Spack DocumentationRelease 0.9

Todd Gamblin

August 31, 2016

Contents

1 Table of Contents 31.1 Feature overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.2 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51.3 Basic usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61.4 Packaging Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401.5 Mirrors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 801.6 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 831.7 Developer Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 861.8 Using Spack for CMake-based Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 901.9 Command index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 921.10 Package List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 931.11 spack package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335

2 Indices and tables 453

Python Module Index 455

i

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Spack is a package management tool designed to support multiple versions and configurations of software on a widevariety of platforms and environments. It was designed for large supercomputing centers, where many users andapplication teams share common installations of software on clusters with exotic architectures, using libraries that donot have a standard ABI. Spack is non-destructive: installing a new version does not break existing installations, somany configurations can coexist on the same system.

Most importantly, Spack is simple. It offers a simple spec syntax so that users can specify versions and configurationoptions concisely. Spack is also simple for package authors: package files are written in pure Python, and specs allowpackage authors to maintain a single file for many different builds of the same package.

See the Feature overview for examples and highlights.

Get spack from the github repository and install your first package:

$ git clone https://github.com/llnl/spack.git$ cd spack/bin$ ./spack install libelf

If you’re new to spack and want to start using it, see Getting Started, or refer to the full manual below.

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2 Contents

CHAPTER 1

Table of Contents

1.1 Feature overview

This is a high-level overview of features that make Spack different from other package managers and port systems.

1.1.1 Simple package installation

Installing the default version of a package is simple. This will install the latest version of the mpileaks package andall of its dependencies:

$ spack install mpileaks

1.1.2 Custom versions & configurations

Spack allows installation to be customized. Users can specify the version, build compiler, compile-time options, andcross-compile platform, all on the command line.

# Install a particular version by appending @$ spack install mpileaks@1.1.2

# Specify a compiler (and its version), with %$ spack install mpileaks@1.1.2 %gcc@4.7.3

# Add special compile-time options by name$ spack install mpileaks@1.1.2 %gcc@4.7.3 debug=True

# Add special boolean compile-time options with +$ spack install mpileaks@1.1.2 %gcc@4.7.3 +debug

# Add compiler flags using the conventional names$ spack install mpileaks@1.1.2 %gcc@4.7.3 cppflags=\"-O3 -floop-block\"

# Cross-compile for a different architecture with arch=$ spack install mpileaks@1.1.2 arch=bgqos_0

Users can specify as many or few options as they care about. Spack will fill in the unspecified values with sensibledefaults. The two listed syntaxes for variants are identical when the value is boolean.

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1.1.3 Customize dependencies

Spack allows dependencies of a particular installation to be customized extensively. Suppose that mpileaks dependsindirectly on libelf and libdwarf. Using ^, users can add custom configurations for the dependencies:

# Install mpileaks and link it with specific versions of libelf and libdwarf$ spack install mpileaks@1.1.2 %gcc@4.7.3 +debug ^libelf@0.8.12 ^libdwarf@20130729+debug

1.1.4 Non-destructive installs

Spack installs every unique package/dependency configuration into its own prefix, so new installs will not breakexisting ones.

1.1.5 Packages can peacefully coexist

Spack avoids library misconfiguration by using RPATH to link dependencies. When a user links a library or runs aprogram, it is tied to the dependencies it was built with, so there is no need to manipulate LD_LIBRARY_PATH atruntime.

1.1.6 Creating packages is easy

To create a new packages, all Spack needs is a URL for the source archive. The spack create command willcreate a boilerplate package file, and the package authors can fill in specific build steps in pure Python.

For example, this command:

$ spack create http://www.mr511.de/software/libelf-0.8.13.tar.gz

creates a simple python file:

from spack import *

class Libelf(Package):"""FIXME: Put a proper description of your package here."""

# FIXME: Add a proper url for your package's homepage here.homepage = "http://www.example.com"url = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"

version('0.8.13', '4136d7b4c04df68b686570afa26988ac')

# FIXME: Add dependencies if required.# depends_on('foo')

def install(self, spec, prefix):# FIXME: Modify the configure line to suit your build system here.configure('--prefix={0}'.format(prefix))

# FIXME: Add logic to build and install here.make()make('install')

It doesn’t take much python coding to get from there to a working package:

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from spack import *

class Libelf(Package):"""libelf lets you read, modify or create ELF object files in an

architecture-independent way. The library takes care of sizeand endian issues, e.g. you can process a file for SPARCprocessors on an Intel-based system."""

homepage = "http://www.mr511.de/software/english.html"url = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"

version('0.8.13', '4136d7b4c04df68b686570afa26988ac')version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7')

provides('elf')

def install(self, spec, prefix):configure("--prefix=" + prefix,

"--enable-shared","--disable-dependency-tracking","--disable-debug")

make()

# The mkdir commands in libelf's install can fail in parallelmake("install", parallel=False)

Spack also provides wrapper functions around common commands like configure, make, and cmake to makewriting packages simple.

1.2 Getting Started

1.2.1 Download

Getting spack is easy. You can clone it from the github repository using this command:

$ git clone https://github.com/llnl/spack.git

This will create a directory called spack. We’ll assume that the full path to this directory is in the SPACK_ROOTenvironment variable. Add $SPACK_ROOT/bin to your path and you’re ready to go:

$ export PATH=$SPACK_ROOT/bin:$PATH$ spack install libelf

For a richer experience, use Spack’s shell support:

# For bash users$ export SPACK_ROOT=/path/to/spack$ . $SPACK_ROOT/share/spack/setup-env.sh

# For tcsh or csh users (note you must set SPACK_ROOT)$ setenv SPACK_ROOT /path/to/spack$ source $SPACK_ROOT/share/spack/setup-env.csh

This automatically adds Spack to your PATH.

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1.2.2 Installation

You don’t need to install Spack; it’s ready to run as soon as you clone it from git.

You may want to run it out of a prefix other than the git repository you cloned. The spack bootstrap commandprovides this functionality. To install spack in a new directory, simply type:

$ spack bootstrap /my/favorite/prefix

This will install a new spack script in /my/favorite/prefix/bin, which you can use just like you would theregular spack script. Each copy of spack installs packages into its own $PREFIX/opt directory.

1.3 Basic usage

The spack command has many subcommands. You’ll only need a small subset of them for typical usage.

Note that Spack colorizes output. less -R should be used with Spack to maintain this colorization. E.g.:

$ spack find | less -R

It is recommend that the following be put in your .bashrc file:

alias less='less -R'

1.3.1 Listing available packages

To install software with Spack, you need to know what software is available. You can see a list of available packagenames at the Package List webpage, or using the spack list command.

spack list

The spack list command prints out a list of all of the packages Spack can install:

$ spack listack llvm qrupdateactiveharmony llvm-lld qtadept-utils lmdb qt-creatoradios lmod qthreadsadol-c lrslib Rallinea-forge lrzip r-abindallinea-reports lua r-assertthatantlr lua-luafilesystem r-base64encape lua-luaposix r-bhapex LuaJIT r-BiocGenericsapr lwgrp r-bootapr-util lwm2 r-brewarmadillo lz4 r-cararpack lzma r-caretarpack-ng lzo r-chronasciidoc m4 r-classastyle mafft r-clusteratk mariadb r-codetoolsatlas matio r-colorspaceatop mbedtls r-crayonautoconf meep r-cubature

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automaded memaxes r-curlautomake mercurial r-datatablebash mesa r-dbibbcp metis r-devtoolsbcftools mfem r-diagrammerbdw-gc Mitos r-dichromatbear mkl r-digestbertini moab r-doparallelbib2xhtml mpc r-dplyrbinutils mpe2 r-dtbison mpfr r-dygraphsbliss mpibash r-e1071blitz mpich r-filehashboost mpileaks r-foreachbowtie2 mrnet r-foreignboxlib msgpack-c r-gdatabpp-core mumps r-geospherebpp-phyl munge r-ggmapbpp-seq muparser r-ggplot2bpp-suite muster r-ggvisbwa mvapich2 r-git2rbzip2 mxml r-glmnetc-blosc nag r-googleviscairo nano r-gridbasecaliper nasm r-gridextracallpath nauty r-gtablecantera nccmp r-gtoolscask ncdu r-htmltoolscblas nco r-htmlwidgetscbtf ncurses r-httpuvcbtf-argonavis ncview r-httrcbtf-krell ndiff r-igraphcbtf-lanl netcdf r-influencercdd netcdf-cxx r-inlinecddlib netcdf-cxx4 r-irlbacdo netcdf-fortran r-iteratorscereal netgauge r-jpegcfitsio netlib-lapack r-jsonlitecgal netlib-scalapack r-labelingcgm nettle r-latticecgns nextflow r-lazyevalcityhash ninja r-leafletcleverleaf numdiff r-lme4cloog nwchem r-lmtestcmake ocaml r-lubridatecmocka oce r-magiccnmem octave r-magrittrcoreutils octave-splines r-mapprojcp2k octopus r-mapscppcheck ompss r-maptoolscram ompt-openmp r-markdowncryptopp opari2 r-masscscope openblas r-matrixcube opencoarrays r-matrixmodelscuda opencv r-memoisecurl openexr r-mgcvczmq openjpeg r-mimedaal openmpi r-minqa

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dakota openspeedshop r-multcompdamselfly openssl r-munselldatamash opium r-mvtnormdbus osu-micro-benchmarks r-ncdf4dealii otf r-networkd3dia otf2 r-nlmedocbook-xml p4est r-nloptrdoxygen panda r-nmfdri2proto pango r-nnetdtcmp papi r-npdyninst paradiseo r-openssleigen parallel r-packratelfutils parallel-netcdf r-pbkrtestelk paraver r-pkgmakerelpa paraview r-plotrixemacs parmetis r-plyrenvironment-modules parmgridgen r-pngespresso parpack r-praiseexodusii patchelf r-protoexonerate pcre r-quantmodexpat pcre2 r-quantregextrae pdt r-R6exuberant-ctags perl r-randomforestfastx_toolkit petsc r-rasterfenics pgi r-rcolorbrewerferret pidx r-rcppfftw pixman r-rcppeigenfish pkg-config r-registryflex plumed r-reshape2fltk pmgr_collective r-rgooglemapsflux pngwriter r-rjavafoam-extend polymake r-rjsonfontconfig porta r-rjsoniofreetype postgresql r-rmysqlgasnet ppl r-rngtoolsgcc prank r-rodbcgdal proj r-roxygen2gdb protobuf r-rpostgresqlgdk-pixbuf psi4 r-rsqlitegeos py-3to2 r-rstangettext py-alabaster r-rstudioapigflags py-argcomplete r-sandwichghostscript py-astroid r-scalesgiflib py-astropy r-shinygit py-autopep8 r-spgl2ps py-babel r-sparsemglib py-basemap r-stanheadersglm py-beautifulsoup4 r-stringiglobal py-biopython r-stringrglog py-blessings r-surveyglpk py-bottleneck r-survivalgmp py-cclib r-tarifxgmsh py-cffi r-testthatgnu-prolog py-coverage r-thdatagnuplot py-csvkit r-threejsgnutls py-cycler r-tibblego py-cython r-tidyrgo-bootstrap py-dask r-ttr

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gobject-introspection py-dateutil r-vcdgoogletest py-dbf r-visnetworkgperf py-decorator r-whiskergperftools py-docutils r-withrgraphlib py-emcee r-xlconnectgraphviz py-epydoc r-xlconnectjarsgromacs py-flake8 r-xlsxgsl py-funcsigs r-xlsxjarsgtkplus py-genders r-xmlgts py-genshi r-xtableguile py-gnuplot r-xtsharfbuzz py-h5py r-yamlharminv py-imagesize r-zoohdf py-iminuit rajahdf5 py-ipython ravelhdf5-blosc py-jdcal readlinehmmer py-jinja2 rosehoomd-blue py-lockfile rsynchpl py-logilab-common rubyhpx5 py-mako rusthtslib py-markupsafe rust-bindgenhub py-matplotlib SAMRAIhwloc py-meep samtoolshydra py-mistune scalascahypre py-mock sconsibmisc py-mpi4py scorepicu py-mpmath scotchicu4c py-mx scrilmbase py-mysqldb1 screenImageMagick py-nestle sedintel py-netcdf seqtkintel-parallel-studio py-networkx serfintltool py-nose siloior py-numexpr slepcipopt py-numpy snappyipp py-openpyxl sparsehashisl py-pandas spindlejasper py-pbr spotjdk py-pep8 sqlitejemalloc py-periodictable statjpeg py-pexpect streamjsoncpp py-phonopy subversionjudy py-pil suite-sparsejulia py-pillow sundialskdiff3 py-ply superlukealib py-pmw superlu-distkripke py-prettytable superlu-mtlaunchmon py-protobuf swiftsimlcms py-py2cairo swigleveldb py-py2neo sympollibaio py-pychecker sziplibarchive py-pycparser tarlibatomic-ops py-pydatalog tasklibcerf py-pyelftools taskdlibcircle py-pygments taulibctl py-pygobject tbblibdrm py-pygtk tcllibdwarf py-pylint tetgen

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libedit py-pypar texinfolibelf py-pyparsing texlivelibepoxy py-pyqt the_platinum_searcherlibevent py-pyside the_silver_searcherlibffi py-pytables thriftlibgcrypt py-python-daemon tklibgd py-pytz tmuxlibgpg-error py-pyyaml tmuxinatorlibgtextutils py-restview treelibhio py-rpy2 trianglelibiconv py-scientificpython trilinoslibjpeg-turbo py-scikit-image turbomolelibjson-c py-scikit-learn udunits2libmng py-scipy uncrustifylibmonitor py-setuptools unibiliumlibNBC py-shiboken unisonlibpciaccess py-sip unixodbclibpng py-six util-linuxlibpthread-stubs py-sncosmo valgrindlibsigsegv py-snowballstemmer vimlibsodium py-sphinx visitlibsplash py-sphinx-rtd-theme vtklibtermkey py-SQLAlchemy wgetlibtiff py-storm wxlibtool py-sympy wxpropgridlibunistring py-tappy xcb-protolibunwind py-tuiview xerces-clibuuid py-twisted xorg-util-macroslibuv py-unittest2 xprotolibvterm py-unittest2py3k xzlibxau py-urwid yasmlibxc py-virtualenv zeromqlibxcb py-wcsaxes zfplibxml2 py-wheel zliblibxpm py-xlrd zoltanlibxshmfence py-yapf zshlibxslt pythonlibxsmm qhull

The packages are listed by name in alphabetical order. If you specify a pattern to match, it will follow this set of rules.A pattern with no wildcards, * or ?, will be treated as though it started and ended with *, so util is equivalent to*util*. A pattern with no capital letters will be treated as case-insensitive. You can also add the -i flag to specifya case insensitive search, or -d to search the description of the package in addition to the name. Some examples:

All packages whose names contain “sql” case insensitive:

$ spack list sqlpostgresql py-mysqldb1 r-rmysql r-rpostgresql r-rsqlite sqlite

All packages whose names start with a capital M:

$ spack list 'M*'Mitos

All packages whose names or descriptions contain Documentation:

$ spack list -d Documentationpy-sphinx r-rcpp

All packages whose names contain documentation case insensitive:

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$ spack list -d documentationdoxygen py-alabaster py-epydoc r-roxygen2 texinfogflags py-docutils r-ggplot2 r-stanheaders

spack info

To get more information on a particular package from spack list, use spack info. Just supply the name of a package:

$ spack info mpichPackage: mpichHomepage: http://www.mpich.org

Safe versions:3.2 http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz3.1.4 http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz3.1.3 http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3.tar.gz3.1.2 http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2.tar.gz3.1.1 http://www.mpich.org/static/downloads/3.1.1/mpich-3.1.1.tar.gz3.1 http://www.mpich.org/static/downloads/3.1/mpich-3.1.tar.gz3.0.4 http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz

Variants:Name Default Description

hydra on Build the hydra process managerpmi on Build with PMI supportverbs off Build support for OpenFabrics verbs.

Build Dependencies:None

Link Dependencies:None

Run Dependencies:None

Virtual packages:mpich@3: provides mpi@:3.0mpich@1: provides mpi@:1.3

Description:MPICH is a high performance and widely portable implementation of theMessage Passing Interface (MPI) standard.

Most of the information is self-explanatory. The safe versions are versions that Spack knows the checksum for, and itwill use the checksum to verify that these versions download without errors or viruses.

Dependencies and virtual dependencies are described in more detail later.

spack versions

To see more available versions of a package, run spack versions. For example:

$ spack versions libelf==> Safe versions (already checksummed):

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0.8.13 0.8.12==> Remote versions (not yet checksummed):

0.8.11 0.8.9 0.8.7 0.8.5 0.8.3 0.8.0 0.6.40.8.10 0.8.8 0.8.6 0.8.4 0.8.2 0.7.0 0.5.2

There are two sections in the output. Safe versions are versions for which Spack has a checksum on file. It can verifythat these versions are downloaded correctly.

In many cases, Spack can also show you what versions are available out on the web—these are remote versions. Spackgets this information by scraping it directly from package web pages. Depending on the package and how its releasesare organized, Spack may or may not be able to find remote versions.

1.3.2 Installing and uninstalling

spack install

spack install will install any package shown by spack list. For example, To install the latest version of thempileaks package, you might type this:

$ spack install mpileaks

If mpileaks depends on other packages, Spack will install the dependencies first. It then fetches the mpileakstarball, expands it, verifies that it was downloaded without errors, builds it, and installs it in its own directory under$SPACK_ROOT/opt. You’ll see a number of messages from spack, a lot of build output, and a message that thepackages is installed:

$ spack install mpileaks==> Installing mpileaks==> mpich is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4.==> callpath is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318.==> adept-utils is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8da.==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz######################################################################## 100.0%==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23/mpileaks-1.0.tar.gz==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23.==> No patches needed for mpileaks.==> Building mpileaks.

... build output ...

==> Successfully installed mpileaks.Fetch: 2.16s. Build: 9.82s. Total: 11.98s.

[+] /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpileaks@1.0-59f6ad23

The last line, with the [+], indicates where the package is installed.

Building a specific version

Spack can also build specific versions of a package. To do this, just add @ after the package name, followed by aversion:

$ spack install mpich@3.0.4

Any number of versions of the same package can be installed at once without interfering with each other. This is goodfor multi-user sites, as installing a version that one user needs will not disrupt existing installations for other users.

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In addition to different versions, Spack can customize the compiler, compile-time options (variants), compiler flags,and platform (for cross compiles) of an installation. Spack is unique in that it can also configure the dependencies apackage is built with. For example, two configurations of the same version of a package, one built with boost 1.39.0,and the other version built with version 1.43.0, can coexist.

This can all be done on the command line using the spec syntax. Spack calls the descriptor used to refer to a particularpackage configuration a spec. In the commands above, mpileaks and mpileaks@3.0.4 are both valid specs.We’ll talk more about how you can use them to customize an installation in Specs & dependencies.

spack uninstall

To uninstall a package, type spack uninstall <package>. This will ask the user for confirmation, and in casewill completely remove the directory in which the package was installed.

$ spack uninstall mpich

If there are still installed packages that depend on the package to be uninstalled, spack will refuse to uninstall it.

To uninstall a package and every package that depends on it, you may give the --dependents option.

$ spack uninstall --dependents mpich

will display a list of all the packages that depend on mpich and, upon confirmation, will uninstall them in the rightorder.

A command like

$ spack uninstall mpich

may be ambiguous if multiple mpich configurations are installed. For example, if both mpich@3.0.2 andmpich@3.1 are installed, mpich could refer to either one. Because it cannot determine which one to uninstall,Spack will ask you either to provide a version number to remove the ambiguity or use the --all option to uninstallall of the matching packages.

You may force uninstall a package with the --force option

$ spack uninstall --force mpich

but you risk breaking other installed packages. In general, it is safer to remove dependent packages before removingtheir dependencies or use the --dependents option.

1.3.3 Seeing installed packages

We know that spack list shows you the names of available packages, but how do you figure out which are alreadyinstalled?

spack find

spack find shows the specs of installed packages. A spec is like a name, but it has a version, compiler, architecture,and build options associated with it. In spack, you can have many installations of the same package with differentspecs.

Running spack find with no arguments lists installed packages:

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$ spack find==> 74 installed packages.-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------ImageMagick@6.8.9-10 libdwarf@20130729 py-dateutil@2.4.0adept-utils@1.0 libdwarf@20130729 py-ipython@2.3.1atk@2.14.0 libelf@0.8.12 py-matplotlib@1.4.2boost@1.55.0 libelf@0.8.13 py-nose@1.3.4bzip2@1.0.6 libffi@3.1 py-numpy@1.9.1cairo@1.14.0 libmng@2.0.2 py-pygments@2.0.1callpath@1.0.2 libpng@1.6.16 py-pyparsing@2.0.3cmake@3.0.2 libtiff@4.0.3 py-pyside@1.2.2dbus@1.8.6 libtool@2.4.2 py-pytz@2014.10dbus@1.9.0 libxcb@1.11 py-setuptools@11.3.1dyninst@8.1.2 libxml2@2.9.2 py-six@1.9.0fontconfig@2.11.1 libxml2@2.9.2 python@2.7.8freetype@2.5.3 llvm@3.0 qhull@1.0gdk-pixbuf@2.31.2 memaxes@0.5 qt@4.8.6glib@2.42.1 mesa@8.0.5 qt@5.4.0graphlib@2.0.0 mpich@3.0.4 readline@6.3gtkplus@2.24.25 mpileaks@1.0 sqlite@3.8.5harfbuzz@0.9.37 mrnet@4.1.0 stat@2.1.0hdf5@1.8.13 ncurses@5.9 tcl@8.6.3icu@54.1 netcdf@4.3.3 tk@srcjpeg@9a openssl@1.0.1h vtk@6.1.0launchmon@1.0.1 pango@1.36.8 xcb-proto@1.11lcms@2.6 pixman@0.32.6 xz@5.2.0libdrm@2.4.33 py-dateutil@2.4.0 zlib@1.2.8

-- linux-debian7-x86_64 / gcc@4.9.2 --------------------------------libelf@0.8.10 mpich@3.0.4

Packages are divided into groups according to their architecture and compiler. Within each group, Spack tries to keepthe view simple, and only shows the version of installed packages.

spack find can filter the package list based on the package name, spec, or a number of properties of their instal-lation status. For example, missing dependencies of a spec can be shown with --missing, packages which wereexplicitly installed with spack install <package> can be singled out with --explicit and those whichhave been pulled in only as dependencies with --implicit.

In some cases, there may be different configurations of the same version of a package installed. For example, thereare two installations of libdwarf@20130729 above. We can look at them in more detail using spack find--deps, and by asking only to show libdwarf packages:

$ spack find --deps libdwarf==> 2 installed packages.-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------

libdwarf@20130729-d9b90962^libelf@0.8.12

libdwarf@20130729-b52fac98^libelf@0.8.13

Now we see that the two instances of libdwarf depend on different versions of libelf: 0.8.12 and 0.8.13. Thisview can become complicated for packages with many dependencies. If you just want to know whether two packages’dependencies differ, you can use spack find --long:

$ spack find --long libdwarf==> 2 installed packages.-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------libdwarf@20130729-d9b90962 libdwarf@20130729-b52fac98

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Now the libdwarf installs have hashes after their names. These are hashes over all of the dependencies of eachpackage. If the hashes are the same, then the packages have the same dependency configuration.

If you want to know the path where each package is installed, you can use spack find --paths:

$ spack find --paths==> 74 installed packages.-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------

ImageMagick@6.8.9-10 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/ImageMagick@6.8.9-10-4df950ddadept-utils@1.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8daatk@2.14.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/atk@2.14.0-3d09ac09boost@1.55.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/boost@1.55.0bzip2@1.0.6 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/bzip2@1.0.6cairo@1.14.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/cairo@1.14.0-fcc2ab44callpath@1.0.2 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318

...

And, finally, you can restrict your search to a particular package by supplying its name:

$ spack find --paths libelf-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------

libelf@0.8.11 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.11libelf@0.8.12 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.12libelf@0.8.13 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.13

spack find actually does a lot more than this. You can use specs to query for specific configurations and builds ofeach package. If you want to find only libelf versions greater than version 0.8.12, you could say:

$ spack find libelf@0.8.12:-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------

libelf@0.8.12 libelf@0.8.13

Finding just the versions of libdwarf built with a particular version of libelf would look like this:

$ spack find --long libdwarf ^libelf@0.8.12==> 1 installed packages.-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------libdwarf@20130729-d9b90962

We can also search for packages that have a certain attribute. For example, spack find libdwarf +debugwill show only installations of libdwarf with the ‘debug’ compile-time option enabled.

The full spec syntax is discussed in detail in Specs & dependencies.

1.3.4 Compiler configuration

Spack has the ability to build packages with multiple compilers and compiler versions. Spack searches for compilerson your machine automatically the first time it is run. It does this by inspecting your PATH.

spack compilers

You can see which compilers spack has found by running spack compilers or spack compiler list:

$ spack compilers==> Available compilers-- gcc ---------------------------------------------------------

gcc@4.9.0 gcc@4.8.0 gcc@4.7.0 gcc@4.6.2 gcc@4.4.7gcc@4.8.2 gcc@4.7.1 gcc@4.6.3 gcc@4.6.1 gcc@4.1.2

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-- intel -------------------------------------------------------intel@15.0.0 intel@14.0.0 intel@13.0.0 intel@12.1.0 intel@10.0intel@14.0.3 intel@13.1.1 intel@12.1.5 intel@12.0.4 intel@9.1intel@14.0.2 intel@13.1.0 intel@12.1.3 intel@11.1intel@14.0.1 intel@13.0.1 intel@12.1.2 intel@10.1

-- clang -------------------------------------------------------clang@3.4 clang@3.3 clang@3.2 clang@3.1

-- pgi ---------------------------------------------------------pgi@14.3-0 pgi@13.2-0 pgi@12.1-0 pgi@10.9-0 pgi@8.0-1pgi@13.10-0 pgi@13.1-1 pgi@11.10-0 pgi@10.2-0 pgi@7.1-3pgi@13.6-0 pgi@12.8-0 pgi@11.1-0 pgi@9.0-4 pgi@7.0-6

Any of these compilers can be used to build Spack packages. More on how this is done is in Specs & dependencies.

spack compiler add

An alias for spack compiler find.

spack compiler find

If you do not see a compiler in this list, but you want to use it with Spack, you can simply run spack compilerfind with the path to where the compiler is installed. For example:

$ spack compiler find /usr/local/tools/ic-13.0.079==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml

intel@13.0.079

Or you can run spack compiler find with no arguments to force auto-detection. This is useful if you do notknow where compilers are installed, but you know that new compilers have been added to your PATH. For example,using dotkit, you might do this:

$ module load gcc-4.9.0$ spack compiler find==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml

gcc@4.9.0

This loads the environment module for gcc-4.9.0 to add it to PATH, and then it adds the compiler to Spack.

spack compiler info

If you want to see specifics on a particular compiler, you can run spack compiler info on it:

$ spack compiler info intel@15intel@15.0.0:

cc = /usr/local/bin/icc-15.0.090cxx = /usr/local/bin/icpc-15.0.090f77 = /usr/local/bin/ifort-15.0.090fc = /usr/local/bin/ifort-15.0.090modules = []operating system = centos6

This shows which C, C++, and Fortran compilers were detected by Spack. Notice also that we didn’t have to be toospecific about the version. We just said intel@15, and information about the only matching Intel compiler wasdisplayed.

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Manual compiler configuration

If auto-detection fails, you can manually configure a compiler by editing your ~/.spack/compilers.yaml file.You can do this by running spack config edit compilers, which will open the file in your $EDITOR.

Each compiler configuration in the file looks like this:

compilers:- compiler:

modules = []operating_system: centos6paths:

cc: /usr/local/bin/icc-15.0.024-betacxx: /usr/local/bin/icpc-15.0.024-betaf77: /usr/local/bin/ifort-15.0.024-betafc: /usr/local/bin/ifort-15.0.024-beta

spec: intel@15.0.0:

For compilers, like clang, that do not support Fortran, put None for f77 and fc:

paths:cc: /usr/bin/clangcxx: /usr/bin/clang++f77: Nonefc: None

spec: clang@3.3svn:

Once you save the file, the configured compilers will show up in the list displayed by spack compilers.

You can also add compiler flags to manually configured compilers. The valid flags are cflags, cxxflags,fflags, cppflags, ldflags, and ldlibs. For example:

compilers:- compiler:

modules = []operating_system: OSpaths:

cc: /usr/local/bin/icc-15.0.024-betacxx: /usr/local/bin/icpc-15.0.024-betaf77: /usr/local/bin/ifort-15.0.024-betafc: /usr/local/bin/ifort-15.0.024-beta

parameters:cppflags: -O3 -fPIC

spec: intel@15.0.0:

These flags will be treated by spack as if they were enterred from the command line each time this compiler is used.The compiler wrappers then inject those flags into the compiler command. Compiler flags enterred from the commandline will be discussed in more detail in the following section.

1.3.5 Specs & dependencies

We know that spack install, spack uninstall, and other commands take a package name with an optionalversion specifier. In Spack, that descriptor is called a spec. Spack uses specs to refer to a particular build configuration(or configurations) of a package. Specs are more than a package name and a version; you can use them to specify thecompiler, compiler version, architecture, compile options, and dependency options for a build. In this section, we’llgo over the full syntax of specs.

Here is an example of a much longer spec than we’ve seen thus far:

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mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt arch=bgq_os ^callpath @1.1 %gcc@4.7.2

If provided to spack install, this will install the mpileaks library at some version between 1.2 and 1.4(inclusive), built using gcc at version 4.7.5 for the Blue Gene/Q architecture, with debug options enabled, and withoutQt support. Additionally, it says to link it with the callpath library (which it depends on), and to build callpathwith gcc 4.7.2. Most specs will not be as complicated as this one, but this is a good example of what is possible withspecs.

More formally, a spec consists of the following pieces:

• Package name identifier (mpileaks above)

• @ Optional version specifier (@1.2:1.4)

• % Optional compiler specifier, with an optional compiler version (gcc or gcc@4.7.3)

• + or - or ~ Optional variant specifiers (+debug, -qt, or ~qt) for boolean variants

• name=<value> Optional variant specifiers that are not restricted to boolean variants

• name=<value> Optional compiler flag specifiers. Valid flag names are cflags, cxxflags, fflags,cppflags, ldflags, and ldlibs.

• target=<value> os=<value> Optional architecture specifier (target=haswell os=CNL10)

• ^ Dependency specs (^callpath@1.1)

There are two things to notice here. The first is that specs are recursively defined. That is, each dependency after ^ isa spec itself. The second is that everything is optional except for the initial package name identifier. Users can be asvague or as specific as they want about the details of building packages, and this makes spack good for beginners andexperts alike.

To really understand what’s going on above, we need to think about how software is structured. An executable or alibrary (these are generally the artifacts produced by building software) depends on other libraries in order to run. Wecan represent the relationship between a package and its dependencies as a graph. Here is the full dependency graphfor mpileaks:

mpileaks

mpich

callpathdyninst

libdwarf

libelf

Each box above is a package and each arrow represents a dependency on some other package. For example, we saythat the package mpileaks depends on callpath and mpich. mpileaks also depends indirectly on dyninst,libdwarf, and libelf, in that these libraries are dependencies of callpath. To install mpileaks, Spack hasto build all of these packages. Dependency graphs in Spack have to be acyclic, and the depends on relationship isdirectional, so this is a directed, acyclic graph or DAG.

The package name identifier in the spec is the root of some dependency DAG, and the DAG itself is implicit. Spackknows the precise dependencies among packages, but users do not need to know the full DAG structure. Each ^ in thefull spec refers to some dependency of the root package. Spack will raise an error if you supply a name after ^ thatthe root does not actually depend on (e.g. mpileaks ^emacs@23.3).

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Spack further simplifies things by only allowing one configuration of each package within any single build. Above,both mpileaks and callpath depend on mpich, but mpich appears only once in the DAG. You cannot build anmpileaks version that depends on one version of mpich and on a callpath version that depends on some otherversion of mpich. In general, such a configuration would likely behave unexpectedly at runtime, and Spack enforcesthis to ensure a consistent runtime environment.

The point of specs is to abstract this full DAG from Spack users. If a user does not care about the DAG at all, shecan refer to mpileaks by simply writing mpileaks. If she knows that mpileaks indirectly uses dyninst and shewants a particular version of dyninst, then she can refer to mpileaks ^dyninst@8.1. Spack will fill in therest when it parses the spec; the user only needs to know package names and minimal details about their relationship.

When spack prints out specs, it sorts package names alphabetically to normalize the way they are displayed, but usersdo not need to worry about this when they write specs. The only restriction on the order of dependencies within a specis that they appear after the root package. For example, these two specs represent exactly the same configuration:

mpileaks ^callpath@1.0 ^libelf@0.8.3mpileaks ^libelf@0.8.3 ^callpath@1.0

You can put all the same modifiers on dependency specs that you would put on the root spec. That is, you canspecify their versions, compilers, variants, and architectures just like any other spec. Specifiers are associated withthe nearest package name to their left. For example, above, @1.1 and %gcc@4.7.2 associates with the callpathpackage, while @1.2:1.4, %gcc@4.7.5, +debug, -qt, and target=haswell os=CNL10 all associate withthe mpileaks package.

In the diagram above, mpileaks depends on mpich with an unspecified version, but packages can depend on otherpackages with constraints by adding more specifiers. For example, mpileaks could depend on mpich@1.2: if itcan only build with version 1.2 or higher of mpich.

Below are more details about the specifiers that you can add to specs.

Version specifier

A version specifier comes somewhere after a package name and starts with @. It can be a single version, e.g. @1.0,@3, or @1.2a7. Or, it can be a range of versions, such as @1.0:1.5 (all versions between 1.0 and 1.5, inclusive).Version ranges can be open, e.g. :3 means any version up to and including 3. This would include 3.4 and 3.4.2.4.2: means any version above and including 4.2. Finally, a version specifier can be a set of arbitrary versions, suchas @1.0,1.5,1.7 (1.0, 1.5, or 1.7). When you supply such a specifier to spack install, it constrains theset of versions that Spack will install.

If the version spec is not provided, then Spack will choose one according to policies set for the particular spackinstallation. If the spec is ambiguous, i.e. it could match multiple versions, Spack will choose a version within thespec’s constraints according to policies set for the particular Spack installation.

Details about how versions are compared and how Spack determines if one version is less than another are discussedin the developer guide.

Compiler specifier

A compiler specifier comes somewhere after a package name and starts with %. It tells Spack what compiler(s)a particular package should be built with. After the % should come the name of some registered Spack compiler.This might include gcc, or intel, but the specific compilers available depend on the site. You can run spackcompilers to get a list; more on this below.

The compiler spec can be followed by an optional compiler version. A compiler version specifier looks exactly likea package version specifier. Version specifiers will associate with the nearest package name or compiler specifier totheir left in the spec.

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If the compiler spec is omitted, Spack will choose a default compiler based on site policies.

Variants

Variants are named options associated with a particular package. They are optional, as each package must pro-vide default values for each variant it makes available. Variants can be specified using a flexible parameter syntaxname=<value>. For example, spack install libelf debug=True will install libelf build with debugflags. The names of particular variants available for a package depend on what was provided by the package author.spack info <package> will provide information on what build variants are available.

For compatibility with earlier versions, variants which happen to be boolean in nature can be specified by a syntax thatrepresents turning options on and off. For example, in the previous spec we could have supplied libelf +debugwith the same effect of enabling the debug compile time option for the libelf package.

Depending on the package a variant may have any default value. For libelf here, debug is False by default, andwe turned it on with debug=True or +debug. If a variant is True by default you can turn it off by either adding-name or ~name to the spec.

There are two syntaxes here because, depending on context, ~ and - may mean different things. In most shells, thefollowing will result in the shell performing home directory substitution:

mpileaks ~debug # shell may try to substitute this!mpileaks~debug # use this instead

If there is a user called debug, the ~ will be incorrectly expanded. In this situation, you would want to write libelf-debug. However, - can be ambiguous when included after a package name without spaces:

mpileaks-debug # wrong!mpileaks -debug # right

Spack allows the - character to be part of package names, so the above will be interpreted as a request for thempileaks-debug package, not a request for mpileaks built without debug options. In this scenario, you shouldwrite mpileaks~debug to avoid ambiguity.

When spack normalizes specs, it prints them out with no spaces boolean variants using the backwards compatibilitysyntax and uses only ~ for disabled boolean variants. We allow - and spaces on the command line is provided forconvenience and legibility.

Compiler Flags

Compiler flags are specified using the same syntax as non-boolean variants, but fulfill a different purpose. While thefunction of a variant is set by the package, compiler flags are used by the compiler wrappers to inject flags into thecompile line of the build. Additionally, compiler flags are inherited by dependencies. spack install libdwarfcppflags=\"-g\" will install both libdwarf and libelf with the -g flag injected into their compile line.

Notice that the value of the compiler flags must be escape quoted on the command line. From within python files, thesame spec would be specified libdwarf cppflags="-g". This is necessary because of how the shell handlesthe quote symbols.

The six compiler flags are injected in the order of implicit make commands in GNU Autotools. If all flags areset, the order is $cppflags $cflags|$cxxflags $ldflags <command> $ldlibs for C and C++ and$fflags $cppflags $ldflags <command> $ldlibs for Fortran.

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Architecture specifiers

The architecture can be specified by using the reserved words target and/or os (target=x86-64os=debian7). You can also use the triplet form of platform, operating system and processor.

$ spack install libelf arch=cray-CNL10-haswell

Users on non-Cray systems won’t have to worry about specifying the architecture. Spack will autodetect what kind ofoperating system is on your machine as well as the processor. For more information on how the architecture can beused on Cray machines, see Spack on Cray

1.3.6 Virtual dependencies

The dependence graph for mpileaks we saw above wasn’t quite accurate. mpileaks uses MPI, which is aninterface that has many different implementations. Above, we showed mpileaks and callpath depending onmpich, which is one particular implementation of MPI. However, we could build either with another implementation,such as openmpi or mvapich.

Spack represents interfaces like this using virtual dependencies. The real dependency DAG for mpileaks looks likethis:

mpi

mpileaks

callpathdyninst

libdwarf

libelf

Notice that mpich has now been replaced with mpi. There is no real MPI package, but some packages provide theMPI interface, and these packages can be substituted in for mpi when mpileaks is built.

You can see what virtual packages a particular package provides by getting info on it:

$ spack info mpichPackage: mpichHomepage: http://www.mpich.org

Safe versions:3.2 http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz3.1.4 http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz3.1.3 http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3.tar.gz3.1.2 http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2.tar.gz3.1.1 http://www.mpich.org/static/downloads/3.1.1/mpich-3.1.1.tar.gz3.1 http://www.mpich.org/static/downloads/3.1/mpich-3.1.tar.gz3.0.4 http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz

Variants:Name Default Description

hydra on Build the hydra process manager

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pmi on Build with PMI supportverbs off Build support for OpenFabrics verbs.

Build Dependencies:None

Link Dependencies:None

Run Dependencies:None

Virtual packages:mpich@3: provides mpi@:3.0mpich@1: provides mpi@:1.3

Description:MPICH is a high performance and widely portable implementation of theMessage Passing Interface (MPI) standard.

Spack is unique in that its virtual packages can be versioned, just like regular packages. A particular version of apackage may provide a particular version of a virtual package, and we can see above that mpich versions 1 and aboveprovide all mpi interface versions up to 1, and mpich versions 3 and above provide mpi versions up to 3. A packagecan depend on a particular version of a virtual package, e.g. if an application needs MPI-2 functions, it can depend onmpi@2: to indicate that it needs some implementation that provides MPI-2 functions.

Constraining virtual packages

When installing a package that depends on a virtual package, you can opt to specify the particular provider you wantto use, or you can let Spack pick. For example, if you just type this:

$ spack install mpileaks

Then spack will pick a provider for you according to site policies. If you really want a particular version, say mpich,then you could run this instead:

$ spack install mpileaks ^mpich

This forces spack to use some version of mpich for its implementation. As always, you can be even more specificand require a particular mpich version:

$ spack install mpileaks ^mpich@3

The mpileaks package in particular only needs MPI-1 commands, so any MPI implementation will do. If anotherpackage depends on mpi@2 and you try to give it an insufficient MPI implementation (e.g., one that provides onlympi@:1), then Spack will raise an error. Likewise, if you try to plug in some package that doesn’t provide MPI,Spack will raise an error.

Specifying Specs by Hash

Complicated specs can become cumbersome to enter on the command line, especially when many of the qualificationsare necessary to distinguish between similar installs, for example when using the uninstall command. To avoidthis, when referencing an existing spec, Spack allows you to reference specs by their hash. We previously discussedthe spec hash that Spack computes. In place of a spec in any command, substitute /<hash> where <hash> is anyamount from the beginning of a spec hash. If the given spec hash is sufficient to be unique, Spack will replace thereference with the spec to which it refers. Otherwise, it will prompt for a more qualified hash.

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Note that this will not work to reinstall a depencency uninstalled by spack uninstall --force.

spack providers

You can see what packages provide a particular virtual package using spack providers. If you wanted to seewhat packages provide mpi, you would just run:

$ spack providers mpiintel-parallel-studio@cluster:+mpi mvapich2@1.9 openmpi@1.7.5:mpich@1: mvapich2@2.0: openmpi@2.0.0:mpich@3: openmpi@1.6.5

And if you only wanted to see packages that provide MPI-2, you would add a version specifier to the spec:

$ spack providers mpi@2intel-parallel-studio@cluster:+mpi mvapich2@2.0: openmpi@2.0.0:mpich@3: openmpi@1.6.5mvapich2@1.9 openmpi@1.7.5:

Notice that the package versions that provide insufficient MPI versions are now filtered out.

1.3.7 Integration with module systems

Note: Environment module support is currently experimental and should not be considered a stable feature of Spack.In particular, the interface and/or generated module names may change in future versions.

Spack provides some integration with Environment Modules and Dotkit to make it easier to use the packages it in-stalled.

Installing Environment Modules

In order to use Spack’s generated environment modules, you must have installed the Environment Modules package.On many Linux distributions, this can be installed from the vendor’s repository:

$ yum install environment-modules # (Fedora/RHEL/CentOS)$ apt-get install environment-modules # (Ubuntu/Debian)

If your Linux distribution does not have Environment Modules, you can get it with Spack:

$ spack install environment-modules

In this case to activate it automatically you need to add the following two lines to your .bashrc profile (or similar):

MODULES_HOME=`spack location -i environment-modules`source ${MODULES_HOME}/Modules/init/bash

If you use a Unix shell other than bash, modify the commands above accordingly and source the appropriate file in${MODULES_HOME}/Modules/init/.

Spack and module systems

You can enable shell support by sourcing some files in the /share/spack directory.

For bash or ksh, run:

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export SPACK_ROOT=/path/to/spack. $SPACK_ROOT/share/spack/setup-env.sh

For csh and tcsh run:

setenv SPACK_ROOT /path/to/spacksource $SPACK_ROOT/share/spack/setup-env.csh

You can put the above code in your .bashrc or .cshrc, and Spack’s shell support will be available on the commandline.

When you install a package with Spack, it automatically generates a module file that lets you add the package to yourenvironment.

Currently, Spack supports the generation of Environment Modules and Dotkit. Generated module files for each ofthese systems can be found in these directories:

$SPACK_ROOT/share/spack/modules$SPACK_ROOT/share/spack/dotkit

The directories are automatically added to your MODULEPATH and DK_NODE environment variables when you enableSpack’s shell support.

Using Modules & Dotkits

If you have shell support enabled you should be able to run either module avail or use -l spack to see whatmodules/dotkits have been installed. Here is sample output of those programs, showing lots of installed packages.

$ module avail

------- /home/gamblin2/spack/share/spack/modules/linux-debian7-x86_64 --------adept-utils@1.0%gcc@4.4.7-5adef8da libelf@0.8.13%gcc@4.4.7automaded@1.0%gcc@4.4.7-d9691bb0 libelf@0.8.13%intel@15.0.0boost@1.55.0%gcc@4.4.7 mpc@1.0.2%gcc@4.4.7-559607f5callpath@1.0.1%gcc@4.4.7-5dce4318 mpfr@3.1.2%gcc@4.4.7dyninst@8.1.2%gcc@4.4.7-b040c20e mpich@3.0.4%gcc@4.4.7gcc@4.9.1%gcc@4.4.7-93ab98c5 mpich@3.0.4%gcc@4.9.0gmp@6.0.0a%gcc@4.4.7 mrnet@4.1.0%gcc@4.4.7-72b7881dgraphlib@2.0.0%gcc@4.4.7 netgauge@2.4.6%gcc@4.9.0-27912b7blaunchmon@1.0.1%gcc@4.4.7 stat@2.1.0%gcc@4.4.7-51101207libNBC@1.1.1%gcc@4.9.0-27912b7b sundials@2.5.0%gcc@4.9.0-27912b7blibdwarf@20130729%gcc@4.4.7-b52fac98

$ use -l spack

spack ----------adept-utils@1.0%gcc@4.4.7-5adef8da - adept-utils @1.0automaded@1.0%gcc@4.4.7-d9691bb0 - automaded @1.0boost@1.55.0%gcc@4.4.7 - boost @1.55.0callpath@1.0.1%gcc@4.4.7-5dce4318 - callpath @1.0.1dyninst@8.1.2%gcc@4.4.7-b040c20e - dyninst @8.1.2gmp@6.0.0a%gcc@4.4.7 - gmp @6.0.0alibNBC@1.1.1%gcc@4.9.0-27912b7b - libNBC @1.1.1libdwarf@20130729%gcc@4.4.7-b52fac98 - libdwarf @20130729libelf@0.8.13%gcc@4.4.7 - libelf @0.8.13libelf@0.8.13%intel@15.0.0 - libelf @0.8.13mpc@1.0.2%gcc@4.4.7-559607f5 - mpc @1.0.2mpfr@3.1.2%gcc@4.4.7 - mpfr @3.1.2

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mpich@3.0.4%gcc@4.4.7 - mpich @3.0.4mpich@3.0.4%gcc@4.9.0 - mpich @3.0.4netgauge@2.4.6%gcc@4.9.0-27912b7b - netgauge @2.4.6sundials@2.5.0%gcc@4.9.0-27912b7b - sundials @2.5.0

The names here should look familiar, they’re the same ones from spack find. You can use the names here directly.For example, you could type either of these commands to load the callpath module:

$ use callpath@1.0.1%gcc@4.4.7-5dce4318

$ module load callpath@1.0.1%gcc@4.4.7-5dce4318

Neither of these is particularly pretty, easy to remember, or easy to type. Luckily, Spack has its own interface for usingmodules and dotkits. You can use the same spec syntax you’re used to:

Environment Modules Dotkitspack load <spec> spack use <spec>spack unload <spec> spack unuse <spec>

And you can use the same shortened names you use everywhere else in Spack. For example, this will add the mpichpackage built with gcc to your path:

$ spack install mpich %gcc@4.4.7

# ... wait for install ...

$ spack use mpich %gcc@4.4.7Prepending: mpich@3.0.4%gcc@4.4.7 (ok)$ which mpicc~/src/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc

Or, similarly with modules, you could type:

$ spack load mpich %gcc@4.4.7

These commands will add appropriate directories to your PATH, MANPATH, CPATH, and LD_LIBRARY_PATH.When you no longer want to use a package, you can type unload or unuse similarly:

$ spack unload mpich %gcc@4.4.7 # modules$ spack unuse mpich %gcc@4.4.7 # dotkit

Note: These use, unuse, load, and unload subcommands are only available if you have enabled Spack’s shellsupport and you have dotkit or modules installed on your machine.

Ambiguous module names

If a spec used with load/unload or use/unuse is ambiguous (i.e. more than one installed package matches it), thenSpack will warn you:

$ spack load libelf==> Error: Multiple matches for spec libelf. Choose one:libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64

You can either type the spack load command again with a fully qualified argument, or you can add just enoughextra constraints to identify one package. For example, above, the key differentiator is that one libelf is built withthe Intel compiler, while the other used gcc. You could therefore just type:

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$ spack load libelf %intel

To identify just the one built with the Intel compiler.

Module files generation and customization

Environment Modules and Dotkit files are generated when packages are installed, and are placed in the followingdirectories under the Spack root:

$SPACK_ROOT/share/spack/modules$SPACK_ROOT/share/spack/dotkit

The content that gets written in each module file can be customized in two ways:

1. overriding part of the spack.Package API within a package.py

2. writing dedicated configuration files

Override Package API

There are currently two methods in spack.Package that may affect the content of module files:

def setup_environment(self, spack_env, run_env):"""Set up the compile and runtime environments for a package."""pass

Recursive Modules

In some cases, it is desirable to load not just a module, but also all the modules it depends on. This is not required formost modules because Spack builds binaries with RPATH support. However, not all packages use RPATH to find theirdependencies: this can be true in particular for Python extensions, which are currently not built with RPATH.

Modules may be loaded recursively with the load command’s --dependencies or -r argument:

$ spack load --dependencies <spec> ...

More than one spec may be placed on the command line here.

Module Commands for Shell Scripts

Although Spack is flexible, the module command is much faster. This could become an issue when emitting a seriesof spack load commands inside a shell script. By adding the --shell flag, spack module find may alsobe used to generate code that can be cut-and-pasted into a shell script. For example:

$ spack module find tcl --dependencies --shell py-numpy git# bzip2@1.0.6%gcc@4.9.3=linux-x86_64module load bzip2-1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx# ncurses@6.0%gcc@4.9.3=linux-x86_64module load ncurses-6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv# zlib@1.2.8%gcc@4.9.3=linux-x86_64module load zlib-1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z# sqlite@3.8.5%gcc@4.9.3=linux-x86_64module load sqlite-3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr# readline@6.3%gcc@4.9.3=linux-x86_64module load readline-6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3

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# python@3.5.1%gcc@4.9.3=linux-x86_64module load python-3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi# py-setuptools@20.5%gcc@4.9.3=linux-x86_64module load py-setuptools-20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2# py-nose@1.3.7%gcc@4.9.3=linux-x86_64module load py-nose-1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli# openblas@0.2.17%gcc@4.9.3+shared=linux-x86_64module load openblas-0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y# py-numpy@1.11.0%gcc@4.9.3+blas+lapack=linux-x86_64module load py-numpy-1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r# curl@7.47.1%gcc@4.9.3=linux-x86_64module load curl-7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi# autoconf@2.69%gcc@4.9.3=linux-x86_64module load autoconf-2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4# cmake@3.5.0%gcc@4.9.3~doc+ncurses+openssl~qt=linux-x86_64module load cmake-3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t# expat@2.1.0%gcc@4.9.3=linux-x86_64module load expat-2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd# git@2.8.0-rc2%gcc@4.9.3+curl+expat=linux-x86_64module load git-2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd

The script may be further edited by removing unnecessary modules. This script may be directly executed in bash via:

source < (spack module find tcl --dependencies --shell py-numpy git)

Regenerating Module files

def setup_dependent_environment(self, spack_env, run_env, dependent_spec):"""Set up the environment of packages that depend on this one"""pass

As briefly stated in the comments, the first method lets you customize the module file content for the package you arecurrently writing, the second allows for modifications to your dependees module file. In both cases one needs to fillrun_env with the desired list of environment modifications.

Example : builtin/packages/python/package.py

The python package that comes with the builtin Spack repository overridessetup_dependent_environment in the following way:

def setup_dependent_environment(self, spack_env, run_env, extension_spec):if extension_spec.package.extends(self.spec):

run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))

to insert the appropriate PYTHONPATH modifications in the module files of python packages.

Configuration files

Another way of modifying the content of module files is writing a modules.yaml configuration file. Followingusual Spack conventions, this file can be placed either at site or user scope.

The default site configuration reads:

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# -------------------------------------------------------------------------# This is the default configuration for Spack's module file generation.## Settings here are versioned with Spack and are intended to provide# sensible defaults out of the box. Spack maintainers should edit this# file to keep it current.## Users can override these settings by editing the following files.## Per-spack-instance settings (overrides defaults):# $SPACK_ROOT/etc/spack/modules.yaml## Per-user settings (overrides default and site settings):# ~/.spack/modules.yaml# -------------------------------------------------------------------------modules:

enable:- tcl- dotkit

prefix_inspections:bin:

- PATHman:

- MANPATHshare/man:

- MANPATHlib:

- LIBRARY_PATH- LD_LIBRARY_PATH

lib64:- LIBRARY_PATH- LD_LIBRARY_PATH

include:- CPATH

lib/pkgconfig:- PKG_CONFIG_PATH

lib64/pkgconfig:- PKG_CONFIG_PATH

'':- CMAKE_PREFIX_PATH

It basically inspects the installation prefixes for the existence of a few folders and, if they exist, it prepends a path to agiven list of environment variables.

For each module system that can be enabled a finer configuration is possible:

modules:tcl:# contains environment modules specific customizations

dotkit:# contains dotkit specific customizations

The structure under the tcl and dotkit keys is almost equal, and will be showcased in the following by someexamples.

Select module files by spec constraints

Using spec syntax it’s possible to have different customizations for different groups of module files.

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Considering :

modules:tcl:all: # Default addition for every package

environment:set:BAR: 'bar'

^openmpi:: # A double ':' overrides previous rulesenvironment:

set:BAR: 'baz'

zlib:environment:

prepend_path:LD_LIBRARY_PATH: 'foo'

zlib%gcc@4.8:environment:

unset:- FOOBAR

what will happen is that:

• every module file will set BAR=bar

• unless the associated spec satisfies ^openmpi in which case BAR=baz

• any spec that satisfies zlib will additionally prepend foo to LD_LIBRARY_PATH

• any spec that satisfies zlib%gcc@4.8 will additionally unset FOOBAR

Note:

Order does matter The modifications associated with the all keyword are always evaluated first, no matter wherethey appear in the configuration file. All the other spec constraints are instead evaluated top to bottom.

Filter modifications out of module files

Modifications to certain environment variables in module files are generated by default. Suppose you would like toavoid having CPATH and LIBRARY_PATH modified by your dotkit modules. Then :

modules:dotkit:all:

filter:# Exclude changes to any of these variablesenvironment_blacklist: ['CPATH', 'LIBRARY_PATH']

will generate dotkit module files that will not contain modifications to either CPATH or LIBRARY_PATH and envi-ronment module files that instead will contain those modifications.

Autoload dependencies

The following lines in modules.yaml:

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modules:tcl:all:

autoload: 'direct'

will produce environment module files that will automatically load their direct dependencies.

Note:

Allowed values for autoload statements Allowed values for autoload statements are either none, direct orall. In tcl configuration it is possible to use the option prerequisites that accepts the same values andwill add prereq statements instead of automatically loading other modules.

Blacklist or whitelist the generation of specific module files

Sometimes it is desirable not to generate module files, a common use case being not providing the users with softwarebuilt using the system compiler.

A configuration file like:

modules:tcl:whitelist: ['gcc', 'llvm'] # Whitelist will have precedence over blacklistblacklist: ['%gcc@4.4.7'] # Assuming gcc@4.4.7 is the system compiler

will skip module file generation for anything that satisfies %gcc@4.4.7, with the exception of specs that satisfy gccor llvm.

Customize the naming scheme and insert conflicts

A configuration file like:

modules:tcl:naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'all:

conflict: ['{name}', 'intel/14.0.1']

will create module files that will conflict with intel/14.0.1 and with the base directory of the same module,effectively preventing the possibility to load two or more versions of the same software at the same time.

Note:

Tokens available for the naming scheme currently only the tokens shown in the example are available to constructthe naming scheme

Note: The conflict option is tcl specific

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Regenerating module files

Sometimes you may need to regenerate the modules files. For example, if newer, fancier module support is added toSpack at some later date, you may want to regenerate all the modules to take advantage of these new features.

spack module refresh

Running spack module refresh will remove the share/spack/modules and share/spack/dotkitdirectories, then regenerate all module and dotkit files from scratch:

$ spack module refresh==> Regenerating tcl module files.==> Regenerating dotkit module files.

1.3.8 Filesystem Views

The Spack installation area allows for many package installation trees to coexist and gives the user choices as towhat versions and variants of packages to use. To use them, the user must rely on a way to aggregate a subset ofthose packages. The section on Environment Modules gives one good way to do that which relies on setting variousenvironment variables. An alternative way to aggregate is through filesystem views.

A filesystem view is a single directory tree which is the union of the directory hierarchies of the individual packageinstallation trees that have been included. The files of the view’s installed packages are brought into the view bysymbolic or hard links back to their location in the original Spack installation area. As the view is formed, any clashesdue to a file having the exact same path in its package installation tree are handled in a first-come-first-served basisand a warning is printed. Packages and their dependencies can be both added and removed. During removal, emptydirectories will be purged. These operations can be limited to pertain to just the packages listed by the user or toexclude specific dependencies and they allow for software installed outside of Spack to coexist inside the filesystemview tree.

By its nature, a filesystem view represents a particular choice of one set of packages among all the versions and variantsthat are available in the Spack installation area. It is thus equivalent to the directory hiearchy that might exist under/usr/local. While this limits a view to including only one version/variant of any package, it provides the benefitsof having a simpler and traditional layout which may be used without any particular knowledge that its packages werebuilt by Spack.

Views can be used for a variety of purposes including:

• A central installation in a traditional layout, eg /usr/local maintained over time by the sysadmin.

• A self-contained installation area which may for the basis of a top-level atomic versioning scheme, eg/opt/pro vs /opt/dev.

• Providing an atomic and monolithic binary distribution, eg for delivery as a single tarball.

• Producing ephemeral testing or developing environments.

Using Filesystem Views

A filesystem view is created and packages are linked in by the spack view command’s symlink and hardlinksub-commands. The spack view remove command can be used to unlink some or all of the filesystem view.

The following example creates a filesystem view based on an installed cmake package and then removes from theview the files in the cmake package while retaining its dependencies.

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$ spack view --verbose symlink myview cmake@3.5.2==> Linking package: "ncurses"==> Linking package: "zlib"==> Linking package: "openssl"==> Linking package: "cmake"

$ ls myview/bin doc etc include lib share

$ ls myview/bin/captoinfo clear cpack ctest infotocap openssl tabs toe tsetccmake cmake c_rehash infocmp ncurses6-config reset tic tput

$ spack view --verbose --dependencies false rm myview cmake@3.5.2==> Removing package: "cmake"

$ ls myview/bin/captoinfo c_rehash infotocap openssl tabs toe tsetclear infocmp ncurses6-config reset tic tput

Limitations of Filesystem Views

This section describes some limitations that should be considered in using filesystems views.

Filesystem views are merely organizational. The binary executable programs, shared libraries and other build productsfound in a view are mere links into the “real” Spack installation area. If a view is built with symbolic links it requiresthe Spack-installed package to be kept in place. Building a view with hardlinks removes this requirement but anyinternal paths (eg, rpath or #! interpreter specifications) will still require the Spack-installed package files to be inplace.

As described above, when a view is built only a single instance of a file may exist in the unified filesystem tree. Ifmore than one package provides a file at the same path (relative to its own root) then it is the first package added to theview that “wins”. A warning is printed and it is up to the user to determine if the conflict matters.

It is up to the user to assure a consistent view is produced. In particular if the user excludes packages, limits thefollowing of dependencies or removes packages the view may become inconsistent. In particular, if two packagesrequire the same sub-tree of dependencies, removing one package (recursively) will remove its dependencies andleave the other package broken.

1.3.9 Extensions & Python support

Spack’s installation model assumes that each package will live in its own install prefix. However, certain packages aretypically installed within the directory hierarchy of other packages. For example, modules in interpreted languageslike Python are typically installed in the $prefix/lib/python-2.7/site-packages directory.

Spack has support for this type of installation as well. In Spack, a package that can live inside the prefix of anotherpackage is called an extension. Suppose you have Python installed like so:

$ spack find python==> 1 installed packages.-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------python@2.7.8

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spack extensions

You can find extensions for your Python installation like this:

$ spack extensions python==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96==> 36 extensions:geos py-ipython py-pexpect py-pyside py-sippy-basemap py-libxml2 py-pil py-pytz py-sixpy-biopython py-mako py-pmw py-rpy2 py-sympypy-cython py-matplotlib py-pychecker py-scientificpython py-virtualenvpy-dateutil py-mpi4py py-pygments py-scikit-learnpy-epydoc py-mx py-pylint py-scipypy-gnuplot py-nose py-pyparsing py-setuptoolspy-h5py py-numpy py-pyqt py-shiboken

==> 12 installed:-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0

==> None activated.

The extensions are a subset of what’s returned by spack list, and they are packages like any other. They areinstalled into their own prefixes, and you can see this with spack find --paths:

$ spack find --paths py-numpy==> 1 installed packages.-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------

py-numpy@1.9.1 /g/g21/gamblin2/src/spack/opt/linux-debian7-x86_64/gcc@4.4.7/py-numpy@1.9.1-66733244

However, even though this package is installed, you cannot use it directly when you run python:

$ spack load python$ pythonPython 2.7.8 (default, Feb 17 2015, 01:35:25)[GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2Type "help", "copyright", "credits" or "license" for more information.>>> import numpyTraceback (most recent call last):

File "<stdin>", line 1, in <module>ImportError: No module named numpy>>>

Extensions & Environment Modules

There are two ways to get numpy working in Python. The first is to use Integration with module systems. You cansimply use or load the module for the extension, and it will be added to the PYTHONPATH in your current shell.

For tcl modules:

$ spack load python$ spack load py-numpy

or, for dotkit:

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$ spack use python$ spack use py-numpy

Now import numpy will succeed for as long as you keep your current session open.

Activating Extensions

It is often desirable to have certain packages always available as part of a Python installation. Spack offers a morepermanent solution for this case. Instead of requiring users to load particular environment modules, you can activatethe package within the Python installation:

spack activate

$ spack activate py-numpy==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=linux-debian7-x86_64-3c74eb69 for python@2.7.8%gcc@4.4.7.==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=linux-debian7-x86_64-5f70f816 for python@2.7.8%gcc@4.4.7.==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7.

Several things have happened here. The user requested that py-numpy be activated in the python installation itwas built with. Spack knows that py-numpy depends on py-nose and py-setuptools, so it activated thosepackages first. Finally, once all dependencies were activated in the python installation, py-numpy was activated aswell.

If we run spack extensions again, we now see the three new packages listed as activated:

$ spack extensions python==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96==> 36 extensions:geos py-ipython py-pexpect py-pyside py-sippy-basemap py-libxml2 py-pil py-pytz py-sixpy-biopython py-mako py-pmw py-rpy2 py-sympypy-cython py-matplotlib py-pychecker py-scientificpython py-virtualenvpy-dateutil py-mpi4py py-pygments py-scikit-learnpy-epydoc py-mx py-pylint py-scipypy-gnuplot py-nose py-pyparsing py-setuptoolspy-h5py py-numpy py-pyqt py-shiboken

==> 12 installed:-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0

==> 3 currently activated:-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------py-nose@1.3.4 py-numpy@1.9.1 py-setuptools@11.3.1

Now, when a user runs python, numpy will be available for import without the user having to explicitly loaded.python@2.7.8 now acts like a system Python installation with numpy installed inside of it.

Spack accomplishes this by symbolically linking the entire prefix of the py-numpy into the prefix of the pythonpackage. To the python interpreter, it looks like numpy is installed in the site-packages directory.

The only limitation of activation is that you can only have a single version of an extension activated at a time. This isbecause multiple versions of the same extension would conflict if symbolically linked into the same prefix. Users who

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want a different version of a package can still get it by using environment modules, but they will have to explicitlyload their preferred version.

spack activate -f

If, for some reason, you want to activate a package without its dependencies, you can use spack activate -f:

$ spack activate -f py-numpy==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7.

spack deactivate

We’ve seen how activating an extension can be used to set up a default version of a Python module. Obviously, youmay want to change that at some point. spack deactivate is the command for this. There are several variants:

• spack deactivate <extension> will deactivate a single extension. If another activated extension de-pends on this one, Spack will warn you and exit with an error.

• spack deactivate --force <extension> deactivates an extension regardless of packages that de-pend on it.

• spack deactivate --all <extension> deactivates an extension and all of its dependencies. Use--force to disregard dependents.

• spack deactivate --all <extendee> deactivates all activated extensions of a package. For exam-ple, to deactivate all python extensions, use:

$ spack deactivate --all python

1.3.10 Filesystem requirements

Spack currently needs to be run from a filesystem that supports flock locking semantics. Nearly all local filesystemsand recent versions of NFS support this, but parallel filesystems may be mounted without flock support enabled.You can determine how your filesystems are mounted with mount -p. The output for a Lustre filesystem might looklike this:

$ mount -l | grep lscratchpilsner-mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)porter-mds1-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)

Note the flock option on both Lustre mounts. If you do not see this or a similar option for your filesystem, you mayneed ot ask your system administrator to enable flock.

This issue typically manifests with the error below:

$ ./spack findTraceback (most recent call last):File "./spack", line 176, in <module>

main()File "./spack", line 154,' in main

return_val = command(parser, args)File "./spack/lib/spack/spack/cmd/find.py", line 170, in find

specs = set(spack.installed_db.query(\**q_args))File "./spack/lib/spack/spack/database.py", line 551, in query

with self.read_transaction():File "./spack/lib/spack/spack/database.py", line 598, in __enter__

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if self._enter() and self._acquire_fn:File "./spack/lib/spack/spack/database.py", line 608, in _enter

return self._db.lock.acquire_read(self._timeout)File "./spack/lib/spack/llnl/util/lock.py", line 103, in acquire_read

self._lock(fcntl.LOCK_SH, timeout) # can raise LockError.File "./spack/lib/spack/llnl/util/lock.py", line 64, in _lock

fcntl.lockf(self._fd, op | fcntl.LOCK_NB)IOError: [Errno 38] Function not implemented

A nicer error message is TBD in future versions of Spack.

1.3.11 Spack on Cray

Spack differs slightly when used on a Cray system. The architecture spec can differentiate between the front-end andback-end processor and operating system. For example, on Edison at NERSC, the back-end target processor is “IvyBridge”, so you can specify to use the back-end this way:

$ spack install zlib target=ivybridge

You can also use the operating system to build against the back-end:

$ spack install zlib os=CNL10

Notice that the name includes both the operating system name and the major version number concatenated together.

Alternatively, if you want to build something for the front-end, you can specify the front-end target processor. Theprocessor for a login node on Edison is “Sandy bridge” so we specify on the command line like so:

$ spack install zlib target=sandybridge

And the front-end operating system is:

$ spack install zlib os=SuSE11

Cray compiler detection

Spack can detect compilers using two methods. For the front-end, we treat everything the same. The difference liesin back-end compiler detection. Back-end compiler detection is made via the Tcl module avail command. Once itdetects the compiler it writes the appropriate PrgEnv and compiler module name to compilers.yaml and sets the pathsto each compiler with Cray’s compiler wrapper names (i.e. cc, CC, ftn). During build time, Spack will load the correctPrgEnv and compiler module and will call appropriate wrapper.

The compilers.yaml config file will also differ. There is a modules section that is filled with the compiler’s Program-ming Environment and module name. On other systems, this field is empty []:

- compiler:modules:

- PrgEnv-intel- intel/15.0.109

As mentioned earlier, the compiler paths will look different on a Cray system. Since most compilers are invoked usingcc, CC and ftn, the paths for each compiler are replaced with their respective Cray compiler wrapper names:

paths:cc: cccxx: CC

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f77: ftnfc: ftn

As opposed to an explicit path to the compiler executable. This allows Spack to call the Cray compiler wrappersduring build time.

For more on compiler configuration, check out Compiler configuration.

Spack sets the default Cray link type to dynamic, to better match other other platforms. Individual packages can enablestatic linking (which is the default outside of Spack on cray systems) using the -static flag.

Setting defaults and using Cray modules

If you want to use default compilers for each PrgEnv and also be able to load cray external modules, you will need toset up a packages.yaml.

Here’s an example of an external configuration for cray modules:

packages:mpi:modules:

mpich@7.3.1%gcc@5.2.0 arch=cray_xc-haswell-CNL10: cray-mpichmpich@7.3.1%intel@16.0.0.109 arch=cray_xc-haswell-CNL10: cray-mpich

This tells Spack that for whatever package that depends on mpi, load the cray-mpich module into the environment.You can then be able to use whatever environment variables, libraries, etc, that are brought into the environment viamodule load.

You can set the default compiler that Spack can use for each compiler type. If you want to use the Cray defaults,then set them under all: in packages.yaml. In the compiler field, set the compiler specs in your order of preference.Whenever you build with that compiler type, Spack will concretize to that version.

Here is an example of a full packages.yaml used at NERSC

packages:mpi:modules:

mpich@7.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-mpichmpich@7.3.1%intel@16.0.0.109 arch=cray_xc-SuSE11-ivybridge: cray-mpich

buildable: Falsenetcdf:modules:

netcdf@4.3.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-netcdfnetcdf@4.3.3.1%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-netcdf

buildable: Falsehdf5:modules:

hdf5@1.8.14%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-hdf5hdf5@1.8.14%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-hdf5

buildable: Falseall:compiler: [gcc@5.2.0, intel@16.0.0.109]

Here we tell spack that whenever we want to build with gcc use version 5.2.0 or if we want to build with intelcompilers, use version 16.0.0.109. We add a spec for each compiler type for each cray modules. This ensures that foreach compiler on our system we can use that external module.

For more on external packages check out the section External Packages.

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1.3.12 Getting Help

spack help

If you don’t find what you need here, the help subcommand will print out out a list of all of spack’s options andsubcommands:

$ spack helpusage: spack [-h] [-d] [-D] [-k] [-m] [-p] [-v] [-V] SUBCOMMAND ...

Spack: the Supercomputing PACKage Manager.

spec expressions:PACKAGE [CONSTRAINTS]

CONSTRAINTS:[0;36m@version[0m[0;32m%compiler @compiler_version[0m[0;94m+variant[0m[0;31m-variant[0m or [0;31m~variant[0m[0;35m=architecture[0m[^DEPENDENCY [CONSTRAINTS] ...]

positional arguments:SUBCOMMANDactivate Activate a package extension.arch Print the architecture for this machinebootstrap Create a new installation of spack in another prefixcd cd to spack directories in the shell.checksum Checksum available versions of a package.clean Remove build stage and source tarball for packages.compiler Manage compilerscompilers List available compilers. Same as 'spack compiler list'.config Get and set configuration options.create Create a new package file from an archive URLdeactivate Deactivate a package extension.dependents Show installed packages that depend on another.diy Do-It-Yourself: build from an existing source directory.doc Run pydoc from within spack.edit Open package files in $EDITORenv Run a command with the install environment for a spec.extensions List extensions for package.fetch Fetch archives for packagesfind Find installed spack packagesgraph Generate graphs of package dependency relationships.help Get help on spack and its commandsinfo Get detailed information on a particular packageinstall Build and install packageslist List available spack packagesload Add package to environment using modules.location Print out locations of various directories used by Spackmd5 Calculate md5 checksums for files/urls.mirror Manage mirrors.module Manipulate module filespackage-list Print a list of all packages in reStructuredText.patch Patch expanded archive sources in preparation for installpkg Query packages associated with particular git revisions.providers List packages that provide a particular virtual package

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purge Remove temporary build files and/or downloaded archivespython Launch an interpreter as spack would launch a commandreindex Rebuild Spack's package database.repo Manage package source repositories.restage Revert checked out package source code.setup Create a configuration script and module, but don't build.spec print out abstract and concrete versions of a spec.stage Expand downloaded archive in preparation for installtest Run unit teststest-install Run package install as a unit test, output formatted results.uninstall Remove an installed packageunload Remove package from environment using module.unuse Remove package from environment using dotkit.url-parse Show parsing of a URL, optionally spider web for versions.urls Inspect urls used by packages in spack.use Add package to environment using dotkit.versions List available versions of a packageview Produce a single-rooted directory view of a spec.

optional arguments:-h, --help show this help message and exit-d, --debug Write out debug logs during compile-D, --pdb Run spack under the pdb debugger-k, --insecure Do not check ssl certificates when downloading.-m, --mock Use mock packages instead of real ones.-p, --profile Profile execution using cProfile.-v, --verbose Print additional output during builds-V, --version show program's version number and exit

Adding an argument, e.g. spack help <subcommand>, will print out usage information for a particular subcom-mand:

$ spack help installusage: spack install [-h] [-i] [-j JOBS] [--keep-prefix] [--keep-stage] [-n]

[-v] [--fake] [--dirty] [--run-tests]...

positional arguments:packages specs of packages to install

optional arguments:-h, --help show this help message and exit-i, --ignore-dependencies

Do not try to install dependencies of requestedpackages.

-j JOBS, --jobs JOBS Explicitly set number of make jobs. Default is #cpus.--keep-prefix Don't remove the install prefix if installation fails.--keep-stage Don't remove the build stage if installation succeeds.-n, --no-checksum Do not check packages against checksum-v, --verbose Display verbose build output while installing.--fake Fake install. Just remove prefix and create a fake

file.--dirty Install a package *without* cleaning the environment.--run-tests Run tests during installation of a package.

Alternately, you can use spack --help in place of spack help, or spack <subcommand> --help to gethelp on a particular subcommand.

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1.4 Packaging Guide

This guide is intended for developers or administrators who want to package software so that Spack can install it. Itassumes that you have at least some familiarity with Python, and that you’ve read the basic usage guide, especially thepart about specs.

There are two key parts of Spack:

1. Specs: expressions for describing builds of software, and

2. Packages: Python modules that describe how to build software according to a spec.

Specs allow a user to describe a particular build in a way that a package author can understand. Packages allowa the packager to encapsulate the build logic for different versions, compilers, options, platforms, and dependencycombinations in one place. Essentially, a package translates a spec into build logic.

Packages in Spack are written in pure Python, so you can do anything in Spack that you can do in Python. Python waschosen as the implementation language for two reasons. First, Python is becoming ubiquitous in the scientific softwarecommunity. Second, it’s a modern language and has many powerful features to help make package writing easy.

1.4.1 Creating & editing packages

spack create

The spack create command creates a directory with the package name and generates a package.py file with aboilerplate package template from a URL. The URL should point to a tarball or other software archive. In most cases,spack create plus a few modifications is all you need to get a package working.

Here’s an example:

$ spack create http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz

Spack examines the tarball URL and tries to figure out the name of the package to be created. Once the name isdetermined a directory in the appropriate repository is created with that name. Spack prefers, but does not require,that names be lower case so the directory name will be lower case when spack create generates it. In caseswhere it is desired to have mixed case or upper case simply rename the directory. Spack also tries to determine whatversion strings look like for this package. Using this information, it will try to find additional versions by spideringthe package’s webpage. If it finds multiple versions, Spack prompts you to tell it how many versions you want todownload and checksum:

$ spack create http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz==> This looks like a URL for cmake version 2.8.12.1.==> Creating template for package cmake==> Found 18 versions of cmake.

2.8.12.1 http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz2.8.12 http://www.cmake.org/files/v2.8/cmake-2.8.12.tar.gz2.8.11.2 http://www.cmake.org/files/v2.8/cmake-2.8.11.2.tar.gz...2.8.0 http://www.cmake.org/files/v2.8/cmake-2.8.0.tar.gz

Include how many checksums in the package file? (default is 5, q to abort)

Spack will automatically download the number of tarballs you specify (starting with the most recent) and checksumeach of them.

You do not have to download all of the versions up front. You can always choose to download just one tarball initially,and run spack checksum later if you need more.

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Note: If spack create fails to detect the package name correctly, you can try supplying it yourself, e.g.:

$ spack create --name cmake http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz

If it fails entirely, you can get minimal boilerplate by using spack edit –force, or you can manually create a directoryand package.py file for the package in var/spack/repos/builtin/packages.

Note: Spack can fetch packages from source code repositories, but, spack create will not currently create aboilerplate package from a repository URL. You will need to use spack edit –force and manually edit the version()directives to fetch from a repo. See Fetching from VCS repositories for details.

Let’s say you download 3 tarballs:

Include how many checksums in the package file? (default is 5, q to abort) 3==> Downloading...==> Fetching http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz###################################################################### 98.6%==> Fetching http://www.cmake.org/files/v2.8/cmake-2.8.12.tar.gz##################################################################### 96.7%==> Fetching http://www.cmake.org/files/v2.8/cmake-2.8.11.2.tar.gz#################################################################### 95.2%

Now Spack generates boilerplate code and opens a new package.py file in your favorite $EDITOR:

1 #2 # This is a template package file for Spack. We've put "FIXME"3 # next to all the things you'll want to change. Once you've handled4 # them, you can save this file and test your package like this:5 #6 # spack install cmake7 #8 # You can edit this file again by typing:9 #

10 # spack edit cmake11 #12 # See the Spack documentation for more information on packaging.13 # If you submit this package back to Spack as a pull request,14 # please first remove this boilerplate and all FIXME comments.15 #16 from spack import *17

18

19 class Cmake(Package):20 """FIXME: Put a proper description of your package here."""21

22 # FIXME: Add a proper url for your package's homepage here.23 homepage = "http://www.example.com"24 url = "http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz"25

26 version('2.8.12.1', '9d38cd4e2c94c3cea97d0e2924814acc')27 version('2.8.12', '105bc6d21cc2e9b6aff901e43c53afea')28 version('2.8.11.2', '6f5d7b8e7534a5d9e1a7664ba63cf882')29

30 # FIXME: Add dependencies if this package requires them.31 # depends_on("foo")32

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33 def install(self, spec, prefix):34 # FIXME: Modify the configure line to suit your build system here.35 configure("--prefix=" + prefix)36

37 # FIXME: Add logic to build and install here38 make()39 make("install")

The tedious stuff (creating the class, checksumming archives) has been done for you.

In the generated package, the download url attribute is already set. All the things you still need to change are markedwith FIXME labels. You can delete the commented instructions between the license and the first import statement afterreading them. The rest of the tasks you need to do are as follows:

1. Add a description.

Immediately inside the package class is a docstring in triple-quotes ("""). It’s used to generate the descriptionshown when users run spack info.

2. Change the homepage to a useful URL.

The homepage is displayed when users run spack info so that they can learn about packages.

3. Add depends_on() calls for the package’s dependencies.

depends_on tells Spack that other packages need to be built and installed before this one. See Dependencies.

4. Get the install() method working.

The install() method implements the logic to build a package. The code should look familiar; it is designedto look like a shell script. Specifics will differ depending on the package, and implementing the install methodis covered in detail later.

Before going into details, we’ll cover a few more basics.

spack edit

One of the easiest ways to learn to write packages is to look at existing ones. You can edit a package file by name withthe spack edit command:

$ spack edit cmake

So, if you used spack create to create a package, then saved and closed the result-ing file, you can get back to it with spack edit. The cmake package actually lives in$SPACK_ROOT/var/spack/repos/builtin/packages/cmake/package.py, but this provides amuch simpler shortcut and saves you the trouble of typing the full path.

If you try to edit a package that doesn’t exist, Spack will recommend using spack create or spack edit--force:

$ spack edit foo==> Error: No package 'foo'. Use spack create, or supply -f/--force to edit a new file.

spack edit --force

spack edit --force can be used to create a new, minimal boilerplate package:

$ spack edit -f foo

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Unlike spack create, which infers names and versions, and which actually downloads the tarball and checksumsit for you, spack edit --force has no such fanciness. It will substitute dummy values for you to fill in yourself:

1 from spack import *2

3 class Foo(Package):4 """Description"""5

6 homepage = "http://www.example.com"7 url = "http://www.example.com/foo-1.0.tar.gz"8

9 version('1.0', '0123456789abcdef0123456789abcdef')10

11 def install(self, spec, prefix):12 configure("--prefix=%s" % prefix)13 make()14 make("install")

This is useful when spack create cannot figure out the name and version of your package from the archive URL.

1.4.2 Naming & directory structure

This section describes how packages need to be named, and where they live in Spack’s directory structure. In general,spack create and spack edit handle creating package files for you, so you can skip most of the details here.

var/spack/repos/builtin/packages

A Spack installation directory is structured like a standard UNIX install prefix (bin, lib, include, var,opt, etc.). Most of the code for Spack lives in $SPACK_ROOT/lib/spack. Packages themselves live in$SPACK_ROOT/var/spack/repos/builtin/packages.

If you cd to that directory, you will see directories for each package:

$ cd $SPACK_ROOT/var/spack/repos/builtin/packages && lsImageMagickLuaJITMitosRSAMRAIackactiveharmonyadept-utilsadiosadol-c...

Each directory contains a file called package.py, which is where all the python code for the package goes. Forexample, the libelf package lives in:

$SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py

Alongside the package.py file, a package may contain extra directories or files (like patches) that it needs to build.

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Package Names

Packages are named after the directory containing package.py. It is preferred, but not required, that the directory,and thus the package name, are lower case. So, libelf‘s package.py lives in a directory called libelf. Thepackage.py file defines a class called Libelf, which extends Spack’s Package class. For example, here is$SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py:

1 from spack import *2

3 class Libelf(Package):4 """ ... description ... """5 homepage = ...6 url = ...7 version(...)8 depends_on(...)9

10 def install():11 ...

The directory name (libelf) determines the package name that users should provide on the command line. e.g., ifyou type any of these:

$ spack install libelf$ spack install libelf@0.8.13

Spack sees the package name in the spec and looks for libelf/package.py invar/spack/repos/builtin/packages. Likewise, if you say spack install py-numpy, thenSpack looks for py-numpy/package.py.

Spack uses the directory name as the package name in order to give packagers more freedom in naming their packages.Package names can contain letters, numbers, dashes, and underscores. Using a Python identifier (e.g., a class name ora module name) would make it difficult to support these options. So, you can name a package 3proxy or _foo andSpack won’t care. It just needs to see that name in the package spec.

Package class names

Spack loads package.py files dynamically, and it needs to find a special class name in the file for the load tosucceed. The class name (Libelf in our example) is formed by converting words separated by - or _ in the file nameto camel case. If the name starts with a number, we prefix the class name with _. Here are some examples:

Module Name Class Namefoo_bar FooBardocbook-xml DocbookXmlFooBar Foobar3proxy _3proxy

In general, you won’t have to remember this naming convention because spack create and spack edit handle the detailsfor you.

1.4.3 Adding new versions

The most straightforward way to add new versions to your package is to add a line like this in the package class:

1 class Foo(Package):2 url = 'http://example.com/foo-1.0.tar.gz'3 version('8.2.1', '4136d7b4c04df68b686570afa26988ac')4 ...

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Versions should be listed with the newest version first.

Version URLs

By default, each version’s URL is extrapolated from the url field in the package. For example, Spack is smart enoughto download version 8.2.1. of the Foo package above from http://example.com/foo-8.2.1.tar.gz.

If spack cannot extrapolate the URL from the url field by default, you can write your own URL generation algorithmin place of the url declaration. For example:

1 class Foo(Package):2 version('8.2.1', '4136d7b4c04df68b686570afa26988ac')3 ...4 def url_for_version(self, version):5 return 'http://example.com/version_%s/foo-%s.tar.gz' \6 % (version, version)7 ...

If a URL cannot be derived systematically, you can add an explicit URL for a particular version:

version('8.2.1', '4136d7b4c04df68b686570afa26988ac',url='http://example.com/foo-8.2.1-special-version.tar.gz')

For the URL above, you might have to add an explicit URL because the version can’t simply be substituted in theoriginal url to construct the new one for 8.2.1.

When you supply a custom URL for a version, Spack uses that URL verbatim and does not perform extrapolation.

Skipping the expand step

Spack normally expands archives automatically after downloading them. If you want to skip this step (e.g., for self-extracting executables and other custom archive types), you can add expand=False to a version directive.

version('8.2.1', '4136d7b4c04df68b686570afa26988ac',url='http://example.com/foo-8.2.1-special-version.tar.gz', expand=False)

When expand is set to False, Spack sets the current working directory to the directory containing the downloadedarchive before it calls your install method. Within install, the path to the downloaded archive is available asself.stage.archive_file.

Here is an example snippet for packages distributed as self-extracting archives. The example sets permissions on thedownloaded file to make it executable, then runs it with some arguments.

def install(self, spec, prefix):set_executable(self.stage.archive_file)installer = Executable(self.stage.archive_file)installer('--prefix=%s' % prefix, 'arg1', 'arg2', 'etc.')

Checksums

Spack uses a checksum to ensure that the downloaded package version is not corrupted or compromised. This is espe-cially important when fetching from insecure sources, like unencrypted http. By default, a package will not be installedif it doesn’t pass a checksum test (though you can override this with spack install --no-checksum).

Spack can currently support checksums using the MD5, SHA-1, SHA-224, SHA-256, SHA-384, and SHA-512 algo-rithms. It determines the algorithm to use based on the hash length.

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spack md5

If you have one or more files to checksum, you can use the spack md5 command to do it:

$ spack md5 foo-8.2.1.tar.gz foo-8.2.2.tar.gz==> 2 MD5 checksums:4136d7b4c04df68b686570afa26988ac foo-8.2.1.tar.gz1586b70a49dfe05da5fcc29ef239dce0 foo-8.2.2.tar.gz

spack md5 also accepts one or more URLs and automatically downloads the files for you:

$ spack md5 http://example.com/foo-8.2.1.tar.gz==> Trying to fetch from http://example.com/foo-8.2.1.tar.gz######################################################################## 100.0%==> 1 MD5 checksum:4136d7b4c04df68b686570afa26988ac foo-8.2.1.tar.gz

Doing this for lots of files, or whenever a new package version is released, is tedious. See spack checksum belowfor an automated version of this process.

spack checksum

If you want to add new versions to a package you’ve already created, this is automated with the spack checksumcommand. Here’s an example for libelf:

$ spack checksum libelf==> Found 16 versions of libelf.

0.8.13 http://www.mr511.de/software/libelf-0.8.13.tar.gz0.8.12 http://www.mr511.de/software/libelf-0.8.12.tar.gz0.8.11 http://www.mr511.de/software/libelf-0.8.11.tar.gz0.8.10 http://www.mr511.de/software/libelf-0.8.10.tar.gz0.8.9 http://www.mr511.de/software/libelf-0.8.9.tar.gz0.8.8 http://www.mr511.de/software/libelf-0.8.8.tar.gz0.8.7 http://www.mr511.de/software/libelf-0.8.7.tar.gz0.8.6 http://www.mr511.de/software/libelf-0.8.6.tar.gz0.8.5 http://www.mr511.de/software/libelf-0.8.5.tar.gz...0.5.2 http://www.mr511.de/software/libelf-0.5.2.tar.gz

How many would you like to checksum? (default is 5, q to abort)

This does the same thing that spack create does, but it allows you to go back and add new versions easily as youneed them (e.g., as they’re released). It fetches the tarballs you ask for and prints out a list of version commandsready to copy/paste into your package file:

==> Checksummed new versions of libelf:version('0.8.13', '4136d7b4c04df68b686570afa26988ac')version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7')version('0.8.11', 'e931910b6d100f6caa32239849947fbf')version('0.8.10', '9db4d36c283d9790d8fa7df1f4d7b4d9')

By default, Spack will search for new tarball downloads by scraping the parent directory of the tarball you gaveit. So, if your tarball is at http://example.com/downloads/foo-1.0.tar.gz, Spack will look inhttp://example.com/downloads/ for links to additional versions. If you need to search another path fordownload links, you can supply some extra attributes that control how your package finds new versions. See thedocumentation on attribute_list_url and attribute_list_depth.

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Note:

• This command assumes that Spack can extrapolate new URLs from an existing URL in the package, and thatSpack can find similar URLs on a webpage. If that’s not possible, e.g. if the package’s developers don’t nametheir tarballs consistently, you’ll need to manually add version calls yourself.

• For spack checksum to work, Spack needs to be able to import your package in Python. That means itcan’t have any syntax errors, or the import will fail. Use this once you’ve got your package in working order.

1.4.4 Fetching from VCS repositories

For some packages, source code is provided in a Version Control System (VCS) repository rather than in a tarball.Spack can fetch packages from VCS repositories. Currently, Spack supports fetching with Git, Mercurial (hg), andSubversion (SVN).

To fetch a package from a source repository, you add a version() call to your package with parameters indicatingthe repository URL and any branch, tag, or revision to fetch. See below for the parameters you’ll need for each VCSsystem.

Repositories and versions

The package author is responsible for coming up with a sensible name for each version to be fetched from a repository.For example, if you’re fetching from a tag like v1.0, you might call that 1.0. If you’re fetching a nameless git commitor an older subversion revision, you might give the commit an intuitive name, like develop for a developmentversion, or some-fancy-new-feature if you want to be more specific.

In general, it’s recommended to fetch tags or particular commits/revisions, NOT branches or the repository mainline,as branches move forward over time and you aren’t guaranteed to get the same thing every time you fetch a particularversion. Life isn’t always simple, though, so this is not strictly enforced.

When fetching from from the branch corresponding to the development version (often called master, trunk, ordev), it is recommended to call this version develop. Spack has special treatment for this version so that @developwill satisfy dependencies like depends_on(abc, when="@x.y.z:"). In other words, @develop is greaterthan any other version. The rationale is that certain features or options first appear in the development branch. There-fore if a package author wants to keep the package on the bleeding edge and provide support for new features, itis advised to use develop for such a version which will greatly simplify writing dependencies and version-relatedconditionals.

In some future release, Spack may support extrapolating repository versions as it does for tarball URLs, but currentlythis is not supported.

Git

Git fetching is enabled with the following parameters to version:

• git: URL of the git repository.

• tag: name of a tag to fetch.

• branch: name of a branch to fetch.

• commit: SHA hash (or prefix) of a commit to fetch.

• submodules: Also fetch submodules when checking out this repository.

Only one of tag, branch, or commit can be used at a time.

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Default branch To fetch a repository’s default branch:

class Example(Package):...version('develop', git='https://github.com/example-project/example.git')

This is not recommended, as the contents of the default branch change over time.

Tags To fetch from a particular tag, use the tag parameter along with git:

version('1.0.1', git='https://github.com/example-project/example.git',tag='v1.0.1')

Branches To fetch a particular branch, use branch instead:

version('experimental', git='https://github.com/example-project/example.git',branch='experimental')

This is not recommended, as the contents of branches change over time.

Commits Finally, to fetch a particular commit, use commit:

version('2014-10-08', git='https://github.com/example-project/example.git',commit='9d38cd4e2c94c3cea97d0e2924814acc')

This doesn’t have to be a full hash; you can abbreviate it as you’d expect with git:

version('2014-10-08', git='https://github.com/example-project/example.git',commit='9d38cd')

It may be useful to provide a saner version for commits like this, e.g. you might use the date as the version, asdone above. Or you could just use the abbreviated commit hash. It’s up to the package author to decide whatmakes the most sense.

Submodules

You can supply submodules=True to cause Spack to fetch submodules along with the repository atfetch time.

version('1.0.1', git='https://github.com/example-project/example.git',tag='v1.0.1', submdoules=True)

Installing

You can fetch and install any of the versions above as you’d expect, by using @<version> in a spec:

$ spack install example@2014-10-08

Git and other VCS versions will show up in the list of versions when a user runs spack info <package name>.

Mercurial

Fetching with mercurial works much like git, but you use the hg parameter.

Default Add the hg parameter with no revision:

version('develop', hg='https://jay.grs.rwth-aachen.de/hg/example')

Note that this is not recommended; try to fetch a particular revision instead.

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Revisions Add hg and revision parameters:

version('1.0', hg='https://jay.grs.rwth-aachen.de/hg/example',revision='v1.0')

Unlike git, which has special parameters for different types of revisions, you can use revision for branches,tags, and commits when you fetch with Mercurial.

As with git, you can fetch these versions using the spack install example@<version> command-line syn-tax.

Subversion

To fetch with subversion, use the svn and revision parameters:

Fetching the head Simply add an svn parameter to version:

version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk')

This is not recommended, as the head will move forward over time.

Fetching a revision To fetch a particular revision, add a revision to the version call:

version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk',revision=128)

Subversion branches are handled as part of the directory structure, so you can check out a branch or tag by changingthe url.

1.4.5 Expanding additional resources in the source tree

Some packages (most notably compilers) provide optional features if additional resources are expanded within theirsource tree before building. In Spack it is possible to describe such a need with the resource directive :

resource(name='cargo',git='https://github.com/rust-lang/cargo.git',tag='0.10.0',destination='cargo'

)

Based on the keywords present among the arguments the appropriate FetchStrategy will be used for the resource.The keyword destination is relative to the source root of the package and should point to where the resource is tobe expanded.

1.4.6 Automatic caching of files fetched during installation

Spack maintains a cache (described here) which saves files retrieved during package installations to avoid re-downloading in the case that a package is installed with a different specification (but the same version) or reinstalledon account of a change in the hashing scheme.

1.4.7 Licensed software

In order to install licensed software, Spack needs to know a few more details about a package. The following classattributes should be defined.

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license_required

Boolean. If set to True, this software requires a license. If set to False, all of the following attributes will beignored. Defaults to False.

license_comment

String. Contains the symbol used by the license manager to denote a comment. Defaults to #.

license_files

List of strings. These are files that the software searches for when looking for a license. All file paths must be relative tothe installation directory. More complex packages like Intel may require multiple licenses for individual components.Defaults to the empty list.

license_vars

List of strings. Environment variables that can be set to tell the software where to look for a license if it is not in theusual location. Defaults to the empty list.

license_url

String. A URL pointing to license setup instructions for the software. Defaults to the empty string.

For example, let’s take a look at the package for the PGI compilers.

# Licensinglicense_required = Truelicense_comment = '#'license_files = ['license.dat']license_vars = ['PGROUPD_LICENSE_FILE', 'LM_LICENSE_FILE']license_url = 'http://www.pgroup.com/doc/pgiinstall.pdf'

As you can see, PGI requires a license. Its license manager, FlexNet, uses the # symbol to denote a comment. Itexpects the license file to be named license.dat and to be located directly in the installation prefix. If you wouldlike the installation file to be located elsewhere, simply set PGROUPD_LICENSE_FILE or LM_LICENSE_FILEafter installation. For further instructions on installation and licensing, see the URL provided.

Let’s walk through a sample PGI installation to see exactly what Spack is and isn’t capable of. Since PGI does notprovide a download URL, it must be downloaded manually. It can either be added to a mirror or located in the currentdirectory when spack install pgi is run. See Mirrors for instructions on setting up a mirror.

After running spack install pgi, the first thing that will happen is Spack will create a global license file locatedat $SPACK_ROOT/etc/spack/licenses/pgi/license.dat. It will then open up the file using the editorset in $EDITOR, or vi if unset. It will look like this:

# A license is required to use pgi.## The recommended solution is to store your license key in this global# license file. After installation, the following symlink(s) will be# added to point to this file (relative to the installation prefix):## license.dat#

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# Alternatively, use one of the following environment variable(s):## PGROUPD_LICENSE_FILE# LM_LICENSE_FILE## If you choose to store your license in a non-standard location, you may# set one of these variable(s) to the full pathname to the license file, or# port@host if you store your license keys on a dedicated license server.# You will likely want to set this variable in a module file so that it# gets loaded every time someone tries to use pgi.## For further information on how to acquire a license, please refer to:## http://www.pgroup.com/doc/pgiinstall.pdf## You may enter your license below.

You can add your license directly to this file, or tell FlexNet to use a license stored on a separate license server. Hereis an example that points to a license server called licman1:

SERVER licman1.mcs.anl.gov 00163eb7fba5 27200USE_SERVER

If your package requires the license to install, you can reference the location of this global license usingself.global_license_file. After installation, symlinks for all of the files given in license_files willbe created, pointing to this global license. If you install a different version or variant of the package, Spack willautomatically detect and reuse the already existing global license.

If the software you are trying to package doesn’t rely on license files, Spack will print a warning message, letting theuser know that they need to set an environment variable or pointing them to installation documentation.

1.4.8 Patches

Depending on the host architecture, package version, known bugs, or other issues, you may need to patch your softwareto get it to build correctly. Like many other package systems, spack allows you to store patches alongside your packagefiles and apply them to source code after it’s downloaded.

patch

You can specify patches in your package file with the patch() directive. patch looks like this:

class Mvapich2(Package):...patch('ad_lustre_rwcontig_open_source.patch', when='@1.9:')

The first argument can be either a URL or a filename. It specifies a patch file that should be applied to your source. Ifthe patch you supply is a filename, then the patch needs to live within the spack source tree. For example, the patchabove lives in a directory structure like this:

$SPACK_ROOT/var/spack/repos/builtin/packages/mvapich2/

package.pyad_lustre_rwcontig_open_source.patch

If you supply a URL instead of a filename, the patch will be fetched from the URL and then applied to your sourcecode.

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Warning: It is generally better to use a filename rather than a URL for your patch. Patches fetched from URLsare not currently checksummed, and adding checksums for them is tedious for the package builder. File patchesgo into the spack repository, which gives you git’s integrity guarantees. URL patches may be removed in a futurespack version.

patch can take two options keyword arguments. They are:

when

If supplied, this is a spec that tells spack when to apply the patch. If the installed package spec matches this spec, thepatch will be applied. In our example above, the patch is applied when mvapich is at version 1.9 or higher.

level

This tells spack how to run the patch command. By default, the level is 1 and spack runs patch -p 1. If level is2, spack will run patch -p 2, and so on.

A lot of people are confused by level, so here’s a primer. If you look in your patch file, you may see something likethis:

1 --- a/src/mpi/romio/adio/ad_lustre/ad_lustre_rwcontig.c 2013-12-10 12:05:44.806417000 -08002 +++ b/src/mpi/romio/adio/ad_lustre/ad_lustre_rwcontig.c 2013-12-10 11:53:03.295622000 -08003 @@ -8,7 +8,7 @@4 * Copyright (C) 2008 Sun Microsystems, Lustre group5 \*/6

7 -#define _XOPEN_SOURCE 6008 +//#define _XOPEN_SOURCE 6009 #include <stdlib.h>

10 #include <malloc.h>11 #include "ad_lustre.h"

Lines 1-2 show paths with synthetic a/ and b/ prefixes. These are placeholders for the two mvapich2 sourcedirectories that diff compared when it created the patch file. This is git’s default behavior when creating patch files,but other programs may behave differently.

-p1 strips off the first level of the prefix in both paths, allowing the patch to be applied from the root of an expandedmvapich2 archive. If you set level to 2, it would strip off src, and so on.

It’s generally easier to just structure your patch file so that it applies cleanly with -p1, but if you’re using a patch youdidn’t create yourself, level can be handy.

Patch functions

In addition to supplying patch files, you can write a custom function to patch a package’s source. For example, thepy-pyside package contains some custom code for tweaking the way the PySide build handles RPATH:

1 def patch(self):2 """Undo PySide RPATH handling and add Spack RPATH."""3 # Figure out the special RPATH4 pypkg = self.spec['python'].package5 rpath = self.rpath6 rpath.append(os.path.join(7 self.prefix, pypkg.site_packages_dir, 'PySide'))

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8

9 # Add Spack's standard CMake args to the sub-builds.10 # They're called BY setup.py so we have to patch it.11 filter_file(12 r'OPTION_CMAKE,',13 r'OPTION_CMAKE, ' + (14 '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", '15 '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)),16 'setup.py')17

18 # PySide tries to patch ELF files to remove RPATHs19 # Disable this and go with the one we set.20 if self.spec.satisfies('@1.2.4:'):21 rpath_file = 'setup.py'22 else:23 rpath_file = 'pyside_postinstall.py'24

25 filter_file(r'(^\s*)(rpath_cmd\(.*\))', r'\1#\2', rpath_file)26

27 # TODO: rpath handling for PySide 1.2.4 still doesn't work.28 # PySide can't find the Shiboken library, even though it comes29 # bundled with it and is installed in the same directory.30

31 # PySide does not provide official support for32 # Python 3.5, but it should work fine33 filter_file("'Programming Language :: Python :: 3.4'",34 "'Programming Language :: Python :: 3.4',\r\n "35 "'Programming Language :: Python :: 3.5'",36 "setup.py")

A patch function, if present, will be run after patch files are applied and before install() is run.

You could put this logic in install(), but putting it in a patch function gives you some benefits. First, spack ensuresthat the patch() function is run once per code checkout. That means that if you run install, hit ctrl-C, and run installagain, the code in the patch function is only run once. Also, you can tell Spack to run only the patching part of thebuild using the spack patch command.

1.4.9 Handling RPATHs

Spack installs each package in a way that ensures that all of its dependencies are found whenit runs. It does this using RPATHs. An RPATH is a search path, stored in a binary (anexecutable or library), that tells the dynamic loader where to find its dependencies at run-time. You may be familiar with LD_LIBRARY_PATH on Linux or DYLD_LIBRARY_PATH<https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/dyld.1.html> onMac OS X. RPATH is similar to these paths, in that it tells the loader where to find libraries. Unlike them, it isembedded in the binary and not set in each user’s environment.

RPATHs in Spack are handled in one of three ways:

1. For most packages, RPATHs are handled automatically using Spack’s compiler wrappers. These wrappers areset in standard variables like CC, CXX, F77, and FC, so most build systems (autotools and many gmake systems)pick them up and use them.

2. CMake also respects Spack’s compiler wrappers, but many CMake builds have logic to overwrite RPATHs whenbinaries are installed. Spack provides the std_cmake_args variable, which includes parameters necessaryfor CMake build use the right installation RPATH. It can be used like this when cmake is invoked:

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class MyPackage(Package):...def install(self, spec, prefix):

cmake('..', *std_cmake_args)make()make('install')

3. If you need to modify the build to add your own RPATHs, you can use the self.rpath property of yourpackage, which will return a list of all the RPATHs that Spack will use when it links. You can see this how thisis used in the PySide example above.

1.4.10 Finding new versions

You’ve already seen the homepage and url package attributes:

1 from spack import *2

3

4 class Mpich(Package):5 """MPICH is a high performance and widely portable implementation of6 the Message Passing Interface (MPI) standard."""7 homepage = "http://www.mpich.org"8 url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"

These are class-level attributes used by Spack to show users information about the package, and to determine whereto download its source code.

Spack uses the tarball URL to extrapolate where to find other tarballs of the same package (e.g. in spack checksum,but this does not always work. This section covers ways you can tell Spack to find tarballs elsewhere.

list_url

When spack tries to find available versions of packages (e.g. with spack checksum), it spiders the parent directory ofthe tarball in the url attribute. For example, for libelf, the url is:

url = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"

Here, Spack spiders http://www.mr511.de/software/ to find similar tarball links and ultimately to make alist of available versions of libelf.

For many packages, the tarball’s parent directory may be unlistable, or it may not contain any links to source codearchives. In fact, many times additional package downloads aren’t even available in the same directory as the downloadURL.

For these, you can specify a separate list_url indicating the page to search for tarballs. For example, libdwarfhas the homepage as the list_url, because that is where links to old versions are:

1 class Libdwarf(Package):2 homepage = "http://www.prevanders.net/dwarf.html"3 url = "http://www.prevanders.net/libdwarf-20130729.tar.gz"4 list_url = homepage

list_depth

libdwarf and many other packages have a listing of available versions on a single webpage, but not all do. Forexample, mpich has a tarball URL that looks like this:

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url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"

But its downloads are in many different subdirectories of http://www.mpich.org/static/downloads/.So, we need to add a list_url and a list_depth attribute:

1 class Mpich(Package):2 homepage = "http://www.mpich.org"3 url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"4 list_url = "http://www.mpich.org/static/downloads/"5 list_depth = 2

By default, Spack only looks at the top-level page available at list_url. list_depth tells it to follow up to 2levels of links from the top-level page. Note that here, this implies two levels of subdirectories, as the mpich websiteis structured much like a filesystem. But list_depth really refers to link depth when spidering the page.

1.4.11 Parallel builds

By default, Spack will invoke make() with a -j <njobs> argument, so that builds run in parallel. It figures outhow many jobs to run by determining how many cores are on the host machine. Specifically, it uses the number ofCPUs reported by Python’s multiprocessing.cpu_count().

If a package does not build properly in parallel, you can override this setting by adding parallel = False toyour package. For example, OpenSSL’s build does not work in parallel, so its package looks like this:

1 class Openssl(Package):2 homepage = "http://www.openssl.org"3 url = "http://www.openssl.org/source/openssl-1.0.1h.tar.gz"4

5 version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')6 depends_on("zlib")7

8 parallel = False

Similarly, you can disable parallel builds only for specific make commands, as libdwarf does:

1 class Libelf(Package):2 ...3

4 def install(self, spec, prefix):5 configure("--prefix=" + prefix,6 "--enable-shared",7 "--disable-dependency-tracking",8 "--disable-debug")9 make()

10

11 # The mkdir commands in libelf's install can fail in parallel12 make("install", parallel=False)

The first make will run in parallel here, but the second will not. If you set parallel to False at the package level,then each call to make() will be sequential by default, but packagers can call make(parallel=True) to overrideit.

1.4.12 Dependencies

We’ve covered how to build a simple package, but what if one package relies on another package to build? How doyou express that in a package file? And how do you refer to the other package in the build script for your own package?

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Spack makes this relatively easy. Let’s take a look at the libdwarf package to see how it’s done:

1 class Libdwarf(Package):2 homepage = "http://www.prevanders.net/dwarf.html"3 url = "http://www.prevanders.net/libdwarf-20130729.tar.gz"4 list_url = homepage5

6 version('20130729', '4cc5e48693f7b93b7aa0261e63c0e21d')7 ...8

9 depends_on("libelf")10

11 def install(self, spec, prefix):12 ...

depends_on()

The highlighted depends_on(’libelf’) call tells Spack that it needs to build and install the libelf packagebefore it builds libdwarf. This means that in your install() method, you are guaranteed that libelf has beenbuilt and installed successfully, so you can rely on it for your libdwarf build.

Dependency specs

depends_on doesn’t just take the name of another package. It takes a full spec. This means that you can restrict theversions or other configuration options of libelf that libdwarf will build with. Here’s an example. Suppose thatin the libdwarf package you write:

depends_on("libelf@0.8:")

Now libdwarf will require a version of libelf version 0.8 or higher in order to build. If some versions oflibelf are installed but they are all older than this, then Spack will build a new version of libelf that satisfies thespec’s version constraint, and it will build libdwarf with that one. You could just as easily provide a version range:

depends_on("libelf@0.8.2:0.8.4:")

Or a requirement for a particular variant or compiler flags:

depends_on("libelf@0.8+debug")depends_on('libelf debug=True')depends_on('libelf cppflags="-fPIC"')

Both users and package authors can use the same spec syntax to refer to different package configurations. Users usethe spec syntax on the command line to find installed packages or to install packages with particular constraints, andpackage authors can use specs to describe relationships between packages.

Additionally, dependencies may be specified for specific use cases:

depends_on("cmake", type="build")depends_on("libelf", type=("build", "link"))depends_on("python", type="run")

The dependency types are:

• “build”: made available during the project’s build. The package will be added to PATH, the compiler includepaths, and PYTHONPATH. Other projects which depend on this one will not have these modified (buildingproject X doesn’t need project Y’s build dependencies).

• “link”: the project is linked to by the project. The package will be added to the current package’s rpath.

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• “run”: the project is used by the project at runtime. The package will be added to PATH and PYTHONPATH.

If not specified, type is assumed to be ("build", "link"). This is the common case for compiled languageusage. Also available are the aliases "alldeps" for all dependency types and "nolink" (("build", "run"))for use by dependencies which are not expressed via a linker (e.g., Python or Lua module loading).

setup_dependent_environment()

Spack provides a mechanism for dependencies to provide variables that can be used in their dependents’ build. Anypackage can declare a setup_dependent_environment() function, and this function will be called before theinstall() method of any dependent packages. This allows dependencies to set up environment variables and otherproperties to be used by dependents.

The function declaration should look like this:

class Qt(Package):...def setup_dependent_environment(self, module, spec, dep_spec):

"""Dependencies of Qt find it using the QTDIR environment variable."""os.environ['QTDIR'] = self.prefix

Here, the Qt package sets the QTDIR environment variable so that packages that depend on a particular Qt installationwill find it.

The arguments to this function are:

• module: the module of the dependent package, where global properties can be assigned.

• spec: the spec of the dependency package (the one the function is called on).

• dep_spec: the spec of the dependent package (i.e. dep_spec depends on spec).

A good example of using these is in the Python package:

1 def setup_dependent_environment(self, spack_env, run_env, extension_spec):2 """Set PYTHONPATH to include site-packages dir for the3 extension and any other python extensions it depends on."""4 pythonhome = self.prefix5 spack_env.set('PYTHONHOME', pythonhome)6

7 python_paths = []8 for d in extension_spec.traverse(deptype=nolink, deptype_query='run'):9 if d.package.extends(self.spec):

10 python_paths.append(join_path(d.prefix,11 self.site_packages_dir))12

13 pythonpath = ':'.join(python_paths)14 spack_env.set('PYTHONPATH', pythonpath)15

16 # For run time environment set only the path for17 # extension_spec and prepend it to PYTHONPATH18 if extension_spec.package.extends(self.spec):19 run_env.prepend_path('PYTHONPATH', join_path(20 extension_spec.prefix, self.site_packages_dir))

The first thing that happens here is that the python command is inserted into module scope of the dependent. Thisallows most python packages to have a very simple install method, like this:

def install(self, spec, prefix):python('setup.py', 'install', '--prefix={0}'.format(prefix))

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Python’s setup_dependent_environment method also sets up some other variables, creates a directory, andsets up the PYTHONPATH so that dependent packages can find their dependencies at build time.

1.4.13 Extensions

Spack’s support for package extensions is documented extensively in Extensions & Python support. This sectiondocuments how to make your own extendable packages and extensions.

To support extensions, a package needs to set its extendable property to True, e.g.:

class Python(Package):...extendable = True...

To make a package into an extension, simply add simply add an extends call in the package definition, and pass itthe name of an extendable package:

class PyNumpy(Package):...extends('python')...

Now, the py-numpy package can be used as an argument to spack activate. When it is activated, all the filesin its prefix will be symbolically linked into the prefix of the python package.

Many packages produce Python extensions for some variants, but not others: they should extend python only if theappropriate variant(s) are selected. This may be accomplished with conditional extends() declarations:

class FooLib(Package):variant('python', default=True, description= \

'Build the Python extension Module')extends('python', when='+python')...

Sometimes, certain files in one package will conflict with those in another, which means they cannot both be activated(symlinked) at the same time. In this case, you can tell Spack to ignore those files when it does the activation:

class PySncosmo(Package):...# py-sncosmo binaries are duplicates of those from py-astropyextends('python', ignore=r'bin/.*')depends_on('py-astropy')...

The code above will prevent everything in the $prefix/bin/ directory from being linked in at activation time.

Note: You can call either depends_on or extends on any one package, but not both. For example you cannot bothdepends_on(’python’) and extends(python) in the same package. extends implies depends_on.

Activation & deactivation

Spack’s Package class has default activate and deactivate implementations that handle symbolically linkingextensions’ prefixes into the directory of the parent package. However, extendable packages can override these meth-ods to add custom activate/deactivate logic of their own. For example, the activate and deactivate methods

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in the Python class use the symbolic linking, but they also handle details surrounding Python’s .pth files, and otheraspects of Python packaging.

Spack’s extensions mechanism is designed to be extensible, so that other packages (like Ruby, R, Perl, etc.) canprovide their own custom extension management logic, as they may not handle modules the same way that Pythondoes.

Let’s look at Python’s activate function:

1 def activate(self, ext_pkg, **args):2 ignore = self.python_ignore(ext_pkg, args)3 args.update(ignore=ignore)4

5 super(Python, self).activate(ext_pkg, **args)6

7 exts = spack.install_layout.extension_map(self.spec)8 exts[ext_pkg.name] = ext_pkg.spec9 self.write_easy_install_pth(exts)

This function is called on the extendee (Python). It first calls activate in the superclass, which handles sym-linking the extension package’s prefix into this package’s prefix. It then does some special handling of theeasy-install.pth file, part of Python’s setuptools.

Deactivate behaves similarly to activate, but it unlinks files:

1 def deactivate(self, ext_pkg, **args):2 args.update(ignore=self.python_ignore(ext_pkg, args))3 super(Python, self).deactivate(ext_pkg, **args)4

5 exts = spack.install_layout.extension_map(self.spec)6 # Make deactivate idempotent7 if ext_pkg.name in exts:8 del exts[ext_pkg.name]9 self.write_easy_install_pth(exts)

Both of these methods call some custom functions in the Python package. See the source for Spack’s Python packagefor details.

Activation arguments

You may have noticed that the activate function defined above takes keyword arguments. These are the keywordarguments from extends(), and they are passed to both activate and deactivate.

This capability allows an extension to customize its own activation by passing arguments to the extendee. Extendeescan likewise implement custom activate() and deactivate() functions to suit their needs.

The only keyword argument supported by default is the ignore argument, which can take a regex, list of regexes, ora predicate to determine which files not to symlink during activation.

1.4.14 Virtual dependencies

In some cases, more than one package can satisfy another package’s dependency. One way this can happen is if apackage depends on a particular interface, but there are multiple implementations of the interface, and the packagecould be built with any of them. A very common interface in HPC is the Message Passing Interface (MPI), which isused in many large-scale parallel applications.

MPI has several different implementations (e.g., MPICH, OpenMPI, and MVAPICH) and scientific applications can bebuilt with any one of them. Complicating matters, MPI does not have a standardized ABI, so a package built with one

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implementation cannot simply be relinked with another implementation. Many package managers handle interfaceslike this by requiring many similar package files, e.g., foo, foo-mvapich, foo-mpich, but Spack avoids thisexplosion of package files by providing support for virtual dependencies.

provides

In Spack, mpi is handled as a virtual package. A package like mpileaks can depend on it just like any otherpackage, by supplying a depends_on call in the package definition. For example:

1 class Mpileaks(Package):2 homepage = "https://github.com/hpc/mpileaks"3 url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"4

5 version('1.0', '8838c574b39202a57d7c2d68692718aa')6

7 depends_on("mpi")8 depends_on("adept-utils")9 depends_on("callpath")

Here, callpath and adept-utils are concrete packages, but there is no actual package file for mpi, so we say itis a virtual package. The syntax of depends_on, is the same for both. If we look inside the package file of an MPIimplementation, say MPICH, we’ll see something like this:

class Mpich(Package):provides('mpi')...

The provides("mpi") call tells Spack that the mpich package can be used to satisfy the dependency of anypackage that depends_on(’mpi’).

Versioned Interfaces

Just as you can pass a spec to depends_on, so can you pass a spec to provides to add constraints. This allowsSpack to support the notion of versioned interfaces. The MPI standard has gone through many revisions, each withnew functions added, and each revision of the standard has a version number. Some packages may require a recentimplementation that supports MPI-3 functions, but some MPI versions may only provide up to MPI-2. Others mayneed MPI 2.1 or higher. You can indicate this by adding a version constraint to the spec passed to provides:

provides("mpi@:2")

Suppose that the above provides call is in the mpich2 package. This says that mpich2 provides MPI support upto version 2, but if a package depends_on("mpi@3"), then Spack will not build that package with mpich2.

provides when

The same package may provide different versions of an interface depending on its version. Above, we simplified theprovides call in mpich to make the explanation easier. In reality, this is how mpich calls provides:

provides('mpi@:3', when='@3:')provides('mpi@:1', when='@1:')

The when argument to provides allows you to specify optional constraints on the providing package, or theprovider. The provider only provides the declared virtual spec when it matches the constraints in the when clause.Here, when mpich is at version 3 or higher, it provides MPI up to version 3. When mpich is at version 1 or higher,it provides the MPI virtual package at version 1.

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The when qualifier ensures that Spack selects a suitably high version of mpich to satisfy some other package thatdepends_on a particular version of MPI. It will also prevent a user from building with too low a version of mpich.For example, suppose the package foo declares this:

class Foo(Package):...depends_on('mpi@2')

Suppose a user invokes spack install like this:

$ spack install foo ^mpich@1.0

Spack will fail with a constraint violation, because the version of MPICH requested is too low for the mpi requirementin foo.

1.4.15 Abstract & concrete specs

Now that we’ve seen how spec constraints can be specified on the command line and within package definitions, wecan talk about how Spack puts all of this information together. When you run this:

$ spack install mpileaks ^callpath@1.0+debug ^libelf@0.8.11

Spack parses the command line and builds a spec from the description. The spec says that mpileaks should bebuilt with the callpath library at 1.0 and with the debug option enabled, and with libelf version 0.8.11. Spackwill also look at the depends_on calls in all of these packages, and it will build a spec from that. The specs fromthe command line and the specs built from package descriptions are then combined, and the constraints are checkedagainst each other to make sure they’re satisfiable.

What we have after this is done is called an abstract spec. An abstract spec is partially specified. In other words, itcould describe more than one build of a package. Spack does this to make things easier on the user: they should onlyhave to specify as much of the package spec as they care about. Here’s an example partial spec DAG, based on theconstraints above:

mpileaks^callpath@1.0+debug

^dyninst^libdwarf

^libelf@0.8.11^mpi

mpileaks

mpi

callpath@1.0+debugdyninst

libdwarf

libelf@0.8.11

This diagram shows a spec DAG output as a tree, where successive levels of indentation represent a depends-onrelationship. In the above DAG, we can see some packages annotated with their constraints, and some packages withno annotations at all. When there are no annotations, it means the user doesn’t care what configuration of that packageis built, just so long as it works.

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Concretization

An abstract spec is useful for the user, but you can’t install an abstract spec. Spack has to take the abstract spec and “fillin” the remaining unspecified parts in order to install. This process is called concretization. Concretization happensin between the time the user runs spack install and the time the install() method is called. The concretizedversion of the spec above might look like this:

mpileaks@2.3%gcc@4.7.3 arch=linux-debian7-x86_64^callpath@1.0%gcc@4.7.3+debug arch=linux-debian7-x86_64

^dyninst@8.1.2%gcc@4.7.3 arch=linux-debian7-x86_64^libdwarf@20130729%gcc@4.7.3 arch=linux-debian7-x86_64

^libelf@0.8.11%gcc@4.7.3 arch=linux-debian7-x86_64^mpich@3.0.4%gcc@4.7.3 arch=linux-debian7-x86_64

mpileaks@2.3%gcc@4.7.3

arch=linux-debian7-x86_64

mpich@3.0.4%gcc@4.7.3

arch=linux-debian7-x86_64

callpath@1.0%gcc@4.7.3+debug

arch=linux-debian7-x86_64dyninst@8.1.2%gcc@4.7.3

arch=linux-debian7-x86_64

libdwarf@20130729%gcc@4.7.3

arch=linux-debian7-x86_64 libelf@0.8.11%gcc@4.7.3

arch=linux-debian7-x86_64

Here, all versions, compilers, and platforms are filled in, and there is a single version (no version ranges) for eachpackage. All decisions about configuration have been made, and only after this point will Spack call the install()method for your package.

Concretization in Spack is based on certain selection policies that tell Spack how to select, e.g., a version, when one isnot specified explicitly. Concretization policies are discussed in more detail in Configuration. Sites using Spack cancustomize them to match the preferences of their own users.

spack spec

For an arbitrary spec, you can see the result of concretization by running spack spec. For example:

$ spack spec dyninst@8.0.1dyninst@8.0.1

^libdwarf^libelf

dyninst@8.0.1%gcc@4.7.3 arch=linux-debian7-x86_64^libdwarf@20130729%gcc@4.7.3 arch=linux-debian7-x86_64

^libelf@0.8.13%gcc@4.7.3 arch=linux-debian7-x86_64

This is useful when you want to know exactly what Spack will do when you ask for a particular spec.

Concretization Policies

A user may have certain preferences for how packages should be concretized on their system. For example, one usermay prefer packages built with OpenMPI and the Intel compiler. Another user may prefer packages be built withMVAPICH and GCC.

See the Concretization Preferences section for more details.

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1.4.16 Implementing the install method

The last element of a package is its install() method. This is where the real work of installation happens, and it’sthe main part of the package you’ll need to customize for each piece of software.

1 def install(self, spec, prefix):2 configure("--prefix=" + prefix,3 "--enable-shared",4 "--disable-dependency-tracking",5 "--disable-debug")6 make()7

8 # The mkdir commands in libelf's install can fail in parallel9 make("install", parallel=False)

install takes a spec: a description of how the package should be built, and a prefix: the path to the directorywhere the software should be installed.

Spack provides wrapper functions for configure and make so that you can call them in a similar way to how you’dcall a shell command. In reality, these are Python functions. Spack provides these functions to make writing packagesmore natural. See the section on shell wrappers.

Now that the metadata is out of the way, we can move on to the install() method. When a user runs spackinstall, Spack fetches an archive for the correct version of the software, expands the archive, and sets the currentworking directory to the root directory of the expanded archive. It then instantiates a package object and calls theinstall() method.

The install() signature looks like this:

class Foo(Package):def install(self, spec, prefix):

...

The parameters are as follows:

self For those not used to Python instance methods, this is the package itself. In this case it’s an instance of Foo,which extends Package. For API docs on Package objects, see Package.

spec This is the concrete spec object created by Spack from an abstract spec supplied by the user. It describes whatshould be installed. It will be of type Spec.

prefix This is the path that your install method should copy build targets into. It acts like a string, but it’s actuallyits own special type, Prefix.

spec and prefix are passed to install for convenience. spec is also available as an attribute on the package(self.spec), and prefix is actually an attribute of spec (spec.prefix).

As mentioned in The install environment, you will usually not need to refer to dependencies explicitly in your packagefile, as the compiler wrappers take care of most of the heavy lifting here. There will be times, though, when youneed to refer to the install locations of dependencies, or when you need to do something different depending on theversion, compiler, dependencies, etc. that your package is built with. These parameters give you access to this type ofinformation.

1.4.17 The install environment

In general, you should not have to do much differently in your install method than you would when installing a packageon the command line. In fact, you may need to do less than you would on the command line.

Spack tries to set environment variables and modify compiler calls so that it appears to the build system that you’rebuilding with a standard system install of everything. Obviously that’s not going to cover all build systems, but it

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should make it easy to port packages to Spack if they use a standard build system. Usually with autotools or cmake,building and installing is easy. With builds that use custom Makefiles, you may need to add logic to modify themakefiles.

The remainder of the section covers the way Spack’s build environment works.

Environment variables

Spack sets a number of standard environment variables that serve two purposes:

1. Make build systems use Spack’s compiler wrappers for their builds.

2. Allow build systems to find dependencies more easily

The Compiler environment variables that Spack sets are:

Variable PurposeCC C compilerCXX C++ compilerF77 Fortran 77 compilerFC Fortran 90 and above compiler

All of these are standard variables respected by most build systems. If your project uses Autotools or CMake,then it should pick them up automatically when you run configure or cmake in the install() function. Manytraditional builds using GNU Make and BSD make also respect these variables, so they may work with these systems.

If your build system does not automatically pick these variables up from the environment, then you can simply passthem on the command line or use a patch as part of your build process to get the correct compilers into the project’sbuild system. There are also some file editing commands you can use – these are described later in the section on filemanipulation.

In addition to the compiler variables, these variables are set before entering install() so that packages can locatedependencies easily:

PATH Set to point to /bin directories of dependenciesCMAKE_PREFIX_PATH Path to dependency prefixes for CMakePKG_CONFIG_PATH Path to any pkgconfig directories for dependenciesPYTHONPATH Path to site-packages dir of any python dependencies

PATH is set up to point to dependencies /bin directories so that you can use tools installed by dependency packagesat build time. For example, $MPICH_ROOT/bin/mpicc is frequently used by dependencies of mpich.

CMAKE_PREFIX_PATH contains a colon-separated list of prefixes where cmakewill search for dependency librariesand headers. This causes all standard CMake find commands to look in the paths of your dependencies, so you do nothave to manually specify arguments like -DDEPENDENCY_DIR=/path/to/dependency to cmake. More onthis is in the CMake documentation.

PKG_CONFIG_PATH is for packages that attempt to discover dependencies using the GNU pkg-config tool. It issimilar to CMAKE_PREFIX_PATH in that it allows a build to automatically discover its dependencies.

If you want to see the environment that a package will build with, or if you want to run commands in that environmentto test them out, you can use the spack env command, documented below.

Compiler interceptors

As mentioned, CC, CXX, F77, and FC are set to point to Spack’s compiler wrappers. These are simply called cc,c++, f77, and f90, and they live in $SPACK_ROOT/lib/spack/env.

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$SPACK_ROOT/lib/spack/env is added first in the PATH environment variable when install() runs so thatsystem compilers are not picked up instead.

All of these compiler wrappers point to a single compiler wrapper script that figures out which real compiler it shouldbe building with. This comes either from spec concretization or from a user explicitly asking for a particular compilerusing, e.g., %intel on the command line.

In addition to invoking the right compiler, the compiler wrappers add flags to the compile line so that dependenciescan be easily found. These flags are added for each dependency, if they exist:

Compile-time library search paths * -L$dep_prefix/lib * -L$dep_prefix/lib64

Runtime library search paths (RPATHs) * $rpath_flag$dep_prefix/lib *$rpath_flag$dep_prefix/lib64

Include search paths * -I$dep_prefix/include

An example of this would be the libdwarf build, which has one dependency: libelf. Every call tocc in the libdwarf build will have -I$LIBELF_PREFIX/include, -L$LIBELF_PREFIX/lib, and$rpath_flag$LIBELF_PREFIX/lib inserted on the command line. This is done transparently to the project’sbuild system, which will just think it’s using a system where libelf is readily available. Because of this, you do nothave to insert extra -I, -L, etc. on the command line.

Another useful consequence of this is that you often do not have to add extra parameters on the configure line toget autotools to find dependencies. The libdwarf install method just calls configure like this:

configure("--prefix=" + prefix)

Because of the -L and -I arguments, configure will successfully find libdwarf.h and libdwarf.so, withoutthe packager having to provide --with-libdwarf=/path/to/libdwarf on the command line.

Note: For most compilers, $rpath_flag is -Wl,-rpath,. However, NAG passes its flagsto GCC instead of passing them directly to the linker. Therefore, its $rpath_flag is doublywrapped: -Wl,-Wl„-rpath,. $rpath_flag can be overriden on a compiler specific basis inlib/spack/spack/compilers/$compiler.py.

The compiler wrappers also pass the compiler flags specified by the user from the command line (cflags,cxxflags, fflags, cppflags, ldflags, and/or ldlibs). They do not override the canonical autotools flagswith the same names (but in ALL-CAPS) that may be passed into the build by particularly challenging package scripts.

Compiler flags

In rare circumstances such as compiling and running small unit tests, a package developer may need to know what arethe appropriate compiler flags to enable features like OpenMP, c++11, c++14 and alike. To that end the compilerclasses in spack implement the following properties: openmp_flag, cxx11_flag, cxx14_flag, which canbe accessed in a package by self.compiler.cxx11_flag and alike. Note that the implementation is such thatif a given compiler version does not support this feature, an error will be produced. Therefore package developerscan also use these properties to assert that a compiler supports the requested feature. This is handy when a packagesupports additional variants like

variant('openmp', default=True, description="Enable OpenMP support.")

Message Parsing Interface (MPI)

It is common for high performance computing software/packages to use MPI. As a result of conretization, agiven package can be built using different implementations of MPI such as Openmpi, MPICH or IntelMPI.

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In some scenarios, to configure a package, one has to provide it with appropriate MPI compiler wrappers suchas mpicc, mpic++. However different implementations of MPI may have different names for those wrap-pers. In order to make package’s install() method indifferent to the choice MPI implementation, eachpackage which implements MPI sets up self.spec.mpicc, self.spec.mpicxx, self.spec.mpifcand self.spec.mpif77 to point to C, C++, Fortran 90 and Fortran 77 MPI wrappers. Package de-velopers are advised to use these variables, for example self.spec[’mpi’].mpicc instead of hard-codingjoin_path(self.spec[’mpi’].prefix.bin, ’mpicc’) for the reasons outlined above.

Blas and Lapack libraries

Different packages provide implementation of Blas and Lapack routines. The names of the resulting staticand/or shared libraries differ from package to package. In order to make the install() method indifferent tothe choice of Blas implementation, each package which provides it sets up self.spec.blas_shared_liband self.spec.blas_static_lib to point to the shared and static Blas libraries, respectively. The sameapplies to packages which provide Lapack. Package developers are advised to use these variables, for examplespec[’blas’].blas_shared_lib instead of hard-coding join_path(spec[’blas’].prefix.lib,’libopenblas.so’).

Forking install()

To give packagers free reign over their install environment, Spack forks a new process each time it invokes a package’sinstall() method. This allows packages to have their own completely sandboxed build environment, withoutimpacting other jobs that the main Spack process runs. Packages are free to change the environment or to modifySpack internals, because each install() call has its own dedicated process.

1.4.18 Failing the build

Sometimes you don’t want a package to successfully install unless some condition is true. You can explicitly causethe build to fail from install() by raising an InstallError, for example:

if spec.architecture.startswith('darwin'):raise InstallError('This package does not build on Mac OS X!')

1.4.19 Prefix objects

Spack passes the prefix parameter to the install method so that you can pass it to configure, cmake, or someother installer, e.g.:

configure('--prefix=' + prefix)

For the most part, prefix objects behave exactly like strings. For packages that do not have their own install target, orfor those that implement it poorly (like libdwarf), you may need to manually copy things into particular directoriesunder the prefix. For this, you can refer to standard subdirectories without having to construct paths yourself, e.g.:

def install(self, spec, prefix):mkdirp(prefix.bin)install('foo-tool', prefix.bin)

mkdirp(prefix.include)install('foo.h', prefix.include)

mkdirp(prefix.lib)install('libfoo.a', prefix.lib)

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Most of the standard UNIX directory names are attributes on the prefix object. Here is a full list:

Prefix Attribute Locationprefix.bin $prefix/binprefix.sbin $prefix/sbinprefix.etc $prefix/etcprefix.include $prefix/includeprefix.lib $prefix/libprefix.lib64 $prefix/lib64prefix.libexec $prefix/libexecprefix.share $prefix/shareprefix.doc $prefix/docprefix.info $prefix/infoprefix.man $prefix/manprefix.man[1-8] $prefix/man/man[1-8]prefix.share_man $prefix/share/manprefix.share_man[1-8] $prefix/share/man[1-8]

1.4.20 Spec objects

When install is called, most parts of the build process are set up for you. The correct version’s tarball has beendownloaded and expanded. Environment variables like CC and CXX are set to point to the correct compiler andversion. An install prefix has already been selected and passed in as prefix. In most cases this is all you need to getconfigure, cmake, or another install working correctly.

There will be times when you need to know more about the build configuration. For example, some soft-ware requires that you pass special parameters to configure, like --with-libelf=/path/to/libelf or--with-mpich. You might also need to supply special compiler flags depending on the compiler. All of thisinformation is available in the spec.

Testing spec constraints

You can test whether your spec is configured a certain way by using the satisfies method. For example, if youwant to check whether the package’s version is in a particular range, you can use specs to do that, e.g.:

configure_args = ['--prefix={0}'.format(prefix)

]

if spec.satisfies('@1.2:1.4'):configure_args.append("CXXFLAGS='-DWITH_FEATURE'")

configure(*configure_args)

This works for compilers, too:

if spec.satisfies('%gcc'):configure_args.append('CXXFLAGS="-g3 -O3"')

if spec.satisfies('%intel'):configure_args.append('CXXFLAGS="-xSSE2 -fast"')

Or for combinations of spec constraints:

if spec.satisfies('@1.2%intel'):tty.error("Version 1.2 breaks when using Intel compiler!")

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You can also do similar satisfaction tests for dependencies:

if spec.satisfies('^dyninst@8.0'):configure_args.append('CXXFLAGS=-DSPECIAL_DYNINST_FEATURE')

This could allow you to easily work around a bug in a particular dependency version.

You can use satisfies() to test for particular dependencies, e.g. foo.satisfies(’^openmpi@1.2’) orfoo.satisfies(’^mpich’), or you can use Python’s built-in in operator:

if 'libelf' in spec:print "this package depends on libelf"

This is useful for virtual dependencies, as you can easily see what implementation was selected for this build:

if 'openmpi' in spec:configure_args.append('--with-openmpi')

elif 'mpich' in spec:configure_args.append('--with-mpich')

elif 'mvapich' in spec:configure_args.append('--with-mvapich')

It’s also a bit more concise than satisfies. The difference between the two functions is that satisfies() testswhether spec constraints overlap at all, while in tests whether a spec or any of its dependencies satisfy the providedspec.

Accessing Dependencies

You may need to get at some file or binary that’s in the prefix of one of your dependencies. You can do that bysub-scripting the spec:

my_mpi = spec['mpi']

The value in the brackets needs to be some package name, and spec needs to depend on that package, or the operationwill fail. For example, the above code will fail if the spec doesn’t depend on mpi. The value returned and assignedto my_mpi, is itself just another Spec object, so you can do all the same things you would do with the package’s ownspec:

mpicc = join_path(my_mpi.prefix.bin, 'mpicc')

Multimethods and @when

Spack allows you to make multiple versions of instance functions in packages, based on whether the package’s specsatisfies particular criteria.

The @when annotation lets packages declare multiple versions of methods like install() that depend on thepackage’s spec. For example:

class SomePackage(Package):...

def install(self, prefix):# Do default install

@when('arch=chaos_5_x86_64_ib')def install(self, prefix):

# This will be executed instead of the default install if# the package's sys_type() is chaos_5_x86_64_ib.

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@when('arch=linux-debian7-x86_64')def install(self, prefix):

# This will be executed if the package's sys_type() is# linux-debian7-x86_64.

In the above code there are three versions of install(), two of which are specialized for particular platforms. Theversion that is called depends on the architecture of the package spec.

Note that this works for methods other than install, as well. So, if you only have part of the install that is platformspecific, you could do something more like this:

class SomePackage(Package):...# virtual dependence on MPI.# could resolve to mpich, mpich2, OpenMPIdepends_on('mpi')

def setup(self):# do nothing in the default casepass

@when('^openmpi')def setup(self):

# do something special when this is built with OpenMPI for# its MPI implementations.

def install(self, prefix):# Do common install stuffself.setup()# Do more common install stuff

You can write multiple @when specs that satisfy the package’s spec, for example:

class SomePackage(Package):...depends_on('mpi')

def setup_mpi(self):# the default, called when no @when specs matchpass

@when('^mpi@3:')def setup_mpi(self):

# this will be called when mpi is version 3 or higherpass

@when('^mpi@2:')def setup_mpi(self):

# this will be called when mpi is version 2 or higherpass

@when('^mpi@1:')def setup_mpi(self):

# this will be called when mpi is version 1 or higherpass

In situations like this, the first matching spec, in declaration order will be called. As before, if no @when spec matches,the default method (the one without the @when decorator) will be called.

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Warning: The default version of decorated methods must always come first. Otherwise it will override all of theplatform-specific versions. There’s not much we can do to get around this because of the way decorators work.

1.4.21 Shell command functions

Recall the install method from libelf:

1 def install(self, spec, prefix):2 configure("--prefix=" + prefix,3 "--enable-shared",4 "--disable-dependency-tracking",5 "--disable-debug")6 make()7

8 # The mkdir commands in libelf's install can fail in parallel9 make("install", parallel=False)

Normally in Python, you’d have to write something like this in order to execute shell commands:

import subprocesssubprocess.check_call('configure', '--prefix={0}'.format(prefix))

We’ve tried to make this a bit easier by providing callable wrapper objects for some shell commands. By default,configure, cmake, and make wrappers are are provided, so you can call them more naturally in your packagefiles.

If you need other commands, you can use which to get them:

sed = which('sed')sed('s/foo/bar/', filename)

The which function will search the PATH for the application.

Callable wrappers also allow spack to provide some special features. For example, in Spack, make is parallel by de-fault, and Spack figures out the number of cores on your machine and passes an appropriate value for -j<numjobs>when it calls make (see the parallel package attribute <attribute_parallel>). In a package file, you can supply akeyword argument, parallel=False, to the make wrapper to disable parallel make. In the libelf package, thisallows us to avoid race conditions in the library’s build system.

1.4.22 Sanity checking an installation

By default, Spack assumes that a build has failed if nothing is written to the install prefix, and that it has succeeded ifanything (a file, a directory, etc.) is written to the install prefix after install() completes.

Consider a simple autotools build like this:

def install(self, spec, prefix):configure("--prefix={0}".format(prefix))make()make("install")

If you are using using standard autotools or CMake, configure and make will not write anything to the installprefix. Only make install writes the files, and only once the build is already complete. Not all builds are likethis. Many builds of scientific software modify the install prefix before make install. Builds like this can falselyreport that they were successfully installed if an error occurs before the install is complete but after files have beenwritten to the prefix.

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sanity_check_is_file and sanity_check_is_dir

You can optionally specify sanity checks to deal with this problem. Add properties like this to your package:

class MyPackage(Package):...

sanity_check_is_file = ['include/libelf.h']sanity_check_is_dir = [lib]

def install(self, spec, prefix):configure("--prefix=" + prefix)make()make("install")

Now, after install() runs, Spack will check whether $prefix/include/libelf.h exists and is a file, andwhether $prefix/lib exists and is a directory. If the checks fail, then the build will fail and the install prefix willbe removed. If they succeed, Spack considers the build successful and keeps the prefix in place.

1.4.23 File manipulation functions

Many builds are not perfect. If a build lacks an install target, or if it does not use systems like CMake or autotools,which have standard ways of setting compilers and options, you may need to edit files or install some files yourself toget them working with Spack.

You can do this with standard Python code, and Python has rich libraries with functions for file manipulation andfiltering. Spack also provides a number of convenience functions of its own to make your life even easier. Thesefunctions are described in this section.

All of the functions in this section can be included by simply running:

from spack import *

This is already part of the boilerplate for packages created with spack create or spack edit.

Filtering functions

filter_file(regex, repl, *filenames, **kwargs) Works like sed but with Python regular expres-sion syntax. Takes a regular expression, a replacement, and a set of files. repl can be a raw string or a callablefunction. If it is a raw string, it can contain \1, \2, etc. to refer to capture groups in the regular expression. Ifit is a callable, it is passed the Python MatchObject and should return a suitable replacement string for theparticular match.

Examples:

1. Filtering a Makefile to force it to use Spack’s compiler wrappers:

filter_file(r'^CC\s*=.*', spack_cc, 'Makefile')filter_file(r'^CXX\s*=.*', spack_cxx, 'Makefile')filter_file(r'^F77\s*=.*', spack_f77, 'Makefile')filter_file(r'^FC\s*=.*', spack_fc, 'Makefile')

2. Replacing #!/usr/bin/perl with #!/usr/bin/env perl in bib2xhtml:

filter_file(r'#!/usr/bin/perl','#!/usr/bin/env perl', join_path(prefix.bin, 'bib2xhtml'))

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3. Switching the compilers used by mpich‘s MPI wrapper scripts from cc, etc. to the compilers used by theSpack build:

filter_file('CC="cc"', 'CC="%s"' % self.compiler.cc,join_path(prefix.bin, 'mpicc'))

filter_file('CXX="c++"', 'CXX="%s"' % self.compiler.cxx,join_path(prefix.bin, 'mpicxx'))

change_sed_delimiter(old_delim, new_delim, *filenames) Some packages, like TAU, have abuild system that can’t install into directories with, e.g. ‘@’ in the name, because they use hard-coded sedcommands in their build.

change_sed_delimiter finds all sed search/replace commands and change the delimiter. e.g., if the filecontains commands that look like s///, you can use this to change them to s@@@.

Example of changing s/// to s@@@ in TAU:

change_sed_delimiter('@', ';', 'configure')change_sed_delimiter('@', ';', 'utils/FixMakefile')change_sed_delimiter('@', ';', 'utils/FixMakefile.sed.default')

File functions

ancestor(dir, n=1) Get the nth ancestor of the directory dir.

can_access(path) True if we can read and write to the file at path. Same as native pythonos.access(file_name, os.R_OK|os.W_OK).

install(src, dest) Install a file to a particular location. For example, install a header into the includedirectory under the install prefix:

install('my-header.h', join_path(prefix.include))

join_path(prefix, *args) Like os.path.join, this joins paths using the OS path separator. However,this version allows an arbitrary number of arguments, so you can string together many path components.

mkdirp(*paths) Create each of the directories in paths, creating any parent directories if they do not exist.

working_dir(dirname, kwargs) This is a Python Context Manager that makes it easier to work with sub-directories in builds. You use this with the Python with statement to change into a working directory, andwhen the with block is done, you change back to the original directory. Think of it as a safe pushd / popdcombination, where popd is guaranteed to be called at the end, even if exceptions are thrown.

Example usage:

1. The libdwarf build first runs configure and make in a subdirectory called libdwarf. It thenimplements the installation code itself. This is natural with working_dir:

with working_dir('libdwarf'):configure("--prefix=" + prefix, "--enable-shared")make()install('libdwarf.a', prefix.lib)

2. Many CMake builds require that you build “out of source”, that is, in a subdirectory. You can handlecreating and cd‘ing to the subdirectory like the LLVM package does:

with working_dir('spack-build', create=True):cmake('..',

'-DLLVM_REQUIRES_RTTI=1',

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'-DPYTHON_EXECUTABLE=/usr/bin/python','-DPYTHON_INCLUDE_DIR=/usr/include/python2.6','-DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so',

*std_cmake_args)make()make("install")

The create=True keyword argument causes the command to create the directory if it does not exist.

touch(path) Create an empty file at path.

1.4.24 Coding Style Guidelines

The following guidelines are provided, in the interests of making Spack packages work in a consistent manner:

Variant Names

Spack packages with variants similar to already-existing Spack packages should use the same name for their variants.Standard variant names are:

Name Default Descriptionshared True Build shared librariesstatic True Build static librariesmpi True Use MPIpython False Build Python extension

If specified in this table, the corresponding default should be used when declaring a variant.

Version Lists

Spack packages should list supported versions with the newest first.

Special Versions

The following special version names may be used when building a package:

@system

Indicates a hook to the OS-installed version of the package. This is useful, for example, to tell Spack to use theOS-installed version in packages.yaml:

openssl:paths:openssl@system: /usr

buildable: False

Certain Spack internals look for the @system version and do appropriate things in that case.

@local

Indicates the version was built manually from some source tree of unknown provenance (see spack setup).

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1.4.25 Packaging workflow commands

When you are building packages, you will likely not get things completely right the first time.

The spack install command performs a number of tasks before it finally installs each package. It downloads anarchive, expands it in a temporary directory, and only then gives control to the package’s install() method. If thebuild doesn’t go as planned, you may want to clean up the temporary directory, or if the package isn’t downloadingproperly, you might want to run only the fetch stage of the build.

A typical package workflow might look like this:

$ spack edit mypackage$ spack install mypackage... build breaks! ...$ spack clean mypackage$ spack edit mypackage$ spack install mypackage... repeat clean/install until install works ...

Below are some commands that will allow you some finer-grained control over the install process.

spack fetch

The first step of spack install. Takes a spec and determines the correct download URL to use for the requestedpackage version, then downloads the archive, checks it against an MD5 checksum, and stores it in a staging directoryif the check was successful. The staging directory will be located under $SPACK_HOME/var/spack.

When run after the archive has already been downloaded, spack fetch is idempotent and will not download thearchive again.

spack stage

The second step in spack install after spack fetch. Expands the downloaded archive in its temporarydirectory, where it will be built by spack install. Similar to fetch, if the archive has already been expanded,stage is idempotent.

spack patch

After staging, Spack applies patches to downloaded packages, if any have been specified in the package file. Thiscommand will run the install process through the fetch, stage, and patch phases. Spack keeps track of whether patcheshave already been applied and skips this step if they have been. If Spack discovers that patches didn’t apply cleanlyon some previous run, then it will restage the entire package before patching.

spack restage

Restores the source code to pristine state, as it was before building.

Does this in one of two ways:

1. If the source was fetched as a tarball, deletes the entire build directory and re-expands the tarball.

2. If the source was checked out from a repository, this deletes the build directory and checks it out again.

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spack clean

Cleans up temporary files for a particular package, by deleting the expanded/checked out source code and any down-loaded archive. If fetch, stage, or install are run again after this, Spack’s build process will start from scratch.

spack purge

Cleans up all of Spack’s temporary and cached files. This can be used to recover disk space if temporary files frominterrupted or failed installs accumulate in the staging area.

When called with --stage or --all (or without arguments, in which case the default is --all) this removes allstaged files; this is equivalent to running spack clean for every package you have fetched or staged.

When called with --cache or --all this will clear all resources cached during installs.

Keeping the stage directory on success

By default, spack install will delete the staging area once a package has been successfully built and installed.Use --keep-stage to leave the build directory intact:

$ spack install --keep-stage <spec>

This allows you to inspect the build directory and potentially debug the build. You can use purge or clean later toget rid of the unwanted temporary files.

Keeping the install prefix on failure

By default, spack installwill delete any partially constructed install prefix if anything fails during install().If you want to keep the prefix anyway (e.g. to diagnose a bug), you can use --keep-prefix:

$ spack install --keep-prefix <spec>

Note that this may confuse Spack into thinking that the package has been installed properly, so you may need to usespack uninstall --force to get rid of the install prefix before you build again:

$ spack uninstall --force <spec>

1.4.26 Graphing dependencies

spack graph

Spack provides the spack graph command for graphing dependencies. The command by default generates anASCII rendering of a spec’s dependency graph. For example:

$ spack graph mpileakso mpileaks|\| |\| o | callpath|/| || |\|| |\ \| | |\ \| | | |\ \

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| | | | | o adept-utils| |_|_|_|/||/| | | |/|o | | | | | mpi/ / / / /

| | o | | dyninst| |/| | ||/|/| | || | |\| || | | |/| | |/|| o | | libdwarf|/ / /o | | libelf/ /

| o cmake|o boost

At the top is the root package in the DAG, with dependency edges emerging from it. On a color terminal, the edgesare colored by which dependency they lead to.

You can also use spack graph to generate graphs in the widely used Dot format. For example:

$ spack graph --dot mpileaksdigraph G {

label = "Spack Dependencies"labelloc = "b"rankdir = "LR"ranksep = "5"

"callpath" [label="callpath"]"adept-utils" [label="adept-utils"]"dyninst" [label="dyninst"]"libdwarf" [label="libdwarf"]"boost" [label="boost"]"cmake" [label="cmake"]"libelf" [label="libelf"]"mpileaks" [label="mpileaks"]"mpi" [label="mpi"]

"callpath" -> "cmake""callpath" -> "dyninst""callpath" -> "adept-utils""callpath" -> "libelf""callpath" -> "mpi""callpath" -> "libdwarf""adept-utils" -> "cmake""adept-utils" -> "boost""adept-utils" -> "mpi""dyninst" -> "cmake""dyninst" -> "boost""dyninst" -> "libelf""dyninst" -> "libdwarf""libdwarf" -> "libelf""boost" -> "python""boost" -> "bzip2""boost" -> "zlib""boost" -> "icu"

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"boost" -> "mpi""cmake" -> "py-sphinx""cmake" -> "bzip2""cmake" -> "expat""cmake" -> "qt""cmake" -> "python""cmake" -> "zlib""cmake" -> "openssl""cmake" -> "libarchive""cmake" -> "xz""cmake" -> "ncurses""cmake" -> "curl""elf" -> "libelf""mpileaks" -> "adept-utils""mpileaks" -> "callpath""mpileaks" -> "mpi"

}

This graph can be provided as input to other graphing tools, such as those in Graphviz.

1.4.27 Interactive shell support

Spack provides some limited shell support to make life easier for packagers. You can enable these commands bysourcing a setup file in the share/spack directory. For bash or ksh, run:

export SPACK_ROOT=/path/to/spack. $SPACK_ROOT/share/spack/setup-env.sh

For csh and tcsh run:

setenv SPACK_ROOT /path/to/spacksource $SPACK_ROOT/share/spack/setup-env.csh

spack cd will then be available.

spack cd

spack cd allows you to quickly cd to pertinent directories in Spack. Suppose you’ve staged a package but you wantto modify it before you build it:

$ spack stage libelf==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz######################################################################## 100.0%==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64/libelf-0.8.13.tar.gz==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64.$ spack cd libelf$ pwd/Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64/libelf-0.8.13

spack cd here changed the current working directory to the directory containing the expanded libelf sourcecode. There are a number of other places you can cd to in the spack directory hierarchy:

$ spack cd -husage: spack cd [-h] [-m | -r | -i | -p | -P | -s | -S | -b] ...

positional arguments:spec spec of package to fetch directory for.

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optional arguments:-h, --help show this help message and exit-m, --module-dir Spack python module directory.-r, --spack-root Spack installation root.-i, --install-dir Install prefix for spec (spec need not be installed).-p, --package-dir Directory enclosing a spec's package.py file.-P, --packages Top-level packages directory for Spack.-s, --stage-dir Stage directory for a spec.-S, --stages Top level Stage directory.-b, --build-dir Checked out or expanded source directory for a spec

(requires it to be staged first).

Some of these change directory into package-specific locations (stage directory, install directory, package directory)and others change to core spack locations. For example, spack cd -m will take you to the main python sourcedirectory of your spack install.

spack env

spack env functions much like the standard unix env command, but it takes a spec as an argument. You can use itto see the environment variables that will be set when a particular build runs, for example:

$ spack env mpileaks@1.1%intel

This will display the entire environment that will be set when the mpileaks@1.1%intel build runs.

To run commands in a package’s build environment, you can simply provide them after the spec argument to spackenv:

$ spack cd mpileaks@1.1%intel$ spack env mpileaks@1.1%intel ./configure

This will cd to the build directory and then run configure in the package’s build environment.

spack location

spack location is the same as spack cd but it does not require shell support. It simply prints out the path youask for, rather than cd’ing to it. In bash, this:

$ cd $(spack location -b <spec>)

is the same as:

$ spack cd -b <spec>

spack location is intended for use in scripts or makefiles that need to know where packages are installed. e.g.,in a makefile you might write:

DWARF_PREFIX = $(spack location -i libdwarf)CXXFLAGS += -I$DWARF_PREFIX/includeCXXFLAGS += -L$DWARF_PREFIX/lib

1.4.28 Build System Configuration Support

Imagine a developer creating a CMake or Autotools-based project in a local directory, which depends on librariesA-Z. Once Spack has installed those dependencies, one would like to run cmake with appropriate command line and

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environment so CMake can find them. The spack setup command does this conveniently, producing a CMakeconfiguration that is essentially the same as how Spack would have configured the project. This can be demonstratedwith a usage example:

$ cd myproject$ spack setup myproject@local$ mkdir build; cd build$ ../spconfig.py ..$ make$ make install

Notes:

• Spack must have myproject/package.py in its repository for this to work.

• spack setup produces the executable script spconfig.py in the local directory, and also creates themodule file for the package. spconfig.py is normally run from the user’s out-of-source build directory.

• The version number given to spack setup is arbitrary, just like spack diy. myproject/package.pydoes not need to have any valid downloadable versions listed (typical when a project is new).

• spconfig.py produces a CMake configuration that does not use the Spack wrappers. Any resulting binaries willnot use RPATH, unless the user has enabled it. This is recommended for development purposes, not production.

• spconfig.py is human readable, and can serve as a developer reference of what dependencies are being used.

• make install installs the package into the Spack repository, where it may be used by other Spack packages.

• CMake-generated makefiles re-run CMake in some circumstances. Use of spconfig.py breaks this behavior,requiring the developer to manually re-run spconfig.py when a CMakeLists.txt file has changed.

CMakePackage

In order to enable spack setup functionality, the author of myproject/package.py must subclass fromCMakePackage instead of the standard Package superclass. Because CMake is standardized, the packager doesnot need to tell Spack how to run cmake; make; make install. Instead the packager only needs to create(optional) methods configure_args() and configure_env(), which provide the arguments (as a list) andextra environment variables (as a dict) to provide to the cmake command. Usually, these will translate variant flagsinto CMake definitions. For example:

def configure_args(self):spec = self.specreturn [

'-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'),'-DBUILD_PYTHON=%s' % ('YES' if '+python' in spec else 'NO'),'-DBUILD_GRIDGEN=%s' % ('YES' if '+gridgen' in spec else 'NO'),'-DBUILD_COUPLER=%s' % ('YES' if '+coupler' in spec else 'NO'),'-DUSE_PISM=%s' % ('YES' if '+pism' in spec else 'NO')

]

If needed, a packager may also override methods defined in StagedPackage (see below).

StagedPackage

CMakePackage is implemented by subclassing the StagedPackage superclass, which breaks down the standardPackage.install() method into several sub-stages: setup, configure, build and install. Details:

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• Instead of implementing the standard install() method, package authors implement the meth-ods for the sub-stages install_setup(), install_configure(), install_build(), andinstall_install().

• The spack install command runs the sub-stages configure, build and install in order. (Thesetup stage is not run by default; see below).

• The spack setup command runs the sub-stages setup and a dummy install (to create the module file).

• The sub-stage install methods take no arguments (other than self). The arguments spec and prefix to thestandard install() method may be accessed via self.spec and self.prefix.

GNU Autotools

The setup functionality is currently only available for CMake-based packages. Extending this functionality to GNUAutotools-based packages would be easy (and should be done by a developer who actively uses Autotools). Packagesthat use non-standard build systems can gain setup functionality by subclassing StagedPackage directly.

1.5 Mirrors

Some sites may not have access to the internet for fetching packages. These sites will need a local repository oftarballs from which they can get their files. Spack has support for this with mirrors. A mirror is a URL that points toa directory, either on the local filesystem or on some server, containing tarballs for all of Spack’s packages.

Here’s an example of a mirror’s directory structure:

mirror/cmake/

cmake-2.8.10.2.tar.gzdyninst/

dyninst-8.1.1.tgzdyninst-8.1.2.tgz

libdwarf/libdwarf-20130126.tar.gzlibdwarf-20130207.tar.gzlibdwarf-20130729.tar.gz

libelf/libelf-0.8.12.tar.gzlibelf-0.8.13.tar.gz

libunwind/libunwind-1.1.tar.gz

mpich/mpich-3.0.4.tar.gz

mvapich2/mvapich2-1.9.tgz

The structure is very simple. There is a top-level directory. The second level directories are named after packages, andthe third level contains tarballs for each package, named after each package.

Note: Archives are not named exactly the way they were in the package’s fetch URL. They have the form<name>-<version>.<extension>, where <name> is Spack’s name for the package, <version> is the ver-sion of the tarball, and <extension> is whatever format the package’s fetch URL contains.

In order to make mirror creation reasonably fast, we copy the tarball in its original format to the mirror directory, butwe do not standardize on a particular compression algorithm, because this would potentially require expanding and

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re-compressing each archive.

1.5.1 spack mirror

Mirrors are managed with the spack mirror command. The help for spack mirror looks like this:

$ spack help mirrorusage: spack mirror [-h] [-n] SUBCOMMAND ...

positional arguments:SUBCOMMANDcreate Create a directory to be used as a spack mirror, and fill

it with package archives.add Add a mirror to Spack.remove (rm) Remove a mirror by name.list Print out available mirrors to the console.

optional arguments:-h, --help show this help message and exit-n, --no-checksum Do not check fetched packages against checksum

The create command actually builds a mirror by fetching all of its packages from the internet and checksummingthem.

The other three commands are for managing mirror configuration. They control the URL(s) from which Spack down-loads its packages.

1.5.2 spack mirror create

You can create a mirror using the spack mirror create command, assuming you’re on a machine where youcan access the internet.

The command will iterate through all of Spack’s packages and download the safe ones into a directory structure likethe one above. Here is what it looks like:

$ spack mirror create libelf libdwarf==> Created new mirror in spack-mirror-2014-06-24==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz########################################################## 81.6%==> Checksum passed for libelf@0.8.13==> Added libelf@0.8.13==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.12.tar.gz###################################################################### 98.6%==> Checksum passed for libelf@0.8.12==> Added libelf@0.8.12==> Trying to fetch from http://www.prevanders.net/libdwarf-20130207.tar.gz###################################################################### 97.3%==> Checksum passed for libdwarf@20130207==> Added libdwarf@20130207==> Trying to fetch from http://www.prevanders.net/libdwarf-20130126.tar.gz######################################################## 78.9%==> Checksum passed for libdwarf@20130126==> Added libdwarf@20130126==> Trying to fetch from http://www.prevanders.net/libdwarf-20130729.tar.gz############################################################# 84.7%==> Added libdwarf@20130729

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==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130729.tar.gz to mirror==> Added python@2.7.8.==> Successfully updated mirror in spack-mirror-2015-02-24.

Archive stats:0 already present5 added0 failed to fetch.

Once this is done, you can tar up the spack-mirror-2014-06-24 directory and copy it over to the machine youwant it hosted on.

Custom package sets

Normally, spack mirror create downloads all the archives it has checksums for. If you want to only create amirror for a subset of packages, you can do that by supplying a list of package specs on the command line after spackmirror create. For example, this command:

$ spack mirror create libelf@0.8.12: boost@1.44:

Will create a mirror for libelf versions greater than or equal to 0.8.12 and boost versions greater than or equal to 1.44.

Mirror files

If you have a very large number of packages you want to mirror, you can supply a file with specs in it, one per line:

$ cat specs.txtlibdwarflibelf@0.8.12:boost@1.44:boost@1.39.0...$ spack mirror create -f specs.txt...

This is useful if there is a specific suite of software managed by your site.

1.5.3 spack mirror add

Once you have a mirror, you need to let spack know about it. This is relatively simple. First, figure out the URL forthe mirror. If it’s a file, you can use a file URL like this one:

file:///Users/gamblin2/spack-mirror-2014-06-24

That points to the directory on the local filesystem. If it were on a web server, you could use a URL like this one:

https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24

Spack will use the URL as the root for all of the packages it fetches. You can tell your Spack installation to use thatmirror like this:

$ spack mirror add local_filesystem file:///Users/gamblin2/spack-mirror-2014-06-24

Each mirror has a name so that you can refer to it again later.

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1.5.4 spack mirror list

To see all the mirrors Spack knows about, run spack mirror list:

$ spack mirror listlocal_filesystem file:///Users/gamblin2/spack-mirror-2014-06-24

1.5.5 spack mirror remove

To remove a mirror by name, run:

$ spack mirror remove local_filesystem$ spack mirror list==> No mirrors configured.

1.5.6 Mirror precedence

Adding a mirror really adds a line in ~/.spack/mirrors.yaml:

mirrors:local_filesystem: file:///Users/gamblin2/spack-mirror-2014-06-24remote_server: https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24

If you want to change the order in which mirrors are searched for packages, you can edit this file and reorder thesections. Spack will search the topmost mirror first and the bottom-most mirror last.

1.5.7 Local Default Cache

Spack caches resources that are downloaded as part of installs. The cache is a valid spack mirror: it uses the same direc-tory structure and naming scheme as other Spack mirrors (so it can be copied anywhere and referenced with a URL likeother mirrors). The mirror is maintained locally (within the Spack installation directory) at var/spack/cache/. Itis always enabled (and is always searched first when attempting to retrieve files for an installation) but can be clearedwith purge; the cache directory can also be deleted manually without issue.

Caching includes retrieved tarball archives and source control repositories, but only resources with an associated digestor commit ID (e.g. a revision number for SVN) will be cached.

1.6 Configuration

1.6.1 Temporary space

Warning: Temporary space configuration will eventually be moved to configuration files, but currently thesesettings are in lib/spack/spack/__init__.py

By default, Spack will try to do all of its building in temporary space. There are two main reasons for this. First,Spack is designed to run out of a user’s home directory, and on may systems the home directory is network mountedand potentially not a very fast filesystem. We create build stages in a temporary directory to avoid this. Second, manysystems impose quotas on home directories, and /tmp or similar directories often have more available space. Thishelps conserve space for installations in users’ home directories.

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You can customize temporary directories by editing lib/spack/spack/__init__.py. Specifically, find thispart of the file:

# Whether to build in tmp space or directly in the stage_path.# If this is true, then spack will make stage directories in# a tmp filesystem, and it will symlink them into stage_path.use_tmp_stage = True

# Locations to use for staging and building, in order of preference# Use a %u to add a username to the stage paths here, in case this# is a shared filesystem. Spack will use the first of these paths# that it can create.tmp_dirs = ['/nfs/tmp2/%u/spack-stage',

'/var/tmp/%u/spack-stage','/tmp/%u/spack-stage']

The use_tmp_stage variable controls whether Spack builds directly inside the var/spack/ directory. Normally,Spack will try to find a temporary directory for a build, then it symlinks that temporary directory into var/spack/so that you can keep track of what temporary directories Spack is using.

The tmp_dirs variable is a list of paths Spack should search when trying to find a temporary directory. They canoptionally contain a %u, which will substitute the current user’s name into the path. The list is searched in order, andSpack will create a temporary stage in the first directory it finds to which it has write access. Add more elements tothe list to indicate where your own site’s temporary directory is.

1.6.2 External Packages

Spack can be configured to use externally-installed packages rather than building its own packages. This may bedesirable if machines ship with system packages, such as a customized MPI that should be used instead of Spackbuilding its own MPI.

External packages are configured through the packages.yaml file found in a Spack installation’s etc/spack/or a user’s ~/.spack/ directory. Here’s an example of an external configuration:

packages:openmpi:paths:

openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debugopenmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel

This example lists three installations of OpenMPI, one built with gcc, one built with gcc and debug information, andanother built with Intel. If Spack is asked to build a package that uses one of these MPIs as a dependency, it will usethe the pre-installed OpenMPI in the given directory. Packages.yaml can also be used to specify modules

Each packages.yaml begins with a packages: token, followed by a list of package names. To specify externals,add a paths or modules token under the package name, which lists externals in a spec: /path or spec:module-name format. Each spec should be as well-defined as reasonably possible. If a package lacks a speccomponent, such as missing a compiler or package version, then Spack will guess the missing component based on itsmost-favored packages, and it may guess incorrectly.

Each package version and compilers listed in an external should have entries in Spack’s packages and compiler con-figuration, even though the package and compiler may not every be built.

The packages configuration can tell Spack to use an external location for certain package versions, but it does notrestrict Spack to using external packages. In the above example, if an OpenMPI 1.8.4 became available Spack maychoose to start building and linking with that version rather than continue using the pre-installed OpenMPI versions.

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To prevent this, the packages.yaml configuration also allows packages to be flagged as non-buildable. The previ-ous example could be modified to be:

packages:openmpi:paths:

openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debugopenmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel

buildable: False

The addition of the buildable flag tells Spack that it should never build its own version of OpenMPI, and it willinstead always rely on a pre-built OpenMPI. Similar to paths, buildable is specified as a property under a packagename.

If an external module is specified as not buildable, then Spack will load the external module into the build environmentwhich can be used for linking.

The buildable does not need to be paired with external packages. It could also be used alone to forbid packagesthat may be buggy or otherwise undesirable.

1.6.3 Concretization Preferences

Spack can be configured to prefer certain compilers, package versions, depends_on, and variants during concretization.The preferred configuration can be controlled via the ~/.spack/packages.yaml file for user configuations, orthe etc/spack/packages.yaml site configuration.

Here’s an example packages.yaml file that sets preferred packages:

packages:opencv:compiler: [gcc@4.9]variants: +debug

gperftools:version: [2.2, 2.4, 2.3]

all:compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi]providers:

mpi: [mvapich, mpich, openmpi]

At a high level, this example is specifying how packages should be concretized. The opencv package should preferusing gcc 4.9 and be built with debug options. The gperftools package should prefer version 2.2 over 2.4. Everypackage on the system should prefer mvapich for its MPI and gcc 4.4.7 (except for opencv, which overrides this bypreferring gcc 4.9). These options are used to fill in implicit defaults. Any of them can be overwritten on the commandline if explicitly requested.

Each packages.yaml file begins with the string packages: and package names are specified on the next level. Thespecial string all applies settings to each package. Underneath each package name is one or more components:compiler, variants, version, or providers. Each component has an ordered list of spec constraints,with earlier entries in the list being preferred over later entries.

Sometimes a package installation may have constraints that forbid the first concretization rule, in which case Spackwill use the first legal concretization rule. Going back to the example, if a user requests gperftools 2.3 or later, thenSpack will install version 2.4 as the 2.4 version of gperftools is preferred over 2.3.

An explicit concretization rule in the preferred section will always take preference over unlisted concretizations. Inthe above example, xlc isn’t listed in the compiler list. Every listed compiler from gcc to pgi will thus be preferredover the xlc compiler.

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The syntax for the provider section differs slightly from other concretization rules. A provider lists a value thatpackages may depend_on (e.g, mpi) and a list of rules for fulfilling that dependency.

1.6.4 Profiling

Spack has some limited built-in support for profiling, and can report statistics using standard Python timing tools. Touse this feature, supply -p to Spack on the command line, before any subcommands.

spack --profile

spack --profile output looks like this:

$ spack --profile graph dyninsto dyninst|\| |\| | |\| o | | libdwarf|/ / /o | | libelf/ /

o | cmake/

o boost915655 function calls (911609 primitive calls) in 0.852 seconds

Ordered by: internal time

ncalls tottime percall cumtime percall filename:lineno(function)224/222 0.133 0.001 0.423 0.002 inspect.py:472(getmodule)169877 0.084 0.000 0.131 0.000 inspect.py:51(ismodule)224749 0.066 0.000 0.066 0.000 {isinstance}

6057 0.059 0.000 0.059 0.000 {posix.stat}95679 0.044 0.000 0.044 0.000 {hasattr}

5604/5224 0.043 0.000 0.603 0.000 inspect.py:440(getsourcefile)4664 0.031 0.000 0.031 0.000 {posix.lstat}

97077 0.022 0.000 0.022 0.000 {method 'get' of 'dict' objects}5835 0.018 0.000 0.053 0.000 inspect.py:398(getfile)

...

The bottom of the output shows the top most time consuming functions, slowest on top. The profiling support is fromPython’s built-in tool, cProfile.

1.7 Developer Guide

This guide is intended for people who want to work on Spack itself. If you just want to develop packages, see thePackaging Guide.

It is assumed that you’ve read the Basic usage and Packaging Guide sections, and that you’re familiar with the conceptsdiscussed there. If you’re not, we recommend reading those first.

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1.7.1 Overview

Spack is designed with three separate roles in mind:

1. Users, who need to install software without knowing all the details about how it is built.

2. Packagers who know how a particular software package is built and encode this information in package files.

3. Developers who work on Spack, add new features, and try to make the jobs of packagers and users easier.

Users could be end users installing software in their home directory, or administrators installing software to a shareddirectory on a shared machine. Packagers could be administrators who want to automate software builds, or applicationdevelopers who want to make their software more accessible to users.

As you might expect, there are many types of users with different levels of sophistication, and Spack is designedto accommodate both simple and complex use cases for packages. A user who only knows that he needs a certainpackage should be able to type something simple, like spack install <package name>, and get the packagethat he wants. If a user wants to ask for a specific version, use particular compilers, or build several versions withdifferent configurations, then that should be possible with a minimal amount of additional specification.

This gets us to the two key concepts in Spack’s software design:

1. Specs: expressions for describing builds of software, and

2. Packages: Python modules that build software according to a spec.

A package is a template for building particular software, and a spec as a descriptor for one or more instances of thattemplate. Users express the configuration they want using a spec, and a package turns the spec into a complete build.

The obvious difficulty with this design is that users under-specify what they want. To build a software package, thepackage object needs a complete specification. In Spack, if a spec describes only one instance of a package, then wesay it is concrete. If a spec could describes many instances, (i.e. it is under-specified in one way or another), then wesay it is abstract.

Spack’s job is to take an abstract spec from the user, find a concrete spec that satisfies the constraints, and hand thetask of building the software off to the package object. The rest of this document describes all the pieces that cometogether to make that happen.

1.7.2 Directory Structure

So that you can familiarize yourself with the project, we’ll start with a high level view of Spack’s directory structure:

spack/ <- installation rootbin/

spack <- main spack executable

etc/spack/ <- Spack config files.

Can be overridden by files in ~/.spack.

var/spack/ <- build & stage directories

repos/ <- contains package repositoriesbuiltin/ <- pkg repository that comes with Spack

repo.yaml <- descriptor for the builtin repositorypackages/ <- directories under here contain packages

cache/ <- saves resources downloaded during installs

opt/spack/ <- packages are installed here

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lib/spack/

docs/ <- source for this documentationenv/ <- compiler wrappers for build environment

external/ <- external libs included in Spack distrollnl/ <- some general-use libraries

spack/ <- spack module; contains Python codecmd/ <- each file in here is a spack subcommandcompilers/ <- compiler description filestest/ <- unit test modulesutil/ <- common code

Spack is designed so that it could live within a standard UNIX directory hierarchy, so lib, var, and opt all containa spack subdirectory in case Spack is installed alongside other software. Most of the interesting parts of Spack livein lib/spack.

Spack has one directory layout and there is no install process. Most Python programs don’t look like this (they usedistutils, setup.py, etc.) but we wanted to make Spack very easy to use. The simple layout spares users from theneed to install Spack into a Python environment. Many users don’t have write access to a Python installation, andinstalling an entire new instance of Python to bootstrap Spack would be very complicated. Users should not haveto install install a big, complicated package to use the thing that’s supposed to spare them from the details of big,complicated packages. The end result is that Spack works out of the box: clone it and add bin to your PATH andyou’re ready to go.

1.7.3 Code Structure

This section gives an overview of the various Python modules in Spack, grouped by functionality.

Package-related modules

spack.package Contains the Package class, which is the superclass for all packages in Spack. Methods onPackage implement all phases of the package lifecycle and manage the build process.

spack.packages Contains all of the packages in Spack and methods for managing them. Functions likepackages.get and class_name_for_package_name handle mapping package module names to classnames and dynamically instantiating packages by name from module files.

spack.relations Relations are relationships between packages, like depends_on and provides. See De-pendencies and Virtual dependencies.

spack.multimethod Implementation of the @when decorator, which allows multimethods in packages.

Spec-related modules

spack.spec Contains Spec and SpecParser. Also implements most of the logic for normalization and con-cretization of specs.

spack.parse Contains some base classes for implementing simple recursive descent parsers: Parser andLexer. Used by SpecParser.

spack.concretize Contains DefaultConcretizer implementation, which allows site administrators tochange Spack’s Concretization Policies.

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spack.version Implements a simple Version class with simple comparison semantics. Also implementsVersionRange and VersionList. All three are comparable with each other and offer union and inter-section operations. Spack uses these classes to compare versions and to manage version constraints on specs.Comparison semantics are similar to the LooseVersion class in distutils and to the way RPM comparesversion strings.

spack.compilers Submodules contains descriptors for all valid compilers in Spack. This is used by the buildsystem to set up the build environment.

Warning: Not yet implemented. Currently has two compiler descriptions, but compilers aren’t fully inte-grated with the build process yet.

spack.architecture architecture.sys_type is used to determine the host architecture while building.

Warning: Not yet implemented. Should eventually have architecture descriptions for cross-compiling.

Build environment

spack.stage Handles creating temporary directories for builds.

spack.compilation This contains utility functions used by the compiler wrapper script, cc.

spack.directory_layout Classes that control the way an installation directory is laid out. Create more imple-mentations of this to change the hierarchy and naming scheme in $spack_prefix/opt

Spack Subcommands

spack.cmd Each module in this package implements a Spack subcommand. See writing commands for details.

Unit tests

spack.test Implements Spack’s test suite. Add a module and put its name in the test suite in __init__.py toadd more unit tests.

spack.test.mock_packages This is a fake package hierarchy used to mock up packages for Spack’s test suite.

Other Modules

spack.globals Includes global settings for Spack. the default policy classes for things like temporary space andconcretization.

spack.tty Basic output functions for all of the messages Spack writes to the terminal.

spack.color Implements a color formatting syntax used by spack.tty.

spack.url URL parsing, for deducing names and versions of packages from tarball URLs.

spack.util In this package are a number of utility modules for the rest of Spack.

spack.error SpackError, the base class for Spack’s exception hierarchy.

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1.7.4 Spec objects

1.7.5 Package objects

Most spack commands look something like this:

1. Parse an abstract spec (or specs) from the command line,

2. Normalize the spec based on information in package files,

3. Concretize the spec according to some customizable policies,

4. Instantiate a package based on the spec, and

5. Call methods (e.g., install()) on the package object.

The information in Package files is used at all stages in this process.

Conceptually, packages are overloaded. They contain:

1.7.6 Stage objects

1.7.7 Writing commands

1.7.8 Unit tests

1.7.9 Unit testing

1.7.10 Developer commands

spack doc

spack test

1.8 Using Spack for CMake-based Development

These are instructions on how to use Spack to aid in the development of a CMake-based project. Spack is used to helpfind the dependencies for the project, configure it at development time, and then package it it in a way that others caninstall. Using Spack for CMake-based development consists of three parts:

1. Setting up the CMake build in your software

2. Writing the Spack Package

3. Using it from Spack.

1.8.1 Setting Up the CMake Build

You should follow standard CMake conventions in setting up your software, your CMake build should NOT dependon or require Spack to build. See here for an example:

https://github.com/citibeth/icebin

Note that there’s one exception here to the rule I mentioned above. In CMakeLists.txt, I have the following line:

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include_directories($ENV{CMAKE_TRANSITIVE_INCLUDE_PATH})

This is a hook into Spack, and it ensures that all transitive dependencies are included in the include path. It’s notneeded if everything is in one tree, but it is (sometimes) in the Spack world; when running without Spack, it has noeffect.

Note that this “feature” is controversial, could break with future versions of GNU ld, and probably not the best to use.The best practice is that you make sure that anything you #include is listed as a dependency in your CMakeLists.txt.

To be more specific: if you #inlcude something from package A and an installed HEADER FILE in A #includessomething from package B, then you should also list B as a dependency in your CMake build. If you depend on A butheader files exported by A do NOT #include things from B, then you do NOT need to list B as a dependency — evenif linking to A links in libB.so as well.

I also recommend that you set up your CMake build to use RPATHs correctly. Not only is this a good idea and nice,but it also ensures that your package will build the same with or without spack install.

1.8.2 Writing the Spack Package

Now that you have a CMake build, you want to tell Spack how to configure it. This is done by writing a Spack packagefor your software. See here for example:

https://github.com/citibeth/spack/blob/efischer/develop/var/spack/repos/builtin/packages/icebin/package.py

You need to subclass CMakePackage, as is done in this example. This enables advanced features of Spack forhelping you in configuring your software (keep reading...). Instead of an install() method used when subclassingPackage, you write configure_args(). See here for more info on how this works:

https://github.com/LLNL/spack/pull/543/files

NOTE: if your software is not publicly available, you do not need to set the URL or version. Or you can set up bogusURLs and versions... whatever causes Spack to not crash.

1.8.3 Using it from Spack

Now that you have a Spack package, you can get Spack to setup your CMake project for you. Use the following tosetup, configure and build your project:

$ cd myproject$ spack spconfig myproject@local$ mkdir build; cd build$ ../spconfig.py ..$ make$ make install

Everything here should look pretty familiar here from a CMake perspective, except that spack spconfig createsthe file spconfig.py, which calls CMake with arguments appropriate for your Spack configuration. Think of it asthe equivalent to running a bunch of spack location -i commands. You will run spconfig.py instead ofrunning CMake directly.

If your project is publicly available (eg on GitHub), then you can ALSO use this setup to “just install” a release versionwithout going through the manual configuration/build step. Just do:

1. Put tag(s) on the version(s) in your GitHub repo you want to be release versions.

2. Set the url in your package.py to download a tarball for the appropriate version. (GitHub will give you atarball for any version in the repo, if you tickle it the right way). For example:

https://github.com/citibeth/icebin/tarball/v0.1.0

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Set up versions as appropriate in your package.py. (Manually download the tarball and run md5sum todetermine the appropriate checksum for it).

3. Now you should be able to say spack install myproject@version and things “just work.”

NOTE... in order to use the features outlined in this post, you currently need to use the following branch of Spack:

https://github.com/citibeth/spack/tree/efischer/develop

There is a pull request open on this branch ( https://github.com/LLNL/spack/pull/543 ) and we are working to get itintegrated into the main develop branch.

1.8.4 Activating your Software

Once you’ve built your software, you will want to load it up. You can use spack load mypackage@local forthat in your .bashrc, but that is slow. Try stuff like the following instead:

The following command will load the Spack-installed packages needed for basic Python use of IceBin:

$ module load `spack module find tcl icebin netcdf cmake@3.5.1`$ module load `spack module find --dependencies tcl py-basemap py-giss`

You can speed up shell startup by turning these into module load commands.

1. Cut-n-paste the script make_spackenv:

#!/bin/sh## Generate commands to load the Spack environment

SPACKENV=$HOME/spackenv.sh

spack module find --shell tcl git icebin@local ibmisc netcdf cmake@3.5.1 > $SPACKENVspack module find --dependencies --shell tcl py-basemap py-giss >> $SPACKENV

2. Add the following to your .bashrc file:

source $HOME/spackenv.sh# Preferentially use your checked-out Python sourceexport PYTHONPATH=$HOME/icebin/pylib:$PYTHONPATH

3. Run sh make_spackenv whenever your Spack installation changes (including right now).

1.8.5 Giving Back

If your software is publicly available, you should submit the package.py for it as a pull request to the main SpackGitHub project. This will ensure that anyone can install your software (almost) painlessly with a simple spackinstall command. See here for how that has turned into detailed instructions that have successfully enabled col-laborators to install complex software:

https://github.com/citibeth/icebin/blob/develop/README.rst

1.9 Command index

This is an alphabetical list of commands with links to the places they appear in the documentation.

• spack activate

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• spack cd• spack checksum• spack clean• spack compiler add• spack compiler find• spack compiler info• spack compilers• spack create• spack deactivate• spack edit• spack edit –force• spack env• spack extensions• spack fetch• spack find• spack graph• spack help• spack info• spack install• spack list• spack location• spack mirror• spack mirror add• spack mirror create• spack mirror list• spack mirror remove• spack module refresh• spack –profile• spack patch• spack providers• spack purge• spack restage• spack spec• spack stage• spack uninstall• spack versions

1.10 Package List

This is a list of things you can install using Spack. It is automatically generated based on the packages in the latestSpack release.

Spack currently has 697 mainline packages:

ack llvm qrupdateactiveharmony llvm-lld qtadept-utils lmdb qt-creatoradios lmod qthreadsadol-c lrslib Rallinea-forge lrzip r-abindallinea-reports lua r-assertthat

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Table 1.1 – continued from previous pageantlr lua-luafilesystem r-base64encape lua-luaposix r-bhapex LuaJIT r-BiocGenericsapr lwgrp r-bootapr-util lwm2 r-brewarmadillo lz4 r-cararpack lzma r-caretarpack-ng lzo r-chronasciidoc m4 r-classastyle mafft r-clusteratk mariadb r-codetoolsatlas matio r-colorspaceatop mbedtls r-crayonautoconf meep r-cubatureautomaded memaxes r-curlautomake mercurial r-datatablebash mesa r-dbibbcp metis r-devtoolsbcftools mfem r-diagrammerbdw-gc Mitos r-dichromatbear mkl r-digestbertini moab r-doparallelbib2xhtml mpc r-dplyrbinutils mpe2 r-dtbison mpfr r-dygraphsbliss mpibash r-e1071blitz mpich r-filehashboost mpileaks r-foreachbowtie2 mrnet r-foreignboxlib msgpack-c r-gdatabpp-core mumps r-geospherebpp-phyl munge r-ggmapbpp-seq muparser r-ggplot2bpp-suite muster r-ggvisbwa mvapich2 r-git2rbzip2 mxml r-glmnetc-blosc nag r-googleviscairo nano r-gridbasecaliper nasm r-gridextracallpath nauty r-gtablecantera nccmp r-gtoolscask ncdu r-htmltoolscblas nco r-htmlwidgetscbtf ncurses r-httpuvcbtf-argonavis ncview r-httrcbtf-krell ndiff r-igraphcbtf-lanl netcdf r-influencercdd netcdf-cxx r-inlinecddlib netcdf-cxx4 r-irlbacdo netcdf-fortran r-iterators

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Table 1.1 – continued from previous pagecereal netgauge r-jpegcfitsio netlib-lapack r-jsonlitecgal netlib-scalapack r-labelingcgm nettle r-latticecgns nextflow r-lazyevalcityhash ninja r-leafletcleverleaf numdiff r-lme4cloog nwchem r-lmtestcmake ocaml r-lubridatecmocka oce r-magiccnmem octave r-magrittrcoreutils octave-splines r-mapprojcp2k octopus r-mapscppcheck ompss r-maptoolscram ompt-openmp r-markdowncryptopp opari2 r-masscscope openblas r-matrixcube opencoarrays r-matrixmodelscuda opencv r-memoisecurl openexr r-mgcvczmq openjpeg r-mimedaal openmpi r-minqadakota openspeedshop r-multcompdamselfly openssl r-munselldatamash opium r-mvtnormdbus osu-micro-benchmarks r-ncdf4dealii otf r-networkd3dia otf2 r-nlmedocbook-xml p4est r-nloptrdoxygen panda r-nmfdri2proto pango r-nnetdtcmp papi r-npdyninst paradiseo r-openssleigen parallel r-packratelfutils parallel-netcdf r-pbkrtestelk paraver r-pkgmakerelpa paraview r-plotrixemacs parmetis r-plyrenvironment-modules parmgridgen r-pngespresso parpack r-praiseexodusii patchelf r-protoexonerate pcre r-quantmodexpat pcre2 r-quantregextrae pdt r-R6exuberant-ctags perl r-randomforestfastx_toolkit petsc r-rasterfenics pgi r-rcolorbrewerferret pidx r-rcppfftw pixman r-rcppeigenfish pkg-config r-registry

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Table 1.1 – continued from previous pageflex plumed r-reshape2fltk pmgr_collective r-rgooglemapsflux pngwriter r-rjavafoam-extend polymake r-rjsonfontconfig porta r-rjsoniofreetype postgresql r-rmysqlgasnet ppl r-rngtoolsgcc prank r-rodbcgdal proj r-roxygen2gdb protobuf r-rpostgresqlgdk-pixbuf psi4 r-rsqlitegeos py-3to2 r-rstangettext py-alabaster r-rstudioapigflags py-argcomplete r-sandwichghostscript py-astroid r-scalesgiflib py-astropy r-shinygit py-autopep8 r-spgl2ps py-babel r-sparsemglib py-basemap r-stanheadersglm py-beautifulsoup4 r-stringiglobal py-biopython r-stringrglog py-blessings r-surveyglpk py-bottleneck r-survivalgmp py-cclib r-tarifxgmsh py-cffi r-testthatgnu-prolog py-coverage r-thdatagnuplot py-csvkit r-threejsgnutls py-cycler r-tibblego py-cython r-tidyrgo-bootstrap py-dask r-ttrgobject-introspection py-dateutil r-vcdgoogletest py-dbf r-visnetworkgperf py-decorator r-whiskergperftools py-docutils r-withrgraphlib py-emcee r-xlconnectgraphviz py-epydoc r-xlconnectjarsgromacs py-flake8 r-xlsxgsl py-funcsigs r-xlsxjarsgtkplus py-genders r-xmlgts py-genshi r-xtableguile py-gnuplot r-xtsharfbuzz py-h5py r-yamlharminv py-imagesize r-zoohdf py-iminuit rajahdf5 py-ipython ravelhdf5-blosc py-jdcal readlinehmmer py-jinja2 rosehoomd-blue py-lockfile rsynchpl py-logilab-common rubyhpx5 py-mako rust

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Table 1.1 – continued from previous pagehtslib py-markupsafe rust-bindgenhub py-matplotlib SAMRAIhwloc py-meep samtoolshydra py-mistune scalascahypre py-mock sconsibmisc py-mpi4py scorepicu py-mpmath scotchicu4c py-mx scrilmbase py-mysqldb1 screenImageMagick py-nestle sedintel py-netcdf seqtkintel-parallel-studio py-networkx serfintltool py-nose siloior py-numexpr slepcipopt py-numpy snappyipp py-openpyxl sparsehashisl py-pandas spindlejasper py-pbr spotjdk py-pep8 sqlitejemalloc py-periodictable statjpeg py-pexpect streamjsoncpp py-phonopy subversionjudy py-pil suite-sparse

julia py-pillow sundialskdiff3 py-ply superlukealib py-pmw superlu-distkripke py-prettytable superlu-mtlaunchmon py-protobuf swiftsimlcms py-py2cairo swigleveldb py-py2neo sympollibaio py-pychecker sziplibarchive py-pycparser tarlibatomic-ops py-pydatalog tasklibcerf py-pyelftools taskdlibcircle py-pygments taulibctl py-pygobject tbblibdrm py-pygtk tcllibdwarf py-pylint tetgenlibedit py-pypar texinfolibelf py-pyparsing texlivelibepoxy py-pyqt the_platinum_searcherlibevent py-pyside the_silver_searcherlibffi py-pytables thriftlibgcrypt py-python-daemon tklibgd py-pytz tmuxlibgpg-error py-pyyaml tmuxinatorlibgtextutils py-restview treelibhio py-rpy2 trianglelibiconv py-scientificpython trilinoslibjpeg-turbo py-scikit-image turbomole

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Table 1.1 – continued from previous pagelibjson-c py-scikit-learn udunits2libmng py-scipy uncrustifylibmonitor py-setuptools unibiliumlibNBC py-shiboken unisonlibpciaccess py-sip unixodbclibpng py-six util-linuxlibpthread-stubs py-sncosmo valgrindlibsigsegv py-snowballstemmer vimlibsodium py-sphinx visitlibsplash py-sphinx-rtd-theme vtklibtermkey py-SQLAlchemy wgetlibtiff py-storm wxlibtool py-sympy wxpropgridlibunistring py-tappy xcb-protolibunwind py-tuiview xerces-clibuuid py-twisted xorg-util-macroslibuv py-unittest2 xprotolibvterm py-unittest2py3k xzlibxau py-urwid yasmlibxc py-virtualenv zeromqlibxcb py-wcsaxes zfplibxml2 py-wheel zliblibxpm py-xlrd zoltanlibxshmfence py-yapf zshlibxslt pythonlibxsmm qhull

1.10.1 ack

Homepage:

• http://beyondgrep.com/

Spack package:

• ack/package.py

Versions: 2.14

Build Dependencies perl

Link Dependencies perl

Description: ack 2.14 is a tool like grep, optimized for programmers. Designed for programmers with large hetero-geneous trees of source code, ack is written purely in portable Perl 5 and takes advantage of the power of Perl’sregular expressions.

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1.10.2 activeharmony

Homepage:

• http://www.dyninst.org/harmony

Spack package:

• activeharmony/package.py

Versions: 4.5

Description: Active Harmony: a framework for auto-tuning (the automated search for values to improve the perfor-mance of a target application).

1.10.3 adept-utils

Homepage:

• https://github.com/llnl/adept-utils

Spack package:

• adept-utils/package.py

Versions: 1.0.1, 1.0

Build Dependencies boost, cmake, mpi

Link Dependencies boost, mpi

Description: Utility libraries for LLNL performance tools.

1.10.4 adios

Homepage:

• http://www.olcf.ornl.gov/center-projects/adios/

Spack package:

• adios/package.py

Versions: 1.10.0, 1.9.0

Build Dependencies hdf5, python, zlib, mpi, libtool, mxml, szip, autoconf , automake, netcdf

Link Dependencies hdf5, zlib, mpi, netcdf , mxml, szip

Description: The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data intheir code that may need to be written, read, or processed outside of the running simulation.

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1.10.5 adol-c

Homepage:

• https://projects.coin-or.org/ADOL-C

Spack package:

• adol-c/package.py

Versions: 2.6.1, head

Description: A package for the automatic differentiation of first and higher derivatives of vector functions in C andC++ programs by operator overloading.

1.10.6 allinea-forge

Homepage:

• http://www.allinea.com/products/develop-allinea-forge

Spack package:

• allinea-forge/package.py

Versions: 6.0.4

Description: Allinea Forge is the complete toolsuite for software development - with everything needed to debug,profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance - from singlethreads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.

1.10.7 allinea-reports

Homepage:

• http://www.allinea.com/products/allinea-performance-reports

Spack package:

• allinea-reports/package.py

Versions: 6.0.4

Description: Allinea Performance Reports are the most effective way to characterize and understand the performanceof HPC application runs. One single-page HTML report elegantly answers a range of vital questions for anyHPC site

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1.10.8 antlr

Homepage:

• http://www.antlr.org

Spack package:

• antlr/package.py

Versions: 2.7.7

Description: ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, pro-cessing, executing, or translating structured text or binary files. It’s widely used to build languages, tools, andframeworks. From a grammar, ANTLR generates a parser that can build and walk parse trees.

1.10.9 ape

Homepage:

• http://www.tddft.org/programs/APE/

Spack package:

• ape/package.py

Versions: 2.2.1

Build Dependencies libxc, gsl

Link Dependencies libxc, gsl

Description: A tool for generating atomic pseudopotentials within a Density- Functional Theory framework

1.10.10 apex

Homepage:

• http://github.com/khuck/xpress-apex

Spack package:

• apex/package.py

Versions: 0.1

Build Dependencies boost, cmake, activeharmony, binutils, ompt-openmp

Link Dependencies boost, activeharmony, binutils, ompt-openmp

Description:

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1.10.11 apr

Homepage:

• https://apr.apache.org/

Spack package:

• apr/package.py

Versions: 1.5.2

Description: Apache portable runtime.

1.10.12 apr-util

Homepage:

• https://apr.apache.org/

Spack package:

• apr-util/package.py

Versions: 1.5.4

Build Dependencies apr

Link Dependencies apr

Description: Apache Portable Runtime Utility

1.10.13 armadillo

Homepage:

• http://arma.sourceforge.net/

Spack package:

• armadillo/package.py

Versions: 7.200.2, 7.200.1

Build Dependencies cmake, superlu, lapack, blas, hdf5, arpack-ng

Link Dependencies lapack, blas, superlu, arpack-ng, hdf5

Description: Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towardsa good balance between speed and ease of use.

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1.10.14 arpack

Homepage:

• http://www.caam.rice.edu/software/ARPACK/

Spack package:

• arpack/package.py

Versions: 96

Build Dependencies lapack, blas

Link Dependencies lapack, blas

Description: A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

1.10.15 arpack-ng

Homepage:

• https://github.com/opencollab/arpack-ng

Spack package:

• arpack-ng/package.py

Versions: 3.4.0, 3.3.0

Build Dependencies cmake, lapack, blas, automake, libtool, autoconf , mpi

Link Dependencies lapack, blas, mpi

Description: ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue prob-lems. Important Features: * Reverse Communication Interface. * Single and Double Precision Real ArithmeticVersions for Symmetric, Non-symmetric, Standard or Generalized Problems. * Single and Double PrecisionComplex Arithmetic Versions for Standard or Generalized Problems. * Routines for Banded Matrices - Stan-dard or Generalized Problems. * Routines for The Singular Value Decomposition. * Example driver routinesthat may be used as templates to implement numerous Shift-Invert strategies for all problem types, data typesand precision. This project is a joint project between Debian, Octave and Scilab in order to provide a commonand maintained version of arpack. Indeed, no single release has been published by Rice university for the lastfew years and since many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifi-cations, arpack-ng aims to tackle this by providing a common repository and maintained versions. arpack-ng isreplacing arpack almost everywhere.

1.10.16 asciidoc

Homepage:

• http://asciidoc.org

Spack package:

• asciidoc/package.py

Versions: 8.6.9

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Build Dependencies libxml2, libxslt

Link Dependencies libxml2, libxslt

Description: A presentable text document format for writing articles, UNIX man pages and other small to mediumsized documents.

1.10.17 astyle

Homepage:

• http://astyle.sourceforge.net/

Spack package:

• astyle/package.py

Versions: 2.04

Description: A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java SourceCode.

1.10.18 atk

Homepage:

• https://developer.gnome.org/atk/

Spack package:

• atk/package.py

Versions: 2.20.0, 2.14.0

Build Dependencies glib, pkg-config

Link Dependencies glib

Description: ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications.Using the ATK interfaces, accessibility tools have full access to view and control running applications.

1.10.19 atlas

Homepage:

• http://math-atlas.sourceforge.net/

Spack package:

• atlas/package.py

Versions: 3.11.34, 3.10.2

Description: Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automaticgeneration and optimization of numerical software. Currently ATLAS supplies optimized versions for the com-plete set of linear algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of thelinear algebra routines in the LAPACK library.

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1.10.20 atop

Homepage:

• http://www.atoptool.nl/index.php

Spack package:

• atop/package.py

Versions: 2.2-3

Description: Atop is an ASCII full-screen performance monitor for Linux

1.10.21 autoconf

Homepage:

• https://www.gnu.org/software/autoconf/

Spack package:

• autoconf/package.py

Versions: 2.69, 2.62

Build Dependencies m4

Description: Autoconf – system configuration part of autotools

1.10.22 automaded

Homepage:

• https://github.com/llnl/AutomaDeD

Spack package:

• automaded/package.py

Versions: 1.0

Build Dependencies boost, cmake, callpath, mpi

Link Dependencies boost, callpath, mpi

Description: AutomaDeD (Automata-based Debugging for Dissimilar parallel tasks) is a tool for automatic diagnosisof performance and correctness problems in MPI applications. It creates control-flow models of each MPIprocess and, when a failure occurs, these models are leveraged to find the origin of problems automatically.MPI calls are intercepted (using wrappers) to create the models. When an MPI application hangs, AutomaDeDcreates a progress-dependence graph that helps finding the process (or group of processes) that caused the hang.

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1.10.23 automake

Homepage:

• http://www.gnu.org/software/automake/

Spack package:

• automake/package.py

Versions: 1.15, 1.14.1, 1.11.6

Build Dependencies autoconf

Link Dependencies autoconf

Description: Automake – make file builder part of autotools

1.10.24 bash

Homepage:

• https://www.gnu.org/software/bash/

Spack package:

• bash/package.py

Versions: 4.3

Build Dependencies readline

Link Dependencies readline

Description: The GNU Project’s Bourne Again SHell.

1.10.25 bbcp

Homepage:

• http://www.slac.stanford.edu/~abh/bbcp/

Spack package:

• bbcp/package.py

Versions: git

Description: Securely and quickly copy data from source to target

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1.10.26 bcftools

Homepage:

• http://samtools.github.io/bcftools/

Spack package:

• bcftools/package.py

Versions: 1.3.1

Build Dependencies zlib

Link Dependencies zlib

Description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binarycounterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

1.10.27 bdw-gc

Homepage:

• http://www.hboehm.info/gc/

Spack package:

• bdw-gc/package.py

Versions: 7.4.4

Build Dependencies libatomic-ops

Link Dependencies libatomic-ops

Description: The Boehm-Demers-Weiser conservative garbage collector is a garbage collecting replacement for Cmalloc or C++ new.

1.10.28 bear

Homepage:

• https://github.com/rizsotto/Bear

Spack package:

• bear/package.py

Versions: 2.0.4

Build Dependencies python, cmake

Link Dependencies python

Description: Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems.

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1.10.29 bertini

Homepage:

• https://bertini.nd.edu/

Spack package:

• bertini/package.py

Versions: 1.5

Build Dependencies flex, gmp, bison, mpfr, mpi

Link Dependencies gmp, mpfr, mpi

Description: Bertini is a general-purpose solver, written in C, that was created for research about polynomial contin-uation. It solves for the numerical solution of systems of polynomial equations using homotopy continuation.

1.10.30 bib2xhtml

Homepage:

• http://www.spinellis.gr/sw/textproc/bib2xhtml/

Spack package:

• bib2xhtml/package.py

Versions: 3.0-15-gf506

Description: bib2xhtml is a program that converts BibTeX files into HTML.

1.10.31 binutils

Homepage:

• http://www.gnu.org/software/binutils/

Spack package:

• binutils/package.py

Versions: 2.26, 2.25, 2.24, 2.23.2, 2.20.1

Build Dependencies m4, bison, flex

Description: GNU binutils, which contain the linker, assembler, objdump and others

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1.10.32 bison

Homepage:

• http://www.gnu.org/software/bison/

Spack package:

• bison/package.py

Versions: 3.0.4

Build Dependencies m4

Description: Bison is a general-purpose parser generator that converts an annotated context-free grammar into adeterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

1.10.33 bliss

Homepage:

• http://www.tcs.hut.fi/Software/bliss/

Spack package:

• bliss/package.py

Versions: 0.73

Build Dependencies gmp, libtool

Link Dependencies gmp

Description: bliss: A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs

1.10.34 blitz

Homepage:

• http://github.com/blitzpp/blitz

Spack package:

• blitz/package.py

Versions: 1.0.0

Description: N-dimensional arrays for C++

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1.10.35 boost

Homepage:

• http://www.boost.org

Spack package:

• boost/package.py

Versions: 1.61.0, 1.60.0, 1.59.0, 1.58.0, 1.57.0, 1.56.0, 1.55.0, 1.54.0, 1.53.0, 1.52.0, 1.51.0, 1.50.0, 1.49.0, 1.48.0,1.47.0, 1.46.1, 1.46.0, 1.45.0, 1.44.0, 1.43.0, 1.42.0, 1.41.0, 1.40.0, 1.39.0, 1.38.0, 1.37.0, 1.36.0, 1.35.0, 1.34.1,1.34.0

Build Dependencies python, bzip2, zlib, icu, mpi

Link Dependencies python, bzip2, zlib, icu, mpi

Description: Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work wellwith the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broadspectrum of applications. The Boost license encourages both commercial and non-commercial use.

1.10.36 bowtie2

Homepage:

• bowtie-bio.sourceforge.net/bowtie2/index.shtml

Spack package:

• bowtie2/package.py

Versions: 2.2.5

Description: Description

1.10.37 boxlib

Homepage:

• https://ccse.lbl.gov/BoxLib/

Spack package:

• boxlib/package.py

Versions: master

Build Dependencies cmake, mpi

Link Dependencies mpi

Description: BoxLib, a software framework for massively parallel block-structured adaptive mesh refinement (AMR)codes.

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1.10.38 bpp-core

Homepage:

• http://biopp.univ-montp2.fr/wiki/index.php/Installation

Spack package:

• bpp-core/package.py

Versions: 2.2.0

Build Dependencies cmake

Description: Bio++ core library.

1.10.39 bpp-phyl

Homepage:

• http://biopp.univ-montp2.fr/wiki/index.php/Installation

Spack package:

• bpp-phyl/package.py

Versions: 2.2.0

Build Dependencies cmake, bpp-core, bpp-seq

Link Dependencies bpp-core, bpp-seq

Description: Bio++ phylogeny library.

1.10.40 bpp-seq

Homepage:

• http://biopp.univ-montp2.fr/wiki/index.php/Installation

Spack package:

• bpp-seq/package.py

Versions: 2.2.0

Build Dependencies cmake, bpp-core

Link Dependencies bpp-core

Description: Bio++ seq library.

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1.10.41 bpp-suite

Homepage:

• http://biopp.univ-montp2.fr/wiki/index.php/BppSuite

Spack package:

• bpp-suite/package.py

Versions: 2.2.0

Build Dependencies bpp-phyl, cmake, texinfo, bpp-core, bpp-seq

Link Dependencies bpp-phyl, bpp-core, bpp-seq

Description: BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.

1.10.42 bwa

Homepage:

• http://github.com/lh3/bwa

Spack package:

• bwa/package.py

Versions: 0.7.15

Build Dependencies zlib

Link Dependencies zlib

Description: Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

1.10.43 bzip2

Homepage:

• http://www.bzip.org

Spack package:

• bzip2/package.py

Versions: 1.0.6

Description: bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files towithin 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst beingaround twice as fast at compression and six times faster at decompression.

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1.10.44 c-blosc

Homepage:

• http://www.blosc.org

Spack package:

• c-blosc/package.py

Versions: 1.9.2, 1.9.1, 1.9.0, 1.8.1, 1.8.0

Build Dependencies snappy, zlib, cmake

Link Dependencies snappy, zlib

Description: Blosc, an extremely fast, multi-threaded, meta-compressor library

1.10.45 cairo

Homepage:

• http://cairographics.org

Spack package:

• cairo/package.py

Versions: 1.14.0

Build Dependencies glib, freetype, fontconfig, libpng, pkg-config, pixman

Link Dependencies glib, libpng, freetype, pixman, fontconfig

Description: Cairo is a 2D graphics library with support for multiple output devices.

1.10.46 caliper

Homepage:

• https://github.com/LLNL/Caliper

Spack package:

• caliper/package.py

Versions: master

Build Dependencies papi, libunwind, cmake, mpi

Link Dependencies libunwind, papi, mpi

Description: Caliper is a generic context annotation system. It gives programmers the ability to provide arbitraryprogram context information to (performance) tools at runtime.

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1.10.47 callpath

Homepage:

• https://github.com/llnl/callpath

Spack package:

• callpath/package.py

Versions: 1.0.2, 1.0.1

Build Dependencies cmake, dyninst, mpi, libelf , adept-utils, libdwarf

Link Dependencies dyninst, mpi, libdwarf , libelf , adept-utils

Description: Library for representing callpaths consistently in distributed-memory performance tools.

1.10.48 cantera

Homepage:

• http://www.cantera.org/docs/sphinx/html/index.html

Spack package:

• cantera/package.py

Versions: 2.2.1

Build Dependencies py-scipy, scons, lapack, blas, sundials, py-numpy, py-cython, python, py-3to2, boost

Link Dependencies lapack, python, blas, sundials, boost

Run Dependencies py-scipy, py-cython, py-3to2, py-numpy

Description: Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermody-namics, and/or transport processes.

1.10.49 cask

Homepage:

• http://cask.readthedocs.io/en/latest/

Spack package:

• cask/package.py

Versions: 0.7.4

Build Dependencies emacs

Run Dependencies emacs

Description: Cask is a project management tool for Emacs Lisp to automate the package development cycle; devel-opment, dependencies, testing, building, packaging and more.

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1.10.50 cblas

Homepage:

• http://www.netlib.org/blas/_cblas/

Spack package:

• cblas/package.py

Versions: 2015-06-06

Build Dependencies blas

Link Dependencies blas

Description: The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks forperforming basic vector and matrix operations.

1.10.51 cbtf

Homepage:

• http://sourceforge.net/p/cbtf/wiki/Home

Spack package:

• cbtf/package.py

Versions: 1.6

Build Dependencies cmake, mrnet, boost, xerces-c, libxml2

Link Dependencies xerces-c, mrnet, boost, libxml2

Description: CBTF project contains the base code for CBTF that supports creating components, component networksand the support to connect these components and component networks into sequential and distributed networktools.

1.10.52 cbtf-argonavis

Homepage:

• http://sourceforge.net/p/cbtf/wiki/Home/

Spack package:

• cbtf-argonavis/package.py

Versions: 1.6

Build Dependencies cmake, mrnet, cbtf-krell, cuda, papi, boost, cbtf

Link Dependencies papi, mrnet, cbtf-krell, cuda, boost, cbtf

Description: CBTF Argo Navis project contains the CUDA collector and supporting libraries that was done as aresult of a DOE SBIR grant.

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1.10.53 cbtf-krell

Homepage:

• http://sourceforge.net/p/cbtf/wiki/Home/

Spack package:

• cbtf-krell/package.py

Versions: 1.6

Build Dependencies mvapich2, mpich2, cmake, boost, dyninst, xerces-c, mrnet, mpt, openmpi, mpich, mvapich,libunwind, papi, cbtf , binutils, libmonitor

Link Dependencies mvapich2, mpich2, mrnet, boost, dyninst, xerces-c, mpt, openmpi, mpich, mvapich, libunwind,papi, cbtf , binutils, libmonitor

Description: CBTF Krell project contains the Krell Institute contributions to the CBTF project. These contributionsinclude many performance data collectors and support libraries as well as some example tools that drive the datacollection at HPC levels of scale.

1.10.54 cbtf-lanl

Homepage:

• http://sourceforge.net/p/cbtf/wiki/Home/

Spack package:

• cbtf-lanl/package.py

Versions: 1.6

Build Dependencies cmake, mrnet, xerces-c, cbtf , cbtf-krell

Link Dependencies cbtf-krell, mrnet, xerces-c, cbtf

Description: CBTF LANL project contains a memory tool and data center type system command monitoring tool.

1.10.55 cdd

Homepage:

• https://www.inf.ethz.ch/personal/fukudak/cdd_home/cdd.html

Spack package:

• cdd/package.py

Versions: 0.61a

Build Dependencies libtool

Description: The program cdd+ (cdd, respectively) is a C++ (ANSI C) implementation of the Double DescriptionMethod [MRTT53] for generating all vertices (i.e. extreme points) and extreme rays of a general convex poly-hedron given by a system of linear inequalities

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1.10.56 cddlib

Homepage:

• https://www.inf.ethz.ch/personal/fukudak/cdd_home/

Spack package:

• cddlib/package.py

Versions: 0.94h

Build Dependencies gmp, libtool

Link Dependencies gmp

Description: The C-library cddlib is a C implementation of the Double Description Method of Motzkin et al. forgenerating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron in R^d given by asystem of linear inequalities

1.10.57 cdo

Homepage:

• https://code.zmaw.de/projects/cdo

Spack package:

• cdo/package.py

Versions: 1.6.9

Build Dependencies netcdf

Link Dependencies netcdf

Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP modelData.

1.10.58 cereal

Homepage:

• http://uscilab.github.io/cereal/

Spack package:

• cereal/package.py

Versions: 1.2.0, 1.1.2, 1.1.1, 1.1.0, 1.0.0, 0.9.1

Build Dependencies cmake

Description: cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turnsthem into different representations, such as compact binary encodings, XML, or JSON. cereal was designed tobe fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with othercode or used standalone.

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1.10.59 cfitsio

Homepage:

• http://heasarc.gsfc.nasa.gov/fitsio/

Spack package:

• cfitsio/package.py

Versions: 3.370

Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (FlexibleImage Transport System) data format.

1.10.60 cgal

Homepage:

• http://www.cgal.org/

Spack package:

• cgal/package.py

Versions: 4.7, 4.6.3

Build Dependencies gmp, zlib, boost, cmake, mpfr

Link Dependencies gmp, zlib, boost, mpfr

Description: CGAL is a software project that provides easy access to efficient and reliable geometric algorithmsin the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geo-graphic information systems, computer aided design, molecular biology, medical imaging, computer graphics,and robotics.

1.10.61 cgm

Homepage:

• http://trac.mcs.anl.gov/projects/ITAPS/wiki/CGM

Spack package:

• cgm/package.py

Versions: 13.1.1, 13.1.0, 13.1

Build Dependencies mpi

Link Dependencies mpi

Description: The Common Geometry Module, Argonne (CGMA) is a code library which provides geometry func-tionality used for mesh generation and other applications.

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1.10.62 cgns

Homepage:

• http://cgns.github.io/

Spack package:

• cgns/package.py

Versions: 3.3.0

Build Dependencies cmake, hdf5

Link Dependencies hdf5

Description: The CFD General Notation System (CGNS) provides a general, portable, and extensible standard forthe storage and retrieval of computational fluid dynamics (CFD) analysis data.

1.10.63 cityhash

Homepage:

• https://github.com/google/cityhash

Spack package:

• cityhash/package.py

Versions: 2013-07-31, master

Description: CityHash, a family of hash functions for strings.

1.10.64 cleverleaf

Homepage:

• http://uk-mac.github.io/CleverLeaf/

Spack package:

• cleverleaf/package.py

Versions: develop

Build Dependencies boost, cmake, SAMRAI, hdf5

Link Dependencies boost, SAMRAI, hdf5

Description: CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with Adaptive Mesh Refinement usingthe SAMRAI toolkit from Lawrence Livermore National Laboratory. The primary goal of CleverLeaf is toevaluate the application of AMR to the Lagrangian-Eulerian hydrodynamics scheme used by CloverLeaf.

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1.10.65 cloog

Homepage:

• http://www.cloog.org

Spack package:

• cloog/package.py

Versions: 0.18.1, 0.18.0, 0.17.0

Build Dependencies gmp, isl

Link Dependencies gmp, isl

Description: CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code(e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra.

1.10.66 cmake

Homepage:

• https://www.cmake.org

Spack package:

• cmake/package.py

Versions: 3.6.1, 3.6.0, 3.5.2, 3.5.1, 3.5.0, 3.4.3, 3.4.0, 3.3.1, 3.0.2, 2.8.10.2

Build Dependencies py-sphinx, bzip2, zlib, qt, python, expat, openssl, libarchive, xz, ncurses, curl

Link Dependencies bzip2, expat, qt, ncurses, zlib, openssl, libarchive, xz, curl

Description: A cross-platform, open-source build system. CMake is a family of tools designed to build, test andpackage software.

1.10.67 cmocka

Homepage:

• https://cmocka.org/

Spack package:

• cmocka/package.py

Versions: 1.0.1

Build Dependencies cmake

Description: Unit-testing framework in pure C

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1.10.68 cnmem

Homepage:

• https://github.com/NVIDIA/cnmem

Spack package:

• cnmem/package.py

Versions: git

Description: CNMem mempool for CUDA devices

1.10.69 coreutils

Homepage:

• http://www.gnu.org/software/coreutils/

Spack package:

• coreutils/package.py

Versions: 8.23

Description: The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operatingsystem. These are the core utilities which are expected to exist on every operating system.

1.10.70 cp2k

Homepage:

• https://www.cp2k.org

Spack package:

• cp2k/package.py

Versions: 3.0

Build Dependencies python, blas, fftw, plumed, lapack, mpi, scalapack

Link Dependencies lapack, blas, fftw, plumed, mpi, scalapack

Description: CP2K is a quantum chemistry and solid state physics software package that can perform atomisticsimulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems

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1.10.71 cppcheck

Homepage:

• http://cppcheck.sourceforge.net/

Spack package:

• cppcheck/package.py

Versions: 1.68

Description: A tool for static C/C++ code analysis.

1.10.72 cram

Homepage:

• https://github.com/llnl/cram

Spack package:

• cram/package.py

Versions: 1.0.1

Build Dependencies python, cmake, mpi

Link Dependencies python, mpi

Description: Cram runs many small MPI jobs inside one large MPI job.

1.10.73 cryptopp

Homepage:

• http://www.cryptopp.com

Spack package:

• cryptopp/package.py

Versions: 5.6.3, 5.6.2, 5.6.1

Description: Crypto++ is an open-source C++ library of cryptographic schemes. The library supports a number ofdifferent cryptography algorithms, including authenticated encryption schemes (GCM, CCM), hash functions(SHA-1, SHA2), public-key encryption (RSA, DSA), and a few obsolete/historical encryption algorithms (MD5,Panama).

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1.10.74 cscope

Homepage:

• http://http://cscope.sourceforge.net/

Spack package:

• cscope/package.py

Versions: 15.8b

Description: Cscope is a developer’s tool for browsing source code.

1.10.75 cube

Homepage:

• http://www.scalasca.org/software/cube-4.x/download.html

Spack package:

• cube/package.py

Versions: 4.3.4, 4.3.3, 4.2.3

Build Dependencies zlib

Link Dependencies zlib

Description: Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performancespace consisting of the dimensions: - performance metric - call path - system resource

1.10.76 cuda

Homepage:

• http://www.nvidia.com/object/cuda_home_new.html

Spack package:

• cuda/package.py

Versions: 7.5.18, 6.5.14

Description: CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dra-matic increases in computing performance by harnessing the power of the graphics processing unit (GPU).Note: NVIDIA does not provide a download URL for CUDA so you will need to download it yourself. Go tohttps://developer.nvidia.com/cuda-downloads and select your Operating System, Architecture, Distribution, andVersion. For the Installer Type, select runfile and click Download. Spack will search your current directory forthis file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up amirror, see http://software.llnl.gov/spack/mirrors.html Note: This package does not currently install the driversnecessary to run CUDA. These will need to be installed manually. See: http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details.

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1.10.77 curl

Homepage:

• http://curl.haxx.se

Spack package:

• curl/package.py

Versions: 7.50.1, 7.49.1, 7.47.1, 7.46.0, 7.45.0, 7.44.0, 7.43.0, 7.42.1

Build Dependencies zlib, openssl

Link Dependencies zlib, openssl

Description: cURL is an open source command line tool and library for transferring data with URL syntax

1.10.78 czmq

Homepage:

• http://czmq.zeromq.org

Spack package:

• czmq/package.py

Versions: 3.0.2

Build Dependencies zeromq, autoconf , libtool, automake, pkg-config

Link Dependencies zeromq

Description: A C interface to the ZMQ library

1.10.79 daal

Homepage:

• https://software.intel.com/en-us/daal

Spack package:

• daal/package.py

Versions: 2016.3.210, 2016.2.181

Description: Intel Data Analytics Acceleration Library. Note: You will have to add the download file to a mirror sothat Spack can find it. For instructions on how to set up a mirror, see http://software.llnl.gov/spack/mirrors.html

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1.10.80 dakota

Homepage:

• https://dakota.sandia.gov/

Spack package:

• dakota/package.py

Versions: 6.3

Build Dependencies cmake, lapack, blas, mpi, python, boost

Link Dependencies lapack, python, blas, boost, mpi

Description: The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systemsanalysis methods. Dakota contains algorithms for: - optimization with gradient and non gradient-based methods;- uncertainty quantification with sampling, reliability, stochastic - expansion, and epistemic methods; - parameterestimation with nonlinear least squares methods; - sensitivity/variance analysis with design of experiments and- parameter study methods. These capabilities may be used on their own or as components within advancedstrategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, oroptimization under uncertainty.

1.10.81 damselfly

Homepage:

• https://github.com/llnl/damselfly

Spack package:

• damselfly/package.py

Versions: 1.0

Build Dependencies cmake

Description: Damselfly is a model-based parallel network simulator.

1.10.82 datamash

Homepage:

• https://www.gnu.org/software/datamash/

Spack package:

• datamash/package.py

Versions: 1.1.0, 1.0.7, 1.0.6, 1.0.5

Description: GNU datamash is a command-line program which performs basic numeric, textual and statistical oper-ations on input textual data files.

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1.10.83 dbus

Homepage:

• http://dbus.freedesktop.org/

Spack package:

• dbus/package.py

Versions: 1.11.2, 1.9.0, 1.8.8, 1.8.6, 1.8.4, 1.8.2

Build Dependencies expat

Link Dependencies expat

Description: D-Bus is a message bus system, a simple way for applications to talk to one another. D-Bus suppliesboth a system daemon (for events such new hardware device printer queue ) and a per-user-login-session daemon(for general IPC needs among user applications). Also, the message bus is built on top of a general one-to-onemessage passing framework, which can be used by any two applications to communicate directly (without goingthrough the message bus daemon).

1.10.84 dealii

Homepage:

• https://www.dealii.org

Spack package:

• dealii/package.py

Versions: develop, 8.4.1, 8.4.0, 8.3.0, 8.2.1, 8.1.0

Build Dependencies zlib, blas, graphviz, netcdf , arpack-ng, bzip2, cmake, lapack, oce, astyle, boost, trilinos, mu-parser, p4est, mpi, suite-sparse, tbb, doxygen, hdf5, slepc, numdiff , metis, petsc, netcdf-cxx, gsl

Link Dependencies zlib, blas, graphviz, netcdf , arpack-ng, bzip2, lapack, oce, astyle, boost, trilinos, muparser,p4est, mpi, suite-sparse, tbb, doxygen, hdf5, slepc, numdiff , metis, petsc, netcdf-cxx, gsl

Description: C++ software library providing well-documented tools to build finite element codes for a broad varietyof PDEs.

1.10.85 dia

Homepage:

• https://wiki.gnome.org/Apps/Dia

Spack package:

• dia/package.py

Versions: 0.97.3

Build Dependencies intltool, python, cairo, swig, gtkplus, libpng, libxslt

Link Dependencies python, cairo, swig, gtkplus, libpng, libxslt

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Description: Dia is a program for drawing structured diagrams.

1.10.86 docbook-xml

Homepage:

• http://www.oasis-open.org/docbook

Spack package:

• docbook-xml/package.py

Versions: 4.5

Description: Docbook DTD XML files.

1.10.87 doxygen

Homepage:

• http://www.stack.nl/~dimitri/doxygen/

Spack package:

• doxygen/package.py

Versions: 1.8.11, 1.8.10

Build Dependencies flex, cmake, bison

Run Dependencies graphviz

Description: Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but italso supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba,Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..

1.10.88 dri2proto

Homepage:

• http://http://cgit.freedesktop.org/xorg/proto/dri2proto/

Spack package:

• dri2proto/package.py

Versions: 2.8

Description: DRI2 Protocol Headers.

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1.10.89 dtcmp

Homepage:

• https://github.com/hpc/dtcmp

Spack package:

• dtcmp/package.py

Versions: 1.0.3

Build Dependencies lwgrp, mpi

Link Dependencies lwgrp, mpi

Description: The Datatype Comparison Library provides comparison operations and parallel sort algorithms for MPIapplications.

1.10.90 dyninst

Homepage:

• https://paradyn.org

Spack package:

• dyninst/package.py

Versions: 9.2.0, 9.1.0, 8.2.1, 8.1.2, 8.1.1

Build Dependencies boost, cmake, libelf , libdwarf

Link Dependencies boost, libelf , libdwarf

Description: API for dynamic binary instrumentation. Modify programs while they are executing without recompil-ing, re-linking, or re-executing.

1.10.91 eigen

Homepage:

• http://eigen.tuxfamily.org/

Spack package:

• eigen/package.py

Versions: 3.2.7

Build Dependencies metis, cmake, fftw, suite-sparse, gmp, scotch, mpfr

Link Dependencies metis, fftw, suite-sparse, gmp, scotch, mpfr

Description: Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and relatedalgorithms.

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1.10.92 elfutils

Homepage:

• https://fedorahosted.org/elfutils/

Spack package:

• elfutils/package.py

Versions: 0.163

Description: elfutils is a collection of various binary tools such as eu-objdump, eu- readelf, and other utilities thatallow you to inspect and manipulate ELF files. Refer to Table 5.Tools Included in elfutils for Red Hat Developerfor a complete list of binary tools that are distributed with the Red Hat Developer Toolset version of elfutils.

1.10.93 elk

Homepage:

• http://elk.sourceforge.net/

Spack package:

• elk/package.py

Versions: 3.3.17

Build Dependencies lapack, blas, fftw, libxc, mpi

Link Dependencies lapack, blas, fftw, libxc, mpi

Description: An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advancedfeatures.

1.10.94 elpa

Homepage:

• http://elpa.mpcdf.mpg.de/

Spack package:

• elpa/package.py

Versions: 2015.11.001

Build Dependencies lapack, blas, scalapack, mpi

Link Dependencies lapack, blas, scalapack, mpi

Description: Eigenvalue solvers for Petaflop-Applications (ELPA)

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1.10.95 emacs

Homepage:

• https://www.gnu.org/software/emacs

Spack package:

• emacs/package.py

Versions: 24.5

Build Dependencies ncurses, libtiff , gtkplus, giflib, libxpm, libpng

Link Dependencies ncurses, libtiff , gtkplus, giflib, libxpm, libpng

Description: The Emacs programmable text editor.

1.10.96 environment-modules

Homepage:

• https://sourceforge.net/p/modules/wiki/Home/

Spack package:

• environment-modules/package.py

Versions: 3.2.10

Build Dependencies tcl

Link Dependencies tcl

Run Dependencies tcl

Description: The Environment Modules package provides for the dynamic modification of a user’s environment viamodulefiles.

1.10.97 espresso

Homepage:

• http://quantum-espresso.org

Spack package:

• espresso/package.py

Versions: 5.4.0, 5.3.0

Build Dependencies lapack, blas, fftw, scalapack, mpi

Link Dependencies lapack, blas, fftw, scalapack, mpi

Description: QE is an integrated suite of Open-Source computer codes for electronic- structure calculations andmaterials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

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1.10.98 exodusii

Homepage:

• https://github.com/gsjaardema/seacas

Spack package:

• exodusii/package.py

Versions: 2016-02-08

Build Dependencies cmake, netcdf , hdf5

Link Dependencies netcdf , hdf5

Description: Exodus II is a C++/Fortran library developed to store and retrieve data for finite element analyses. It’sused for preprocessing (problem definition), postprocessing (results visualization), and data transfer betweencodes. An Exodus II data file is a random access, machine independent, binary file that is written and read viaC, C++, or Fortran API routines.

1.10.99 exonerate

Homepage:

• http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Spack package:

• exonerate/package.py

Versions: 2.4.0

Build Dependencies glib, pkg-config

Link Dependencies glib

Description: Pairwise sequence alignment of DNA and proteins

1.10.100 expat

Homepage:

• http://expat.sourceforge.net/

Spack package:

• expat/package.py

Versions: 2.2.0, 2.1.0

Description: <eXpat/> is an XML parser library written in C

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1.10.101 extrae

Homepage:

• http://www.bsc.es/computer-sciences/extrae

Spack package:

• extrae/package.py

Versions: 3.0.1

Build Dependencies papi, dyninst, mpi, libunwind, boost, libdwarf

Link Dependencies papi, dyninst, mpi, libunwind, boost, libdwarf

Description: Extrae is the package devoted to generate tracefiles which can be analyzed later by Paraver. Extrae isa tool that uses different interposition mechanisms to inject probes into the target application so as to gatherinformation regarding the application performance. The Extrae instrumentation package can instrument theMPI programin model, and the following parallel programming models either alone or in conjunction with MPI: OpenMP, CUDA, OpenCL, pthread, OmpSs

1.10.102 exuberant-ctags

Homepage:

• ctags.sourceforge.net

Spack package:

• exuberant-ctags/package.py

Versions: 5.8

Description: The canonical ctags generator

1.10.103 fastx_toolkit

Homepage:

• http://hannonlab.cshl.edu/fastx_toolkit/

Spack package:

• fastx_toolkit/package.py

Versions: 0.0.14

Build Dependencies libgtextutils

Link Dependencies libgtextutils

Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files prepro-cessing.

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1.10.104 fenics

Homepage:

• http://fenicsproject.org/

Spack package:

• fenics/package.py

Versions: 1.6.0, 1.5.0

Build Dependencies py-sphinx, suite-sparse, cmake, eigen, hdf5, python, slepc, swig, parmetis, py-numpy, py-six,py-ply, trilinos, boost, py-setuptools, petsc, mpi, scotch, vtk, qt

Link Dependencies py-sphinx, suite-sparse, cmake, eigen, hdf5, python, slepc, swig, parmetis, py-numpy, py-six,py-ply, trilinos, boost, py-setuptools, petsc, mpi, scotch, vtk, qt

Description: FEniCS is organized as a collection of interoperable components that together form the FEniCS Project.These components include the problem- solving environment DOLFIN, the form compiler FFC, the finite ele-ment tabulator FIAT, the just-in-time compiler Instant, the code generation interface UFC, the form languageUFL and a range of additional components.

1.10.105 ferret

Homepage:

• http://ferret.noaa.gov/Ferret/

Spack package:

• ferret/package.py

Versions: 6.96

Build Dependencies readline, zlib, netcdf , netcdf-fortran, hdf5

Link Dependencies readline, zlib, netcdf , netcdf-fortran, hdf5

Description: Ferret is an interactive computer visualization and analysis environment designed to meet the needs ofoceanographers and meteorologists analyzing large and complex gridded data sets.

1.10.106 fftw

Homepage:

• http://www.fftw.org

Spack package:

• fftw/package.py

Versions: 3.3.5, 3.3.4

Build Dependencies mpi

Link Dependencies mpi

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Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or moredimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. thediscrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should becomethe FFT library of choice for most applications.

1.10.107 fish

Homepage:

• http://fishshell.com/

Spack package:

• fish/package.py

Versions: 2.2.0

Description: fish is a smart and user-friendly command line shell for OS X, Linux, and the rest of the family.

1.10.108 flex

Homepage:

• http://flex.sourceforge.net/

Spack package:

• flex/package.py

Versions: 2.6.0, 2.5.39

Build Dependencies m4, bison

Description: Flex is a tool for generating scanners.

1.10.109 fltk

Homepage:

• http://www.fltk.org/

Spack package:

• fltk/package.py

Versions: 1.3.3

Description: FLTK (pronounced “fulltick”) is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), MicrosoftWindows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphicsvia OpenGL and its built-in GLUT emulation. FLTK is designed to be small and modular enough to be staticallylinked, but works fine as a shared library. FLTK also includes an excellent UI builder called FLUID that can beused to create applications in minutes.

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1.10.110 flux

Homepage:

• https://github.com/flux-framework/flux-core

Spack package:

• flux/package.py

Versions: master

Build Dependencies hwloc, docbook-xml, python, czmq, munge, asciidoc, lua, py-cffi, libxslt, zeromq, libjson-c

Link Dependencies hwloc, python, czmq, munge, lua, py-cffi, libxslt, zeromq, libjson-c

Description: A next-generation resource manager (pre-alpha)

1.10.111 foam-extend

Homepage:

• http://www.extend-project.de/

Spack package:

• foam-extend/package.py

Versions: 3.2, 3.1, 3.0

Build Dependencies flex, zlib, cmake, python, metis, mpi, parmgridgen, scotch, parmetis, paraview

Link Dependencies flex, zlib, python, metis, mpi, parmgridgen, scotch, parmetis, paraview

Description: The foam-extend project is a fork of the OpenFOAM open source library for Computational FluidDynamics (CFD).

1.10.112 fontconfig

Homepage:

• http://www.freedesktop.org/wiki/Software/fontconfig/

Spack package:

• fontconfig/package.py

Versions: 2.11.1

Build Dependencies libxml2, freetype

Link Dependencies libxml2, freetype

Description: Fontconfig customizing font access

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1.10.113 freetype

Homepage:

• http://http://www.freetype.org

Spack package:

• freetype/package.py

Versions: 2.5.3

Build Dependencies libpng

Link Dependencies libpng

Description: Font package

1.10.114 gasnet

Homepage:

• http://gasnet.lbl.gov

Spack package:

• gasnet/package.py

Versions: 1.24.0

Description: GASNet is a language-independent, low-level networking layer that provides network-independent,high-performance communication primitives tailored for implementing parallel global address space SPMDlanguages and libraries such as UPC, Co-Array Fortran, SHMEM, Cray Chapel, and Titanium.

1.10.115 gcc

Homepage:

• https://gcc.gnu.org

Spack package:

• gcc/package.py

Versions: 6.2.0, 6.1.0, 5.4.0, 5.3.0, 5.2.0, 5.1.0, 4.9.4, 4.9.3, 4.9.2, 4.9.1, 4.8.5, 4.8.4, 4.7.4, 4.6.4, 4.5.4

Build Dependencies mpfr, gmp, mpc, binutils, isl

Link Dependencies mpfr, gmp, mpc, binutils, isl

Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, and Java.

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1.10.116 gdal

Homepage:

• http://www.gdal.org/

Spack package:

• gdal/package.py

Versions: 2.0.2

Build Dependencies libtiff , hdf5, python, swig, zlib, py-numpy, hdf , netcdf , proj, libpng, openjpeg, kealib, geos

Link Dependencies libtiff , hdf5, python, swig, zlib, hdf , netcdf , proj, libpng, openjpeg, kealib, geos

Run Dependencies py-numpy

Description: GDAL is a translator library for raster and vector geospatial data formats that is released under anX/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a singleraster abstract data model and vector abstract data model to the calling application for all supported formats. Italso comes with a variety of useful command line utilities for data translation and processing.

1.10.117 gdb

Homepage:

• https://www.gnu.org/software/gdb

Spack package:

• gdb/package.py

Versions: 7.11, 7.10.1, 7.10, 7.9.1, 7.9, 7.8.2

Build Dependencies texinfo

Description: GDB, the GNU Project debugger, allows you to see what is going on ‘inside’ another program while itexecutes – or what another program was doing at the moment it crashed.

1.10.118 gdk-pixbuf

Homepage:

• https://developer.gnome.org/gdk-pixbuf/

Spack package:

• gdk-pixbuf/package.py

Versions: 2.31.2

Build Dependencies glib, libpng, libtiff , jpeg

Link Dependencies glib, libpng, libtiff , jpeg

Description: The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 andGTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off intoa separate package in preparation for the change to GTK+ 3.

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1.10.119 geos

Homepage:

• http://trac.osgeo.org/geos/

Spack package:

• geos/package.py

Versions: 3.5.0, 3.4.2, 3.4.1, 3.4.0, 3.3.9, 3.3.8, 3.3.7, 3.3.6, 3.3.5, 3.3.4, 3.3.3

Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, itaims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features forSQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

1.10.120 gettext

Homepage:

• https://www.gnu.org/software/gettext/

Spack package:

• gettext/package.py

Versions: 0.19.8.1, 0.19.7

Build Dependencies bzip2, tar, libunistring, ncurses, libxml2, xz

Link Dependencies bzip2, tar, libunistring, ncurses, libxml2, xz

Description: GNU internationalization (i18n) and localization (l10n) library.

1.10.121 gflags

Homepage:

• https://gflags.github.io/gflags

Spack package:

• gflags/package.py

Versions: 2.1.2

Build Dependencies cmake

Description: The gflags package contains a C++ library that implements commandline flags processing. It includesbuilt-in support for standard types such as string and the ability to define flags in the source file in which theyare used. Online documentation available at: https://gflags.github.io/gflags/

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1.10.122 ghostscript

Homepage:

• http://ghostscript.com/

Spack package:

• ghostscript/package.py

Versions: 9.18

Build Dependencies libtiff

Link Dependencies libtiff

Description: An interpreter for the PostScript language and for PDF.

1.10.123 giflib

Homepage:

• http://giflib.sourceforge.net/

Spack package:

• giflib/package.py

Versions: 5.1.4

Description: The GIFLIB project maintains the giflib service library, which has been pulling images out of GIFssince 1989.

1.10.124 git

Homepage:

• http://git-scm.com

Spack package:

• git/package.py

Versions: 2.9.3, 2.9.2, 2.9.1, 2.9.0, 2.8.4, 2.8.3, 2.8.2, 2.8.1, 2.8.0, 2.7.3, 2.7.1

Build Dependencies pcre, expat, zlib, openssl, gettext, perl, curl, autoconf

Link Dependencies pcre, expat, zlib, openssl, gettext, perl, curl

Description: Git is a free and open source distributed version control system designed to handle everything fromsmall to very large projects with speed and efficiency.

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1.10.125 gl2ps

Homepage:

• http://www.geuz.org/gl2ps/

Spack package:

• gl2ps/package.py

Versions: 1.3.9

Build Dependencies libpng

Link Dependencies libpng

Description: GL2PS is a C library providing high quality vector output for any OpenGL application.

1.10.126 glib

Homepage:

• https://developer.gnome.org/glib/

Spack package:

• glib/package.py

Versions: 2.49.4, 2.48.1, 2.42.1

Build Dependencies libffi, pcre, zlib, gettext, pkg-config

Link Dependencies libffi, pcre, zlib, gettext

Description: The GLib package contains a low-level libraries useful for providing data structure handling for C,portability wrappers and interfaces for such runtime functionality as an event loop, threads, dynamic loadingand an object system.

1.10.127 glm

Homepage:

• https://github.com/g-truc/glm

Spack package:

• glm/package.py

Versions: 0.9.7.1

Build Dependencies cmake

Description: OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based onthe OpenGL Shading Language (GLSL) specification.

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1.10.128 global

Homepage:

• http://www.gnu.org/software/global

Spack package:

• global/package.py

Versions: 6.5

Build Dependencies ncurses, exuberant-ctags

Link Dependencies ncurses

Run Dependencies exuberant-ctags

Description: The Gnu Global tagging system

1.10.129 glog

Homepage:

• https://github.com/google/glog

Spack package:

• glog/package.py

Versions: 0.3.3

Description: C++ implementation of the Google logging module.

1.10.130 glpk

Homepage:

• https://www.gnu.org/software/glpk

Spack package:

• glpk/package.py

Versions: 4.57

Build Dependencies gmp

Link Dependencies gmp

Description: The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear program-ming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSIC and organized in the form of a callable library

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1.10.131 gmp

Homepage:

• https://gmplib.org

Spack package:

• gmp/package.py

Versions: 6.1.1, 6.1.0, 6.0.0a, 6.0.0

Build Dependencies m4

Description: GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers,and floating-point numbers.

1.10.132 gmsh

Homepage:

• http://gmsh.info

Spack package:

• gmsh/package.py

Versions: 2.12.0, 2.11.0

Build Dependencies cmake, fltk, hdf5, lapack, blas, zlib, oce, mpi, petsc, gmp, slepc

Link Dependencies fltk, hdf5, lapack, blas, zlib, oce, mpi, petsc, gmp, slepc

Description: Gmsh is a free 3D finite element grid generator with a built-in CAD engine and post-processor. Itsdesign goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visu-alization capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. Thespecification of any input to these modules is done either interactively using the graphical user interface or inASCII text files using Gmsh’s own scripting language.

1.10.133 gnu-prolog

Homepage:

• http://www.gprolog.org/

Spack package:

• gnu-prolog/package.py

Versions: 1.4.4

Description: A free Prolog compiler with constraint solving over finite domains.

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1.10.134 gnuplot

Homepage:

• http://www.gnuplot.info

Spack package:

• gnuplot/package.py

Versions: 5.0.1

Build Dependencies cairo, libcerf , libgd, pango, readline, wx

Link Dependencies cairo, libcerf , libgd, pango, readline, wx

Description: Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS,and many other platforms. The source code is copyrighted but freely distributed (i.e., you don’t have to pay forit). It was originally created to allow scientists and students to visualize mathematical functions and data inter-actively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plottingengine by third-party applications like Octave. Gnuplot has been supported and under active development since1986

1.10.135 gnutls

Homepage:

• http://www.gnutls.org

Spack package:

• gnutls/package.py

Versions: 3.3.9

Build Dependencies nettle

Link Dependencies nettle

Description: GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols andtechnologies around them. It provides a simple C language application programming interface (API) to accessthe secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and otherrequired structures. It is aimed to be portable and efficient with focus on security and interoperability.

1.10.136 go

Homepage:

• https://golang.org

Spack package:

• go/package.py

Versions: 1.6.2, 1.5.4

Build Dependencies go-bootstrap, git

Link Dependencies git

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Run Dependencies git

Description: The golang compiler and build environment

1.10.137 go-bootstrap

Homepage:

• https://golang.org

Spack package:

• go-bootstrap/package.py

Versions: 1.4.2

Build Dependencies git

Link Dependencies git

Description: Old C-bootstrapped go to bootstrap real go

1.10.138 gobject-introspection

Homepage:

• https://wiki.gnome.org/Projects/GObjectIntrospection

Spack package:

• gobject-introspection/package.py

Versions: 1.48.0

Build Dependencies glib, python, cairo

Link Dependencies glib, python, cairo

Description: The GObject Introspection is used to describe the program APIs and collect them in a uniform, machinereadable format.Cairo is a 2D graphics library with support for multiple output

1.10.139 googletest

Homepage:

• https://github.com/google/googletest

Spack package:

• googletest/package.py

Versions: 1.7.0

Build Dependencies cmake

Description: Google test framework for C++. Also called gtest.

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1.10.140 gperf

Homepage:

• https://www.gnu.org/software/gperf/

Spack package:

• gperf/package.py

Versions: 3.0.4

Description: GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash functionand hash table, in form of C or C++ code, for looking up a value depending on the input string. The hashfunction is perfect, which means that the hash table has no collisions, and the hash table lookup needs a singlestring comparison only.

1.10.141 gperftools

Homepage:

• https://code.google.com/p/gperftools

Spack package:

• gperftools/package.py

Versions: 2.4, 2.3

Build Dependencies libunwind

Link Dependencies libunwind

Description: Google’s fast malloc/free implementation, especially for multi-threaded applications. Contains tcmal-loc, heap-checker, heap-profiler, and cpu- profiler.

1.10.142 graphlib

Homepage:

• https://github.com/LLNL/graphlib

Spack package:

• graphlib/package.py

Versions: 3.0.0, 2.0.0

Build Dependencies cmake

Description: Library to create, manipulate, and export graphs Graphlib.

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1.10.143 graphviz

Homepage:

• http://www.graphviz.org

Spack package:

• graphviz/package.py

Versions: 2.38.0

Build Dependencies python, swig, ghostscript, pkg-config

Link Dependencies python, swig, ghostscript

Description: Graph Visualization Software

1.10.144 gromacs

Homepage:

• http://www.gromacs.org

Spack package:

• gromacs/package.py

Versions: 5.1.2

Build Dependencies mpi, fftw, cmake, plumed

Link Dependencies mpi, fftw, plumed

Description: GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primar-ily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the BiophysicalChemistry department of University of Groningen, and is now maintained by contributors in universities and re-search centers across the world. GROMACS is one of the fastest and most popular software packages availableand can run on CPUs as well as GPUs. It is free, open source released under the GNU General Public License.Starting from version 4.6, GROMACS is released under the GNU Lesser General Public License.

1.10.145 gsl

Homepage:

• http://www.gnu.org/software/gsl

Spack package:

• gsl/package.py

Versions: 2.1, 2.0, 1.16

Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free softwareunder the GNU General Public License. The library provides a wide range of mathematical routines such asrandom number generators, special functions and least-squares fitting. There are over 1000 functions in totalwith an extensive test suite.

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1.10.146 gtkplus

Homepage:

• http://www.gtk.org

Spack package:

• gtkplus/package.py

Versions: 2.24.25

Build Dependencies gdk-pixbuf , pango, atk

Link Dependencies gdk-pixbuf , pango, atk

Description: The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

1.10.147 gts

Homepage:

• http://gts.sourceforge.net/index.html

Spack package:

• gts/package.py

Versions: 121130

Build Dependencies glib

Link Dependencies glib

Description: GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Libraryintended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. Thesource code is available free of charge under the Free Software LGPL license. The code is written entirely in Cwith an object-oriented approach based mostly on the design of GTK+. Careful attention is paid to performancerelated issues as the initial goal of GTS is to provide a simple and efficient library to scientists dealing with 3Dcomputational surface meshes.

1.10.148 guile

Homepage:

• https://www.gnu.org/software/guile/

Spack package:

• guile/package.py

Versions: 2.0.11

Build Dependencies libunistring, gettext, bdw-gc, libtool, libffi, readline, gmp, pkg-config

Link Dependencies libunistring, gettext, bdw-gc, libtool, libffi, readline, gmp

Description: Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language forthe GNU operating system.

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1.10.149 harfbuzz

Homepage:

• http://www.freedesktop.org/wiki/Software/HarfBuzz/

Spack package:

• harfbuzz/package.py

Versions: 0.9.37

Build Dependencies glib, cairo, freetype, zlib, icu

Link Dependencies glib, cairo, freetype, zlib, icu

Description: The Harfbuzz package contains an OpenType text shaping engine.

1.10.150 harminv

Homepage:

• http://ab-initio.mit.edu/wiki/index.php/Harminv

Spack package:

• harminv/package.py

Versions: 1.4

Build Dependencies lapack, blas

Link Dependencies lapack, blas

Description: Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion -given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponen-tially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases ofthose sinusoids.

1.10.151 hdf

Homepage:

• https://www.hdfgroup.org/products/hdf4/

Spack package:

• hdf/package.py

Versions: 4.2.11

Build Dependencies zlib, szip, jpeg

Link Dependencies zlib, szip, jpeg

Description: HDF4 (also known as HDF) is a library and multi-object file format for storing and managing databetween machines.

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1.10.152 hdf5

Homepage:

• http://www.hdfgroup.org/HDF5/

Spack package:

• hdf5/package.py

Versions: 1.10.0-patch1, 1.10.0, 1.8.16, 1.8.15, 1.8.13

Build Dependencies zlib, szip, mpi

Link Dependencies zlib, szip, mpi

Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimitedvariety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

1.10.153 hdf5-blosc

Homepage:

• https://github.com/Blosc/hdf5-blosc

Spack package:

• hdf5-blosc/package.py

Versions: master

Build Dependencies c-blosc, libtool, hdf5

Link Dependencies c-blosc, hdf5

Description: Blosc filter for HDF5

1.10.154 hmmer

Homepage:

• http://www.hmmer.org

Spack package:

• hmmer/package.py

Versions: 3.1b2, 3.0, 2.4i, 2.3.2, 2.3.1

Build Dependencies gsl, mpi

Link Dependencies gsl, mpi

Description: HMMER is used for searching sequence databases for sequence homologs, and for making sequencealignments. It implements methods using probabilistic models called profile hidden Markov models (profileHMMs).

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1.10.155 hoomd-blue

Homepage:

• https://codeblue.umich.edu/hoomd-blue/index.html

Spack package:

• hoomd-blue/package.py

Versions: 1.3.3

Build Dependencies doxygen, cmake, python, py-numpy, cuda, mpi, boost

Link Dependencies python, boost, cuda, mpi

Run Dependencies py-numpy

Description: HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core tothousands of GPUs. You define particle initial conditions and interactions in a high-level python script. Thentell HOOMD-blue how you want to execute the job and it takes care of the rest. Python job scripts give youunlimited flexibility to create custom initialization routines, control simulation parameters, and perform in situanalysis.

1.10.156 hpl

Homepage:

• http://www.netlib.org/benchmark/hpl/

Spack package:

• hpl/package.py

Versions: 2.2

Build Dependencies blas, mpi

Link Dependencies blas, mpi

Description: HPL is a software package that solves a (random) dense linear system in double precision (64 bits)arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely availableimplementation of the High Performance Computing Linpack Benchmark.

1.10.157 hpx5

Homepage:

• http://hpx.crest.iu.edu

Spack package:

• hpx5/package.py

Versions: 2.0.0, 1.3.0, 1.2.0, 1.1.0, 1.0.0

Build Dependencies mpi

Link Dependencies mpi

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Description: The HPX-5 Runtime System. HPX-5 (High Performance ParalleX) is an open source, portable,performance-oriented runtime developed at CREST (Indiana University). HPX-5 provides a distributed pro-gramming model allowing programs to run unmodified on systems from a single SMP to large clusters andsupercomputers with thousands of nodes. HPX-5 supports a wide variety of Intel and ARM platforms. It isbeing used by a broad range of scientific applications enabling scientists to write code that performs and scalesbetter than contemporary runtimes.

1.10.158 htslib

Homepage:

• https://github.com/samtools/htslib

Spack package:

• htslib/package.py

Versions: 1.3.1

Build Dependencies zlib

Link Dependencies zlib

Description: C library for high-throughput sequencing data formats.

1.10.159 hub

Homepage:

• https://github.com/github/hub

Spack package:

• hub/package.py

Versions: 2.2.3, 2.2.2, 2.2.1, 2.2.0, 1.12.4, head

Build Dependencies go

Link Dependencies go

Description: The github git wrapper

1.10.160 hwloc

Homepage:

• http://www.open-mpi.org/projects/hwloc/

Spack package:

• hwloc/package.py

Versions: 1.11.3, 1.11.2, 1.11.1, 1.9

Build Dependencies libpciaccess

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Link Dependencies libpciaccess

Description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS,versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memorynodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributessuch as cache and memory information as well as the locality of I/O devices such as network interfaces, In-finiBand HCAs or GPUs. It primarily aims at helping applications with gathering information about moderncomputing hardware so as to exploit it accordingly and efficiently.

1.10.161 hydra

Homepage:

• http://www.mpich.org

Spack package:

• hydra/package.py

Versions: 3.2

Description: Hydra is a process management system for starting parallel jobs. Hydra is designed to natively workwith existing launcher daemons (such as ssh, rsh, fork), as well as natively integrate with resource managementsystems (such as slurm, pbs, sge).

1.10.162 hypre

Homepage:

• http://computation.llnl.gov/project/linear_solvers/software.php

Spack package:

• hypre/package.py

Versions: 2.10.1, 2.10.0b

Build Dependencies lapack, blas, mpi

Link Dependencies lapack, blas, mpi

Description: Hypre is a library of high performance preconditioners that features parallel multigrid methods for bothstructured and unstructured grid problems.

1.10.163 ibmisc

Homepage:

• https://github.com/citibeth/ibmisc

Spack package:

• ibmisc/package.py

Versions: 0.1.0

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Build Dependencies doxygen, cmake, eigen, python, netcdf-cxx4, blitz, everytrace, py-numpy, py-cython, udunits2,googletest, proj, boost

Link Dependencies eigen, python, netcdf-cxx4, blitz, everytrace, udunits2, proj, boost

Run Dependencies py-cython, py-numpy

Description: Misc. reusable utilities used by IceBin.

1.10.164 icu

Homepage:

• http://www.example.com

Spack package:

• icu/package.py

Versions: 54.1

Description: The International Components for Unicode (ICU) package is a mature, widely used set of C/C++ li-braries providing Unicode and Globalization support for software applications. ICU is widely portable andgives applications the same results on all platforms.

1.10.165 icu4c

Homepage:

• http://site.icu-project.org/

Spack package:

• icu4c/package.py

Versions: 54_1

Description: ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalizationsupport for software applications.

1.10.166 ilmbase

Homepage:

• http://www.openexr.com/

Spack package:

• ilmbase/package.py

Versions: 2.2.0, 2.1.0, 2.0.1, 1.0.2, 0.9.0

Description: OpenEXR ILM Base libraries (high dynamic-range image file format)

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1.10.167 ImageMagick

Homepage:

• http://www.imagemagick.org

Spack package:

• ImageMagick/package.py

Versions: 7.0.2-7, 7.0.2-6

Build Dependencies freetype, ghostscript, libtiff , jpeg, fontconfig, libtool, libpng

Link Dependencies freetype, ghostscript, libtiff , jpeg, fontconfig, libpng

Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images.

1.10.168 intel

Homepage:

• https://software.intel.com/en-us/intel-parallel-studio-xe

Spack package:

• intel/package.py

Versions: 16.0.3, 16.0.2

Description: Intel Compilers. Note: You will have to add the download file to a mirror so that Spack can find it. Forinstructions on how to set up a mirror, see http://software.llnl.gov/spack/mirrors.html

1.10.169 intel-parallel-studio

Homepage:

• https://software.intel.com/en-us/intel-parallel-studio-xe

Spack package:

• intel-parallel-studio/package.py

Versions: professional.2016.3, professional.2016.2, composer.2016.3, composer.2016.2, cluster.2016.3, clus-ter.2016.2

Description: Intel Parallel Studio. Note: You will have to add the download file to a mirror so that Spack can find it.For instructions on how to set up a mirror, see http://software.llnl.gov/spack/mirrors.html

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1.10.170 intltool

Homepage:

• https://freedesktop.org/wiki/Software/intltool/

Spack package:

• intltool/package.py

Versions: 0.51.0

Description: intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

1.10.171 ior

Homepage:

• https://github.com/LLNL/ior

Spack package:

• ior/package.py

Versions: 3.0.1

Build Dependencies mpi, netcdf , hdf5

Link Dependencies mpi, netcdf , hdf5

Description: The IOR software is used for benchmarking parallel file systems using POSIX, MPI-IO, or HDF5interfaces.

1.10.172 ipopt

Homepage:

• https://projects.coin-or.org/Ipopt

Spack package:

• ipopt/package.py

Versions: 3.12.4, 3.12.3, 3.12.2, 3.12.1, 3.12.0

Build Dependencies lapack, blas, mumps, pkg-config

Link Dependencies lapack, blas, mumps

Description: Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlin-ear optimization.

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1.10.173 ipp

Homepage:

• https://software.intel.com/en-us/intel-ipp

Spack package:

• ipp/package.py

Versions: 9.0.3.210

Description: Intel Integrated Performance Primitives. Note: You will have to add the download file to a mirror sothat Spack can find it. For instructions on how to set up a mirror, see http://software.llnl.gov/spack/mirrors.html

1.10.174 isl

Homepage:

• http://isl.gforge.inria.fr

Spack package:

• isl/package.py

Versions: 0.14

Build Dependencies gmp

Link Dependencies gmp

Description: isl is a thread-safe C library for manipulating sets and relations of integer points bounded by affineconstraints.

1.10.175 jasper

Homepage:

• https://www.ece.uvic.ca/~frodo/jasper/

Spack package:

• jasper/package.py

Versions: 1.900.1

Build Dependencies libjpeg-turbo

Link Dependencies libjpeg-turbo

Description: Library for manipulating JPEG-2000 images

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1.10.176 jdk

Homepage:

• http://www.oracle.com/technetwork/java/javase/downloads/index.html

Spack package:

• jdk/package.py

Versions: 8u92-linux-x64, 8u66-linux-x64

Description: The Java Development Kit (JDK) released by Oracle Corporation in the form of a binary product aimedat Java developers.

1.10.177 jemalloc

Homepage:

• http://www.canonware.com/jemalloc/

Spack package:

• jemalloc/package.py

Versions: 4.1.0, 4.0.4

Description: jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance andscalable concurrency support.

1.10.178 jpeg

Homepage:

• http://www.ijg.org

Spack package:

• jpeg/package.py

Versions: 9b, 9a

Description: libjpeg is a widely used free library with functions for handling the JPEG image data format. It imple-ments a JPEG codec (encoding and decoding) alongside various utilities for handling JPEG data.

1.10.179 jsoncpp

Homepage:

• https://github.com/open-source-parsers/jsoncpp

Spack package:

• jsoncpp/package.py

Versions: 1.7.3

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Build Dependencies cmake

Description: JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserializa-tion to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it aconvenient format to store user input files.

1.10.180 judy

Homepage:

• http://judy.sourceforge.net/

Spack package:

• judy/package.py

Versions: 1.0.5

Description: Judy: General-purpose dynamic array, associative array and hash-trie.

1.10.181 julia

Homepage:

• http://julialang.org

Spack package:

• julia/package.py

Versions: 0.4.6, 0.4.5, 0.4.3, release-0.5, release-0.4, master

Build Dependencies git, cmake, python, openssl, m4, curl, binutils

Link Dependencies git, cmake, python, openssl, curl, binutils

Run Dependencies py-matplotlib, mpi, hdf5

Description: The Julia Language: A fresh approach to technical computing

1.10.182 kdiff3

Homepage:

• http://kdiff3.sourceforge.net/

Spack package:

• kdiff3/package.py

Versions: 0.9.98

Build Dependencies qt

Link Dependencies qt

Description: Compare and merge 2 or 3 files or directories.

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1.10.183 kealib

Homepage:

• http://kealib.org/

Spack package:

• kealib/package.py

Versions: 1.4.5

Build Dependencies hdf5

Link Dependencies hdf5

Description: An HDF5 Based Raster File Format KEALib provides an implementation of the GDAL data model.The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handlingvery large files and compression throughout. Based on the HDF5 standard, it also provides a base from whichother formats can be derived and is a good choice for long term data archiving. An independent software library(libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to beused from any GDAL supported software. Development work on this project has been funded by LandcareResearch.

1.10.184 kripke

Homepage:

• https://codesign.llnl.gov/kripke.php

Spack package:

• kripke/package.py

Versions: 1.1

Build Dependencies mpi

Link Dependencies mpi

Description: Kripke is a simple, scalable, 3D Sn deterministic particle transport proxy/mini app.

1.10.185 launchmon

Homepage:

• https://github.com/LLNL/LaunchMON

Spack package:

• launchmon/package.py

Versions: 1.0.2

Build Dependencies autoconf , libtool, libgcrypt, libgpg-error, automake

Link Dependencies libgcrypt, libgpg-error

Description: Software infrastructure that enables HPC run-time tools to co-locate tool daemons with a parallel job.

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1.10.186 lcms

Homepage:

• http://www.littlecms.com

Spack package:

• lcms/package.py

Versions: 2.6

Build Dependencies libtiff , zlib, jpeg

Link Dependencies libtiff , zlib, jpeg

Description: Little cms is a color management library. Implements fast transforms between ICC profiles. It is focusedon speed, and is portable across several platforms (MIT license).

1.10.187 leveldb

Homepage:

• https://github.com/google/leveldb

Spack package:

• leveldb/package.py

Versions: 1.18

Build Dependencies snappy

Link Dependencies snappy

Description: LevelDB is a fast key-value storage library written at Google that provides an ordered mapping fromstring keys to string values.

1.10.188 libaio

Homepage:

• https://git.fedorahosted.org/cgit/libaio.git

Spack package:

• libaio/package.py

Versions: 0.3.110-1

Description: This is the linux native Asynchronous I/O interface library.

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1.10.189 libarchive

Homepage:

• http://www.libarchive.org

Spack package:

• libarchive/package.py

Versions: 3.2.1, 3.1.2, 3.1.1, 3.1.0

Build Dependencies lzma, xz, bzip2, zlib, libxml2, expat, lz4, openssl, nettle, lzo

Link Dependencies lzma, xz, bzip2, zlib, libxml2, expat, lz4, openssl, nettle, lzo

Description: libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and otherarchive formats.

1.10.190 libatomic-ops

Homepage:

• https://github.com/ivmai/libatomic_ops

Spack package:

• libatomic-ops/package.py

Versions: 7.4.4

Description: This package provides semi-portable access to hardware-provided atomic memory update operations ona number architectures.

1.10.191 libcerf

Homepage:

• http://sourceforge.net/projects/libcerf

Spack package:

• libcerf/package.py

Versions: 1.3

Description: A self-contained C library providing complex error functions, based on Faddeeva’s plasma dispersionfunction w(z). Also provides Dawson’s integral and Voigt’s convolution of a Gaussian and a Lorentzian

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1.10.192 libcircle

Homepage:

• https://github.com/hpc/libcircle

Spack package:

• libcircle/package.py

Versions: 0.2.1-rc.1

Build Dependencies mpi

Link Dependencies mpi

Description: libcircle provides an efficient distributed queue on a cluster, using self-stabilizing work stealing.

1.10.193 libctl

Homepage:

• http://ab-initio.mit.edu/wiki/index.php/Libctl

Spack package:

• libctl/package.py

Versions: 3.2.2

Build Dependencies guile

Link Dependencies guile

Description: libctl is a free Guile-based library implementing flexible control files for scientific simulations.

1.10.194 libdrm

Homepage:

• http://dri.freedesktop.org/libdrm/

Spack package:

• libdrm/package.py

Versions: 2.4.59, 2.4.33

Build Dependencies libpciaccess

Link Dependencies libpciaccess

Description: A userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other oper-ating systems that support the ioctl interface.

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1.10.195 libdwarf

Homepage:

• http://www.prevanders.net/dwarf.html

Spack package:

• libdwarf/package.py

Versions: 20160507, 20130729, 20130207, 20130126

Build Dependencies libelf

Link Dependencies libelf

Description: The DWARF Debugging Information Format is of interest to programmers working on compilers anddebuggers (and any one interested in reading or writing DWARF information). It was developed by a committee(known as the PLSIG at the time) starting around 1991. Starting around 1991 SGI developed the libdwarf anddwarfdump tools for internal use and as part of SGI IRIX developer tools. Since that time dwarfdump andlibdwarf have been shipped (as an executable and archive respectively, not source) with every release of the SGIMIPS/IRIX C compiler.

1.10.196 libedit

Homepage:

• http://thrysoee.dk/editline/

Spack package:

• libedit/package.py

Versions: 3.1

Build Dependencies ncurses

Link Dependencies ncurses

Description: An autotools compatible port of the NetBSD editline library

1.10.197 libelf

Homepage:

• http://www.mr511.de/software/english.html

Spack package:

• libelf/package.py

Versions: 0.8.13, 0.8.12

Description: libelf lets you read, modify or create ELF object files in an architecture-independent way. The librarytakes care of size and endian issues, e.g. you can process a file for SPARC processors on an Intel- based system.

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1.10.198 libepoxy

Homepage:

• https://github.com/anholt/libepoxy

Spack package:

• libepoxy/package.py

Versions: 1.3.1

Description: Epoxy is a library for handling OpenGL function pointer management for you.

1.10.199 libevent

Homepage:

• http://libevent.org

Spack package:

• libevent/package.py

Versions: 2.0.21, 2.0.20, 2.0.19, 2.0.18, 2.0.17, 2.0.16, 2.0.15, 2.0.14, 2.0.13, 2.0.12

Build Dependencies openssl

Link Dependencies openssl

Description: The libevent API provides a mechanism to execute a callback function when a specific event occurs ona file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signalsor regular timeouts.

1.10.200 libffi

Homepage:

• https://sourceware.org/libffi/

Spack package:

• libffi/package.py

Versions: 3.2.1

Description: The libffi library provides a portable, high level programming interface to various calling conventions.This allows a programmer to call any function specified by a call interface description at run time.

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1.10.201 libgcrypt

Homepage:

• http://www.gnu.org/software/libgcrypt/

Spack package:

• libgcrypt/package.py

Versions: 1.6.2

Build Dependencies libgpg-error

Link Dependencies libgpg-error

Description: Libgcrypt is a general purpose cryptographic library based on the code from GnuPG. It provides func-tions for all cryptographic building blocks: symmetric ciphers, hash algorithms, MACs, public key algorithms,large integer functions, random numbers and a lot of supporting functions.

1.10.202 libgd

Homepage:

• https://github.com/libgd/libgd

Spack package:

• libgd/package.py

Versions: 2.1.1

Build Dependencies libpng, cmake

Link Dependencies libpng

Description: GD is an open source code library for the dynamic creation of images by programmers. GD is written inC, and “wrappers” are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM,BMP images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and mostanything else, on the fly. While not restricted to use on the web, the most common applications of GD involvewebsite development.

1.10.203 libgpg-error

Homepage:

• https://www.gnupg.org/related_software/libgpg-error

Spack package:

• libgpg-error/package.py

Versions: 1.21, 1.18

Description: Libgpg-error is a small library that defines common error values for all GnuPG components. Amongthese are GPG, GPGSM, GPGME, GPG-Agent, libgcrypt, Libksba, DirMngr, Pinentry, SmartCard Daemon andpossibly more in the future.

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1.10.204 libgtextutils

Homepage:

• https://github.com/agordon/libgtextutils

Spack package:

• libgtextutils/package.py

Versions: 0.7

Description: Gordon’s Text utils Library.

1.10.205 libhio

Homepage:

• https://github.com/hpc/libhio/

Spack package:

• libhio/package.py

Versions: 1.3.0.1

Build Dependencies libjson-c, bzip2, pkg-config

Link Dependencies libjson-c, bzip2

Description: A library for writing to hierarchical data store systems.

1.10.206 libiconv

Homepage:

• https://www.gnu.org/software/libiconv/

Spack package:

• libiconv/package.py

Versions: 1.14

Description: GNU libiconv provides an implementation of the iconv() function and the iconv program for characterset conversion.

1.10.207 libjpeg-turbo

Homepage:

• http://libjpeg-turbo.virtualgl.org

Spack package:

• libjpeg-turbo/package.py

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Versions: 1.3.1

Build Dependencies yasm, nasm

Description: libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compres-sion and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

1.10.208 libjson-c

Homepage:

• https://github.com/json-c/json-c/wiki

Spack package:

• libjson-c/package.py

Versions: 0.11

Description: A JSON implementation in C

1.10.209 libmng

Homepage:

• http://sourceforge.net/projects/libmng/

Spack package:

• libmng/package.py

Versions: 2.0.2

Build Dependencies zlib, jpeg, lcms

Link Dependencies zlib, jpeg, lcms

Description: libmng -THE reference library for reading, displaying, writing and examining Multiple-Image NetworkGraphics. MNG is the animation extension to the popular PNG image-format.

1.10.210 libmonitor

Homepage:

• https://github.com/HPCToolkit/libmonitor

Spack package:

• libmonitor/package.py

Versions: 20130218

Description: Libmonitor is a library for process and thread control.

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1.10.211 libNBC

Homepage:

• http://unixer.de/research/nbcoll/libnbc/

Spack package:

• libNBC/package.py

Versions: 1.1.1

Build Dependencies mpi

Link Dependencies mpi

Description: LibNBC is a prototypic implementation of a nonblocking interface for MPI collective operations. Basedon ANSI C and MPI-1, it supports all MPI-1 collective operations in a nonblocking manner. LibNBC is dis-tributed under the BSD license.

1.10.212 libpciaccess

Homepage:

• http://cgit.freedesktop.org/xorg/lib/libpciaccess/

Spack package:

• libpciaccess/package.py

Versions: 0.13.4

Build Dependencies libtool

Description: Generic PCI access library.

1.10.213 libpng

Homepage:

• http://www.libpng.org/pub/png/libpng.html

Spack package:

• libpng/package.py

Versions: 1.6.16, 1.6.15, 1.6.14, 1.5.26, 1.4.19, 1.2.56

Build Dependencies zlib

Link Dependencies zlib

Description: libpng graphics file format

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1.10.214 libpthread-stubs

Homepage:

• http://xcb.freedesktop.org/

Spack package:

• libpthread-stubs/package.py

Versions: 0.3

Description: The libpthread-stubs package provides weak aliases for pthread functions not provided in libc or other-wise available by default.

1.10.215 libsigsegv

Homepage:

• https://www.gnu.org/software/libsigsegv/

Spack package:

• libsigsegv/package.py

Versions: 2.10

Description: GNU libsigsegv is a library for handling page faults in user mode.

1.10.216 libsodium

Homepage:

• https://download.libsodium.org/doc/

Spack package:

• libsodium/package.py

Versions: 1.0.3, 1.0.2, 1.0.1, 1.0.0, 0.7.1

Description: Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hash-ing and more.

1.10.217 libsplash

Homepage:

• https://github.com/ComputationalRadiationPhysics/libSplash

Spack package:

• libsplash/package.py

Versions: 1.4.0, 1.3.1, 1.2.4

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Build Dependencies hdf5, cmake, mpi

Link Dependencies hdf5, mpi

Description: libSplash aims at developing a HDF5-based I/O library for HPC simulations. It is created as an easy-to-use frontend for the standard HDF5 library with support for MPI processes in a cluster environment. Whilethe standard HDF5 library provides detailed low-level control, libSplash simplifies tasks commonly found inlarge-scale HPC simulations, such as iterative computations and MPI distributed processes.

1.10.218 libtermkey

Homepage:

• http://www.leonerd.org.uk/code/libtermkey/

Spack package:

• libtermkey/package.py

Versions: 0.18, 0.17, 0.16, 0.15b, 0.14

Description: Easy keyboard entry processing for terminal programs

1.10.219 libtiff

Homepage:

• http://www.remotesensing.org/libtiff/

Spack package:

• libtiff/package.py

Versions: 4.0.3

Build Dependencies xz, zlib, jpeg

Link Dependencies xz, zlib, jpeg

Description: libtiff graphics format library

1.10.220 libtool

Homepage:

• https://www.gnu.org/software/libtool/

Spack package:

• libtool/package.py

Versions: 2.4.6, 2.4.2

Build Dependencies m4

Description: libtool – library building part of autotools

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1.10.221 libunistring

Homepage:

• https://www.gnu.org/software/libunistring/

Spack package:

• libunistring/package.py

Versions: 0.9.6

Description: This library provides functions for manipulating Unicode strings and for manipulating C strings accord-ing to the Unicode standard.

1.10.222 libunwind

Homepage:

• http://www.nongnu.org/libunwind/

Spack package:

• libunwind/package.py

Versions: 1.1

Description: A portable and efficient C programming interface (API) to determine the call-chain of a program.

1.10.223 libuuid

Homepage:

• http://sourceforge.net/projects/libuuid/

Spack package:

• libuuid/package.py

Versions: 1.0.3

Description: Portable uuid C library

1.10.224 libuv

Homepage:

• http://libuv.org

Spack package:

• libuv/package.py

Versions: 1.9.0

Build Dependencies autoconf , libtool, automake

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Description: Multi-platform library with a focus on asynchronous IO

1.10.225 libvterm

Homepage:

• http://www.leonerd.org.uk/code/libvterm/

Spack package:

• libvterm/package.py

Versions: 681

Description: An abstract library implementation of a terminal emulator

1.10.226 libxau

Homepage:

• http://xcb.freedesktop.org/

Spack package:

• libxau/package.py

Versions: 1.0.8

Build Dependencies xproto, pkg-config

Link Dependencies xproto

Description: The libXau package contains a library implementing the X11 Authorization Protocol. This is useful forrestricting client access to the display.

1.10.227 libxc

Homepage:

• http://www.tddft.org/programs/octopus/wiki/index.php/Libxc

Spack package:

• libxc/package.py

Versions: 2.2.2

Description: Libxc is a library of exchange-correlation functionals for density- functional theory.

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1.10.228 libxcb

Homepage:

• http://xcb.freedesktop.org/

Spack package:

• libxcb/package.py

Versions: 1.11.1, 1.11

Build Dependencies python, libpthread-stubs, libxau, xcb-proto, pkg-config

Link Dependencies libpthread-stubs, xcb-proto, libxau

Description: The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latencyhiding, direct access to the protocol, improved threading support, and extensibility.

1.10.229 libxml2

Homepage:

• http://xmlsoft.org

Spack package:

• libxml2/package.py

Versions: 2.9.4, 2.9.2

Build Dependencies python, xz, zlib

Link Dependencies python, xz, zlib

Description: Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of theGnome platform), it is free software available under the MIT License.

1.10.230 libxpm

Homepage:

• https://www.x.org/

Spack package:

• libxpm/package.py

Versions: 3.5.11, 3.5.10, 3.5.9, 3.5.8, 3.5.7

Description: Xpm file format library

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1.10.231 libxshmfence

Homepage:

• http://keithp.com/blogs/dri3_extension/

Spack package:

• libxshmfence/package.py

Versions: 1.2

Description: This is a tiny library that exposes a event API on top of Linux futexes.

1.10.232 libxslt

Homepage:

• http://www.xmlsoft.org/XSLT/index.html

Spack package:

• libxslt/package.py

Versions: 1.1.28

Build Dependencies xz, libxml2, zlib, libgcrypt

Link Dependencies xz, libxml2, zlib, libgcrypt

Description: Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML languageto define transformation for XML. Libxslt is based on libxml2 the XML C library developed for the GNOMEproject. It also implements most of the EXSLT set of processor-portable extensions functions and some ofSaxon’s evaluate and expressions extensions.

1.10.233 libxsmm

Homepage:

• https://github.com/hfp/libxsmm

Spack package:

• libxsmm/package.py

Versions: 1.4.3, 1.4.2, 1.4.1, 1.4

Description: LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting IntelArchitecture (x86).

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1.10.234 llvm

Homepage:

• http://llvm.org/

Spack package:

• llvm/package.py

Versions: 3.8.0, 3.7.1, 3.7.0, 3.6.2, 3.5.1, 3.0, trunk

Build Dependencies cmake, libedit, python, swig, ncurses, isl, gmp, binutils

Link Dependencies libedit, python, swig, ncurses, isl, gmp, binutils

Description: The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despiteits name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries thatcan be used to build them. The name “LLVM” itself is not an acronym; it is the full name of the project.

1.10.235 llvm-lld

Homepage:

• http://lld.llvm.org

Spack package:

• llvm-lld/package.py

Versions: 3.4

Build Dependencies llvm, cmake

Link Dependencies llvm

Description: lld - The LLVM Linker lld is a new set of modular code for creating linker tools.

1.10.236 lmdb

Homepage:

• http://www.openldap.org/software/repo.html

Spack package:

• lmdb/package.py

Versions: 0.9.16

Description: Read-only mirror of official repo on openldap.org. Issues and pull requests here are ignored. UseOpenLDAP ITS for issues. http://www.openldap.org/software/repo.html

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1.10.237 lmod

Homepage:

• https://www.tacc.utexas.edu/research-development/tacc-projects/lmod

Spack package:

• lmod/package.py

Versions: 6.4.5, 6.4.1, 6.3.7, 6.0.1

Build Dependencies lua, tcl, lua-luaposix, lua-luafilesystem

Link Dependencies lua

Run Dependencies tcl, lua-luaposix, lua-luafilesystem

Description: Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem.Environment Modules provide a convenient way to dynamically change the users’ environment through mod-ulefiles. This includes easily adding or removing directories to the PATH environment variable. Modulefiles forLibrary packages provide environment variables that specify where the library and header files can be found.

1.10.238 lrslib

Homepage:

• http://cgm.cs.mcgill.ca/~avis/C/lrs.html

Spack package:

• lrslib/package.py

Versions: 6.2, 6.1, 6.0, 5.1, 4.3

Build Dependencies gmp, libtool

Link Dependencies gmp

Description: lrslib Ver 6.2 is a self-contained ANSI C implementation of the reverse search algorithm for vertexenumeration/convex hull problems and comes with a choice of three arithmetic packages

1.10.239 lrzip

Homepage:

• http://lrzip.kolivas.org

Spack package:

• lrzip/package.py

Versions: 0.630, 0.621, 0.616, 0.615, master

Build Dependencies bzip2, zlib, lzo

Link Dependencies bzip2, zlib, lzo

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Description: A compression utility that excels at compressing large files (usually > 10-50 MB). Larger files and/ormore free RAM means that the utility will be able to more effectively compress your files (ie: faster / smallersize), especially if the filesize(s) exceed 100 MB. You can either choose to optimise for speed (fast compression/ decompression) or size, but not both.

1.10.240 lua

Homepage:

• http://www.lua.org

Spack package:

• lua/package.py

Versions: 5.3.2, 5.3.1, 5.3.0, 5.2.4, 5.2.3, 5.2.2, 5.2.1, 5.2.0, 5.1.5, 5.1.4, 5.1.3

Build Dependencies ncurses, readline

Link Dependencies ncurses, readline

Description: The Lua programming language interpreter and library

1.10.241 lua-luafilesystem

Homepage:

• http://keplerproject.github.io/luafilesystem

Spack package:

• lua-luafilesystem/package.py

Versions: 1_6_3

Build Dependencies lua

Link Dependencies lua

Description: LuaFileSystem is a Lua library developed to complement the set of functions related to file systemsoffered by the standard Lua distribution. LuaFileSystem offers a portable way to access the underlying directorystructure and file attributes. LuaFileSystem is free software and uses the same license as Lua 5.1

1.10.242 lua-luaposix

Homepage:

• https://github.com/luaposix/luaposix/

Spack package:

• lua-luaposix/package.py

Versions: 33.4.0

Build Dependencies lua

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Link Dependencies lua

Description: Lua posix bindings, including ncurses

1.10.243 LuaJIT

Homepage:

• http://www.luajit.org

Spack package:

• LuaJIT/package.py

Versions: 2.0.4

Description: Flast flexible JITed lua

1.10.244 lwgrp

Homepage:

• https://github.com/hpc/lwgrp

Spack package:

• lwgrp/package.py

Versions: 1.0.2

Build Dependencies mpi

Link Dependencies mpi

Description: Thie light-weight group library provides process group representations using O(log N) space and time.

1.10.245 lwm2

Homepage:

• https://jay.grs.rwth-aachen.de/redmine/projects/lwm2

Spack package:

• lwm2/package.py

Versions: torus

Build Dependencies papi, mpi

Link Dependencies papi, mpi

Description: LWM2: Light Weight Measurement Module. This is a PMPI module that can collect a number oftime-sliced MPI and POSIX I/O measurements from a program.

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1.10.246 lz4

Homepage:

• http://cyan4973.github.io/lz4/

Spack package:

• lz4/package.py

Versions: 131

Description: LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalablewith multi-cores CPU. It also features an extremely fast decoder, with speed in multiple GB/s per core, typicallyreaching RAM speed limits on multi-core systems.

1.10.247 lzma

Homepage:

• http://tukaani.org/lzma/

Spack package:

• lzma/package.py

Versions: 4.32.7

Description: LZMA Utils are legacy data compression software with high compression ratio. LZMA Utils are nolonger developed, although critical bugs may be fixed as long as fixing them doesn’t require huge changes to thecode. Users of LZMA Utils should move to XZ Utils. XZ Utils support the legacy .lzma format used by LZMAUtils, and can also emulate the command line tools of LZMA Utils. This should make transition from LZMAUtils to XZ Utils relatively easy.

1.10.248 lzo

Homepage:

• https://www.oberhumer.com/opensource/lzo/

Spack package:

• lzo/package.py

Versions: 2.09, 2.08, 2.07, 2.06, 2.05

Description: Real-time data compression library

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1.10.249 m4

Homepage:

• https://www.gnu.org/software/m4/m4.html

Spack package:

• m4/package.py

Versions: 1.4.17

Build Dependencies libsigsegv

Link Dependencies libsigsegv

Description: GNU M4 is an implementation of the traditional Unix macro processor.

1.10.250 mafft

Homepage:

• http://mafft.cbrc.jp/alignment/software/index.html

Spack package:

• mafft/package.py

Versions: 7.221

Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a rangeof multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; foralignment of <~30,000 sequences), etc.

1.10.251 mariadb

Homepage:

• https://mariadb.org/about/

Spack package:

• mariadb/package.py

Versions: 10.1.14, 5.5.49

Build Dependencies libaio, cmake, libedit, ncurses, zlib, libevent, jemalloc, boost

Link Dependencies libaio, cmake, libedit, ncurses, zlib, libevent, jemalloc, boost

Description: MariaDB turns data into structured information in a wide array of applications, ranging from bankingto websites. It is an enhanced, drop- in replacement for MySQL. MariaDB is used because it is fast, scalableand robust, with a rich ecosystem of storage engines, plugins and many other tools make it very versatile for awide variety of use cases.

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1.10.252 matio

Homepage:

• http://sourceforge.net/projects/matio/

Spack package:

• matio/package.py

Versions: 1.5.2

Description: matio is an C library for reading and writing Matlab MAT files

1.10.253 mbedtls

Homepage:

• https://tls.mbed.org

Spack package:

• mbedtls/package.py

Versions: 2.2.1, 2.2.0, 2.1.4, 2.1.3, 1.3.16

Build Dependencies cmake

Description: mbed TLS (formerly known as PolarSSL) makes it trivially easy for developers to include cryptographicand SSL/TLS capabilities in their (embedded) products, facilitating this functionality with a minimal codingfootprint.

1.10.254 meep

Homepage:

• http://ab-initio.mit.edu/wiki/index.php/Meep

Spack package:

• meep/package.py

Versions: 1.3, 1.2.1, 1.1.1

Build Dependencies guile, hdf5, lapack, blas, harminv, mpi, libctl, gsl

Link Dependencies guile, hdf5, lapack, blas, harminv, mpi, libctl, gsl

Description: Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developedat MIT to model electromagnetic systems.

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1.10.255 memaxes

Homepage:

• https://github.com/llnl/MemAxes

Spack package:

• memaxes/package.py

Versions: 0.5

Build Dependencies cmake, qt

Link Dependencies qt

Description: MemAxes is a visualizer for sampled memory trace data.

1.10.256 mercurial

Homepage:

• https://www.mercurial-scm.org

Spack package:

• mercurial/package.py

Versions: 3.9, 3.8.4, 3.8.3, 3.8.2, 3.8.1

Build Dependencies python, py-docutils

Link Dependencies python

Description: Mercurial is a free, distributed source control management tool.

1.10.257 mesa

Homepage:

• http://www.mesa3d.org

Spack package:

• mesa/package.py

Versions: 8.0.5

Build Dependencies libxml2, libdrm, llvm

Link Dependencies libxml2, libdrm, llvm

Description: Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive3D graphics.

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1.10.258 metis

Homepage:

• http://glaros.dtc.umn.edu/gkhome/metis/metis/overview

Spack package:

• metis/package.py

Versions: 5.1.0, 5.0.2, 4.0.3

Build Dependencies cmake

Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and pro-ducing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on themultilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

1.10.259 mfem

Homepage:

• http://www.mfem.org

Spack package:

• mfem/package.py

Versions: 3.2, 3.1

Build Dependencies hypre, cmake, lapack, blas, metis, mpi, suite-sparse

Link Dependencies hypre, lapack, blas, metis, mpi, suite-sparse

Description: Free, lightweight, scalable C++ library for finite element methods.

1.10.260 Mitos

Homepage:

• https://github.com/llnl/Mitos

Spack package:

• Mitos/package.py

Versions: 0.9.2, 0.9.1

Build Dependencies dyninst, cmake, hwloc, mpi

Link Dependencies dyninst, hwloc, mpi

Description: Mitos is a library and a tool for collecting sampled memory performance data to view with MemAxes

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1.10.261 mkl

Homepage:

• https://software.intel.com/en-us/intel-mkl

Spack package:

• mkl/package.py

Versions: 11.3.3.210, 11.3.2.181

Description: Intel Math Kernel Library. Note: You will have to add the download file to a mirror so that Spack canfind it. For instructions on how to set up a mirror, see http://software.llnl.gov/spack/mirrors.html. To set thethreading layer at run time set MKL_THREADING_LAYER variable to one of the following values: INTEL(default), SEQUENTIAL, PGI. To set interface layer at run time, use set the MKL_INTERFACE_LAYERvariable to LP64 (default) or ILP64.

1.10.262 moab

Homepage:

• https://bitbucket.org/fathomteam/moab

Spack package:

• moab/package.py

Versions: 4.9.1, 4.9.0, 4.8.2

Build Dependencies trilinos, mpi, netcdf , parmetis, hdf5

Link Dependencies trilinos, mpi, netcdf , parmetis, hdf5

Description: MOAB is a component for representing and evaluating mesh data. MOAB can store structured andunstructured mesh, consisting of elements in the finite element ‘zoo.’ The functional interface to MOAB issimple yet powerful, allowing the representation of many types of metadata commonly found on the mesh.MOAB is optimized for efficiency in space and time, based on access to mesh in chunks rather than throughindividual entities, while also versatile enough to support individual entity access.

1.10.263 mpc

Homepage:

• http://www.multiprecision.org

Spack package:

• mpc/package.py

Versions: 1.0.3, 1.0.2

Build Dependencies gmp, mpfr

Link Dependencies gmp, mpfr

Description: Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correctrounding of the result.

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1.10.264 mpe2

Homepage:

• http://www.mcs.anl.gov/research/projects/perfvis/software/MPE/

Spack package:

• mpe2/package.py

Versions: 1.3.0

Build Dependencies mpi

Link Dependencies mpi

Description: Message Passing Extensions (MPE): Parallel, shared X window graphics

1.10.265 mpfr

Homepage:

• http://www.mpfr.org

Spack package:

• mpfr/package.py

Versions: 3.1.4, 3.1.3, 3.1.2

Build Dependencies gmp

Link Dependencies gmp

Description: The MPFR library is a C library for multiple-precision floating-point computations with correct round-ing.

1.10.266 mpibash

Homepage:

• http://www.ccs3.lanl.gov/~pakin/software/mpibash-4.3.html

Spack package:

• mpibash/package.py

Versions: 4.3

Build Dependencies autoconf , libcircle, mpi

Link Dependencies libcircle, mpi

Description: Parallel scripting right from the Bourne-Again Shell (Bash)

1.10. Package List 185

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1.10.267 mpich

Homepage:

• http://www.mpich.org

Spack package:

• mpich/package.py

Versions: 3.2, 3.1.4, 3.1.3, 3.1.2, 3.1.1, 3.1, 3.0.4

Description: MPICH is a high performance and widely portable implementation of the Message Passing Interface(MPI) standard.

1.10.268 mpileaks

Homepage:

• https://github.com/hpc/mpileaks

Spack package:

• mpileaks/package.py

Versions: 1.0

Build Dependencies mpi, callpath, adept-utils

Link Dependencies mpi, callpath, adept-utils

Description: Tool to detect and report leaked MPI objects like MPI_Requests and MPI_Datatypes.

1.10.269 mrnet

Homepage:

• http://paradyn.org/mrnet

Spack package:

• mrnet/package.py

Versions: 5.0.1-2, 5.0.1, 4.1.0, 4.0.0

Build Dependencies boost

Link Dependencies boost

Description: The MRNet Multi-Cast Reduction Network.

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1.10.270 msgpack-c

Homepage:

• http://www.msgpack.org

Spack package:

• msgpack-c/package.py

Versions: 1.4.1

Build Dependencies cmake

Description: A small, fast binary interchange format convertible to/from JSON

1.10.271 mumps

Homepage:

• http://mumps.enseeiht.fr

Spack package:

• mumps/package.py

Versions: 5.0.1

Build Dependencies scotch, blas, metis, mpi, scalapack, parmetis

Link Dependencies scotch, blas, metis, mpi, scalapack, parmetis

Description: MUMPS: a MUltifrontal Massively Parallel sparse direct Solver

1.10.272 munge

Homepage:

• https://code.google.com/p/munge/

Spack package:

• munge/package.py

Versions: 0.5.11

Build Dependencies openssl, libgcrypt

Link Dependencies openssl, libgcrypt

Description: MUNGE Uid ‘N’ Gid Emporium

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1.10.273 muparser

Homepage:

• http://muparser.beltoforion.de/

Spack package:

• muparser/package.py

Versions: 2.2.5

Description: C++ math expression parser library.

1.10.274 muster

Homepage:

• https://github.com/llnl/muster

Spack package:

• muster/package.py

Versions: 1.0.1, 1.0

Build Dependencies boost, cmake, mpi

Link Dependencies boost, mpi

Description: The Muster library provides implementations of sequential and parallel K-Medoids clustering algo-rithms. It is intended as a general framework for parallel cluster analysis, particularly for performance dataanalysis on systems with very large numbers of processes.

1.10.275 mvapich2

Homepage:

• http://mvapich.cse.ohio-state.edu/

Spack package:

• mvapich2/package.py

Versions: 2.2rc2, 2.2b, 2.2a, 2.1, 2.0, 1.9

Build Dependencies libpciaccess

Link Dependencies libpciaccess

Description: MVAPICH2 is an MPI implementation for Infiniband networks.

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1.10.276 mxml

Homepage:

• http://www.msweet.org

Spack package:

• mxml/package.py

Versions: 2.9, 2.8, 2.7, 2.6, 2.5

Description: Mini-XML is a small XML library that you can use to read and write XML and XML-like data files inyour application without requiring large non- standard libraries.

1.10.277 nag

Homepage:

• http://www.nag.com/nagware/np.asp

Spack package:

• nag/package.py

Versions: 6.1, 6.0

Description: The NAG Fortran Compiler.

1.10.278 nano

Homepage:

• http://www.nano-editor.org

Spack package:

• nano/package.py

Versions: 2.6.3, 2.6.2

Description: Tiny little text editor

1.10.279 nasm

Homepage:

• http://www.nasm.us

Spack package:

• nasm/package.py

Versions: 2.11.06

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Description: NASM (Netwide Assembler) is an 80x86 assembler designed for portability and modularity. It includesa disassembler as well.

1.10.280 nauty

Homepage:

• http://pallini.di.uniroma1.it/index.html

Spack package:

• nauty/package.py

Versions: 2.6r7, 2.6r5, 2.5r9

Description: nauty and Traces are programs for computing automorphism groups of graphsq and digraphs

1.10.281 nccmp

Homepage:

• http://nccmp.sourceforge.net/

Spack package:

• nccmp/package.py

Versions: 1.8.2.0

Build Dependencies netcdf

Link Dependencies netcdf

Description: Compare NetCDF Files

1.10.282 ncdu

Homepage:

• http://dev.yorhel.nl/ncdu

Spack package:

• ncdu/package.py

Versions: 1.11, 1.10, 1.9, 1.8, 1.7

Build Dependencies ncurses

Link Dependencies ncurses

Description: Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remoteserver where you don’t have an entire gaphical setup available, but it is a useful tool even on regular desktopsystems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-likeenvironment with ncurses installed.

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1.10.283 nco

Homepage:

• https://sourceforge.net/projects/nco

Spack package:

• nco/package.py

Versions: 4.5.5

Build Dependencies antlr, udunits2, netcdf , gsl

Link Dependencies antlr, udunits2, netcdf , gsl

Description: The NCO toolkit manipulates and analyzes data stored in netCDF- accessible formats

1.10.284 ncurses

Homepage:

• http://invisible-island.net/ncurses/ncurses.html

Spack package:

• ncurses/package.py

Versions: 6.0, 5.9

Description: The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, andmore. It uses terminfo format, supports pads and color and multiple highlights and forms characters andfunction-key mapping, and has all the other SYSV-curses enhancements over BSD curses.

1.10.285 ncview

Homepage:

• http://meteora.ucsd.edu/~pierce/ncview_home_page.html

Spack package:

• ncview/package.py

Versions: 2.1.7

Build Dependencies udunits2, netcdf

Link Dependencies udunits2, netcdf

Description: Simple viewer for NetCDF files.

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1.10.286 ndiff

Homepage:

• http://ftp.math.utah.edu/pub/ndiff/

Spack package:

• ndiff/package.py

Versions: 2.00, 1.00

Description: The ndiff tool is a binary utility that compares putatively similar files while ignoring small numericdifferernces. This utility is most often used to compare files containing a lot of floating-point numeric data thatmay be slightly different due to numeric error.

1.10.287 netcdf

Homepage:

• http://www.unidata.ucar.edu/software/netcdf

Spack package:

• netcdf/package.py

Versions: 4.4.1, 4.4.0, 4.3.3

Build Dependencies m4, curl, zlib, hdf , hdf5

Link Dependencies hdf , curl, zlib, hdf5

Description: NetCDF is a set of software libraries and self-describing, machine- independent data formats that sup-port the creation, access, and sharing of array-oriented scientific data.

1.10.288 netcdf-cxx

Homepage:

• http://www.unidata.ucar.edu/software/netcdf

Spack package:

• netcdf-cxx/package.py

Versions: 4.2

Build Dependencies netcdf

Link Dependencies netcdf

Description: Deprecated C++ compatibility bindings for NetCDF. These do NOT read or write NetCDF-4 files, andare no longer maintained by Unidata. Developers should migrate to current NetCDF C++ bindings, in Spackpackage netcdf-cxx4.

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1.10.289 netcdf-cxx4

Homepage:

• http://www.unidata.ucar.edu/software/netcdf

Spack package:

• netcdf-cxx4/package.py

Versions: 4.3.0, 4.2.1

Build Dependencies autoconf , netcdf

Link Dependencies netcdf

Description: C++ interface for NetCDF4

1.10.290 netcdf-fortran

Homepage:

• http://www.unidata.ucar.edu/software/netcdf

Spack package:

• netcdf-fortran/package.py

Versions: 4.4.4, 4.4.3

Build Dependencies netcdf

Link Dependencies netcdf

Description: Fortran interface for NetCDF4

1.10.291 netgauge

Homepage:

• http://unixer.de/research/netgauge/

Spack package:

• netgauge/package.py

Versions: 2.4.6

Build Dependencies mpi

Link Dependencies mpi

Description: Netgauge is a high-precision network parameter measurement tool. It supports benchmarking of manydifferent network protocols and communication patterns. The main focus lies on accuracy, statistical analysisand easy extensibility.

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1.10.292 netlib-lapack

Homepage:

• http://www.netlib.org/lapack/

Spack package:

• netlib-lapack/package.py

Versions: 3.6.0, 3.5.0, 3.4.2, 3.4.1, 3.4.0, 3.3.1

Build Dependencies blas, cmake

Link Dependencies blas

Description: LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations includ-ing matrix inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular valuedecomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the scien-tific community.

1.10.293 netlib-scalapack

Homepage:

• http://www.netlib.org/scalapack/

Spack package:

• netlib-scalapack/package.py

Versions: 2.0.2, 2.0.1, 2.0.0

Build Dependencies lapack, cmake, mpi

Link Dependencies lapack, mpi

Description: ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memorymachines

1.10.294 nettle

Homepage:

• https://www.lysator.liu.se/~nisse/nettle/

Spack package:

• nettle/package.py

Versions: 3.2, 2.7

Build Dependencies gmp

Link Dependencies gmp

Description: The Nettle package contains the low-level cryptographic library that is designed to fit easily in manycontexts.

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1.10.295 nextflow

Homepage:

• http://www.nextflow.io

Spack package:

• nextflow/package.py

Versions: 0.20.1

Build Dependencies jdk

Link Dependencies jdk

Description: Data-driven computational pipelines

1.10.296 ninja

Homepage:

• https://martine.github.io/ninja/

Spack package:

• ninja/package.py

Versions: 1.6.0

Build Dependencies python

Link Dependencies python

Description: A small, fast Make alternative

1.10.297 numdiff

Homepage:

• https://www.nongnu.org/numdiff

Spack package:

• numdiff/package.py

Versions: 5.8.1

Description: Numdiff is a little program that can be used to compare putatively similar files line by line and field byfield, ignoring small numeric differences or/and different numeric formats.

1.10. Package List 195

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1.10.298 nwchem

Homepage:

• http://www.nwchem-sw.org

Spack package:

• nwchem/package.py

Versions: 6.6

Build Dependencies lapack, python, blas, scalapack, mpi

Link Dependencies lapack, blas, scalapack, mpi

Run Dependencies python

Description: High-performance computational chemistry software

1.10.299 ocaml

Homepage:

• http://ocaml.org/

Spack package:

• ocaml/package.py

Versions: 4.03.0

Build Dependencies ncurses

Link Dependencies ncurses

Description: OCaml is an industrial strength programming language supporting functional, imperative and object-oriented styles

1.10.300 oce

Homepage:

• https://github.com/tpaviot/oce

Spack package:

• oce/package.py

Versions: 0.17.2, 0.17.1, 0.17, 0.16.1, 0.16

Build Dependencies tbb, cmake

Link Dependencies tbb

Description: Open CASCADE Community Edition: patches/improvements/experiments contributed by users overthe official Open CASCADE library.

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1.10.301 octave

Homepage:

• https://www.gnu.org/software/octave/

Spack package:

• octave/package.py

Versions: 4.0.2, 4.0.0

Build Dependencies zlib, ImageMagick, qhull, blas, curl, qrupdate, pcre, fltk, gnuplot, lapack, fontconfig, gl2ps,freetype, llvm, suite-sparse, readline, glpk, qt, jdk, hdf5, fftw, arpack, pkg-config

Link Dependencies zlib, ImageMagick, qhull, blas, curl, qrupdate, pcre, fltk, gnuplot, lapack, fontconfig, gl2ps,freetype, llvm, suite-sparse, readline, glpk, qt, jdk, hdf5, fftw, arpack

Description: GNU Octave is a high-level language, primarily intended for numerical computations. It provides aconvenient command line interface for solving linear and nonlinear problems numerically, and for performingother numerical experiments using a language that is mostly compatible with Matlab. It may also be used as abatch-oriented language.

1.10.302 octave-splines

Homepage:

• http://octave.sourceforge.net/splines/index.html

Spack package:

• octave-splines/package.py

Versions: 1.3.1

Build Dependencies octave

Link Dependencies octave

Description: Additional spline functions.

1.10.303 octopus

Homepage:

• http://www.tddft.org/programs/octopus/

Spack package:

• octopus/package.py

Versions: 5.0.1

Build Dependencies libxc, lapack, blas, fftw, mpi, gsl

Link Dependencies libxc, lapack, blas, fftw, mpi, gsl

Description: A real-space finite-difference (time-dependent) density-functional theory code.

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1.10.304 ompss

Homepage:

• http://pm.bsc.es/

Spack package:

• ompss/package.py

Versions: 14.10

Build Dependencies hwloc, extrae, mpi

Link Dependencies hwloc, extrae, mpi

Description: OmpSs is an effort to integrate features from the StarSs programming model developed by BSC intoa single programming model. In particular, our objective is to extend OpenMP with new directives to supportasynchronous parallelism and heterogeneity (devices like GPUs). However, it can also be understood as newdirectives extending other accelerator based APIs like CUDA or OpenCL. Our OmpSs environment is built ontop of our Mercurium compiler and Nanos++ runtime system.

1.10.305 ompt-openmp

Homepage:

• https://github.com/OpenMPToolsInterface/LLVM-openmp

Spack package:

• ompt-openmp/package.py

Versions: 0.1

Build Dependencies cmake

Description: LLVM/Clang OpenMP runtime with OMPT support. This is a fork of theOpenMPToolsInterface/LLVM-openmp fork of the official LLVM OpenMP mirror. This library providesa drop-in replacement of the OpenMP runtimes for GCC, Intel and LLVM/Clang.

1.10.306 opari2

Homepage:

• http://www.vi-hps.org/projects/score-p

Spack package:

• opari2/package.py

Versions: 2.0, 1.1.4, 1.1.2

Description: OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMPdirectives and runtime library calls with calls to the POMP2 measurement interface. OPARI2 will provideyou with a new initialization method that allows for multi-directory and parallel builds as well as the usageof pre-instrumented libraries. Furthermore, an efficient way of tracking parent-child relationships was added.Additionally, we extended OPARI2 to support instrumentation of OpenMP 3.0 tied tasks.

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1.10.307 openblas

Homepage:

• http://www.openblas.net

Spack package:

• openblas/package.py

Versions: 0.2.18, 0.2.17, 0.2.16, 0.2.15

Description: OpenBLAS: An optimized BLAS library

1.10.308 opencoarrays

Homepage:

• http://www.opencoarrays.org/

Spack package:

• opencoarrays/package.py

Versions: 1.6.2

Build Dependencies cmake, mpi

Link Dependencies mpi

Description: OpenCoarrays is an open-source software project that produces an application binary interface (ABI)supporting coarray Fortran (CAF) compilers, an application programming interface (API) that supports users ofnon-CAF compilers, and an associated compiler wrapper and program launcher.

1.10.309 opencv

Homepage:

• http://opencv.org/

Spack package:

• opencv/package.py

Versions: 3.1.0

Build Dependencies zlib, cmake, eigen, jdk, python, libjpeg-turbo, vtk, libtiff , gtkplus, cuda, jasper, libpng, py-numpy, qt

Link Dependencies zlib, qt, jdk, python, libjpeg-turbo, vtk, libtiff , gtkplus, jasper, libpng, cuda

Run Dependencies py-numpy

Description: OpenCV is released under a BSD license and hence it’s free for both academic and commercial use. Ithas C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV wasdesigned for computational efficiency and with a strong focus on real- time applications. Written in optimizedC/C++, the library can take advantage of multi-core processing. Enabled with OpenCL, it can take advantageof the hardware acceleration of the underlying heterogeneous compute platform. Adopted all around the world,OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 9

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million. Usage ranges from interactive art, to mines inspection, stitching maps on the web or through advancedrobotics.

1.10.310 openexr

Homepage:

• http://www.openexr.com/

Spack package:

• openexr/package.py

Versions: 2.2.0, 2.1.0, 2.0.1, 1.7.0, 1.6.1, 1.5.0, 1.4.0a, 1.3.2

Build Dependencies ilmbase, pkg-config

Link Dependencies ilmbase

Description: OpenEXR Graphics Tools (high dynamic-range image file format)

1.10.311 openjpeg

Homepage:

• https://github.com/uclouvain/openjpeg

Spack package:

• openjpeg/package.py

Versions: 2.1, 2.0.1, 2.0, 1.5.2, 1.5.1

Build Dependencies cmake

Description: OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order topromote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group(JPEG). Since April 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.

1.10.312 openmpi

Homepage:

• http://www.open-mpi.org

Spack package:

• openmpi/package.py

Versions: 2.0.0, 1.10.3, 1.10.2, 1.10.1, 1.10.0, 1.8.8, 1.6.5

Build Dependencies hwloc, sqlite

Link Dependencies hwloc, sqlite

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Description: Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2compliant implementation, Open MPI offers advantages for system and software vendors, application developersand computer science researchers.

1.10.313 openspeedshop

Homepage:

• http://www.openspeedshop.org

Spack package:

• openspeedshop/package.py

Versions: 2.2

Build Dependencies mvapich2, sqlite, mrnet, cbtf , libmonitor, cmake, openmpi, mpich, bison, boost, flex, mpich2,papi, python, dyninst, mpt, libunwind, mvapich, qt, cbtf-argonavis, cbtf-krell, libelf , binutils, libdwarf

Link Dependencies mvapich2, sqlite, mpich2, mrnet, qt, python, dyninst, cbtf-argonavis, mpt, openmpi, cbtf-krell,libelf , mvapich, mpich, papi, libunwind, libdwarf , boost, cbtf , libmonitor

Description: OpenSpeedShop is a community effort by The Krell Institute with current direct funding from DOEsNNSA. It builds on top of a broad list of community infrastructures, most notably Dyninst and MRNet fromUW, libmonitor from Rice, and PAPI from UTK. OpenSpeedShop is an open source multi platform Linuxperformance tool which is targeted to support performance analysis of applications running on both single nodeand large scale IA64, IA32, EM64T, AMD64, PPC, ARM, Blue Gene and Cray platforms. OpenSpeedShopdevelopment is hosted by the Krell Institute. The infrastructure and base components of OpenSpeedShop arereleased as open source code primarily under LGPL.

1.10.314 openssl

Homepage:

• http://www.openssl.org

Spack package:

• openssl/package.py

Versions: 1.0.2h, 1.0.2g, 1.0.2f, 1.0.2e, 1.0.2d, 1.0.1t, 1.0.1r, 1.0.1h

Build Dependencies zlib

Link Dependencies zlib

Description: The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, andOpen Source toolkit implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLSv1) protocols as well as a full-strength general purpose cryptography library.

1.10. Package List 201

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1.10.315 opium

Homepage:

• https://opium.sourceforge.net/index.html

Spack package:

• opium/package.py

Versions: 3.8

Build Dependencies lapack, blas

Link Dependencies lapack, blas

Description: DFT pseudopotential generation project

1.10.316 osu-micro-benchmarks

Homepage:

• http://mvapich.cse.ohio-state.edu/benchmarks/

Spack package:

• osu-micro-benchmarks/package.py

Versions: 5.3

Build Dependencies cuda, mpi

Link Dependencies cuda, mpi

Description: The Ohio MicroBenchmark suite is a collection of independent MPI message passing performancemicrobenchmarks developed and written at The Ohio State University. It includes traditional benchmarks andperformance measures such as latency, bandwidth and host overhead and can be used for both traditional andGPU-enhanced nodes.

1.10.317 otf

Homepage:

• http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/otf/index_html/document_view?set_language=en

Spack package:

• otf/package.py

Versions: 1.12.5salmon

Build Dependencies zlib

Link Dependencies zlib

Description: To improve scalability for very large and massively parallel traces the Open Trace Format (OTF) isdeveloped at ZIH as a successor format to the Vampir Trace Format (VTF3).

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1.10.318 otf2

Homepage:

• http://www.vi-hps.org/score-p

Spack package:

• otf2/package.py

Versions: 2.0, 1.5.1, 1.4, 1.3.1, 1.2.1

Description: The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus supportlibrary.

1.10.319 p4est

Homepage:

• http://www.p4est.org

Spack package:

• p4est/package.py

Versions: 1.1

Build Dependencies mpi, zlib, automake, lua, libtool, autoconf

Link Dependencies lua, zlib, mpi

Description: Dynamic management of a collection (a forest) of adaptive octrees in parallel

1.10.320 panda

Homepage:

• http://comopt.ifi.uni-heidelberg.de/software/PANDA/index.html

Spack package:

• panda/package.py

Versions: current

Build Dependencies cmake, mpi

Link Dependencies mpi

Description: PANDA: Parallel AdjaceNcy Decomposition Algorithm

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1.10.321 pango

Homepage:

• http://www.pango.org

Spack package:

• pango/package.py

Versions: 1.40.1, 1.36.8

Build Dependencies cairo, harfbuzz

Link Dependencies cairo, harfbuzz

Description: Pango is a library for laying out and rendering of text, with an emphasis on internationalization. It canbe used anywhere that text layout is needed, though most of the work on Pango so far has been done in thecontext of the GTK+ widget toolkit.

1.10.322 papi

Homepage:

• http://icl.cs.utk.edu/papi/index.html

Spack package:

• papi/package.py

Versions: 5.4.3, 5.4.1, 5.3.0

Description: PAPI provides the tool designer and application engineer with a consistent interface and methodologyfor use of the performance counter hardware found in most major microprocessors. PAPI enables softwareengineers to see, in near real time, the relation between software performance and processor events. In ad-dition Component PAPI provides access to a collection of components that expose performance measurementopportunites across the hardware and software stack.

1.10.323 paradiseo

Homepage:

• http://paradiseo.gforge.inria.fr/

Spack package:

• paradiseo/package.py

Versions: head, dev-safe

Build Dependencies doxygen, cmake, eigen, gnuplot, mpi, boost

Link Dependencies boost, gnuplot, mpi

Description: A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics.

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1.10.324 parallel

Homepage:

• http://www.gnu.org/software/parallel/

Spack package:

• parallel/package.py

Versions: 20160422, 20160322

Description: GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be asingle command or a small script that has to be run for each of the lines in the input.

1.10.325 parallel-netcdf

Homepage:

• https://trac.mcs.anl.gov/projects/parallel-netcdf

Spack package:

• parallel-netcdf/package.py

Versions: 1.7.0, 1.6.1

Build Dependencies m4, mpi

Link Dependencies mpi

Description: Parallel netCDF (PnetCDF) is a library providing high-performance parallel I/O while still maintainingfile-format compatibility with Unidata’s NetCDF.

1.10.326 paraver

Homepage:

• http://www.bsc.es/computer-sciences/performance-tools/paraver

Spack package:

• paraver/package.py

Versions: 4.5.3

Build Dependencies boost, wxpropgrid, wx

Link Dependencies boost, wxpropgrid, wx

Description: “A very powerful performance visualization and analysis tool based on traces that can be used to analyseany information that is expressed on its input trace format. Traces for parallel MPI, OpenMP and other programscan be genereated with Extrae.

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1.10.327 paraview

Homepage:

• http://www.paraview.org

Spack package:

• paraview/package.py

Versions: 5.0.0, 4.4.0

Build Dependencies bzip2, libtiff , cmake, qt, python, libxml2, zlib, freetype, jpeg, mpi, tcl, libpng

Link Dependencies bzip2, libtiff , qt, python, libxml2, zlib, freetype, jpeg, mpi, tcl, libpng

Run Dependencies py-matplotlib, py-numpy

Description:

1.10.328 parmetis

Homepage:

• http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview

Spack package:

• parmetis/package.py

Versions: 4.0.3, 4.0.2

Build Dependencies metis, cmake, mpi

Link Dependencies metis, mpi

Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioningunstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.

1.10.329 parmgridgen

Homepage:

• http://www-users.cs.umn.edu/~moulitsa/software.html

Spack package:

• parmgridgen/package.py

Versions: 1.0

Build Dependencies mpi

Link Dependencies mpi

Description: MGRIDGEN is a serial library written entirely in ANSI C that implements (serial) algorithms for obtain-ing a sequence of successive coarse grids that are well-suited for geometric multigrid methods. ParMGridGenis the parallel version of MGridGen

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1.10.330 parpack

Homepage:

• http://www.caam.rice.edu/software/ARPACK/download.html

Spack package:

• parpack/package.py

Versions: 96

Build Dependencies lapack, blas, mpi

Link Dependencies lapack, blas, mpi

Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

1.10.331 patchelf

Homepage:

• https://nixos.org/patchelf.html

Spack package:

• patchelf/package.py

Versions: 0.8

Description: PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

1.10.332 pcre

Homepage:

• http://www.pcre.org

Spack package:

• pcre/package.py

Versions: 8.39, 8.38

Description: The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for imple-menting regular expression pattern matching using the same syntax and semantics as Perl 5.

1.10.333 pcre2

Homepage:

• http://www.pcre.org

Spack package:

• pcre2/package.py

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Versions: 10.20

Description: The PCRE2 package contains Perl Compatible Regular Expression libraries. These are useful for im-plementing regular expression pattern matching using the same syntax and semantics as Perl 5.

1.10.334 pdt

Homepage:

• https://www.cs.uoregon.edu/research/pdt/home.php

Spack package:

• pdt/package.py

Versions: 3.22.1, 3.22, 3.21, 3.19, 3.18.1

Description: Program Database Toolkit (PDT) is a framework for analyzing source code written in several program-ming languages and for making rich program knowledge accessible to developers of static and dynamic analysistools. PDT implements a standard program representation, the program database (PDB), that can be accessed ina uniform way through a class library supporting common PDB operations.

1.10.335 perl

Homepage:

• http://www.perl.org

Spack package:

• perl/package.py

Versions: 5.24.0, 5.22.2, 5.20.3

Description: Perl 5 is a highly capable, feature-rich programming language with over 27 years of development.

1.10.336 petsc

Homepage:

• http://www.mcs.anl.gov/petsc/index.html

Spack package:

• petsc/package.py

Versions: 3.7.2, 3.6.4, 3.6.3, 3.5.3, 3.5.2, 3.5.1, 3.4.4

Build Dependencies hypre, superlu-dist, hdf5, lapack, boost, blas, metis, mpi, python, mumps, scalapack, parmetis

Link Dependencies hypre, superlu-dist, hdf5, lapack, boost, blas, metis, mpi, python, mumps, scalapack, parmetis

Description: PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applica-tions modeled by partial differential equations.

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1.10.337 pgi

Homepage:

• http://www.pgroup.com/

Spack package:

• pgi/package.py

Versions: 16.5, 16.3

Description: PGI optimizing multi-core x64 compilers for Linux, MacOS & Windows with support for debuggingand profiling of local MPI processes. Note: The PGI compilers are licensed software. You will need to create anaccount on the PGI homepage and download PGI yourself. Once the download finishes, rename the file (whichmay contain information such as the architecture) to the format: pgi-<version>.tar.gz. Spack will search yourcurrent directory for a file of this format. Alternatively, add this file to a mirror so that Spack can find it. Forinstructions on how to set up a mirror, see http://software.llnl.gov/spack/mirrors.html

1.10.338 pidx

Homepage:

• http://www.cedmav.com/pidx

Spack package:

• pidx/package.py

Versions: 1.0

Build Dependencies cmake, mpi

Link Dependencies mpi

Description: PIDX Parallel I/O Library. PIDX is an efficient parallel I/O library that reads and writes multiresolutionIDX data files.

1.10.339 pixman

Homepage:

• http://www.pixman.org

Spack package:

• pixman/package.py

Versions: 0.32.6

Build Dependencies libpng, pkg-config

Link Dependencies libpng

Description: The Pixman package contains a library that provides low-level pixel manipulation features such as imagecompositing and trapezoid rasterization.

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1.10.340 pkg-config

Homepage:

• http://www.freedesktop.org/wiki/Software/pkg-config/

Spack package:

• pkg-config/package.py

Versions: 0.29.1, 0.28

Description: pkg-config is a helper tool used when compiling applications and libraries

1.10.341 plumed

Homepage:

• http://www.plumed.org/

Spack package:

• plumed/package.py

Versions: 2.2.3

Build Dependencies lapack, blas, zlib, gsl, mpi

Link Dependencies lapack, blas, zlib, gsl, mpi

Description: PLUMED is an open source library for free energy calculations in molecular systems which workstogether with some of the most popular molecular dynamics engines. Free energy calculations can be performedas a function of many order parameters with a particular focus on biological problems, using state of the artmethods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software,written in C++, can be easily interfaced with both fortran and C/C++ codes.

1.10.342 pmgr_collective

Homepage:

• http://www.sourceforge.net/projects/pmgrcollective

Spack package:

• pmgr_collective/package.py

Versions: 1.0

Description: PMGR_COLLECTIVE provides a scalable network for bootstrapping MPI jobs.

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1.10.343 pngwriter

Homepage:

• http://pngwriter.sourceforge.net/

Spack package:

• pngwriter/package.py

Versions: 0.5.6

Build Dependencies libpng, freetype, zlib, cmake

Link Dependencies libpng, freetype, zlib

Description: PNGwriter is a very easy to use open source graphics library that uses PNG as its output format. Theinterface has been designed to be as simple and intuitive as possible. It supports plotting and reading pixels inthe RGB (red, green, blue), HSV (hue, saturation, value/brightness) and CMYK (cyan, magenta, yellow, black)colour spaces, basic shapes, scaling, bilinear interpolation, full TrueType antialiased and rotated text support,bezier curves, opening existing PNG images and more.

1.10.344 polymake

Homepage:

• https://polymake.org/doku.php

Spack package:

• polymake/package.py

Versions: 3.0r2, 3.0r1

Build Dependencies ppl, bliss, cddlib, lrslib, gmp, boost, mpfr

Link Dependencies ppl, bliss, cddlib, lrslib, gmp, boost, mpfr

Description: polymake is open source software for research in polyhedral geometry

1.10.345 porta

Homepage:

• http://porta.zib.de

Spack package:

• porta/package.py

Versions: 1.4.1

Build Dependencies libtool

Description: PORTA is a collection of routines for analyzing polytopes and polyhedra

1.10. Package List 211

Spack Documentation, Release 0.9

1.10.346 postgresql

Homepage:

• http://www.postgresql.org/

Spack package:

• postgresql/package.py

Versions: 9.5.3, 9.3.4

Build Dependencies readline, openssl

Link Dependencies readline, openssl

Description: PostgreSQL is a powerful, open source object-relational database system. It has more than 15 years ofactive development and a proven architecture that has earned it a strong reputation for reliability, data integrity,and correctness.

1.10.347 ppl

Homepage:

• http://bugseng.com/products/ppl/

Spack package:

• ppl/package.py

Versions: 1.1

Build Dependencies gmp

Link Dependencies gmp

Description: The Parma Polyhedra Library (PPL) provides numerical abstractions especially targeted at applicationsin the field of analysis and verification of complex systems. These abstractions include convex polyhedra,some special classes of polyhedra shapes that offer interesting complexity/precision tradeoffs, and grids whichrepresent regularly spaced points that satisfy a set of linear congruence relations. The library also supports finitepowersets and products of polyhedra and grids, a mixed integer linear programming problem solver using anexact-arithmetic version of the simplex algorithm, a parametric integer programming solver, and primitives fortermination analysis via the automatic synthesis of linear ranking functions.

1.10.348 prank

Homepage:

• http://wasabiapp.org/software/prank/

Spack package:

• prank/package.py

Versions: 150803

Build Dependencies bpp-suite, exonerate, mafft

Link Dependencies bpp-suite, exonerate, mafft

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Description: A powerful multiple sequence alignment browser.

1.10.349 proj

Homepage:

• https://github.com/OSGeo/proj.4/wiki

Spack package:

• proj/package.py

Versions: 4.9.2, 4.9.1, 4.8.0, 4.7.0, 4.6.1

Description: Cartographic Projections

1.10.350 protobuf

Homepage:

• https://developers.google.com/protocol-buffers

Spack package:

• protobuf/package.py

Versions: 2.5.0

Description: Google’s data interchange format.

1.10.351 psi4

Homepage:

• http://www.psicode.org/

Spack package:

• psi4/package.py

Versions: 0.5

Build Dependencies cmake, lapack, blas, py-numpy, python, boost

Link Dependencies lapack, python, blas, boost

Run Dependencies py-numpy

Description: Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.

1.10. Package List 213

Spack Documentation, Release 0.9

1.10.352 py-3to2

Homepage:

• https://pypi.python.org/pypi/3to2

Spack package:

• py-3to2/package.py

Versions: 1.1.1

Build Dependencies python

Link Dependencies python

Description: lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Pythonversion 2.x.

1.10.353 py-alabaster

Homepage:

• https://pypi.python.org/pypi/alabaster

Spack package:

• py-alabaster/package.py

Versions: 0.7.9

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Alabaster is a visually (c)lean, responsive, configurable theme for the Sphinx documentation system.

1.10.354 py-argcomplete

Homepage:

• https://pypi.python.org/pypi/argcomplete

Spack package:

• py-argcomplete/package.py

Versions: 1.1.1

Build Dependencies python

Link Dependencies python

Description: Bash tab completion for argparse.

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1.10.355 py-astroid

Homepage:

• https://www.astroid.org/

Spack package:

• py-astroid/package.py

Versions: 1.4.5, 1.4.4, 1.4.3, 1.4.2, 1.4.1

Build Dependencies python, py-six, py-logilab-common, py-setuptools

Link Dependencies python

Run Dependencies py-six, py-logilab-common

Description:

1.10.356 py-astropy

Homepage:

• http://www.astropy.org/

Spack package:

• py-astropy/package.py

Versions: 1.1.2, 1.1.post1

Build Dependencies py-scipy, py-scikit-image, py-pyyaml, python, libxml2, cfitsio, expat, py-h5py, py-numpy, py-pandas, py-beautifulsoup4, py-pytz, py-matplotlib

Link Dependencies python, libxml2, cfitsio, expat

Run Dependencies py-scipy, py-scikit-image, py-pyyaml, py-h5py, py-numpy, py-pandas, py-beautifulsoup4, py-pytz,py-matplotlib

Description: The Astropy Project is a community effort to develop a single core package for Astronomy in Pythonand foster interoperability between Python astronomy packages.

1.10.357 py-autopep8

Homepage:

• https://github.com/hhatto/autopep8

Spack package:

• py-autopep8/package.py

Versions: 1.2.2

Build Dependencies python, py-pep8, py-setuptools

Link Dependencies python

Run Dependencies py-pep8

1.10. Package List 215

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Description: Automatic pep8 formatter

1.10.358 py-babel

Homepage:

• http://babel.pocoo.org/en/latest/

Spack package:

• py-babel/package.py

Versions: 2.3.4

Build Dependencies python, py-pytz, py-setuptools

Link Dependencies python

Run Dependencies py-pytz

Description: Babel is an integrated collection of utilities that assist in internationalizing and localizing Python appli-cations, with an emphasis on web-based applications.

1.10.359 py-basemap

Homepage:

• http://matplotlib.org/basemap/

Spack package:

• py-basemap/package.py

Versions: 1.0.7

Build Dependencies pil, python, geos, py-numpy, py-setuptools, py-matplotlib

Link Dependencies python, geos

Run Dependencies py-matplotlib, pil, py-numpy

Description: The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python.

1.10.360 py-beautifulsoup4

Homepage:

• https://www.crummy.com/software/BeautifulSoup

Spack package:

• py-beautifulsoup4/package.py

Versions: 4.4.1

Build Dependencies python

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Link Dependencies python

Description: Beautiful Soup is a Python library for pulling data out of HTML and XML files. It works with yourfavorite parser to provide idiomatic ways of navigating, searching, and modifying the parse tree.

1.10.361 py-biopython

Homepage:

• http://biopython.org/wiki/Main_Page

Spack package:

• py-biopython/package.py

Versions: 1.65

Build Dependencies python, py-mx, py-numpy

Link Dependencies python

Run Dependencies py-mx, py-numpy

Description: A distributed collaborative effort to develop Python libraries and applications which address the needsof current and future work in bioinformatics.

1.10.362 py-blessings

Homepage:

• https://github.com/erikrose/blessings

Spack package:

• py-blessings/package.py

Versions: 1.6

Build Dependencies python, py-setuptools

Link Dependencies python

Description: A nicer, kinder way to write to the terminal

1.10.363 py-bottleneck

Homepage:

• https://pypi.python.org/pypi/Bottleneck/1.0.0

Spack package:

• py-bottleneck/package.py

Versions: 1.0.0

Build Dependencies python, py-numpy

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Link Dependencies python

Run Dependencies py-numpy

Description: A collection of fast NumPy array functions written in Cython.

1.10.364 py-cclib

Homepage:

• https://cclib.github.io/

Spack package:

• py-cclib/package.py

Versions: 1.5

Build Dependencies python, py-numpy

Link Dependencies python

Run Dependencies py-numpy

Description: Open source library for parsing and interpreting the results of computational chemistry packages

1.10.365 py-cffi

Homepage:

• http://cffi.readthedocs.org/en/latest/

Spack package:

• py-cffi/package.py

Versions: 1.1.2

Build Dependencies python, libffi, py-pycparser, py-setuptools

Link Dependencies python, libffi

Run Dependencies py-pycparser

Description: Foreign Function Interface for Python calling C code

1.10.366 py-coverage

Homepage:

• http://nedbatchelder.com/code/coverage/

Spack package:

• py-coverage/package.py

Versions: 4.0a6

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Build Dependencies python, py-setuptools

Link Dependencies python

Description: Testing coverage checker for python

1.10.367 py-csvkit

Homepage:

• http://csvkit.rtfd.org/

Spack package:

• py-csvkit/package.py

Versions: 0.9.1

Build Dependencies py-dbf , python, py-SQLAlchemy, py-dateutil, py-openpyxl, py-six, py-xlrd

Link Dependencies python

Run Dependencies py-openpyxl, py-SQLAlchemy, py-dbf , py-dateutil, py-six, py-xlrd

Description: A library of utilities for working with CSV, the king of tabular file formats

1.10.368 py-cycler

Homepage:

• http://matplotlib.org/cycler/

Spack package:

• py-cycler/package.py

Versions: 0.10.0

Build Dependencies python, py-six, py-setuptools

Link Dependencies python

Run Dependencies py-six

Description: Composable style cycles.

1.10.369 py-cython

Homepage:

• https://pypi.python.org/pypi/cython

Spack package:

• py-cython/package.py

Versions: 0.23.5, 0.23.4, 0.22, 0.21.2

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Build Dependencies python

Link Dependencies python

Description: The Cython compiler for writing C extensions for the Python language.

1.10.370 py-dask

Homepage:

• https://github.com/dask/dask/

Spack package:

• py-dask/package.py

Versions: 0.8.1

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Minimal task scheduling abstraction

1.10.371 py-dateutil

Homepage:

• https://pypi.python.org/pypi/dateutil

Spack package:

• py-dateutil/package.py

Versions: 2.5.2, 2.4.2, 2.4.0

Build Dependencies python, py-six, py-setuptools

Link Dependencies python

Run Dependencies py-six

Description: Extensions to the standard Python datetime module.

1.10.372 py-dbf

Homepage:

• https://pypi.python.org/pypi/dbf

Spack package:

• py-dbf/package.py

Versions: 0.96.005

Build Dependencies python

220 Chapter 1. Table of Contents

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Link Dependencies python

Description: Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro .dbf files (including memos)

1.10.373 py-decorator

Homepage:

• https://github.com/micheles/decorator

Spack package:

• py-decorator/package.py

Versions: 4.0.9

Build Dependencies python, py-setuptools

Link Dependencies python

Description: The aim of the decorator module it to simplify the usage of decorators for the average programmer, andto popularize decorators by showing various non-trivial examples.

1.10.374 py-docutils

Homepage:

• http://docutils.sourceforge.net/

Spack package:

• py-docutils/package.py

Versions: 0.12

Build Dependencies python

Link Dependencies python

Description: Docutils is an open-source text processing system for processing plaintext documentation into usefulformats, such as HTML, LaTeX, man- pages, open-document or XML. It includes reStructuredText, the easy toread, easy to use, what-you-see-is-what-you-get plaintext markup language.

1.10.375 py-emcee

Homepage:

• http://dan.iel.fm/emcee/current/

Spack package:

• py-emcee/package.py

Versions: 2.1.0

Build Dependencies python, py-numpy

1.10. Package List 221

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Link Dependencies python

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Description: emcee is an MIT licensed pure-Python implementation of Goodman & Weare’s Affine Invariant Markovchain Monte Carlo (MCMC) Ensemble sampler.

1.10.376 py-epydoc

Homepage:

• https://pypi.python.org/pypi/epydoc

Spack package:

• py-epydoc/package.py

Versions: 3.0.1

Build Dependencies python

Link Dependencies python

Description: Epydoc is a tool for generating API documentation documentation for Python modules, based on theirdocstrings.

1.10.377 py-flake8

Homepage:

• http://flake8.readthedocs.io/en/latest/

Spack package:

• py-flake8/package.py

Versions: 2.5.4

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Flake8 is a wrapper around PyFlakes, pep8 and Ned Batchelder’s McCabe script.

1.10.378 py-funcsigs

Homepage:

• https://pypi.python.org/pypi/funcsigs

Spack package:

• py-funcsigs/package.py

Versions: 0.4

Build Dependencies python, py-setuptools

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Link Dependencies python

Description: Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2.

1.10.379 py-genders

Homepage:

• https://github.com/chaos/genders

Spack package:

• py-genders/package.py

Versions: 1.22

Build Dependencies python

Link Dependencies python

Description: Genders is a static cluster configuration database used for cluster configuration management. It is usedby a variety of tools and scripts for management of large clusters.

1.10.380 py-genshi

Homepage:

• https://genshi.edgewall.org/

Spack package:

• py-genshi/package.py

Versions: 0.7, 0.6.1, 0.6

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Python toolkit for generation of output for the web

1.10.381 py-gnuplot

Homepage:

• http://gnuplot-py.sourceforge.net/

Spack package:

• py-gnuplot/package.py

Versions: 1.8

Build Dependencies python, py-numpy

Link Dependencies python

1.10. Package List 223

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Run Dependencies py-numpy

Description: Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplotplotting program.

1.10.382 py-h5py

Homepage:

• https://pypi.python.org/pypi/h5py

Spack package:

• py-h5py/package.py

Versions: 2.6.0, 2.5.0, 2.4.0

Build Dependencies py-cython, hdf5, python, mpi, py-six, py-setuptools, py-numpy, py-mpi4py, pkg-config

Link Dependencies python, mpi, py-mpi4py, hdf5

Run Dependencies py-six, py-numpy

Description: The h5py package provides both a high- and low-level interface to the HDF5 library from Python.

1.10.383 py-imagesize

Homepage:

• https://pypi.python.org/pypi/imagesize

Spack package:

• py-imagesize/package.py

Versions: 0.7.1

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Parses image file headers and returns image size. Supports PNG, JPEG, JPEG2000, and GIF image fileformats.

1.10.384 py-iminuit

Homepage:

• https://pypi.python.org/pypi/iminuit

Spack package:

• py-iminuit/package.py

Versions: 1.2

Build Dependencies python, py-cython, py-numpy, py-setuptools, py-matplotlib

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Run Dependencies py-numpy, py-matplotlib

Description: Interactive IPython-Friendly Minimizer based on SEAL Minuit2.

1.10.385 py-ipython

Homepage:

• https://pypi.python.org/pypi/ipython

Spack package:

• py-ipython/package.py

Versions: 3.1.0, 2.3.1

Build Dependencies python, py-pygments, py-setuptools

Link Dependencies python

Run Dependencies py-pygments, py-setuptools

Description: IPython provides a rich toolkit to help you make the most out of using Python interactively.

1.10.386 py-jdcal

Homepage:

• http://github.com/phn/jdcal

Spack package:

• py-jdcal/package.py

Versions: 1.2

Build Dependencies python

Link Dependencies python

Description: Julian dates from proleptic Gregorian and Julian calendars

1.10.387 py-jinja2

Homepage:

• http://jinja.pocoo.org/

Spack package:

• py-jinja2/package.py

Versions: 2.8, 2.7.3, 2.7.2, 2.7.1, 2.7

Build Dependencies python, py-markupsafe, py-babel, py-setuptools

1.10. Package List 225

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Link Dependencies python

Run Dependencies py-markupsafe, py-babel

Description: Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax butsupports inline expressions and an optional sandboxed environment.

1.10.388 py-lockfile

Homepage:

• https://pypi.python.org/pypi/lockfile

Spack package:

• py-lockfile/package.py

Versions: 0.10.2

Build Dependencies python, py-setuptools

Link Dependencies python

Description: The lockfile package exports a LockFile class which provides a simple API for locking files. Unlikethe Windows msvcrt.locking function, the fcntl.lockf and flock functions, and the deprecated posixfile module,the API is identical across both Unix (including Linux and Mac) and Windows platforms. The lock mechanismrelies on the atomic nature of the link (on Unix) and mkdir (on Windows) system calls. An implementation basedon SQLite is also provided, more as a demonstration of the possibilities it provides than as production-qualitycode.

1.10.389 py-logilab-common

Homepage:

• https://www.logilab.org/project/logilab-common

Spack package:

• py-logilab-common/package.py

Versions: 1.2.0

Build Dependencies python, py-six, py-setuptools

Link Dependencies python

Run Dependencies py-six

Description: Common modules used by Logilab projects

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1.10.390 py-mako

Homepage:

• https://pypi.python.org/pypi/mako

Spack package:

• py-mako/package.py

Versions: 1.0.1

Build Dependencies python, py-setuptools

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Description: A super-fast templating language that borrows the best ideas from the existing templating languages.

1.10.391 py-markupsafe

Homepage:

• http://www.pocoo.org/projects/markupsafe/

Spack package:

• py-markupsafe/package.py

Versions: 0.23, 0.22, 0.21, 0.20, 0.19

Build Dependencies python, py-setuptools

Link Dependencies python

Description: MarkupSafe is a library for Python that implements a unicode string that is aware of HTML escapingrules and can be used to implement automatic string escaping. It is used by Jinja 2, the Mako templating engine,the Pylons web framework and many more.

1.10.392 py-matplotlib

Homepage:

• https://pypi.python.org/pypi/matplotlib

Spack package:

• py-matplotlib/package.py

Versions: 1.5.1, 1.4.3, 1.4.2

Build Dependencies py-pyparsing, freetype, py-ipython, ImageMagick, qt, python, qhull, py-setuptools, py-dateutil,py-numpy, py-six, py-pillow, py-mock, py-nose, tk, py-pytz, py-cycler, libpng, py-pyside, pkg-config

Link Dependencies freetype, py-ipython, ImageMagick, qt, python, qhull, py-mock, py-nose, tk, libpng

Run Dependencies py-pyparsing, py-pillow, py-dateutil, py-numpy, py-six, py-pytz, py-cycler, py-pyside

Description: matplotlib is a python 2D plotting library which produces publication quality figures in a variety ofhardcopy formats and interactive environments across platforms.

1.10. Package List 227

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1.10.393 py-meep

Homepage:

• https://launchpad.net/python-meep

Spack package:

• py-meep/package.py

Versions: 1.4.2

Build Dependencies py-scipy, python, swig, py-numpy, mpi, meep, py-matplotlib

Link Dependencies python, swig, meep, mpi

Run Dependencies py-scipy, py-matplotlib, py-numpy

Description: Python-meep is a wrapper around libmeep. It allows the scripting of Meep-simulations with Python

1.10.394 py-mistune

Homepage:

• http://mistune.readthedocs.org/en/latest/

Spack package:

• py-mistune/package.py

Versions: 0.7.1, 0.7, 0.6, 0.5.1, 0.5

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Python markdown parser

1.10.395 py-mock

Homepage:

• https://github.com/testing-cabal/mock

Spack package:

• py-mock/package.py

Versions: 1.3.0

Build Dependencies python, py-pbr, py-setuptools

Link Dependencies python

Run Dependencies py-pbr

Description: mock is a library for testing in Python. It allows you to replace parts of your system under test withmock objects and make assertions about how they have been used.

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1.10.396 py-mpi4py

Homepage:

• https://pypi.python.org/pypi/mpi4py

Spack package:

• py-mpi4py/package.py

Versions: 2.0.0, 1.3.1

Build Dependencies python, py-setuptools, mpi

Link Dependencies python, mpi

Description: This package provides Python bindings for the Message Passing Interface (MPI) standard. It is imple-mented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++bindings.

1.10.397 py-mpmath

Homepage:

• http://mpmath.org

Spack package:

• py-mpmath/package.py

Versions: 0.19

Build Dependencies python

Link Dependencies python

Description: A Python library for arbitrary-precision floating-point arithmetic.

1.10.398 py-mx

Homepage:

• http://www.egenix.com/products/python/mxBase/

Spack package:

• py-mx/package.py

Versions: 3.2.8

Build Dependencies python

Link Dependencies python

Description: The eGenix.com mx Base Distribution for Python is a collection of professional quality software toolswhich enhance Python’s usability in many important areas such as fast text searching, date/time processing andhigh speed data types.

1.10. Package List 229

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1.10.399 py-mysqldb1

Homepage:

• https://github.com/farcepest/MySQLdb1

Spack package:

• py-mysqldb1/package.py

Versions: 1.2.5

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Legacy mysql bindings for python

1.10.400 py-nestle

Homepage:

• http://kbarbary.github.io/nestle/

Spack package:

• py-nestle/package.py

Versions: 0.1.1

Build Dependencies python, py-scipy, py-numpy

Link Dependencies python

Run Dependencies py-scipy, py-numpy

Description: Nested sampling algorithms for evaluating Bayesian evidence.

1.10.401 py-netcdf

Homepage:

• http://unidata.github.io/netcdf4-python

Spack package:

• py-netcdf/package.py

Versions: 1.2.3.1

Build Dependencies python, py-cython, netcdf , py-numpy

Link Dependencies python, netcdf

Run Dependencies py-cython, py-numpy

Description: Python interface to the netCDF Library.

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1.10.402 py-networkx

Homepage:

• http://networkx.github.io/

Spack package:

• py-networkx/package.py

Versions: 1.11

Build Dependencies python, py-decorator, py-setuptools

Link Dependencies python

Run Dependencies py-decorator

Description: NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, andfunctions of complex networks.

1.10.403 py-nose

Homepage:

• https://pypi.python.org/pypi/nose

Spack package:

• py-nose/package.py

Versions: 1.3.7, 1.3.6, 1.3.4

Build Dependencies python, py-setuptools

Link Dependencies python

Description: nose extends the test loading and running features of unittest, making it easier to write, find and runtests.

1.10.404 py-numexpr

Homepage:

• https://pypi.python.org/pypi/numexpr

Spack package:

• py-numexpr/package.py

Versions: 2.5, 2.4.6

Build Dependencies python, py-numpy

Link Dependencies python

Run Dependencies py-numpy

Description: Fast numerical expression evaluator for NumPy

1.10. Package List 231

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1.10.405 py-numpy

Homepage:

• http://www.numpy.org/

Spack package:

• py-numpy/package.py

Versions: 1.11.0, 1.10.4, 1.9.2, 1.9.1

Build Dependencies python, lapack, blas, py-nose, py-setuptools

Link Dependencies python, lapack, blas

Description: NumPy is the fundamental package for scientific computing with Python. It contains among otherthings: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integratingC/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities

1.10.406 py-openpyxl

Homepage:

• http://openpyxl.readthedocs.org/

Spack package:

• py-openpyxl/package.py

Versions: 2.4.0-a1

Build Dependencies python, py-jdcal, py-setuptools

Link Dependencies python

Run Dependencies py-jdcal

Description: A Python library to read/write Excel 2007 xlsx/xlsm files

1.10.407 py-pandas

Homepage:

• http://pandas.pydata.org/

Spack package:

• py-pandas/package.py

Versions: 0.18.0, 0.16.1, 0.16.0

Build Dependencies py-numexpr, py-bottleneck, python, py-dateutil, py-numpy, py-pytz, py-setuptools

Link Dependencies python

Run Dependencies py-pytz, py-numpy, py-numexpr, py-bottleneck, py-dateutil

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Description: pandas is a Python package providing fast, flexible, and expressive data structures designed to makeworking with relational or labeled data both easy and intuitive. It aims to be the fundamental high-level buildingblock for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becomingthe most powerful and flexible open source data analysis / manipulation tool available in any language.

1.10.408 py-pbr

Homepage:

• https://pypi.python.org/pypi/pbr

Spack package:

• py-pbr/package.py

Versions: 1.8.1

Build Dependencies python, py-setuptools

Link Dependencies python

Description: PBR is a library that injects some useful and sensible default behaviors into your setuptools run.

1.10.409 py-pep8

Homepage:

• https://github.com/PyCQA/pycodestyle

Spack package:

• py-pep8/package.py

Versions: 1.7.0

Build Dependencies python, py-setuptools

Link Dependencies python

Description: python pep8 format checker

1.10.410 py-periodictable

Homepage:

• https://pypi.python.org/pypi/periodictable

Spack package:

• py-periodictable/package.py

Versions: 1.4.1

Build Dependencies python, py-pyparsing, py-numpy

Link Dependencies python

1.10. Package List 233

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Run Dependencies py-pyparsing, py-numpy

Description: nose extends the test loading and running features of unittest, making it easier to write, find and runtests.

1.10.411 py-pexpect

Homepage:

• https://pypi.python.org/pypi/pexpect

Spack package:

• py-pexpect/package.py

Versions: 3.3

Build Dependencies python

Link Dependencies python

Description: Pexpect allows easy control of interactive console applications.

1.10.412 py-phonopy

Homepage:

• http://atztogo.github.io/phonopy/index.html

Spack package:

• py-phonopy/package.py

Versions: 1.10.0

Build Dependencies python, py-scipy, py-numpy, py-pyyaml, py-matplotlib

Link Dependencies python

Run Dependencies py-scipy, py-numpy, py-pyyaml, py-matplotlib

Description: Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.

1.10.413 py-pil

Homepage:

• http://www.pythonware.com/products/pil/

Spack package:

• py-pil/package.py

Versions: 1.1.7

Build Dependencies python

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Description: The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. Thislibrary supports many file formats, and provides powerful image processing and graphics capabilities.

1.10.414 py-pillow

Homepage:

• https://python-pillow.org/

Spack package:

• py-pillow/package.py

Versions: 3.3.0.dev0, 3.2.0, 3.0.0

Build Dependencies freetype, libtiff , python, zlib, jpeg, py-setuptools, openjpeg, binutils, lcms

Link Dependencies freetype, libtiff , python, zlib, jpeg, openjpeg, lcms

Description: Pillow is a fork of the Python Imaging Library (PIL). It adds image processing capabilities to yourPython interpreter. This library supports many file formats, and provides powerful image processing and graph-ics capabilities.

1.10.415 py-ply

Homepage:

• http://www.dabeaz.com/ply

Spack package:

• py-ply/package.py

Versions: 3.8

Build Dependencies python

Link Dependencies python

Description: PLY is nothing more than a straightforward lex/yacc implementation.

1.10.416 py-pmw

Homepage:

• https://pypi.python.org/pypi/Pmw

Spack package:

• py-pmw/package.py

Versions: 2.0.0

Build Dependencies python

1.10. Package List 235

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Description: Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using otherwidgets as component parts.

1.10.417 py-prettytable

Homepage:

• https://code.google.com/archive/p/prettytable/

Spack package:

• py-prettytable/package.py

Versions: 0.7.2

Build Dependencies python, py-setuptools

Link Dependencies python

Description: PrettyTable is a simple Python library designed to make it quick and easy to represent tabular data invisually appealing ASCII tables.

1.10.418 py-protobuf

Homepage:

• https://developers.google.com/protocol-buffers/

Spack package:

• py-protobuf/package.py

Versions: 3.0.0b2, 2.6.1, 2.5.0, 2.4.1, 2.3.0

Build Dependencies python, py-setuptools

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Description: Protocol buffers are Google’s language-neutral, platform-neutral, extensible mechanism for serializingstructured data - think XML, but smaller, faster, and simpler. You define how you want your data to be structuredonce, then you can use special generated source code to easily write and read your structured data to and froma variety of data streams and using a variety of languages.

1.10.419 py-py2cairo

Homepage:

• https://pypi.python.org/pypi/pycairo

Spack package:

• py-py2cairo/package.py

Versions: 1.10.0

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Build Dependencies python, cairo, pixman

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Description: bindings for the Cairo for Python 2, to be used in Python.

1.10.420 py-py2neo

Homepage:

• http://www.example.com

Spack package:

• py-py2neo/package.py

Versions: 2.0.8, 2.0.7, 2.0.6, 2.0.5, 2.0.4

Build Dependencies python, py-setuptools

Link Dependencies python

Description: FIXME: put a proper description of your package here.

1.10.421 py-pychecker

Homepage:

• http://pychecker.sourceforge.net/

Spack package:

• py-pychecker/package.py

Versions: 0.8.19

Build Dependencies python

Link Dependencies python

Description:

1.10.422 py-pycparser

Homepage:

• https://github.com/eliben/pycparser

Spack package:

• py-pycparser/package.py

Versions: 2.13

Build Dependencies python, py-setuptools

Link Dependencies python

1.10. Package List 237

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Description: A complete parser of the C language, written in pure python.

1.10.423 py-pydatalog

Homepage:

• https://pypi.python.org/pypi/pyDatalog/

Spack package:

• py-pydatalog/package.py

Versions: 0.17.1

Build Dependencies python

Link Dependencies python

Description: pyDatalog adds logic programming to Python.

1.10.424 py-pyelftools

Homepage:

• https://pypi.python.org/pypi/pyelftools

Spack package:

• py-pyelftools/package.py

Versions: 0.23

Build Dependencies python

Link Dependencies python

Description: A pure-Python library for parsing and analyzing ELF files and DWARF debugging information

1.10.425 py-pygments

Homepage:

• https://pypi.python.org/pypi/pygments

Spack package:

• py-pygments/package.py

Versions: 2.1.3, 2.0.2, 2.0.1

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Pygments is a syntax highlighting package written in Python.

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1.10.426 py-pygobject

Homepage:

• https://pypi.python.org/pypi/pygobject

Spack package:

• py-pygobject/package.py

Versions: 2.28.3

Build Dependencies python, libffi, py-py2cairo, glib, gobject-introspection

Link Dependencies python, libffi, py-py2cairo, glib, gobject-introspection

Description: bindings for the GLib, and GObject, to be used in Python.

1.10.427 py-pygtk

Homepage:

• http://www.pygtk.org/

Spack package:

• py-pygtk/package.py

Versions: 2.24.0

Build Dependencies glib, py-pygobject, python, cairo, py-py2cairo, gtkplus, libffi

Link Dependencies glib, py-pygobject, python, cairo, py-py2cairo, gtkplus, libffi

Description: bindings for the Gtk in Python

1.10.428 py-pylint

Homepage:

• https://pypi.python.org/pypi/pylint

Spack package:

• py-pylint/package.py

Versions: 1.4.3, 1.4.1

Build Dependencies python, py-nose, py-setuptools

Link Dependencies python

Description: array processing for numbers, strings, records, and objects.

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1.10.429 py-pypar

Homepage:

• http://code.google.com/p/pypar/

Spack package:

• py-pypar/package.py

Versions: 2.1.5_108

Build Dependencies python, mpi

Link Dependencies python, mpi

Description: Pypar is an efficient but easy-to-use module that allows programs written in Python to run in parallel onmultiple processors and communicate using MPI.

1.10.430 py-pyparsing

Homepage:

• https://pypi.python.org/pypi/pyparsing

Spack package:

• py-pyparsing/package.py

Versions: 2.0.3

Build Dependencies python

Link Dependencies python

Description: A Python Parsing Module.

1.10.431 py-pyqt

Homepage:

• http://www.riverbankcomputing.com/software/pyqt/intro

Spack package:

• py-pyqt/package.py

Versions: 4.11.3

Build Dependencies python, py-sip, qt

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Run Dependencies py-sip

Description: PyQt is a set of Python v2 and v3 bindings for Digia’s Qt application framework and runs on all plat-forms supported by Qt including Windows, MacOS/X and Linux.

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1.10.432 py-pyside

Homepage:

• https://pypi.python.org/pypi/pyside

Spack package:

• py-pyside/package.py

Versions: 1.2.4, 1.2.2

Build Dependencies cmake, qt, python, libxml2, py-setuptools, libxslt

Link Dependencies python, libxml2, qt, libxslt

Description: Python bindings for Qt.

1.10.433 py-pytables

Homepage:

• http://www.pytables.org/

Spack package:

• py-pytables/package.py

Versions: 3.2.2

Build Dependencies py-numexpr, hdf5, python, py-numpy, py-cython, py-setuptools

Link Dependencies python, hdf5

Run Dependencies py-cython, py-numexpr, py-numpy

Description: PyTables is a package for managing hierarchical datasets and designed to efficiently and easily copewith extremely large amounts of data.

1.10.434 py-python-daemon

Homepage:

• https://pypi.python.org/pypi/python-daemon/

Spack package:

• py-python-daemon/package.py

Versions: 2.0.5

Build Dependencies python, py-lockfile, py-setuptools

Link Dependencies python

Run Dependencies py-lockfile

1.10. Package List 241

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Description: Library to implement a well-behaved Unix daemon process. This library implements the well-behaveddaemon specification of PEP Standard daemon process. A well-behaved Unix daemon process is tricky to getright, but the required steps are much the same for every daemon program. A DaemonContext instance holdsthe behaviour and configured process environment for the program; use the instance as a context manager toenter a daemon state.

1.10.435 py-pytz

Homepage:

• https://pypi.python.org/pypi/pytz

Spack package:

• py-pytz/package.py

Versions: 2016.6.1, 2016.3, 2015.4, 2014.10

Build Dependencies python, py-setuptools

Link Dependencies python

Description: World timezone definitions, modern and historical.

1.10.436 py-pyyaml

Homepage:

• http://pyyaml.org/wiki/PyYAML

Spack package:

• py-pyyaml/package.py

Versions: 3.11

Build Dependencies python

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Description: PyYAML is a YAML parser and emitter for Python.

1.10.437 py-restview

Homepage:

• https://mg.pov.lt/restview/

Spack package:

• py-restview/package.py

Versions: 2.6.1

Build Dependencies python, py-docutils, py-pygments

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Run Dependencies py-docutils, py-pygments

Description: A viewer for ReStructuredText documents that renders them on the fly.

1.10.438 py-rpy2

Homepage:

• https://pypi.python.org/pypi/rpy2

Spack package:

• py-rpy2/package.py

Versions: 2.5.6, 2.5.4

Build Dependencies python, R, py-setuptools

Link Dependencies python, R

Description: rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposedhigh-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.

1.10.439 py-scientificpython

Homepage:

• https://sourcesup.renater.fr/projects/scientific-py/

Spack package:

• py-scientificpython/package.py

Versions: 2.8.1

Build Dependencies python

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Description: ScientificPython is a collection of Python modules for scientific computing. It contains support forgeometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.

1.10.440 py-scikit-image

Homepage:

• http://scikit-image.org/

Spack package:

• py-scikit-image/package.py

Versions: 0.12.3

Build Dependencies py-scipy, pil, python, py-six, py-dask, py-networkx, py-setuptools, py-matplotlib

1.10. Package List 243

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Link Dependencies python

Run Dependencies py-scipy, pil, py-six, py-dask, py-networkx, py-matplotlib

Description: Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipula-tion, object detection, etc.

1.10.441 py-scikit-learn

Homepage:

• https://pypi.python.org/pypi/scikit-learn

Spack package:

• py-scikit-learn/package.py

Versions: 0.17.1, 0.16.1, 0.15.2

Build Dependencies python, py-scipy, py-setuptools, py-numpy

Link Dependencies python

Run Dependencies py-scipy, py-numpy

Description:

1.10.442 py-scipy

Homepage:

• http://www.scipy.org/

Spack package:

• py-scipy/package.py

Versions: 0.17.0, 0.15.1, 0.15.0

Build Dependencies python, py-nose, py-numpy

Link Dependencies python

Run Dependencies py-numpy

Description: Scientific Library for Python.

1.10.443 py-setuptools

Homepage:

• https://pypi.python.org/pypi/setuptools

Spack package:

• py-setuptools/package.py

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Versions: 25.2.0, 20.7.0, 20.6.7, 20.5, 19.2, 18.1, 16.0, 11.3.1

Build Dependencies python

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Description: A Python utility that aids in the process of downloading, building, upgrading, installing, and uninstallingPython packages.

1.10.444 py-shiboken

Homepage:

• https://shiboken.readthedocs.org/

Spack package:

• py-shiboken/package.py

Versions: 1.2.2

Build Dependencies python, libxml2, cmake, qt, py-setuptools

Link Dependencies python, libxml2, qt

Description: Shiboken generates bindings for C++ libraries using CPython.

1.10.445 py-sip

Homepage:

• http://www.riverbankcomputing.com/software/sip/intro

Spack package:

• py-sip/package.py

Versions: 4.16.7, 4.16.5

Build Dependencies python

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Description: SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.

1.10.446 py-six

Homepage:

• https://pypi.python.org/pypi/six

Spack package:

• py-six/package.py

Versions: 1.10.0, 1.9.0

1.10. Package List 245

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Build Dependencies python, py-setuptools

Link Dependencies python

Description: Python 2 and 3 compatibility utilities.

1.10.447 py-sncosmo

Homepage:

• http://sncosmo.readthedocs.io/

Spack package:

• py-sncosmo/package.py

Versions: 1.2.0

Build Dependencies py-scipy, py-emcee, python, py-nestle, py-numpy, py-astropy, py-iminuit, py-matplotlib

Link Dependencies python

Run Dependencies py-scipy, py-emcee, py-nestle, py-numpy, py-astropy, py-iminuit, py-matplotlib

Description: SNCosmo is a Python library for high-level supernova cosmology analysis.

1.10.448 py-snowballstemmer

Homepage:

• https://pypi.python.org/pypi/snowballstemmer

Spack package:

• py-snowballstemmer/package.py

Versions: 1.2.1

Build Dependencies python

Link Dependencies python

Description: This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowballalgorithms.

1.10.449 py-sphinx

Homepage:

• http://sphinx-doc.org

Spack package:

• py-sphinx/package.py

Versions: 1.4.5, 1.3.1

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Build Dependencies py-pygments, python, py-setuptools, py-alabaster, py-sphinx-rtd-theme, py-six, py-babel, py-snowballstemmer, py-docutils, py-jinja2, py-imagesize

Link Dependencies python

Run Dependencies py-babel, py-setuptools, py-alabaster, py-sphinx-rtd-theme, py-six, py-pygments, py-snowballstemmer, py-docutils, py-jinja2, py-imagesize

Description: Sphinx Documentation Generator.

1.10.450 py-sphinx-rtd-theme

Homepage:

• https://pypi.python.org/pypi/sphinx_rtd_theme

Spack package:

• py-sphinx-rtd-theme/package.py

Versions: 0.1.10a0

Build Dependencies python, py-setuptools

Link Dependencies python

Description: ReadTheDocs.org theme for Sphinx.

1.10.451 py-SQLAlchemy

Homepage:

• http://www.sqlalchemy.org/

Spack package:

• py-SQLAlchemy/package.py

Versions: 1.0.12

Build Dependencies python

Link Dependencies python

Description: The Python SQL Toolkit and Object Relational Mapper

1.10.452 py-storm

Homepage:

• https://storm.canonical.com/

Spack package:

• py-storm/package.py

Versions: 0.20

1.10. Package List 247

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Build Dependencies python, py-setuptools

Link Dependencies python

Description: Storm is an object-relational mapper (ORM) for Python

1.10.453 py-sympy

Homepage:

• https://pypi.python.org/pypi/sympy

Spack package:

• py-sympy/package.py

Versions: 1.0, 0.7.6

Build Dependencies python, py-mpmath

Link Dependencies python, py-mpmath

Description: SymPy is a Python library for symbolic mathematics.

1.10.454 py-tappy

Homepage:

• https://github.com/mblayman/tappy

Spack package:

• py-tappy/package.py

Versions: 1.6

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Python TAP interface module for unit tests

1.10.455 py-tuiview

Homepage:

• https://bitbucket.org/chchrsc/tuiview

Spack package:

• py-tuiview/package.py

Versions: 1.1.7

Build Dependencies python, py-pyqt, gdal, py-numpy

Link Dependencies python, gdal

248 Chapter 1. Table of Contents

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Description: TuiView is a lightweight raster GIS with powerful raster attribute table manipulation abilities.

1.10.456 py-twisted

Homepage:

• https://twistedmatrix.com/

Spack package:

• py-twisted/package.py

Versions: 15.4.0, 15.3.0

Build Dependencies python, py-setuptools

Link Dependencies python

Description: An asynchronous networking framework written in Python

1.10.457 py-unittest2

Homepage:

• https://pypi.python.org/pypi/unittest2

Spack package:

• py-unittest2/package.py

Versions: 1.1.0

Build Dependencies python, py-setuptools

Link Dependencies python

Description: unittest2 is a backport of the new features added to the unittest testing framework in Python 2.7 andonwards.

1.10.458 py-unittest2py3k

Homepage:

• https://pypi.python.org/pypi/unittest2py3k

Spack package:

• py-unittest2py3k/package.py

Versions: 0.5.1

Build Dependencies python, py-setuptools

Link Dependencies python

1.10. Package List 249

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Description: unittest2 is a backport of the new features added to the unittest testing framework in Python 2.7 and 3.2.This is a Python 3 compatible version of unittest2.

1.10.459 py-urwid

Homepage:

• http://urwid.org/

Spack package:

• py-urwid/package.py

Versions: 1.3.0

Build Dependencies python, py-setuptools

Link Dependencies python

Description: A full-featured console UI library

1.10.460 py-virtualenv

Homepage:

• http://virtualenv.readthedocs.org/projects/virtualenv/

Spack package:

• py-virtualenv/package.py

Versions: 15.0.1, 13.0.1, 1.11.6

Build Dependencies python, py-setuptools

Link Dependencies python

Description: virtualenv is a tool to create isolated Python environments.

1.10.461 py-wcsaxes

Homepage:

• http://wcsaxes.readthedocs.io/en/latest/index.html

Spack package:

• py-wcsaxes/package.py

Versions: 0.8

Build Dependencies python, py-astropy, py-numpy, py-matplotlib

Link Dependencies python

Run Dependencies py-astropy, py-numpy, py-matplotlib

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Description: WCSAxes is a framework for making plots of Astronomical data in Matplotlib.

1.10.462 py-wheel

Homepage:

• https://pypi.python.org/pypi/wheel

Spack package:

• py-wheel/package.py

Versions: 0.26.0

Build Dependencies python, py-setuptools

Link Dependencies python

Description: A built-package format for Python.

1.10.463 py-xlrd

Homepage:

• http://www.python-excel.org/

Spack package:

• py-xlrd/package.py

Versions: 0.9.4

Build Dependencies python

Link Dependencies python

Description: Library for developers to extract data from Microsoft Excel (tm) spreadsheet files

1.10.464 py-yapf

Homepage:

• https://github.com/google/yapf

Spack package:

• py-yapf/package.py

Versions: 0.2.1

Build Dependencies python, py-setuptools

Link Dependencies python

Description: Yet Another Python Formatter

1.10. Package List 251

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1.10.465 python

Homepage:

• http://www.python.org

Spack package:

• python/package.py

Versions: 3.5.2, 3.5.1, 3.5.0, 3.4.3, 3.3.6, 3.2.6, 3.1.5, 2.7.12, 2.7.11, 2.7.10, 2.7.9, 2.7.8

Build Dependencies bzip2, ncurses, zlib, openssl, sqlite, tcl, tk, readline

Link Dependencies bzip2, ncurses, zlib, openssl, sqlite, tcl, tk, readline

Description: The Python programming language.

1.10.466 qhull

Homepage:

• http://www.qhull.org

Spack package:

• qhull/package.py

Versions: 2015.2, 2012.1

Build Dependencies cmake

Description: Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection abouta point, furt hest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Ithandles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximationsto the convex hull.

1.10.467 qrupdate

Homepage:

• http://sourceforge.net/projects/qrupdate/

Spack package:

• qrupdate/package.py

Versions: 1.1.2

Build Dependencies lapack, blas

Link Dependencies lapack, blas

Description: qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.

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1.10.468 qt

Homepage:

• http://qt.io

Spack package:

• qt/package.py

Versions: 5.7.0, 5.5.1, 5.4.2, 5.4.0, 5.3.2, 5.2.1, 4.8.6, 3.3.8b

Build Dependencies zlib, libxml2, dbus, libtiff , jpeg, gtkplus, libxcb, libpng, libmng, mesa

Link Dependencies zlib, libxml2, dbus, libtiff , jpeg, gtkplus, libxcb, libpng, libmng, mesa

Description: Qt is a comprehensive cross-platform C++ application framework.

1.10.469 qt-creator

Homepage:

• https://www.qt.io/ide/

Spack package:

• qt-creator/package.py

Versions: 4.1.0

Build Dependencies qt

Link Dependencies qt

Description: The Qt Creator IDE.

1.10.470 qthreads

Homepage:

• http://www.cs.sandia.gov/qthreads/

Spack package:

• qthreads/package.py

Versions: 1.10

Build Dependencies hwloc, autoconf

Link Dependencies hwloc

Description: The qthreads API is designed to make using large numbers of threads convenient and easy, and to allowportable access to threading constructs used in massively parallel shared memory environments. The API mapswell to both MTA-style threading and PIM-style threading, and we provide an implementation of this interfacein both a standard SMP context as well as the SST context. The qthreads API provides access to full/empty-bit(FEB) semantics, where every word of memory can be marked either full or empty, and a thread can wait forany word to attain either state.

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1.10.471 R

Homepage:

• https://www.r-project.org

Spack package:

• R/package.py

Versions: 3.3.1, 3.3.0, 3.2.3, 3.2.2, 3.2.1, 3.2.0, 3.1.3, 3.1.2

Build Dependencies glib, pcre, bzip2, zlib, pango, jdk, lapack, cairo, blas, libtiff , freetype, jpeg, ncurses, tcl, tk,readline, curl, icu

Link Dependencies glib, pcre, bzip2, zlib, pango, jdk, lapack, cairo, blas, libtiff , freetype, jpeg, ncurses, tcl, tk,readline, curl, icu

Description: R is ‘GNU S’, a freely available language and environment for statistical computing and graphics whichprovides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests,time series analysis, classification, clustering, etc. Please consult the R project homepage for further informa-tion.

1.10.472 r-abind

Homepage:

• https://cran.r-project.org/

Spack package:

• r-abind/package.py

Versions: 1.4-3

Build Dependencies R

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Description: Combine multidimensional arrays into a single array. This is a generalization of ‘cbind’ and ‘rbind’.Works with vectors, matrices, and higher-dimensional arrays. Also provides functions ‘adrop’, ‘asub’, and ‘afill’for manipulating, extracting and replacing data in arrays.

1.10.473 r-assertthat

Homepage:

• https://cran.r-project.org/web/packages/assertthat/index.html

Spack package:

• r-assertthat/package.py

Versions: 0.1

Build Dependencies R

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Description: assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that youcode should satisfy, while also producing friendly error messages so that your users know what they’ve donewrong.

1.10.474 r-base64enc

Homepage:

• http://www.rforge.net/base64enc

Spack package:

• r-base64enc/package.py

Versions: 0.1-3

Build Dependencies R

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Description: This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64package.

1.10.475 r-bh

Homepage:

• https://cran.r-project.org/web/packages/BH/index.html

Spack package:

• r-bh/package.py

Versions: 1.60.0-2

Build Dependencies R

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Description: Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided asC++ template code which is resolved entirely at compile-time without linking. This package aims to providethe most useful subset of Boost libraries for template use among CRAN package. By placing these libraries inthis package, we offer a more efficient distribution system for CRAN as replication of this code in the sources ofother packages is avoided. As of release 1.60.0-2, the following Boost libraries are included: ‘algorithm’ ‘any’‘bimap’ ‘bind’ ‘circular_buffer’ ‘concept’ ‘config’ ‘container’ ‘date’_’time’ ‘detail’ ‘dynamic_bitset’ ‘excep-tion’ ‘filesystem’ ‘flyweight’ ‘foreach’ ‘functional’ ‘fusion’ ‘geometry’ ‘graph’ ‘heap’ ‘icl’ ‘integer’ ‘interpro-cess’ ‘intrusive’ ‘io’ ‘iostreams’ ‘iterator’ ‘math’ ‘move’ ‘mpl’ ‘multiprcecision’ ‘numeric’ ‘pending’ ‘phoenix’‘preprocessor’ ‘random’ ‘range’ ‘smart_ptr’ ‘spirit’ ‘tuple’ ‘type_trains’ ‘typeof’ ‘unordered’ ‘utility’ ‘uuid’.

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1.10.476 r-BiocGenerics

Homepage:

• https://bioconductor.org/packages/BiocGenerics/

Spack package:

• r-BiocGenerics/package.py

Versions: bioc-3.3, bioc-3.2

Build Dependencies R

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Description: S4 generic functions needed by many Bioconductor packages.

1.10.477 r-boot

Homepage:

• https://cran.r-project.org/package=boot

Spack package:

• r-boot/package.py

Versions: 1.3-18

Build Dependencies R

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Description: Functions and datasets for bootstrapping from the book “Bootstrap Methods and Their Application” byA. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.

1.10.478 r-brew

Homepage:

• https://cran.r-project.org/package=brew

Spack package:

• r-brew/package.py

Versions: 1.0-6

Build Dependencies R

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Description: brew implements a templating framework for mixing text and R code for report generation. brew tem-plate syntax is similar to PHP, Ruby’s erb module, Java Server Pages, and Python’s psp module.

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1.10.479 r-car

Homepage:

• https://r-forge.r-project.org/projects/car/

Spack package:

• r-car/package.py

Versions: 2.1-2

Build Dependencies r-nnet, r-mass, R, r-pbkrtest, r-quantreg, r-mgcv

Link Dependencies R

Run Dependencies r-pbkrtest, r-mass, r-quantreg, r-mgcv, r-nnet

Description: Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression,Second Edition, Sage, 2011.

1.10.480 r-caret

Homepage:

• https://github.com/topepo/caret/

Spack package:

• r-caret/package.py

Versions: 6.0-70

Build Dependencies r-plyr, r-lattice, r-foreach, r-reshape2, r-car, R, r-nlme, r-ggplot2

Link Dependencies R

Run Dependencies r-plyr, r-lattice, r-foreach, r-reshape2, r-car, r-nlme, r-ggplot2

Description: Misc functions for training and plotting classification and regression models.

1.10.481 r-chron

Homepage:

• https://cran.r-project.org/package=chron

Spack package:

• r-chron/package.py

Versions: 2.3-47

Build Dependencies R

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Description: Chronological objects which can handle dates and times.

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1.10.482 r-class

Homepage:

• http://www.stats.ox.ac.uk/pub/MASS4/

Spack package:

• r-class/package.py

Versions: 7.3-14

Build Dependencies r-mass, R

Link Dependencies R

Run Dependencies r-mass

Description: Various functions for classification, including k-nearest neighbour, Learning Vector Quantization andSelf-Organizing Maps.

1.10.483 r-cluster

Homepage:

• https://cran.r-project.org/web/packages/cluster/index.html

Spack package:

• r-cluster/package.py

Versions: 2.0.4

Build Dependencies R

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Description: Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and MiaHubert, based on Kaufman and Rousseeuw (1990) “Finding Groups in Data”.

1.10.484 r-codetools

Homepage:

• https://cran.r-project.org/web/packages/codetools/index.html

Spack package:

• r-codetools/package.py

Versions: 0.2-14

Build Dependencies R

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Description: Code analysis tools for R.

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1.10.485 r-colorspace

Homepage:

• https://cran.r-project.org/web/packages/colorspace/index.html

Spack package:

• r-colorspace/package.py

Versions: 1.2-6

Build Dependencies R

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Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV,HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes basedon HCL colors are provided.

1.10.486 r-crayon

Homepage:

• https://github.com/gaborcsardi/crayon

Spack package:

• r-crayon/package.py

Versions: 1.3.2

Build Dependencies R

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Description: Colored terminal output on terminals that support ‘ANSI’ color and highlight codes. It also works in‘Emacs’ ‘ESS’. ‘ANSI’ color support is automatically detected. Colors and highlighting can be combined andnested. New styles can also be created easily. This package was inspired by the ‘chalk’ ‘JavaScript’ project.

1.10.487 r-cubature

Homepage:

• https://cran.r-project.org/package=cubature

Spack package:

• r-cubature/package.py

Versions: 1.1-2

Build Dependencies R

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Description: Adaptive multivariate integration over hypercubes

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1.10.488 r-curl

Homepage:

• https://github.com/jeroenooms/curl

Spack package:

• r-curl/package.py

Versions: 1.0, 0.9.7

Build Dependencies curl, R

Link Dependencies curl, R

Description: The curl() and curl_download() functions provide highly configurable drop-in replacements for baseurl() and download.file() with better performance, support for encryption (https, ftps), gzip compression, au-thentication, and other libcurl goodies. The core of the package implements a framework for performing fullycustomized requests where data can be processed either in memory, on disk, or streaming via the callback orconnection interfaces. Some knowledge of libcurl is recommended; for a more-user-friendly web client see the‘httr’ package which builds on this package with http specific tools and logic.

1.10.489 r-datatable

Homepage:

• https://github.com/Rdatatable/data.table/wiki

Spack package:

• r-datatable/package.py

Versions: 1.9.6

Build Dependencies R, r-chron

Link Dependencies R

Run Dependencies r-chron

Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete ofcolumns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexiblesyntax, for faster development.

1.10.490 r-dbi

Homepage:

• https://github.com/rstats-db/DBI

Spack package:

• r-dbi/package.py

Versions: 0.4-1

Build Dependencies R

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Description: A database interface definition for communication between R and relational database management sys-tems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

1.10.491 r-devtools

Homepage:

• https://github.com/hadley/devtools

Spack package:

• r-devtools/package.py

Versions: 1.11.1

Build Dependencies r-withr, r-rstudioapi, r-httr, r-whisker, r-git2r, r-jsonlite, R, r-digest, r-memoise

Link Dependencies R

Run Dependencies r-withr, r-rstudioapi, r-httr, r-whisker, r-git2r, r-jsonlite, r-digest, r-memoise

Description: Collection of package development tools.

1.10.492 r-diagrammer

Homepage:

• https://github.com/rich-iannone/DiagrammeR

Spack package:

• r-diagrammer/package.py

Versions: 0.8.4

Build Dependencies r-rstudioapi, r-influencer, r-igraph, R, r-htmlwidgets, r-stringr, r-visnetwork, r-scales

Link Dependencies R

Run Dependencies r-rstudioapi, r-influencer, r-igraph, r-htmlwidgets, r-stringr, r-visnetwork, r-scales

Description: Create graph diagrams and flowcharts using R.

1.10.493 r-dichromat

Homepage:

• https://cran.r-project.org/web/packages/dichromat/index.html

Spack package:

• r-dichromat/package.py

Versions: 2.0-0

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Build Dependencies R

Link Dependencies R

Description: Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.

1.10.494 r-digest

Homepage:

• http://dirk.eddelbuettel.com/code/digest.html

Spack package:

• r-digest/package.py

Versions: 0.6.9

Build Dependencies R

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Description: Implementation of a function ‘digest()’ for the creation of hash digests of arbitrary R objects (using themd5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R languageobjects, as well as a function ‘hmac()’ to create hash-based message authentication code. The md5 algorithm byRon Rivest is specified in RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described in ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5,sha-1, sha-256 and aes, this package uses small standalone implementations that were provided by ChristopheDevine. For crc32, code from the zlib library is used. For sha-512, an implementation by Aaron D. Gifford isused. For xxhash, the implementation by Yann Collet is used. For murmurhash, an implementation by ShaneDay is used. Please note that this package is not meant to be deployed for cryptographic purposes for whichmore comprehensive (and widely tested) libraries such as OpenSSL should be used.

1.10.495 r-doparallel

Homepage:

• https://cran.r-project.org/web/packages/doParallel/index.html

Spack package:

• r-doparallel/package.py

Versions: 1.0.10

Build Dependencies R, r-iterators, r-foreach

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Run Dependencies r-iterators, r-foreach

Description: Provides a parallel backend for the %dopar% function using the parallel package.

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1.10.496 r-dplyr

Homepage:

• https://github.com/hadley/dplyr

Spack package:

• r-dplyr/package.py

Versions: 0.5.0

Build Dependencies r-tibble, r-assertthat, r-lazyeval, r-R6, R, r-bh, r-dbi, r-rcpp, r-magrittr

Link Dependencies R

Run Dependencies r-tibble, r-dbi, r-assertthat, r-lazyeval, r-bh, r-R6, r-rcpp, r-magrittr

Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.

1.10.497 r-dt

Homepage:

• http://rstudio.github.io/DT

Spack package:

• r-dt/package.py

Versions: 0.1

Build Dependencies R, r-htmltools, r-htmlwidgets, r-magrittr

Link Dependencies R

Run Dependencies r-htmltools, r-htmlwidgets, r-magrittr

Description: Data objects in R can be rendered as HTML tables using the JavaScript library ‘DataTables’ (typicallyvia R Markdown or Shiny). The ‘DataTables’ library has been included in this R package. The package name‘DT’ is an abbreviation of ‘DataTables’.

1.10.498 r-dygraphs

Homepage:

• https://cran.r-project.org/web/packages/dygraphs/index.html

Spack package:

• r-dygraphs/package.py

Versions: 0.9

Build Dependencies r-zoo, R, r-magrittr, r-htmlwidgets, r-xts

Link Dependencies R

Run Dependencies r-zoo, r-xts, r-magrittr, r-htmlwidgets

1.10. Package List 263

Spack Documentation, Release 0.9

Description: An R interface to the ‘dygraphs’ JavaScript charting library (a copy of which is included in the package).Provides rich facilities for charting time-series data in R, including highly configurable series- and axis- displayand interactive features like zoom/pan and series/point highlighting.

1.10.499 r-e1071

Homepage:

• https://cran.r-project.org/package=e1071

Spack package:

• r-e1071/package.py

Versions: 1.6-7

Build Dependencies R, r-class

Link Dependencies R

Run Dependencies r-class

Description: Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector ma-chines, shortest path computation, bagged clustering, naive Bayes classifier, ...

1.10.500 r-filehash

Homepage:

• https://cran.r-project.org/

Spack package:

• r-filehash/package.py

Versions: 2.3

Build Dependencies R

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Description: Implements a simple key-value style database where character string keys are associated with datavalues that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data fromthe database. Utilities are provided that allow ‘filehash’ databases to be treated much like environments and listsare already used in R. These utilities are provided to encourage interactive and exploratory analysis on largedatasets. Three different file formats for representing the database are currently available and new formats caneasily be incorporated by third parties for use in the ‘filehash’ framework.

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1.10.501 r-foreach

Homepage:

• https://cran.r-project.org/web/packages/foreach/index.html

Spack package:

• r-foreach/package.py

Versions: 1.4.3

Build Dependencies R, r-codetools, r-iterators

Link Dependencies R

Run Dependencies r-codetools, r-iterators

Description: Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elementsin a collection, without the use of an explicit loop counter. This package in particular is intended to be usedfor its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function,but doesn’t require the evaluation of a function. Using foreach without side effects also facilitates executing theloop in parallel.

1.10.502 r-foreign

Homepage:

• https://cran.r-project.org/web/packages/foreign/index.html

Spack package:

• r-foreign/package.py

Versions: 0.8-66

Build Dependencies R

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Description: Functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS,Stata, Systat and Weka and for reading and writing some dBase files.

1.10.503 r-gdata

Homepage:

• https://cran.r-project.org/package=gdata

Spack package:

• r-gdata/package.py

Versions: 2.17.0

Build Dependencies R, r-gtools

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Run Dependencies r-gtools

1.10. Package List 265

Spack Documentation, Release 0.9

Description: Various R programming tools for data manipulation, including: - medical unit conversions (‘Con-vertMedUnits’, ‘MedUnits’), - combining objects (‘bindData’, ‘cbindX’, ‘combine’, ‘interleave’), - char-acter vector operations (‘centerText’, ‘startsWith’, ‘trim’), - factor manipulation (‘levels’, ‘reorder.factor’,‘mapLevels’), - obtaining information about R objects (‘object.size’, ‘elem’, ‘env’, ‘humanReadable’, ‘is.what’,‘ll’, ‘keep’, ‘ls.funs’, ‘Args’,’nPairs’, ‘nobs’), - manipulating MS- Excel formatted files (‘read.xls’, ‘installXL-SXsupport’, ‘sheetCount’, ‘xlsFormats’), - generating fixed-width format files (‘write.fwf’), - extricating com-ponents of date & time objects (‘getYear’, ‘getMonth’, ‘getDay’, ‘getHour’, ‘getMin’, ‘getSec’), - operationson columns of data frames (‘matchcols’, ‘rename.vars’), - matrix operations (‘unmatrix’, ‘upperTriangle’, ‘low-erTriangle’), - operations on vectors (‘case’, ‘unknownToNA’, ‘duplicated2’, ‘trimSum’), - operations on dataframes (‘frameApply’, ‘wideByFactor’), - value of last evaluated expression (‘ans’), and - wrapper for ‘sample’that ensures consistent behavior for both scalar and vector arguments (‘resample’).

1.10.504 r-geosphere

Homepage:

• https://cran.r-project.org/package=geosphere

Spack package:

• r-geosphere/package.py

Versions: 1.5-5

Build Dependencies r-sp, R

Link Dependencies R

Run Dependencies r-sp

Description: Spherical trigonometry for geographic applications. That is, compute distances and related measuresfor angular (longitude/latitude) locations.

1.10.505 r-ggmap

Homepage:

• https://github.com/dkahle/ggmap

Spack package:

• r-ggmap/package.py

Versions: 2.6.1

Build Dependencies r-geosphere, r-mapproj, r-ggplot2, r-png, r-proto, r-rjson, r-plyr, r-reshape2, R, r-rgooglemaps,r-digest, r-jpeg, r-scales

Link Dependencies R

Run Dependencies r-geosphere, r-mapproj, r-ggplot2, r-png, r-proto, r-rjson, r-plyr, r-reshape2, r-jpeg, r-rgooglemaps, r-digest, r-scales

Description: A collection of functions to visualize spatial data and models on top of static maps from various onlinesources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions forgeolocation and routing.

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1.10.506 r-ggplot2

Homepage:

• http://ggplot2.org/

Spack package:

• r-ggplot2/package.py

Versions: 2.1.0

Build Dependencies r-mass, r-plyr, r-gtable, r-reshape2, R, r-digest, r-scales

Link Dependencies R

Run Dependencies r-mass, r-plyr, r-gtable, r-reshape2, r-digest, r-scales

Description: An implementation of the grammar of graphics in R. It combines the advantages of both base andlattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plotstep by step from multiple data sources. It also implements a sophisticated multidimensional conditioningsystem and a consistent interface to map data to aesthetic attributes. See http://ggplot2.org for more information,documentation and examples.

1.10.507 r-ggvis

Homepage:

• http://ggvis.rstudio.com/

Spack package:

• r-ggvis/package.py

Versions: 0.4.2

Build Dependencies r-jsonlite, r-htmltools, r-shiny, r-assertthat, r-lazyeval, R, r-dplyr, r-magrittr

Link Dependencies R

Run Dependencies r-jsonlite, r-htmltools, r-shiny, r-assertthat, r-lazyeval, r-dplyr, r-magrittr

Description: An implementation of an interactive grammar of graphics, taking the best parts of ‘ggplot2’, combiningthem with the reactive framework from ‘shiny’ and web graphics from ‘vega’.

1.10.508 r-git2r

Homepage:

• https://github.com/ropensci/git2r

Spack package:

• r-git2r/package.py

Versions: 0.15.0

Build Dependencies R, zlib, openssl

Link Dependencies R, zlib, openssl

1.10. Package List 267

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Description: Interface to the ‘libgit2’ library, which is a pure C implementation of the ‘Git’ core methods. Providesaccess to ‘Git’ repositories to extract data and running some basic ‘Git’ commands.

1.10.509 r-glmnet

Homepage:

• http://www.jstatsoft.org/v33/i01/

Spack package:

• r-glmnet/package.py

Versions: 2.0-5

Build Dependencies r-matrix, R, r-foreach

Link Dependencies R

Run Dependencies r-matrix, r-foreach

Description: Extremely efficient procedures for fitting the entire lasso or elastic- net regularization path for linearregression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent ad-ditions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinatedescent in a path- wise fashion, as described in the paper linked to via the URL below.

1.10.510 r-googlevis

Homepage:

• https://github.com/mages/googleVis#googlevis

Spack package:

• r-googlevis/package.py

Versions: 0.6.0

Build Dependencies R, r-jsonlite

Link Dependencies R

Run Dependencies r-jsonlite

Description: R interface to Google Charts API, allowing users to create interactive charts based on data frames.Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection isrequired and for some charts a Flash player. The data remains local and is not uploaded to Google.

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1.10.511 r-gridbase

Homepage:

• https://cran.r-project.org/web/packages/gridBase/index.html

Spack package:

• r-gridbase/package.py

Versions: 0.4-7

Build Dependencies R

Link Dependencies R

Description: Integration of base and grid graphics.

1.10.512 r-gridextra

Homepage:

• https://github.com/baptiste/gridextra

Spack package:

• r-gridextra/package.py

Versions: 2.2.1

Build Dependencies r-gtable, R

Link Dependencies R

Run Dependencies r-gtable

Description: Provides a number of user-level functions to work with “grid” graphics, notably to arrange multiplegrid-based plots on a page, and draw tables.

1.10.513 r-gtable

Homepage:

• https://cran.r-project.org/web/packages/gtable/index.html

Spack package:

• r-gtable/package.py

Versions: 0.2.0

Build Dependencies R

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Description: Tools to make it easier to work with “tables” of ‘grobs’.

1.10. Package List 269

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1.10.514 r-gtools

Homepage:

• https://cran.r-project.org/package=gtools

Spack package:

• r-gtools/package.py

Versions: 3.5.0

Build Dependencies R

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Description: Functions to assist in R programming, including: - assist in developing, updating, and maintainingR and R packages (‘ask’, ‘checkRVersion’, ‘getDependencies’, ‘keywords’, ‘scat’), - calculate the logit andinverse logit transformations (‘logit’, ‘inv.logit’), - test if a value is missing, empty or contains only NA andNULL values (‘invalid’), - manipulate R’s .Last function (‘addLast’), - define macros (‘defmacro’), - detect oddand even integers (‘odd’, ‘even’), - convert strings containing non-ASCII characters (like single quotes) to plainASCII (‘ASCIIfy’), - perform a binary search (‘binsearch’), - sort strings containing both numeric and charactercomponents (‘mixedsort’), - create a factor variable from the quantiles of a continuous variable (‘quantcut’),- enumerate permutations and combinations (‘combinations’, ‘permutation’), - calculate and convert betweenfold-change and log- ratio (‘foldchange’, ‘logratio2foldchange’, ‘foldchange2logratio’), - calculate probabilitiesand generate random numbers from Dirichlet distributions (‘rdirichlet’, ‘ddirichlet’), - apply a function overadjacent subsets of a vector (‘running’), - modify the TCP_NODELAY (‘de-Nagle’) flag for socket objects, -efficient ‘rbind’ of data frames, even if the column names don’t match (‘smartbind’), - generate significancestars from p-values (‘stars.pval’), - convert characters to/from ASCII codes.

1.10.515 r-htmltools

Homepage:

• https://github.com/rstudio/htmltools

Spack package:

• r-htmltools/package.py

Versions: 0.3.5

Build Dependencies R, r-digest, r-rcpp

Link Dependencies R

Run Dependencies r-digest, r-rcpp

Description: Tools for HTML generation and output.

1.10.516 r-htmlwidgets

Homepage:

• https://github.com/ramnathv/htmlwidgets

Spack package:

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• r-htmlwidgets/package.py

Versions: 0.6

Build Dependencies r-yaml, R, r-htmltools, r-jsonlite

Link Dependencies R

Run Dependencies r-yaml, r-jsonlite, r-htmltools

Description: A framework for creating HTML widgets that render in various contexts including the R console, ‘RMarkdown’ documents, and ‘Shiny’ web applications.

1.10.517 r-httpuv

Homepage:

• https://github.com/rstudio/httpuv

Spack package:

• r-httpuv/package.py

Versions: 1.3.3

Build Dependencies R, r-rcpp

Link Dependencies R

Run Dependencies r-rcpp

Description: Provides low-level socket and protocol support for handling HTTP and WebSocket requests directlyfrom within R. It is primarily intended as a building block for other packages, rather than making it particularlyeasy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parserC libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http- parser licenseinformation.)

1.10.518 r-httr

Homepage:

• https://github.com/hadley/httr

Spack package:

• r-httr/package.py

Versions: 1.1.0

Build Dependencies r-R6, r-jsonlite, r-mime, r-openssl, R, r-curl

Link Dependencies R

Run Dependencies r-curl, r-R6, r-mime, r-jsonlite, r-openssl

Description: Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configurationfunctions make it easy to control additional request components (authenticate(), add_headers() and so on).

1.10. Package List 271

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1.10.519 r-igraph

Homepage:

• http://igraph.org/

Spack package:

• r-igraph/package.py

Versions: 1.0.1

Build Dependencies r-matrix, libxml2, r-irlba, r-nmf , R, gmp, r-magrittr

Link Dependencies libxml2, R, gmp

Run Dependencies r-matrix, r-irlba, r-nmf , r-magrittr

Description: Routines for simple graphs and network analysis. It can handle large graphs very well and providesfunctions for generating random and regular graphs, graph visualization, centrality methods and much more.

1.10.520 r-influencer

Homepage:

• https://github.com/rcc-uchicago/influenceR

Spack package:

• r-influencer/package.py

Versions: 0.1.0

Build Dependencies r-matrix, R, r-igraph

Link Dependencies R

Run Dependencies r-matrix, r-igraph

Description: Provides functionality to compute various node centrality measures on networks. Included are functionsto compute betweenness centrality (by utilizing Madduri and Bader’s SNAP library), implementations of Burt’sconstraint and effective network size (ENS) metrics, Borgatti’s algorithm to identify key players, and Valente’sbridging metric. On Unix systems, the betweenness, Key Players, and bridging implementations are parallelizedwith OpenMP, which may run faster on systems which have OpenMP configured.

1.10.521 r-inline

Homepage:

• https://cran.r-project.org/web/packages/inline/index.html

Spack package:

• r-inline/package.py

Versions: 0.3.14

Build Dependencies R

Link Dependencies R

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Description: Functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran codesupporting .C and .Call calling conventions.

1.10.522 r-irlba

Homepage:

• https://cran.r-project.org/web/packages/irlba/index.html

Spack package:

• r-irlba/package.py

Versions: 2.0.0

Build Dependencies r-matrix, R

Link Dependencies R

Run Dependencies r-matrix

Description: Fast and memory efficient methods for truncated singular and eigenvalue decompositions and principalcomponent analysis of large sparse or dense matrices.

1.10.523 r-iterators

Homepage:

• https://cran.r-project.org/web/packages/iterators/index.html

Spack package:

• r-iterators/package.py

Versions: 1.0.8

Build Dependencies R

Link Dependencies R

Description: Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, orother collection of data.

1.10.524 r-jpeg

Homepage:

• http://www.rforge.net/jpeg/

Spack package:

• r-jpeg/package.py

Versions: 0.1-8

Build Dependencies R, jpeg

1.10. Package List 273

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Link Dependencies R, jpeg

Description: This package provides an easy and simple way to read, write and display bitmap images stored in theJPEG format. It can read and write both files and in-memory raw vectors.

1.10.525 r-jsonlite

Homepage:

• https://github.com/jeroenooms/jsonlite

Spack package:

• r-jsonlite/package.py

Versions: 1.0, 0.9.21

Build Dependencies R

Link Dependencies R

Description: A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of‘RJSONIO’, but has been completely rewritten in recent versions. The package offers flexible, robust, highperformance tools for working with JSON in R and is particularly powerful for building pipelines and inter-acting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014).In addition to converting JSON data from/to R objects, ‘jsonlite’ contains functions to stream, validate, andprettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decodedconsistently for use with dynamic data in systems and applications.

1.10.526 r-labeling

Homepage:

• https://cran.r-project.org/web/packages/labeling/index.html

Spack package:

• r-labeling/package.py

Versions: 0.3

Build Dependencies R

Link Dependencies R

Description: Provides a range of axis labeling algorithms.

1.10.527 r-lattice

Homepage:

• http://lattice.r-forge.r-project.org/

Spack package:

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• r-lattice/package.py

Versions: 0.20-33

Build Dependencies R

Link Dependencies R

Description: A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an em-phasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handlemost nonstandard requirements. See ?Lattice for an introduction.

1.10.528 r-lazyeval

Homepage:

• https://cran.r-project.org/web/packages/lazyeval/index.html

Spack package:

• r-lazyeval/package.py

Versions: 0.2.0

Build Dependencies R

Link Dependencies R

Description: An alternative approach to non-standard evaluation using formulas. Provides a full implementation ofLISP style ‘quasiquotation’, making it easier to generate code with other code.

1.10.529 r-leaflet

Homepage:

• http://rstudio.github.io/leaflet/

Spack package:

• r-leaflet/package.py

Versions: 1.0.1

Build Dependencies r-rcolorbrewer, r-png, r-htmltools, r-markdown, r-sp, R, r-raster, r-base64enc, r-htmlwidgets,r-magrittr, r-scales

Link Dependencies R

Run Dependencies r-rcolorbrewer, r-png, r-htmltools, r-markdown, r-sp, r-raster, r-base64enc, r-htmlwidgets, r-magrittr, r-scales

Description: Create and customize interactive maps using the ‘Leaflet’ JavaScript library and the ‘htmlwidgets’ pack-age. These maps can be used directly from the R console, from ‘RStudio’, in Shiny apps and R Markdowndocuments.

1.10. Package List 275

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1.10.530 r-lme4

Homepage:

• https://github.com/lme4/lme4/

Spack package:

• r-lme4/package.py

Versions: 1.1-12

Build Dependencies r-matrix, r-minqa, r-lattice, r-rcppeigen, r-mass, r-nloptr, R, r-nlme, r-rcpp

Link Dependencies R

Run Dependencies r-matrix, r-minqa, r-lattice, r-rcppeigen, r-mass, r-nloptr, r-nlme, r-rcpp

Description: Fit linear and generalized linear mixed-effects models. The models and their components are repre-sented using S4 classes and methods. The core computational algorithms are implemented using the ‘Eigen’C++ library for numerical linear algebra and ‘RcppEigen’ “glue”.

1.10.531 r-lmtest

Homepage:

• https://cran.r-project.org/package=lmtest

Spack package:

• r-lmtest/package.py

Versions: 0.9-34

Build Dependencies r-zoo, R

Link Dependencies R

Run Dependencies r-zoo

Description: A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Fur-thermore, some generic tools for inference in parametric models are provided.

1.10.532 r-lubridate

Homepage:

• https://cran.r-project.org/web/packages/lubridate/index.html

Spack package:

• r-lubridate/package.py

Versions: 1.5.6

Build Dependencies R, r-stringr

Link Dependencies R

Run Dependencies r-stringr

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Description: Functions to work with date-times and timespans: fast and user friendly parsing of date-time data,extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), alge-braic manipulation on date-time and timespan objects. The ‘lubridate’ package has a consistent and memorablesyntax that makes working with dates easy and fun.

1.10.533 r-magic

Homepage:

• https://cran.r-project.org/

Spack package:

• r-magic/package.py

Versions: 1.5-6

Build Dependencies r-abind, R

Link Dependencies R

Run Dependencies r-abind

Description: A collection of efficient, vectorized algorithms for the creation and investigation of magic squares andhypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.

1.10.534 r-magrittr

Homepage:

• https://cran.r-project.org/web/packages/magrittr/index.html

Spack package:

• r-magrittr/package.py

Versions: 1.5

Build Dependencies R

Link Dependencies R

Description: Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operatorwill forward a value, or the result of an expression, into the next function call/expression. There is flexiblesupport for the type of right-hand side expressions. For more information, see package vignette.

1.10.535 r-mapproj

Homepage:

• https://cran.r-project.org/package=mapproj

Spack package:

• r-mapproj/package.py

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Spack Documentation, Release 0.9

Versions: 1.2-4

Build Dependencies r-maps, R

Link Dependencies R

Run Dependencies r-maps

Description: Converts latitude/longitude into projected coordinates.

1.10.536 r-maps

Homepage:

• https://cran.r-project.org/

Spack package:

• r-maps/package.py

Versions: 3.1.1

Build Dependencies R

Link Dependencies R

Description: Display of maps. Projection code and larger maps are in separate packages (‘mapproj’ and ‘mapdata’).

1.10.537 r-maptools

Homepage:

• http://r-forge.r-project.org/projects/maptools/

Spack package:

• r-maptools/package.py

Versions: 0.8-39

Build Dependencies r-sp, R, r-foreign, r-lattice

Link Dependencies R

Run Dependencies r-sp, r-foreign, r-lattice

Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code usedfrom shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrap-pers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap,WinBUGS, Mondrian, and others.

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1.10.538 r-markdown

Homepage:

• https://github.com/rstudio/markdown

Spack package:

• r-markdown/package.py

Versions: 0.7.7

Build Dependencies R, r-mime

Link Dependencies R

Run Dependencies r-mime

Description: Provides R bindings to the ‘Sundown’ ‘Markdown’ rendering library(https://github.com/vmg/sundown). ‘Markdown’ is a plain-text formatting syntax that can be convertedto ‘XHTML’ or other formats. See http://en.wikipedia.org/wiki/Markdown for more information about‘Markdown’.

1.10.539 r-mass

Homepage:

• http://www.stats.ox.ac.uk/pub/MASS4/

Spack package:

• r-mass/package.py

Versions: 7.3-45

Build Dependencies R

Link Dependencies R

Description: Functions and datasets to support Venables and Ripley, “Modern Applied Statistics with S” (4th edition,2002).

1.10.540 r-matrix

Homepage:

• http://matrix.r-forge.r-project.org/

Spack package:

• r-matrix/package.py

Versions: 1.2-6

Build Dependencies r-lattice, R

Link Dependencies R

Run Dependencies r-lattice

1.10. Package List 279

Spack Documentation, Release 0.9

Description: Classes and methods for dense and sparse matrices and operations on them using ‘LAPACK’ and‘SuiteSparse’.

1.10.541 r-matrixmodels

Homepage:

• http://matrix.r-forge.r-project.org/

Spack package:

• r-matrixmodels/package.py

Versions: 0.4-1

Build Dependencies r-matrix, R

Link Dependencies R

Run Dependencies r-matrix

Description: Modelling with sparse and dense ‘Matrix’ matrices, using modular prediction and response moduleclasses.

1.10.542 r-memoise

Homepage:

• https://github.com/hadley/memoise

Spack package:

• r-memoise/package.py

Versions: 1.0.0

Build Dependencies R, r-digest

Link Dependencies R

Run Dependencies r-digest

Description: Cache the results of a function so that when you call it again with the same arguments it returns thepre-computed value.

1.10.543 r-mgcv

Homepage:

• https://cran.r-project.org/package=mgcv

Spack package:

• r-mgcv/package.py

Versions: 1.8-13

280 Chapter 1. Table of Contents

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Build Dependencies r-matrix, r-nlme, R

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Run Dependencies r-matrix, r-nlme

Description: GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimationby GCV, REML or UBRE/AIC. Includes a gam() function, a wide variety of smoothers, JAGS support anddistributions beyond the exponential family.

1.10.544 r-mime

Homepage:

• https://github.com/yihui/mime

Spack package:

• r-mime/package.py

Versions: 0.5, 0.4

Build Dependencies R

Link Dependencies R

Description: Guesses the MIME type from a filename extension using the data derived from /etc/mime.types inUNIX-type systems.

1.10.545 r-minqa

Homepage:

• http://optimizer.r-forge.r-project.org/

Spack package:

• r-minqa/package.py

Versions: 1.2.4

Build Dependencies R, r-rcpp

Link Dependencies R

Run Dependencies r-rcpp

Description: Derivative-free optimization by quadratic approximation based on an interface to Fortran implementa-tions by M. J. D. Powell.

1.10. Package List 281

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1.10.546 r-multcomp

Homepage:

• http://multcomp.r-forge.r-project.org/

Spack package:

• r-multcomp/package.py

Versions: 1.4-6

Build Dependencies r-survival, r-codetools, r-thdata, r-mvtnorm, r-sandwich, R

Link Dependencies R

Run Dependencies r-mvtnorm, r-codetools, r-survival, r-sandwich, r-thdata

Description: Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, includ-ing linear, generalized linear, linear mixed effects, and survival models. The package includes demos repro-ducing analyzes presented in the book “Multiple Comparisons Using R” (Bretz, Hothorn, Westfall, 2010, CRCPress).

1.10.547 r-munsell

Homepage:

• https://cran.r-project.org/web/packages/munsell/index.html

Spack package:

• r-munsell/package.py

Versions: 0.4.3

Build Dependencies r-colorspace, R

Link Dependencies R

Run Dependencies r-colorspace

Description: Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Mun-sell’s original notation (e.g. “5R 5/10”) and hexadecimal strings suitable for use directly in R graphics. Alsoprovides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and displaycolour palettes.

1.10.548 r-mvtnorm

Homepage:

• http://mvtnorm.r-forge.r-project.org/

Spack package:

• r-mvtnorm/package.py

Versions: 1.0-5

Build Dependencies R

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Description: Computes multivariate normal and t probabilities, quantiles, random deviates and densities.

1.10.549 r-ncdf4

Homepage:

• http://cirrus.ucsd.edu/~pierce/ncdf

Spack package:

• r-ncdf4/package.py

Versions: 1.15

Build Dependencies R, netcdf

Link Dependencies R, netcdf

Description: Provides a high-level R interface to data files written using Unidata’s netCDF library (version 4 orearlier), which are binary data files that are portable across platforms and include metadata information inaddition to the data sets. Using this package, netCDF files (either version 4 or “classic” version 3) can beopened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, ineither version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdfpackage, which only worked with netcdf version 3 files. For various reasons the names of the functions havehad to be changed from the names in the ncdf package. The old ncdf package is still available at the URLgiven below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4packages installed simultaneously without a problem. However, the ncdf package does not provide an interfacefor netcdf version 4 files.

1.10.550 r-networkd3

Homepage:

• http://cran.r-project.org/package=networkD3

Spack package:

• r-networkd3/package.py

Versions: 0.2.12

Build Dependencies R, r-igraph, r-magrittr, r-htmlwidgets

Link Dependencies R

Run Dependencies r-igraph, r-magrittr, r-htmlwidgets

Description: Creates ‘D3’ ‘JavaScript’ network, tree, dendrogram, and Sankey graphs from ‘R’.

1.10. Package List 283

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1.10.551 r-nlme

Homepage:

• https://cran.r-project.org/package=nlme

Spack package:

• r-nlme/package.py

Versions: 3.1-128

Build Dependencies r-lattice, R

Link Dependencies R

Run Dependencies r-lattice

Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.

1.10.552 r-nloptr

Homepage:

• https://cran.r-project.org/package=nloptr

Spack package:

• r-nloptr/package.py

Versions: 1.0.4

Build Dependencies R

Link Dependencies R

Description: nloptr is an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, provid-ing a common interface for a number of different free optimization routines available online as well as originalimplementations of various other algorithms. See http://ab- initio.mit.edu/wiki/index.php/NLopt_Introductionfor more information on the available algorithms. During installation on Unix the NLopt code is downloadedand compiled from the NLopt website.

1.10.553 r-nmf

Homepage:

• http://renozao.github.io/NMF

Spack package:

• r-nmf/package.py

Versions: 0.20.6

Build Dependencies r-digest, r-cluster, r-rcolorbrewer, r-doparallel, r-gridbase, r-stringr, r-registry, r-foreach, r-reshape2, r-colorspace, R, r-rngtools, r-ggplot2, r-pkgmaker

Link Dependencies R

284 Chapter 1. Table of Contents

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Run Dependencies r-digest, r-cluster, r-rcolorbrewer, r-doparallel, r-gridbase, r-stringr, r-registry, r-foreach, r-reshape2, r-colorspace, r-rngtools, r-ggplot2, r-pkgmaker

Description: Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implementsa set of already published algorithms and seeding methods, and provides a framework to test, develop and plugnew/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interfacefunction provides an easy way of performing parallel computations on multicore machines..

1.10.554 r-nnet

Homepage:

• http://www.stats.ox.ac.uk/pub/MASS4/

Spack package:

• r-nnet/package.py

Versions: 7.3-12

Build Dependencies R

Link Dependencies R

Description: Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linearmodels.

1.10.555 r-np

Homepage:

• https://github.com/JeffreyRacine/R-Package-np/

Spack package:

• r-np/package.py

Versions: 0.60-2

Build Dependencies R, r-cubature, r-boot

Link Dependencies R

Run Dependencies r-cubature, r-boot

Description: This package provides a variety of nonparametric (and semiparametric) kernel methods that seamlesslyhandle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledgesupport from the Natural Sciences and Engineering Research Council of Canada (NSERC:www.nserc.ca), theSocial Sciences and Humanities Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierar-chical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).

1.10. Package List 285

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1.10.556 r-openssl

Homepage:

• https://github.com/jeroenooms/openssl#readme

Spack package:

• r-openssl/package.py

Versions: 0.9.4

Build Dependencies R, openssl

Link Dependencies R, openssl

Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA andEC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually orvia x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric(public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES forencrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc),base64 encoder, a secure random number generator, and ‘bignum’ math methods for manually performing cryptocalculations on large multibyte integers.

1.10.557 r-packrat

Homepage:

• https://github.com/rstudio/packrat/

Spack package:

• r-packrat/package.py

Versions: 0.4.7-1

Build Dependencies R

Link Dependencies R

Description: Manage the R packages your project depends on in an isolated, portable, and reproducible way.

1.10.558 r-pbkrtest

Homepage:

• http://people.math.aau.dk/~sorenh/software/pbkrtest/

Spack package:

• r-pbkrtest/package.py

Versions: 0.4-6

Build Dependencies r-matrix, r-mass, R, r-lme4

Link Dependencies R

Run Dependencies r-matrix, r-mass, r-lme4

286 Chapter 1. Table of Contents

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Description: Test in mixed effects models. Attention is on mixed effects models as implemented in the ‘lme4’package. This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests forlinear mixed effects models and a parametric bootstrap test for generalized linear mixed models.

1.10.559 r-pkgmaker

Homepage:

• https://renozao.github.io/pkgmaker

Spack package:

• r-pkgmaker/package.py

Versions: 0.22

Build Dependencies r-codetools, r-stringr, r-registry, R, r-xtable, r-digest

Link Dependencies R

Run Dependencies r-digest, r-codetools, r-xtable, r-registry, r-stringr

Description: This package provides some low-level utilities to use for package development. It currently providesmanagers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. Itserves as a base package for packages like NMF, RcppOctave, doRNG, and as an incubator package for othergeneral purposes utilities, that will eventually be packaged separately. It is still under heavy development andchanges in the interface(s) are more than likely to happen.

1.10.560 r-plotrix

Homepage:

• https://cran.r-project.org/package=plotrix

Spack package:

• r-plotrix/package.py

Versions: 3.6-3

Build Dependencies R

Link Dependencies R

Description: Lots of plots, various labeling, axis and color scaling functions.

1.10.561 r-plyr

Homepage:

• http://had.co.nz/plyr

Spack package:

• r-plyr/package.py

1.10. Package List 287

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Versions: 1.8.4

Build Dependencies R, r-rcpp

Link Dependencies R

Run Dependencies r-rcpp

Description: A set of tools that solves a common set of problems: you need to break a big problem down intomanageable pieces, operate on each piece and then put all the pieces back together. For example, you mightwant to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of ‘plyr’ has been generously supported by‘Becton Dickinson’.

1.10.562 r-png

Homepage:

• http://www.rforge.net/png/

Spack package:

• r-png/package.py

Versions: 0.1-7

Build Dependencies libpng, R

Link Dependencies libpng, R

Description: This package provides an easy and simple way to read, write and display bitmap images stored in thePNG format. It can read and write both files and in-memory raw vectors.

1.10.563 r-praise

Homepage:

• https://github.com/gaborcsardi/praise

Spack package:

• r-praise/package.py

Versions: 1.0.0

Build Dependencies R

Link Dependencies R

Description: Build friendly R packages that praise their users if they have done something good, or they just need itto feel better.

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1.10.564 r-proto

Homepage:

• http://r-proto.googlecode.com/

Spack package:

• r-proto/package.py

Versions: 0.3-10

Build Dependencies R

Link Dependencies R

Description: An object oriented system using object-based, also called prototype- based, rather than class-basedobject oriented ideas.

1.10.565 r-quantmod

Homepage:

• http://www.quantmod.com/

Spack package:

• r-quantmod/package.py

Versions: 0.4-5

Build Dependencies r-zoo, R, r-ttr, r-xts

Link Dependencies R

Run Dependencies r-zoo, r-xts, r-ttr

Description: Specify, build, trade, and analyse quantitative financial trading strategies.

1.10.566 r-quantreg

Homepage:

• https://cran.r-project.org/package=quantreg

Spack package:

• r-quantreg/package.py

Versions: 5.26

Build Dependencies r-matrix, r-matrixmodels, R, r-sparsem

Link Dependencies R

Run Dependencies r-matrix, r-matrixmodels, r-sparsem

Description: Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametricand non-parametric (total variation penalized) models for conditional quantiles of a univariate response andseveral methods for handling censored survival data. Portfolio selection methods based on expected shortfallrisk are also included.

1.10. Package List 289

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1.10.567 r-R6

Homepage:

• https://github.com/wch/R6/

Spack package:

• r-R6/package.py

Versions: 2.1.2

Build Dependencies R

Link Dependencies R

Description: The R6 package allows the creation of classes with reference semantics, similar to R’s built-in referenceclasses. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4classes so they do not require the methods package. These classes allow public and private members, and theysupport inheritance, even when the classes are defined in different packages.

1.10.568 r-randomforest

Homepage:

• https://www.stat.berkeley.edu/~breiman/RandomForests/

Spack package:

• r-randomforest/package.py

Versions: 4.6-12

Build Dependencies R

Link Dependencies R

Description: Classification and regression based on a forest of trees using random inputs.

1.10.569 r-raster

Homepage:

• http://cran.r-project.org/package=raster

Spack package:

• r-raster/package.py

Versions: 2.5-8

Build Dependencies r-sp, R, r-rcpp

Link Dependencies R

Run Dependencies r-sp, r-rcpp

290 Chapter 1. Table of Contents

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Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package imple-ments basic and high-level functions. Processing of very large files is supported.

1.10.570 r-rcolorbrewer

Homepage:

• http://colorbrewer2.org

Spack package:

• r-rcolorbrewer/package.py

Versions: 1.1-2

Build Dependencies R

Link Dependencies R

Description: Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described athttp://colorbrewer2.org

1.10.571 r-rcpp

Homepage:

• http://dirk.eddelbuettel.com/code/rcpp.html

Spack package:

• r-rcpp/package.py

Versions: 0.12.6, 0.12.5

Build Dependencies R

Link Dependencies R

Description: The ‘Rcpp’ package provides R functions as well as C++ classes which offer a seamless integration of Rand C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates bothwriting of new code as well as easier integration of third-party libraries. Documentation about ‘Rcpp’ is providedby several vignettes included in this package, via the ‘Rcpp Gallery’ site at <http://gallery.rcpp.org>, the paperby Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see ‘citation(“Rcpp”)’for details on these last two.

1.10.572 r-rcppeigen

Homepage:

• http://eigen.tuxfamily.org/

Spack package:

• r-rcppeigen/package.py

1.10. Package List 291

Spack Documentation, Release 0.9

Versions: 0.3.2.8.1

Build Dependencies r-matrix, R, r-rcpp

Link Dependencies R

Run Dependencies r-matrix, r-rcpp

Description: R and ‘Eigen’ integration using ‘Rcpp’. ‘Eigen’ is a C++ template library for linear algebra: matrices,vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating pointand complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance onmany algorithms is comparable with some of the best implementations based on ‘Lapack’ and level-3 ‘BLAS’.The ‘RcppEigen’ package includes the header files from the ‘Eigen’ C++ template library (currently version3.2.8). Thus users do not need to install ‘Eigen’ itself in order to use ‘RcppEigen’. Since version 3.1.1, ‘Eigen’is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPLversion 3 or later. ‘RcppEigen’ (the ‘Rcpp’ bindings/bridge to ‘Eigen’) is licensed under the GNU GPL version2 or later, as is the rest of ‘Rcpp’.

1.10.573 r-registry

Homepage:

• https://cran.r-project.org/web/packages/registry/index.html

Spack package:

• r-registry/package.py

Versions: 0.3

Build Dependencies R

Link Dependencies R

Description: Provides a generic infrastructure for creating and using registries.

1.10.574 r-reshape2

Homepage:

• https://github.com/hadley/reshape

Spack package:

• r-reshape2/package.py

Versions: 1.4.1

Build Dependencies r-plyr, R, r-rcpp, r-stringr

Link Dependencies R

Run Dependencies r-plyr, r-rcpp, r-stringr

Description: Flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).

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1.10.575 r-rgooglemaps

Homepage:

• https://cran.r-project.org/package=RgoogleMaps

Spack package:

• r-rgooglemaps/package.py

Versions: 1.2.0.7

Build Dependencies R, r-rjsonio, r-png

Link Dependencies R

Run Dependencies r-rjsonio, r-png

Description: This package serves two purposes: (i) Provide a comfortable R interface to query the Google serverfor static maps, and (ii) Use the map as a background image to overlay plots within R. This requires propercoordinate scaling.

1.10.576 r-rjava

Homepage:

• http://www.rforge.net/rJava/

Spack package:

• r-rjava/package.py

Versions: 0.9-8

Build Dependencies R, jdk

Link Dependencies R, jdk

Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, callingmethods and accessing fields.

1.10.577 r-rjson

Homepage:

• https://cran.r-project.org/package=rjson

Spack package:

• r-rjson/package.py

Versions: 0.2.15

Build Dependencies R

Link Dependencies R

Description: Converts R object into JSON objects and vice-versa.

1.10. Package List 293

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1.10.578 r-rjsonio

Homepage:

• https://cran.r-project.org/package=RJSONIO

Spack package:

• r-rjsonio/package.py

Versions: 1.3-0

Build Dependencies R

Link Dependencies R

Description: This is a package that allows conversion to and from data in Javascript object notation (JSON) format.This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmersto read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that wastoo slow for converting large R objects to JSON and was not extensible. rjson’s performance is now similar tothis package, and perhaps slightly faster in some cases. This package uses methods and is readily extensibleby defining methods for different classes, vectorized operations, and C code and callbacks to R functions fordeserializing JSON objects to R. The two packages intentionally share the same basic interface. This package(RJSONIO) has many additional options to allow customizing the generation and processing of JSON content.This package uses libjson rather than implementing yet another JSON parser. The aim is to support other generalprojects by building on their work, providing feedback and benefit from their ongoing development.

1.10.579 r-rmysql

Homepage:

• https://github.com/rstats-db/rmysql

Spack package:

• r-rmysql/package.py

Versions: 0.10.9

Build Dependencies R, r-dbi, mariadb

Link Dependencies R, mariadb

Run Dependencies r-dbi

Description: Implements ‘DBI’ Interface to ‘MySQL’ and ‘MariaDB’ Databases.

1.10.580 r-rngtools

Homepage:

• https://renozao.github.io/rngtools

Spack package:

• r-rngtools/package.py

Versions: 1.2.4

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Build Dependencies r-pkgmaker, R, r-digest, r-stringr

Link Dependencies R

Run Dependencies r-pkgmaker, r-digest, r-stringr

Description: This package contains a set of functions for working with Random Number Generators (RNGs). Inparticular, it defines a generic S4 framework for getting/setting the current RNG, or RNG data that are embeddedinto objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNGsettings can be changed.

1.10.581 r-rodbc

Homepage:

• https://cran.rstudio.com/web/packages/RODBC/

Spack package:

• r-rodbc/package.py

Versions: 1.3-13

Build Dependencies unixodbc, R

Link Dependencies unixodbc, R

Description: An ODBC database interface.

1.10.582 r-roxygen2

Homepage:

• https://github.com/klutometis/roxygen

Spack package:

• r-roxygen2/package.py

Versions: 5.0.1

Build Dependencies r-stringi, R, r-stringr, r-digest, r-rcpp, r-brew

Link Dependencies R

Run Dependencies r-rcpp, r-digest, r-stringi, r-brew, r-stringr

Description: A ‘Doxygen’-like in-source documentation system for Rd, collation, and ‘NAMESPACE’ files.

1.10. Package List 295

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1.10.583 r-rpostgresql

Homepage:

• https://code.google.com/p/rpostgresql/

Spack package:

• r-rpostgresql/package.py

Versions: 0.4-1

Build Dependencies R, postgresql, r-dbi

Link Dependencies R, postgresql

Run Dependencies r-dbi

Description: Database interface and PostgreSQL driver for R This package provides a Database Interface (DBI)compliant driver for R to access PostgreSQL database systems. In order to build and install this package fromsource, PostgreSQL itself must be present your system to provide PostgreSQL functionality via its libraries andheader files. These files are provided as postgresql-devel package under some Linux distributions. On MicrosoftWindows system the attached libpq library source will be used. A wiki and issue tracking system for the packageare available at Google Code at https://code.google.com/p/rpostgresql/.

1.10.584 r-rsqlite

Homepage:

• https://github.com/rstats-db/RSQLite

Spack package:

• r-rsqlite/package.py

Versions: 1.0.0

Build Dependencies R, r-dbi

Link Dependencies R

Run Dependencies r-dbi

Description: This package embeds the SQLite database engine in R and provides an interface compliant with theDBI package. The source for the SQLite engine (version 3.8.6) is included.

1.10.585 r-rstan

Homepage:

• http://mc-stan.org/

Spack package:

• r-rstan/package.py

Versions: 2.10.1

Build Dependencies r-gridextra, r-inline, r-stanheaders, r-rcppeigen, R, r-bh, r-ggplot2, r-rcpp

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Link Dependencies R

Run Dependencies r-gridextra, r-inline, r-stanheaders, r-rcppeigen, r-bh, r-ggplot2, r-rcpp

Description: User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by ac-cessing the header-only Stan library provided by the ‘StanHeaders’ package. The Stan project develops a prob-abilistic programming language that implements full Bayesian statistical inference via Markov Chain MonteCarlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihoodestimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evalu-ate gradients without burdening the user with the need to derive the partial derivatives.

1.10.586 r-rstudioapi

Homepage:

• https://cran.r-project.org/web/packages/rstudioapi/index.html

Spack package:

• r-rstudioapi/package.py

Versions: 0.6, 0.5

Build Dependencies R

Link Dependencies R

Description: Access the RStudio API (if available) and provide informative error messages when it’s not.

1.10.587 r-sandwich

Homepage:

• https://cran.r-project.org/package=sandwich

Spack package:

• r-sandwich/package.py

Versions: 2.3-4

Build Dependencies r-zoo, R

Link Dependencies R

Run Dependencies r-zoo

Description: Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.

1.10. Package List 297

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1.10.588 r-scales

Homepage:

• https://github.com/hadley/scales

Spack package:

• r-scales/package.py

Versions: 0.4.0

Build Dependencies r-rcolorbrewer, r-labeling, r-plyr, r-munsell, R, r-dichromat, r-rcpp

Link Dependencies R

Run Dependencies r-rcolorbrewer, r-labeling, r-plyr, r-munsell, r-dichromat, r-rcpp

Description: Graphical scales map data to aesthetics, and provide methods for automatically determining breaks andlabels for axes and legends.

1.10.589 r-shiny

Homepage:

• http://shiny.rstudio.com/

Spack package:

• r-shiny/package.py

Versions: 0.13.2

Build Dependencies r-digest, r-httpuv, r-jsonlite, r-htmltools, r-mime, R, r-xtable, r-R6

Link Dependencies R

Run Dependencies r-digest, r-httpuv, r-jsonlite, r-htmltools, r-mime, r-xtable, r-R6

Description: Makes it incredibly easy to build interactive web applications with R. Automatic “reactive” bindingbetween inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, andpowerful applications with minimal effort.

1.10.590 r-sp

Homepage:

• https://github.com/edzer/sp/

Spack package:

• r-sp/package.py

Versions: 1.2-3

Build Dependencies r-lattice, R

Link Dependencies R

Run Dependencies r-lattice

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Description: Classes and methods for spatial data; the classes document where the spatial location information re-sides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as wellas methods for retrieving coordinates, for subsetting, print, summary, etc.

1.10.591 r-sparsem

Homepage:

• http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html

Spack package:

• r-sparsem/package.py

Versions: 1.7

Build Dependencies R

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Description: Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decompo-sition and backsolving as well as standard R subsetting and Kronecker products.

1.10.592 r-stanheaders

Homepage:

• http://mc-stan.org/

Spack package:

• r-stanheaders/package.py

Versions: 2.10.0-2

Build Dependencies R

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Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, vi-gnettes, or function documentation. There is a shared object containing part of the CVODES library, but it isnot accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directiveof their package’s DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies.The Stan project develops a probabilistic programming language that implements full or approximate Bayesianstatistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally pe-nalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automaticdifferentiation scheme, templated statistical and linear algebra functions that can handle the automatically dif-ferentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The ‘rstan’ package providesuser-facing R functions to parse, compile, test, estimate, and analyze Stan models.

1.10. Package List 299

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1.10.593 r-stringi

Homepage:

• http://www.gagolewski.com/software/stringi/

Spack package:

• r-stringi/package.py

Versions: 1.1.1

Build Dependencies R, icu

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Description: Allows for fast, correct, consistent, portable, as well as convenient character string/text processing inevery locale and any native encoding. Owing to the use of the ICU library, the package provides R users withplatform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among availablefeatures there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Al-gorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization,date-time formatting and parsing, etc.

1.10.594 r-stringr

Homepage:

• https://cran.r-project.org/web/packages/stringr/index.html

Spack package:

• r-stringr/package.py

Versions: 1.0.0

Build Dependencies R, r-stringi, r-magrittr

Link Dependencies R

Run Dependencies r-stringi, r-magrittr

Description: A consistent, simple and easy to use set of wrappers around the fantastic ‘stringi’ package. All functionand argument names (and positions) are consistent, all functions deal with “NA“‘s and zero length vectors inthe same way, and the output from one function is easy to feed into the input of another.

1.10.595 r-survey

Homepage:

• http://r-survey.r-forge.r-project.org/survey/

Spack package:

• r-survey/package.py

Versions: 3.30-3

Build Dependencies R

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Link Dependencies R

Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Coxmodels, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights.Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling withoutreplacement. Principal components, factor analysis.

1.10.596 r-survival

Homepage:

• https://cran.r-project.org/package=survival

Spack package:

• r-survival/package.py

Versions: 2.39-5

Build Dependencies r-matrix, R

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Run Dependencies r-matrix

Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier andAalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

1.10.597 r-tarifx

Homepage:

• https://cran.r-project.org/package=taRifx

Spack package:

• r-tarifx/package.py

Versions: 1.0.6

Build Dependencies r-plyr, r-reshape2, R

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Run Dependencies r-plyr, r-reshape2

Description: A collection of various utility and convenience functions.

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1.10.598 r-testthat

Homepage:

• https://github.com/hadley/testthat

Spack package:

• r-testthat/package.py

Versions: 1.0.2

Build Dependencies r-R6, r-praise, R, r-crayon, r-digest, r-magrittr

Link Dependencies R

Run Dependencies r-digest, r-crayon, r-R6, r-magrittr, r-praise

Description: A unit testing system designed to be fun, flexible and easy to set up.

1.10.599 r-thdata

Homepage:

• https://cran.r-project.org/package=TH.data

Spack package:

• r-thdata/package.py

Versions: 1.0-7

Build Dependencies r-mass, R, r-survival

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Run Dependencies r-mass, r-survival

Description: Contains data sets used in other packages Torsten Hothorn maintains.

1.10.600 r-threejs

Homepage:

• http://bwlewis.github.io/rthreejs

Spack package:

• r-threejs/package.py

Versions: 0.2.2

Build Dependencies r-matrix, R, r-base64enc, r-jsonlite, r-htmlwidgets

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Run Dependencies r-matrix, r-jsonlite, r-base64enc, r-htmlwidgets

Description: Create interactive 3D scatter plots, network plots, and globes using the ‘three.js’ visualization library(“http://threejs.org”).

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1.10.601 r-tibble

Homepage:

• https://github.com/hadley/tibble

Spack package:

• r-tibble/package.py

Versions: 1.1

Build Dependencies r-lazyeval, R, r-rcpp, r-assertthat

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Run Dependencies r-lazyeval, r-rcpp, r-assertthat

Description: Provides a ‘tbl_df’ class that offers better checking and printing capabilities than traditional data frames.

1.10.602 r-tidyr

Homepage:

• https://github.com/hadley/tidyr

Spack package:

• r-tidyr/package.py

Versions: 0.5.1

Build Dependencies r-tibble, r-stringi, r-lazyeval, R, r-dplyr, r-rcpp, r-magrittr

Link Dependencies R

Run Dependencies r-tibble, r-stringi, r-lazyeval, r-dplyr, r-rcpp, r-magrittr

Description: An evolution of ‘reshape2’. It’s designed specifically for data tidying (not general reshaping or aggre-gating) and works well with ‘dplyr’ data pipelines.

1.10.603 r-ttr

Homepage:

• https://github.com/joshuaulrich/TTR

Spack package:

• r-ttr/package.py

Versions: 0.23-1

Build Dependencies r-zoo, R, r-xts

Link Dependencies R

Run Dependencies r-zoo, r-xts

Description: Functions and data to construct technical trading rules with R.

1.10. Package List 303

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1.10.604 r-vcd

Homepage:

• https://cran.r-project.org/package=vcd

Spack package:

• r-vcd/package.py

Versions: 1.4-1

Build Dependencies r-mass, r-colorspace, R, r-lmtest

Link Dependencies R

Run Dependencies r-mass, r-colorspace, r-lmtest

Description: Visualization techniques, data sets, summary and inference procedures aimed particularly at categoricaldata. Special emphasis is given to highly extensible grid graphics. The package was package was originallyinspired by the book “Visualizing Categorical Data” by Michael Friendly and is now the main support packagefor a new book, “Discrete Data Analysis with R” by Michael Friendly and David Meyer (2015).

1.10.605 r-visnetwork

Homepage:

• https://github.com/datastorm-open/visNetwork

Spack package:

• r-visnetwork/package.py

Versions: 1.0.1

Build Dependencies r-htmlwidgets, R, r-htmltools, r-jsonlite, r-magrittr

Link Dependencies R

Run Dependencies r-jsonlite, r-htmlwidgets, r-htmltools, r-magrittr

Description: Provides an R interface to the ‘vis.js’ JavaScript charting library. It allows an interactive visualizationof networks.

1.10.606 r-whisker

Homepage:

• http://github.com/edwindj/whisker

Spack package:

• r-whisker/package.py

Versions: 0.3-2

Build Dependencies R

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Description: logicless templating, reuse templates in many programming languages including R

1.10.607 r-withr

Homepage:

• http://github.com/jimhester/withr

Spack package:

• r-withr/package.py

Versions: 1.0.1

Build Dependencies R

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Description: A set of functions to run code ‘with’ safely and temporarily modified global state. Many of these func-tions were originally a part of the ‘devtools’ package, this provides a simple package with limited dependenciesto provide access to these functions.

1.10.608 r-xlconnect

Homepage:

• http://miraisolutions.wordpress.com/

Spack package:

• r-xlconnect/package.py

Versions: 0.2-12, 0.2-11

Build Dependencies r-xlconnectjars, R, r-rjava

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Run Dependencies r-xlconnectjars, r-rjava

Description: Provides comprehensive functionality to read, write and format Excel data.

1.10.609 r-xlconnectjars

Homepage:

• http://miraisolutions.wordpress.com/

Spack package:

• r-xlconnectjars/package.py

Versions: 0.2-12, 0.2-9

Build Dependencies R, r-rjava

Link Dependencies R

1.10. Package List 305

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Run Dependencies r-rjava

Description: Provides external JAR dependencies for the XLConnect package.

1.10.610 r-xlsx

Homepage:

• http://code.google.com/p/rexcel/

Spack package:

• r-xlsx/package.py

Versions: 0.5.7

Build Dependencies R, r-rjava, r-xlsxjars

Link Dependencies R

Run Dependencies r-rjava, r-xlsxjars

Description: Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.

1.10.611 r-xlsxjars

Homepage:

• https://cran.rstudio.com/web/packages/xlsxjars/index.html

Spack package:

• r-xlsxjars/package.py

Versions: 0.6.1

Build Dependencies R, r-rjava

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Run Dependencies r-rjava

Description: The xlsxjars package collects all the external jars required for the xlxs package. This release correspondsto POI 3.10.1.

1.10.612 r-xml

Homepage:

• http://www.omegahat.net/RSXML

Spack package:

• r-xml/package.py

Versions: 3.98-1

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Build Dependencies libxml2, R

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Description: Many approaches for both reading and creating XML (and HTML) documents (including DTDs), bothlocal and accessible via HTTP or FTP. Also offers access to an ‘XPath’ “interpreter”.

1.10.613 r-xtable

Homepage:

• http://xtable.r-forge.r-project.org/

Spack package:

• r-xtable/package.py

Versions: 1.8-2

Build Dependencies R

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Description: Coerce data to LaTeX and HTML tables.

1.10.614 r-xts

Homepage:

• http://r-forge.r-project.org/projects/xts/

Spack package:

• r-xts/package.py

Versions: 0.9-7

Build Dependencies r-zoo, R

Link Dependencies R

Run Dependencies r-zoo

Description: Provide for uniform handling of R’s different time-based data classes by extending zoo, maximizing na-tive format information preservation and allowing for user level customization and extension, while simplifyingcross-class interoperability.

1.10.615 r-yaml

Homepage:

• https://cran.r-project.org/web/packages/yaml/index.html

Spack package:

• r-yaml/package.py

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Versions: 2.1.13

Build Dependencies R

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Description: This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML)for R.

1.10.616 r-zoo

Homepage:

• http://zoo.r-forge.r-project.org/

Spack package:

• r-zoo/package.py

Versions: 1.7-13

Build Dependencies r-lattice, R

Link Dependencies R

Run Dependencies r-lattice

Description: An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregulartime series of numeric vectors/matrices and factors. zoo’s key design goals are independence of a particularindex/date/time class and consistency with ts and base R by providing methods to extend standard generics.

1.10.617 raja

Homepage:

• http://software.llnl.gov/RAJA/

Spack package:

• raja/package.py

Versions: git

Description: RAJA Parallel Framework.

1.10.618 ravel

Homepage:

• https://github.com/llnl/ravel

Spack package:

• ravel/package.py

Versions: 1.0.0

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Build Dependencies muster, otf2, cmake, qt, otf

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Description: Ravel is a parallel communication trace visualization tool that orders events according to logical time.

1.10.619 readline

Homepage:

• http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html

Spack package:

• readline/package.py

Versions: 6.3

Build Dependencies ncurses

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Description: The GNU Readline library provides a set of functions for use by applications that allow users to editcommand lines as they are typed in. Both Emacs and vi editing modes are available. The Readline libraryincludes additional functions to maintain a list of previously-entered command lines, to recall and perhapsreedit those lines, and perform csh-like history expansion on previous commands.

1.10.620 rose

Homepage:

• http://rosecompiler.org/

Spack package:

• rose/package.py

Versions: master

Build Dependencies libtool, autoconf , boost, jdk, automake

Link Dependencies boost, jdk

Description: A compiler infrastructure to build source-to-source program transformation and analysis tools. (Devel-oped at Lawrence Livermore National Lab)

1.10.621 rsync

Homepage:

• https://rsync.samba.org

Spack package:

• rsync/package.py

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Versions: 3.1.2, 3.1.1

Description: An open source utility that provides fast incremental file transfer.

1.10.622 ruby

Homepage:

• https://www.ruby-lang.org/

Spack package:

• ruby/package.py

Versions: 2.2.0

Build Dependencies libffi, readline, zlib, openssl

Link Dependencies libffi, readline, zlib, openssl

Description: A dynamic, open source programming language with a focus on simplicity and productivity.

1.10.623 rust

Homepage:

• http://www.rust-lang.org

Spack package:

• rust/package.py

Versions: 1.8.0

Build Dependencies git, cmake, python, openssl, llvm, curl

Link Dependencies git, cmake, python, openssl, llvm, curl

Description: The rust programming language toolchain

1.10.624 rust-bindgen

Homepage:

• http://www.rust-lang.org

Spack package:

• rust-bindgen/package.py

Versions: 0.16

Build Dependencies llvm, rust

Link Dependencies llvm, rust

Description: The rust programming language toolchain

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1.10.625 SAMRAI

Homepage:

• https://computation.llnl.gov/project/SAMRAI/

Spack package:

• SAMRAI/package.py

Versions: 3.9.1, 3.8.0, 3.7.3, 3.7.2, 3.6.3-beta, 3.5.2-beta, 3.5.0-beta, 3.4.1-beta, 3.3.3-beta, 3.3.2-beta, 2.4.4

Build Dependencies mpi, zlib, boost, hdf5

Link Dependencies mpi, zlib, boost, hdf5

Description: SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) is an object-oriented C++software library enables exploration of numerical, algorithmic, parallel computing, and software issues associ-ated with applying structured adaptive mesh refinement (SAMR) technology in large-scale parallel applicationdevelopment.

1.10.626 samtools

Homepage:

• www.htslib.org

Spack package:

• samtools/package.py

Versions: 1.3.1, 1.2

Build Dependencies ncurses, htslib, zlib

Link Dependencies ncurses, htslib, zlib

Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting,merging, indexing and generating alignments in a per-position format

1.10.627 scalasca

Homepage:

• http://www.scalasca.org

Spack package:

• scalasca/package.py

Versions: 2.2.2, 2.1

Build Dependencies cube, scorep, mpi

Link Dependencies cube, scorep, mpi

Description: Scalasca is a software tool that supports the performance optimization of parallel programs by measuringand analyzing their runtime behavior. The analysis identifies potential performance bottlenecks - in particularthose concerning communication and synchronization - and offers guidance in exploring their causes.

1.10. Package List 311

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1.10.628 scons

Homepage:

• http://scons.org

Spack package:

• scons/package.py

Versions: 2.5.0

Build Dependencies python

Link Dependencies python

Description: SCons is a software construction tool

1.10.629 scorep

Homepage:

• http://www.vi-hps.org/projects/score-p

Spack package:

• scorep/package.py

Versions: 2.0.2, 1.4.2, 1.3

Build Dependencies otf2, opari2, cube, papi, mpi

Link Dependencies otf2, opari2, cube, papi, mpi

Description: The Score-P measurement infrastructure is a highly scalable and easy-to- use tool suite for profiling,event tracing, and online analysis of HPC applications.

1.10.630 scotch

Homepage:

• http://www.labri.fr/perso/pelegrin/scotch/

Spack package:

• scotch/package.py

Versions: 6.0.3, 6.0.0, 5.1.10b

Build Dependencies flex, zlib, bison, mpi

Link Dependencies zlib, mpi

Description: Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, and sparsematrix ordering.

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1.10.631 scr

Homepage:

• https://computation.llnl.gov/project/scr/

Spack package:

• scr/package.py

Versions: 1.1.8, 1.1-7

Build Dependencies mpi

Link Dependencies mpi

Description: SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast,scalable checkpoint/restart capability for MPI codes

1.10.632 screen

Homepage:

• https://www.gnu.org/software/screen/

Spack package:

• screen/package.py

Versions: 4.3.1, 4.3.0, 4.2.1, 4.2.0, 4.0.3, 4.0.2, 3.9.15, 3.9.11, 3.9.10, 3.9.9, 3.9.8, 3.9.4, 3.7.6, 3.7.4, 3.7.2, 3.7.1

Build Dependencies ncurses

Link Dependencies ncurses

Description: Screen is a full-screen window manager that multiplexes a physical terminal between several processes,typically interactive shells.

1.10.633 sed

Homepage:

• http://www.gnu.org/software/sed/

Spack package:

• sed/package.py

Versions: 4.2.2

Description: GNU implementation of the famous stream editor.

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1.10.634 seqtk

Homepage:

• https://github.com/lh3/seqtk

Spack package:

• seqtk/package.py

Versions: 1.2, 1.1

Build Dependencies zlib

Link Dependencies zlib

Description: Toolkit for processing sequences in FASTA/Q formats.

1.10.635 serf

Homepage:

• https://serf.apache.org/

Spack package:

• serf/package.py

Versions: 1.3.8

Build Dependencies expat, apr, zlib, openssl, apr-util, scons

Link Dependencies apr, apr-util, zlib, expat, openssl

Description: Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime(APR) library

1.10.636 silo

Homepage:

• http://wci.llnl.gov/simulation/computer-codes/silo

Spack package:

• silo/package.py

Versions: 4.10.2, 4.9, 4.8

Build Dependencies qt, hdf5

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Description: Silo is a library for reading and writing a wide variety of scientific data to binary, disk files.

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1.10.637 slepc

Homepage:

• http://www.grycap.upv.es/slepc

Spack package:

• slepc/package.py

Versions: 3.7.1, 3.6.3, 3.6.2

Build Dependencies petsc, arpack-ng

Link Dependencies petsc, arpack-ng

Description: Scalable Library for Eigenvalue Problem Computations.

1.10.638 snappy

Homepage:

• https://code.google.com/p/snappy

Spack package:

• snappy/package.py

Versions: 1.1.3

Description: A fast compressor/decompressor: https://code.google.com/p/snappy

1.10.639 sparsehash

Homepage:

• https://github.com/sparsehash/sparsehash

Spack package:

• sparsehash/package.py

Versions: 2.0.3

Description: Sparse and dense hash-tables for C++ by Google

1.10.640 spindle

Homepage:

• https://computation.llnl.gov/project/spindle/

Spack package:

• spindle/package.py

Versions: 0.8.1

1.10. Package List 315

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Link Dependencies launchmon

Description: Spindle improves the library-loading performance of dynamically linked HPC applications. WithoutSpindle large MPI jobs can overload on a shared file system when loading dynamically linked libraries, causingsite-wide performance problems.

1.10.641 spot

Homepage:

• https://spot.lrde.epita.fr/index.html

Spack package:

• spot/package.py

Versions: 1.99.3

Build Dependencies python

Link Dependencies python

Description: Spot is a C++11 library for omega-automata manipulation and model checking.

1.10.642 sqlite

Homepage:

• www.sqlite.org

Spack package:

• sqlite/package.py

Versions: 3.8.5

Description: SQLite3 is an SQL database engine in a C library. Programs that link the SQLite3 library can have SQLdatabase access without running a separate RDBMS process.

1.10.643 stat

Homepage:

• http://paradyn.org/STAT/STAT.html

Spack package:

• stat/package.py

Versions: 3.0.0b, 2.2.0, 2.1.0, 2.0.0

Build Dependencies autoconf , launchmon, py-pygtk, swig, automake, python, mrnet, libtool, libelf , graphviz,graphlib, mpi, dyninst, libdwarf

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Run Dependencies graphviz

Description: Library to create, manipulate, and export graphs Graphlib.

1.10.644 stream

Homepage:

• https://www.cs.virginia.edu/stream/ref.html

Spack package:

• stream/package.py

Versions: 5.10

Description: The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memorybandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.

1.10.645 subversion

Homepage:

• https://subversion.apache.org/

Spack package:

• subversion/package.py

Versions: 1.9.3, 1.8.13

Build Dependencies apr, apr-util, sqlite, zlib, serf

Link Dependencies apr, apr-util, sqlite, zlib, serf

Description: Apache Subversion - an open source version control system.

1.10.646 suite-sparse

Homepage:

• http://faculty.cse.tamu.edu/davis/suitesparse.html

Spack package:

• suite-sparse/package.py

Versions: 4.5.3, 4.5.1

Build Dependencies lapack, blas, tbb, metis

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Description: SuiteSparse is a suite of sparse matrix algorithms

1.10. Package List 317

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1.10.647 sundials

Homepage:

• http://computation.llnl.gov/casc/sundials/

Spack package:

• sundials/package.py

Versions: 2.6.2

Build Dependencies superlu-mt, cmake, lapack, blas, mpi, suite-sparse

Link Dependencies superlu-mt, lapack, blas, suite-sparse, mpi

Description: SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)

1.10.648 superlu

Homepage:

• http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu

Spack package:

• superlu/package.py

Versions: 5.2.1

Build Dependencies blas

Link Dependencies blas

Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems oflinear equations on high performance machines. SuperLU is designed for sequential machines.

1.10.649 superlu-dist

Homepage:

• http://crd-legacy.lbl.gov/~xiaoye/SuperLU/

Spack package:

• superlu-dist/package.py

Versions: 5.0.0, 4.3, 4.2, 4.1, 4.0

Build Dependencies lapack, blas, metis, parmetis, mpi

Link Dependencies lapack, blas, metis, parmetis, mpi

Description: A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equa-tions on high performance machines.

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1.10.650 superlu-mt

Homepage:

• http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu_mt

Spack package:

• superlu-mt/package.py

Versions: 3.1

Build Dependencies blas

Link Dependencies blas

Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systemsof linear equations on high performance machines. SuperLU_MT is designed for shared memory parallel ma-chines.

1.10.651 swiftsim

Homepage:

• http://icc.dur.ac.uk/swift/

Spack package:

• swiftsim/package.py

Versions: 0.3.0

Build Dependencies hdf5, metis, mpi, m4, libtool, autoconf , automake

Link Dependencies mpi, metis, hdf5

Description: SPH With Inter-dependent Fine-grained Tasking (SWIFT) provides astrophysicists with a state of theart framework to perform particle based simulations.

1.10.652 swig

Homepage:

• http://www.swig.org

Spack package:

• swig/package.py

Versions: 3.0.10, 3.0.8, 3.0.2, 2.0.12, 2.0.2, 1.3.40

Build Dependencies pcre

Link Dependencies pcre

Description: SWIG is an interface compiler that connects programs written in C and C++ with scripting languagessuch as Perl, Python, Ruby, and Tcl. It works by taking the declarations found in C/C++ header files andusing them to generate the wrapper code that scripting languages need to access the underlying C/C++ code. Inaddition, SWIG provides a variety of customization features that let you tailor the wrapping process to suit yourapplication.

1.10. Package List 319

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1.10.653 sympol

Homepage:

• http://www.math.uni-rostock.de/~rehn/software/sympol.html

Spack package:

• sympol/package.py

Versions: 0.1.8

Build Dependencies lrslib, boost, cmake, bliss, gmp

Link Dependencies lrslib, boost, gmp, bliss

Description: SymPol is a C++ tool to work with symmetric polyhedra

1.10.654 szip

Homepage:

• https://www.hdfgroup.org/doc_resource/SZIP/

Spack package:

• szip/package.py

Versions: 2.1

Description: An implementation of the extended-Rice lossless compression algorithm. It provides lossless compres-sion of scientific data, and is provided with HDF software products.

1.10.655 tar

Homepage:

• https://www.gnu.org/software/tar/

Spack package:

• tar/package.py

Versions: 1.29, 1.28

Description: GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.

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1.10.656 task

Homepage:

• http://www.taskwarrior.org

Spack package:

• task/package.py

Versions: 2.4.4

Build Dependencies gnutls, libuuid, cmake

Link Dependencies gnutls, libuuid

Description: Feature-rich console based todo list manager

1.10.657 taskd

Homepage:

• http://www.taskwarrior.org

Spack package:

• taskd/package.py

Versions: 1.1.0

Build Dependencies gnutls, libuuid, cmake

Link Dependencies gnutls, libuuid

Description: TaskWarrior task synchronization daemon

1.10.658 tau

Homepage:

• http://www.cs.uoregon.edu/research/tau

Spack package:

• tau/package.py

Versions: 2.25, 2.24.1, 2.24, 2.23.1

Build Dependencies pdt, scorep, binutils, mpi

Link Dependencies pdt, scorep, binutils, mpi

Description: A portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran,C, C++, UPC, Java, Python.

1.10. Package List 321

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1.10.659 tbb

Homepage:

• http://www.threadingbuildingblocks.org/

Spack package:

• tbb/package.py

Versions: 4.4.4, 4.4.3

Description: Widely used C++ template library for task parallelism. Intel Threading Building Blocks (Intel TBB)lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portableand composable, and that have future-proof scalability.

1.10.660 tcl

Homepage:

• http://www.tcl.tk

Spack package:

• tcl/package.py

Versions: 8.6.5, 8.6.4, 8.6.3, 8.5.19

Build Dependencies zlib

Link Dependencies zlib

Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language,suitable for a very wide range of uses, including web and desktop applications, networking, administration,testing and many more. Open source and business-friendly, Tcl is a mature yet evolving language that is trulycross platform, easily deployed and highly extensible.

1.10.661 tetgen

Homepage:

• http://www.tetgen.org

Spack package:

• tetgen/package.py

Versions: 1.5.0, 1.4.3

Build Dependencies cmake

Description: TetGen is a program and library that can be used to generate tetrahedral meshes for given 3D polyhedraldomains. TetGen generates exact constrained Delaunay tetrahedralizations, boundary conforming Delaunaymeshes, and Voronoi paritions.

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1.10.662 texinfo

Homepage:

• https://www.gnu.org/software/texinfo/

Spack package:

• texinfo/package.py

Versions: 6.0, 5.2, 5.1, 5.0

Description: Texinfo is the official documentation format of the GNU project. It was invented by Richard Stallmanand Bob Chassell many years ago, loosely based on Brian Reid’s Scribe and other formatting languages of thetime. It is used by many non-GNU projects as well.FIXME: put a proper description of your package here.

1.10.663 texlive

Homepage:

• http://www.tug.org/texlive

Spack package:

• texlive/package.py

Versions: live

Build Dependencies perl

Description: TeX Live is a free software distribution for the TeX typesetting system

1.10.664 the_platinum_searcher

Homepage:

• https://github.com/monochromegane/the_platinum_searcher

Spack package:

• the_platinum_searcher/package.py

Versions: head

Build Dependencies go

Link Dependencies go

Description: Fast parallel recursive grep alternative

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1.10.665 the_silver_searcher

Homepage:

• http://geoff.greer.fm/ag/

Spack package:

• the_silver_searcher/package.py

Versions: 0.32.0, 0.30.0

Build Dependencies pcre, xz, pkg-config

Link Dependencies pcre, xz

Description: Fast recursive grep alternative

1.10.666 thrift

Homepage:

• http://thrift.apache.org

Spack package:

• thrift/package.py

Versions: 0.9.2

Build Dependencies flex, jdk, python, zlib, openssl, automake, libtool, libevent, bison, autoconf , boost

Link Dependencies jdk, python, zlib, openssl, libevent, boost

Description: Software framework for scalable cross-language services development. Thrift combines a softwarestack with a code generation engine to build services that work efficiently and seamlessly between C++, Java,Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi andother languages.

1.10.667 tk

Homepage:

• http://www.tcl.tk

Spack package:

• tk/package.py

Versions: 8.6.5, 8.6.3

Build Dependencies tcl

Link Dependencies tcl

Description: Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level thanconventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, andcan produce rich, native applications that run unchanged across Windows, Mac OS X, Linux and more.

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1.10.668 tmux

Homepage:

• http://tmux.github.io

Spack package:

• tmux/package.py

Versions: 2.2, 2.1, 1.9a

Build Dependencies ncurses, libevent

Link Dependencies ncurses, libevent

Description: tmux is a terminal multiplexer. What is a terminal multiplexer? It lets you switch easily between severalprograms in one terminal, detach them (they keep running in the background) and reattach them to a differentterminal. And do a lot more.

1.10.669 tmuxinator

Homepage:

• https://github.com/tmuxinator/tmuxinator

Spack package:

• tmuxinator/package.py

Versions: 0.6.11

Build Dependencies ruby

Link Dependencies ruby

Description: A session configuration creator and manager for tmux

1.10.670 tree

Homepage:

• http://mama.indstate.edu/users/ice/tree/

Spack package:

• tree/package.py

Versions: 1.7.0

Description: Tree is a recursive directory listing command that produces a depth indented listing of files, which iscolorized ala dircolors if the LS_COLORS environment variable is set and output is to tty. Tree has been portedand reported to work under the following operating systems: Linux, FreeBSD, OS X, Solaris, HP/UX, Cygwin,HP Nonstop and OS/2.

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1.10.671 triangle

Homepage:

• http://www.cs.cmu.edu/~quake/triangle.html

Spack package:

• triangle/package.py

Versions: 1.6

Description: Triangle is a two-dimensional mesh generator and Delaunay triangulator. Triangle generates exact De-launay triangulations, constrained Delaunay triangulations, conforming Delaunay triangulations, Voronoi dia-grams, and high-quality triangular meshes.

1.10.672 trilinos

Homepage:

• https://trilinos.org/

Spack package:

• trilinos/package.py

Versions: 12.6.4, 12.6.3, 12.6.2, 12.6.1, 12.4.2, 12.2.1, 12.0.1, 11.14.3, 11.14.2, 11.14.1

Build Dependencies superlu-dist, matio, cmake, glm, hypre, lapack, boost, swig, metis, parmetis, mpi, suite-sparse,netcdf , mumps, python, py-numpy, scalapack, blas, hdf5

Link Dependencies superlu-dist, matio, glm, hypre, lapack, boost, swig, metis, parmetis, mpi, suite-sparse, netcdf ,mumps, python, py-numpy, scalapack, blas, hdf5

Description: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientificproblems. A unique design feature of Trilinos is its focus on packages.

1.10.673 turbomole

Homepage:

• http://www.turbomole-gmbh.com/

Spack package:

• turbomole/package.py

Versions: 7.0.2

Description: TURBOMOLE: Program Package for ab initio Electronic Structure Calculations. NB: Requires a li-cense to download.

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1.10.674 udunits2

Homepage:

• http://www.unidata.ucar.edu/software/udunits

Spack package:

• udunits2/package.py

Versions: 2.2.20

Build Dependencies expat

Link Dependencies expat

Description: Automated units conversion

1.10.675 uncrustify

Homepage:

• http://uncrustify.sourceforge.net/

Spack package:

• uncrustify/package.py

Versions: 0.61

Description: Source Code Beautifier for C, C++, C#, ObjectiveC, Java, and others.

1.10.676 unibilium

Homepage:

• https://github.com/mauke/unibilium

Spack package:

• unibilium/package.py

Versions: 1.2.0

Description: A terminfo parsing library

1.10.677 unison

Homepage:

• https://www.cis.upenn.edu/~bcpierce/unison/

Spack package:

• unison/package.py

Versions: 2.48.4

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Build Dependencies ocaml

Description: Unison is a file-synchronization tool for OSX, Unix, and Windows. It allows two replicas of a collectionof files and directories to be stored on different hosts (or different disks on the same host), modified separately,and then brought up to date by propagating the changes in each replica to the other.

1.10.678 unixodbc

Homepage:

• http://www.unixodbc.org/

Spack package:

• unixodbc/package.py

Versions: 2.3.4

Description: ODBC is an open specification for providing application developers with a predictable API with whichto access Data Sources. Data Sources include SQL Servers and any Data Source with an ODBC Driver.

1.10.679 util-linux

Homepage:

• http://freecode.com/projects/util-linux

Spack package:

• util-linux/package.py

Versions: 2.25

Build Dependencies python

Link Dependencies python

Description: Util-linux is a suite of essential utilities for any Linux system.

1.10.680 valgrind

Homepage:

• http://valgrind.org/

Spack package:

• valgrind/package.py

Versions: 3.11.0, 3.10.1, 3.10.0

Build Dependencies boost, mpi

Link Dependencies boost, mpi

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Description: An instrumentation framework for building dynamic analysis. There are Valgrind tools that can auto-matically detect many memory management and threading bugs, and profile your programs in detail. You canalso use Valgrind to build new tools. Valgrind is Open Source / Free Software, and is freely available under theGNU General Public License, version 2.

1.10.681 vim

Homepage:

• http://www.vim.org

Spack package:

• vim/package.py

Versions: 7.4, 7.3, 7.2, 7.1, 7.0, 6.4, 6.3, 6.2, 6.1.405, 6.1, 6.0

Build Dependencies python, ruby

Link Dependencies python, ruby

Run Dependencies cscope

Description: Vim is a highly configurable text editor built to enable efficient text editing. It is an improved versionof the vi editor distributed with most UNIX systems. Vim is often called a “programmer’s editor,” and so usefulfor programming that many consider it an entire IDE. It’s not just for programmers, though. Vim is perfect forall kinds of text editing, from composing email to editing configuration files.

1.10.682 visit

Homepage:

• https://wci.llnl.gov/simulation/computer-codes/visit/

Spack package:

• visit/package.py

Versions: 2.10.2, 2.10.1

Build Dependencies python, vtk, qt, silo

Link Dependencies python, vtk, qt, silo

Description: VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.

1.10.683 vtk

Homepage:

• http://www.vtk.org

Spack package:

• vtk/package.py

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Versions: 7.0.0, 6.3.0, 6.1.0

Build Dependencies cmake, qt

Link Dependencies qt

Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computergraphics, image processing and visualization.

1.10.684 wget

Homepage:

• http://www.gnu.org/software/wget/

Spack package:

• wget/package.py

Versions: 1.17, 1.16

Build Dependencies openssl

Link Dependencies openssl

Description: GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non- interactive commandline tool, so it may easily be called from scripts, cronjobs, terminals without X-Windows support, etc.

1.10.685 wx

Homepage:

• http://www.wxwidgets.org/

Spack package:

• wx/package.py

Versions: 3.0.1, 2.8.12

Build Dependencies gtkplus

Link Dependencies gtkplus

Description: wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux andother platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many otherlanguages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feelbecause it uses the platform’s native API rather than emulating the GUI. It’s also extensive, free, open-sourceand mature.

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1.10.686 wxpropgrid

Homepage:

• http://wxpropgrid.sourceforge.net/

Spack package:

• wxpropgrid/package.py

Versions: 1.4.15

Build Dependencies wx

Link Dependencies wx

Description: wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.

1.10.687 xcb-proto

Homepage:

• http://xcb.freedesktop.org/

Spack package:

• xcb-proto/package.py

Versions: 1.11

Description: Protocol for libxcb

1.10.688 xerces-c

Homepage:

• https://xerces.apache.org/xerces-c

Spack package:

• xerces-c/package.py

Versions: 3.1.4

Description: Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes iteasy to give your application the ability to read and write XML data. A shared library is provided for parsing,generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.

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1.10.689 xorg-util-macros

Homepage:

• http://www.example.com

Spack package:

• xorg-util-macros/package.py

Versions: 1.19.0

Description: The m4 macros used by all of the Xorg packages.

1.10.690 xproto

Homepage:

• http://www.x.org/

Spack package:

• xproto/package.py

Versions: 7.0.29

Build Dependencies xorg-util-macros

Link Dependencies xorg-util-macros

Description: The Xorg protocol headers provide the header files required to build the system, and to allow otherapplications to build against the installed X Window system.

1.10.691 xz

Homepage:

• http://tukaani.org/xz/

Spack package:

• xz/package.py

Versions: 5.2.2, 5.2.0

Description: XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils werewritten for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor toLZMA Utils.

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1.10.692 yasm

Homepage:

• http://yasm.tortall.net

Spack package:

• yasm/package.py

Versions: 1.3.0

Description: Yasm is a complete rewrite of the NASM-2.11.06 assembler. It supports the x86 and AMD64 instructionsets, accepts NASM and GAS assembler syntaxes and outputs binary, ELF32 and ELF64 object formats.

1.10.693 zeromq

Homepage:

• http://zguide.zeromq.org/

Spack package:

• zeromq/package.py

Versions: 4.1.2, 4.1.1, 4.0.7, 4.0.6, 4.0.5

Build Dependencies libsodium

Link Dependencies libsodium

Description: The ZMQ networking/concurrency library and core API

1.10.694 zfp

Homepage:

• http://computation.llnl.gov/projects/floating-point-compression

Spack package:

• zfp/package.py

Versions: 0.5.0

Description: zfp is an open source C library for compressed floating-point arrays that supports very high throughputread and write random acces, target error bounds or bit rates. Although bit-for-bit lossless compression is notalways possible, zfp is usually accurate to within machine epsilon in near-lossless mode, and is often orders ofmagnitude more accurate than other lossy compressors.

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1.10.695 zlib

Homepage:

• http://zlib.net

Spack package:

• zlib/package.py

Versions: 1.2.8

Description: A free, general-purpose, legally unencumbered lossless data-compression library.

1.10.696 zoltan

Homepage:

• http://www.cs.sandia.gov/zoltan

Spack package:

• zoltan/package.py

Versions: 3.83, 3.8, 3.6, 3.3

Build Dependencies mpi

Link Dependencies mpi

Description: The Zoltan library is a toolkit of parallel combinatorial algorithms for parallel, unstructured, and/oradaptive scientific applications. Zoltan’s largest component is a suite of dynamic load-balancing and paritioningalgorithms that increase applications’ parallel performance by reducing idle time. Zoltan also has graph coloringand graph ordering algorithms, which are useful in task schedulers and parallel preconditioners.

1.10.697 zsh

Homepage:

• http://www.zsh.org

Spack package:

• zsh/package.py

Versions: 5.1.1

Build Dependencies pcre

Link Dependencies pcre

Description: Zsh is a shell designed for interactive use, although it is also a powerful scripting language. Many ofthe useful features of bash, ksh, and tcsh were incorporated into zsh; many original features were added.

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1.11 spack package

1.11.1 Subpackages

spack.cmd package

Subpackages

spack.cmd.common package

Submodules

spack.cmd.common.arguments modulespack.cmd.common.arguments.add_common_arguments(parser, list_of_arguments)

Module contents

Submodules

spack.cmd.activate module

spack.cmd.activate.activate(parser, args)

spack.cmd.activate.setup_parser(subparser)

spack.cmd.arch module

spack.cmd.arch.arch(parser, args)

spack.cmd.bootstrap module

spack.cmd.bootstrap.bootstrap(parser, args)

spack.cmd.bootstrap.get_origin_info(remote)

spack.cmd.bootstrap.setup_parser(subparser)

spack.cmd.cd module

spack.cmd.cd.cd(parser, args)

spack.cmd.cd.setup_parser(subparser)This is for decoration – spack cd is used through spack’s shell support. This allows spack cd to print a descriptivehelp message when called with -h.

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spack.cmd.checksum module

spack.cmd.checksum.checksum(parser, args)

spack.cmd.checksum.get_checksums(versions, urls, **kwargs)

spack.cmd.checksum.setup_parser(subparser)

spack.cmd.clean module

spack.cmd.clean.clean(parser, args)

spack.cmd.clean.setup_parser(subparser)

spack.cmd.compiler module

spack.cmd.compiler.compiler(parser, args)

spack.cmd.compiler.compiler_find(args)Search either $PATH or a list of paths OR MODULES for compilers and add them to Spack’s configuration.

spack.cmd.compiler.compiler_info(args)Print info about all compilers matching a spec.

spack.cmd.compiler.compiler_list(args)

spack.cmd.compiler.compiler_remove(args)

spack.cmd.compiler.setup_parser(subparser)

spack.cmd.compilers module

spack.cmd.compilers.compilers(parser, args)

spack.cmd.compilers.setup_parser(subparser)

spack.cmd.config module

spack.cmd.config.config(parser, args)

spack.cmd.config.config_edit(args)

spack.cmd.config.config_get(args)

spack.cmd.config.setup_parser(subparser)

spack.cmd.create module

class spack.cmd.create.BuildSystemGuesserBases: object

spack.cmd.create.create(parser, args)

spack.cmd.create.fetch_tarballs(url, name, version)Try to find versions of the supplied archive by scraping the web. Prompts the user to select how many todownload if many are found.

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spack.cmd.create.find_repository(spec, args)

spack.cmd.create.guess_name_and_version(url, args)

spack.cmd.create.make_version_calls(ver_hash_tuples)Adds a version() call to the package for each version found.

spack.cmd.create.setup_parser(subparser)

spack.cmd.deactivate module

spack.cmd.deactivate.deactivate(parser, args)

spack.cmd.deactivate.setup_parser(subparser)

spack.cmd.dependents module

spack.cmd.dependents.dependents(parser, args)

spack.cmd.dependents.setup_parser(subparser)

spack.cmd.diy module

spack.cmd.diy.diy(self, args)

spack.cmd.diy.setup_parser(subparser)

spack.cmd.doc module

spack.cmd.doc.doc(parser, args)

spack.cmd.doc.setup_parser(subparser)

spack.cmd.edit module

spack.cmd.edit.edit(parser, args)

spack.cmd.edit.edit_package(name, repo_path, namespace, force=False)

spack.cmd.edit.setup_parser(subparser)

spack.cmd.env module

spack.cmd.env.env(parser, args)

spack.cmd.env.setup_parser(subparser)

spack.cmd.extensions module

spack.cmd.extensions.extensions(parser, args)

spack.cmd.extensions.setup_parser(subparser)

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spack.cmd.fetch module

spack.cmd.fetch.fetch(parser, args)

spack.cmd.fetch.setup_parser(subparser)

spack.cmd.find module

spack.cmd.find.find(parser, args)

spack.cmd.find.query_arguments(args)

spack.cmd.find.setup_parser(subparser)

spack.cmd.graph module

spack.cmd.graph.graph(parser, args)

spack.cmd.graph.setup_parser(subparser)

spack.cmd.help module

spack.cmd.help.help(parser, args)

spack.cmd.help.setup_parser(subparser)

spack.cmd.info module

spack.cmd.info.info(parser, args)

spack.cmd.info.padder(str_list, extra=0)Return a function to pad elements of a list.

spack.cmd.info.print_text_info(pkg)Print out a plain text description of a package.

spack.cmd.info.setup_parser(subparser)

spack.cmd.install module

spack.cmd.install.install(parser, args)

spack.cmd.install.setup_parser(subparser)

spack.cmd.list module

spack.cmd.list.list(parser, args)

spack.cmd.list.setup_parser(subparser)

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spack.cmd.load module

spack.cmd.load.load(parser, args)

spack.cmd.load.setup_parser(subparser)Parser is only constructed so that this prints a nice help message with -h.

spack.cmd.location module

spack.cmd.location.location(parser, args)

spack.cmd.location.setup_parser(subparser)

spack.cmd.md5 module

spack.cmd.md5.compute_md5_checksum(url)

spack.cmd.md5.md5(parser, args)

spack.cmd.md5.setup_parser(subparser)

spack.cmd.mirror module

spack.cmd.mirror.mirror(parser, args)

spack.cmd.mirror.mirror_add(args)Add a mirror to Spack.

spack.cmd.mirror.mirror_create(args)Create a directory to be used as a spack mirror, and fill it with package archives.

spack.cmd.mirror.mirror_list(args)Print out available mirrors to the console.

spack.cmd.mirror.mirror_remove(args)Remove a mirror by name.

spack.cmd.mirror.setup_parser(subparser)

spack.cmd.module module

exception spack.cmd.module.MultipleMatchesBases: exceptions.Exception

exception spack.cmd.module.NoMatchBases: exceptions.Exception

spack.cmd.module.find(mtype, specs, args)Look at all installed packages and see if the spec provided matches any. If it does, check whether there isa module file of type <mtype> there, and print out the name that the user should type to use that package’smodule.

spack.cmd.module.loads(mtype, specs, args)Prompt the list of modules associated with a list of specs

spack.cmd.module.module(parser, args)

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spack.cmd.module.refresh(mtype, specs, args)Regenerate module files for item in specs

spack.cmd.module.rm(mtype, specs, args)Deletes module files associated with items in specs

spack.cmd.module.setup_parser(subparser)

spack.cmd.module.subcommand(subparser_name)Registers a function in the callbacks dictionary

spack.cmd.package_list module

spack.cmd.package_list.github_url(pkg)Link to a package file on github.

spack.cmd.package_list.package_list(parser, args)

spack.cmd.package_list.print_rst_package_list()Print out information on all packages in restructured text.

spack.cmd.package_list.rst_table(elts)Print out a RST-style table.

spack.cmd.patch module

spack.cmd.patch.patch(parser, args)

spack.cmd.patch.setup_parser(subparser)

spack.cmd.pkg module

spack.cmd.pkg.diff_packages(rev1, rev2)

spack.cmd.pkg.get_git()

spack.cmd.pkg.list_packages(rev)

spack.cmd.pkg.pkg(parser, args)

spack.cmd.pkg.pkg_add(args)

spack.cmd.pkg.pkg_added(args)Show packages added since a commit.

spack.cmd.pkg.pkg_diff(args)Compare packages available in two different git revisions.

spack.cmd.pkg.pkg_list(args)List packages associated with a particular spack git revision.

spack.cmd.pkg.pkg_removed(args)Show packages removed since a commit.

spack.cmd.pkg.setup_parser(subparser)

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spack.cmd.providers module

spack.cmd.providers.providers(parser, args)

spack.cmd.providers.setup_parser(subparser)

spack.cmd.purge module

spack.cmd.purge.purge(parser, args)

spack.cmd.purge.setup_parser(subparser)

spack.cmd.python module

spack.cmd.python.python(parser, args)

spack.cmd.python.setup_parser(subparser)

spack.cmd.reindex module

spack.cmd.reindex.reindex(parser, args)

spack.cmd.repo module

spack.cmd.repo.repo(parser, args)

spack.cmd.repo.repo_add(args)Add a package source to Spack’s configuration.

spack.cmd.repo.repo_create(args)Create a new package repository.

spack.cmd.repo.repo_list(args)Show registered repositories and their namespaces.

spack.cmd.repo.repo_remove(args)Remove a repository from Spack’s configuration.

spack.cmd.repo.setup_parser(subparser)

spack.cmd.restage module

spack.cmd.restage.restage(parser, args)

spack.cmd.restage.setup_parser(subparser)

spack.cmd.setup module

spack.cmd.setup.setup(self, args)

spack.cmd.setup.setup_parser(subparser)

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spack.cmd.spec module

spack.cmd.spec.setup_parser(subparser)

spack.cmd.spec.spec(parser, args)

spack.cmd.stage module

spack.cmd.stage.setup_parser(subparser)

spack.cmd.stage.stage(parser, args)

spack.cmd.test module

class spack.cmd.test.MockCacheBases: object

fetcher(targetPath, digest)

store(copyCmd, relativeDst)

class spack.cmd.test.MockCacheFetcherBases: object

fetch()

set_stage(stage)

spack.cmd.test.setup_parser(subparser)

spack.cmd.test.test(parser, args)

spack.cmd.test_install module

class spack.cmd.test_install.TestCase(classname, name, time=None)Bases: object

results = {0: None, 1: ‘failure’, 2: ‘skipped’, 3: ‘error’}

set_result(result_type, message=None, error_type=None, text=None)

class spack.cmd.test_install.TestResultBases: object

ERRORED = 3

FAILED = 1

PASSED = 0

SKIPPED = 2

class spack.cmd.test_install.TestSuite(filename)Bases: object

append(item)

spack.cmd.test_install.failed_dependencies(spec)

spack.cmd.test_install.fetch_log(path)

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spack.cmd.test_install.get_filename(args, top_spec)

spack.cmd.test_install.get_top_spec_or_die(args)

spack.cmd.test_install.install_single_spec(spec, number_of_jobs)

spack.cmd.test_install.setup_parser(subparser)

spack.cmd.test_install.test_install(parser, args)

spack.cmd.uninstall module

spack.cmd.uninstall.concretize_specs(specs, allow_multiple_matches=False, force=False)Returns a list of specs matching the non necessarily concretized specs given from cli

Args: specs: list of specs to be matched against installed packages allow_multiple_matches : if True multiplematches are admitted

Return: list of specs

spack.cmd.uninstall.do_uninstall(specs, force)Uninstalls all the specs in a list.

Args: specs: list of specs to be uninstalled force: force uninstallation (boolean)

spack.cmd.uninstall.installed_dependents(specs)Returns a dictionary that maps a spec with a list of its installed dependents

Args: specs: list of specs to be checked for dependents

Returns: dictionary of installed dependents

spack.cmd.uninstall.setup_parser(subparser)

spack.cmd.uninstall.uninstall(parser, args)

spack.cmd.unload module

spack.cmd.unload.setup_parser(subparser)Parser is only constructed so that this prints a nice help message with -h.

spack.cmd.unload.unload(parser, args)

spack.cmd.unuse module

spack.cmd.unuse.setup_parser(subparser)Parser is only constructed so that this prints a nice help message with -h.

spack.cmd.unuse.unuse(parser, args)

spack.cmd.url_parse module

spack.cmd.url_parse.print_name_and_version(url)

spack.cmd.url_parse.setup_parser(subparser)

spack.cmd.url_parse.url_parse(parser, args)

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spack.cmd.urls module

spack.cmd.urls.setup_parser(subparser)

spack.cmd.urls.urls(parser, args)

spack.cmd.use module

spack.cmd.use.setup_parser(subparser)Parser is only constructed so that this prints a nice help message with -h.

spack.cmd.use.use(parser, args)

spack.cmd.versions module

spack.cmd.versions.setup_parser(subparser)

spack.cmd.versions.versions(parser, args)

spack.cmd.view module

Produce a “view” of a Spack DAG.

A “view” is file hierarchy representing the union of a number of Spack-installed package file hierarchies. The unionis formed from:

• specs resolved from the package names given by the user (the seeds)

• all depenencies of the seeds unless user specifies –no-depenencies

• less any specs with names matching the regular expressions given by –exclude

The view can be built and tore down via a number of methods (the “actions”):

• symlink :: a file system view which is a directory hierarchy that is the union of the hierarchies of the installedpackages in the DAG where installed files are referenced via symlinks.

• hardlink :: like the symlink view but hardlinks are used.

• statlink :: a view producing a status report of a symlink or hardlink view.

The file system view concept is imspired by Nix, implemented by brett.viren@gmail.com ca 2016.

spack.cmd.view.assuredir(path)Assure path exists as a directory

spack.cmd.view.check_one(spec, path, verbose=False)Check status of view in path against spec

spack.cmd.view.filter_exclude(specs, exclude)Filter specs given sequence of exclude regex

spack.cmd.view.flatten(seeds, descend=True)Normalize and flattend seed specs and descend hiearchy

spack.cmd.view.link_one(spec, path, link=<built-in function symlink>, verbose=False)Link all files in spec into directory path.

spack.cmd.view.purge_empty_directories(path)Ascend up from the leaves accessible from path and remove empty directories.

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spack.cmd.view.relative_to(prefix, path)Return end of path relative to prefix

spack.cmd.view.remove_one(spec, path, verbose=False)Remove any files found in spec from path and purge empty directories.

spack.cmd.view.setup_parser(sp)

spack.cmd.view.transform_path(spec, path, prefix=None)Return the a relative path corresponding to given path spec.prefix

spack.cmd.view.view(parser, args)Produce a view of a set of packages.

spack.cmd.view.visitor_add(specs, args)Symlink all files found in specs

spack.cmd.view.visitor_check(specs, args)Give status of view in args.path relative to specs

spack.cmd.view.visitor_hard(specs, args)Hardlink all files found in specs

spack.cmd.view.visitor_hardlink(specs, args)Hardlink all files found in specs

spack.cmd.view.visitor_remove(specs, args)Remove all files and directories found in specs from args.path

spack.cmd.view.visitor_rm(specs, args)Remove all files and directories found in specs from args.path

spack.cmd.view.visitor_soft(specs, args)Symlink all files found in specs

spack.cmd.view.visitor_statlink(specs, args)Give status of view in args.path relative to specs

spack.cmd.view.visitor_status(specs, args)Give status of view in args.path relative to specs

spack.cmd.view.visitor_symlink(specs, args)Symlink all files found in specs

Module contents

spack.cmd.ask_for_confirmation(message)

spack.cmd.disambiguate_spec(spec)

spack.cmd.display_specs(specs, **kwargs)

spack.cmd.elide_list(line_list, max_num=10)Takes a long list and limits it to a smaller number of elements, replacing intervening elements with ‘...’. Forexample:

elide_list([1,2,3,4,5,6], 4)

gives:

[1, 2, 3, '...', 6]

spack.cmd.get_cmd_function_name(name)

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spack.cmd.get_command(name)Imports the command’s function from a module and returns it.

spack.cmd.get_module(name)Imports the module for a particular command name and returns it.

spack.cmd.gray_hash(spec, length)

spack.cmd.parse_specs(args, **kwargs)Convenience function for parsing arguments from specs. Handles common exceptions and dies if there areerrors.

spack.compilers package

Submodules

spack.compilers.cce module

class spack.compilers.cce.Cce(cspec, operating_system, paths, modules=[], alias=None, **kwargs)Bases: spack.compiler.Compiler

Cray compiler environment compiler.

PrgEnv = ‘PrgEnv-cray’

PrgEnv_compiler = ‘cce’

cc_names = [’cc’]

cxx_names = [’CC’]

classmethod default_version(comp)

f77_names = [’ftn’]

fc_names = [’ftn’]

link_paths = {‘cc’: ‘cc’, ‘cxx’: ‘c++’, ‘f77’: ‘f77’, ‘fc’: ‘fc’}

suffixes = [’-mp-\\d\\.\\d’]

spack.compilers.clang module

class spack.compilers.clang.Clang(cspec, operating_system, paths, modules=[], alias=None,**kwargs)

Bases: spack.compiler.Compiler

cc_names = [’clang’]

cxx11_flag

cxx_names = [’clang++’]

classmethod default_version(comp)The ‘–version’ option works for clang compilers. On most platforms, output looks like this:

clang version 3.1 (trunk 149096)Target: x86_64-unknown-linux-gnuThread model: posix

On Mac OS X, it looks like this:

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f77_names = []

fc_names = []

is_apple

link_paths = {‘cc’: ‘clang/clang’, ‘cxx’: ‘clang/clang++’, ‘f77’: ‘f77’, ‘fc’: ‘f90’}

openmp_flag

spack.compilers.gcc module

class spack.compilers.gcc.Gcc(cspec, operating_system, paths, modules=[], alias=None, **kwargs)Bases: spack.compiler.Compiler

PrgEnv = ‘PrgEnv-gnu’

PrgEnv_compiler = ‘gcc’

cc_names = [’gcc’]

cxx11_flag

cxx14_flag

cxx_names = [’g++’]

f77_names = [’gfortran’]

classmethod f77_version(f77)

fc_names = [’gfortran’]

classmethod fc_version(fc)

link_paths = {‘cc’: ‘gcc/gcc’, ‘cxx’: ‘gcc/g++’, ‘f77’: ‘gcc/gfortran’, ‘fc’: ‘gcc/gfortran’}

openmp_flag

suffixes = [’-mp-\\d\\.\\d’, ‘-\\d\\.\\d’, ‘-\\d’]

spack.compilers.intel module

class spack.compilers.intel.Intel(cspec, operating_system, paths, modules=[], alias=None,**kwargs)

Bases: spack.compiler.Compiler

PrgEnv = ‘PrgEnv-intel’

PrgEnv_compiler = ‘intel’

cc_names = [’icc’]

cxx11_flag

cxx_names = [’icpc’]

classmethod default_version(comp)The ‘–version’ option seems to be the most consistent one for intel compilers. Output looks like this:

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icpc (ICC) 12.1.5 20120612Copyright (C) 1985-2012 Intel Corporation. All rights reserved.

or:

ifort (IFORT) 12.1.5 20120612Copyright (C) 1985-2012 Intel Corporation. All rights reserved.

f77_names = [’ifort’]

fc_names = [’ifort’]

link_paths = {‘cc’: ‘intel/icc’, ‘cxx’: ‘intel/icpc’, ‘f77’: ‘intel/ifort’, ‘fc’: ‘intel/ifort’}

openmp_flag

spack.compilers.nag module

class spack.compilers.nag.Nag(cspec, operating_system, paths, modules=[], alias=None, **kwargs)Bases: spack.compiler.Compiler

cc_names = []

cxx11_flag

cxx_names = []

classmethod default_version(comp)The ‘-V’ option works for nag compilers. Output looks like this:

NAG Fortran Compiler Release 6.0(Hibiya) Build 1037Product NPL6A60NA for x86-64 Linux

f77_names = [’nagfor’]

f77_rpath_arg

fc_names = [’nagfor’]

fc_rpath_arg

link_paths = {‘cc’: ‘cc’, ‘cxx’: ‘c++’, ‘f77’: ‘nag/nagfor’, ‘fc’: ‘nag/nagfor’}

openmp_flag

spack.compilers.pgi module

class spack.compilers.pgi.Pgi(cspec, operating_system, paths, modules=[], alias=None, **kwargs)Bases: spack.compiler.Compiler

PrgEnv = ‘PrgEnv-pgi’

PrgEnv_compiler = ‘pgi’

cc_names = [’pgcc’]

cxx11_flag

cxx_names = [’pgc++’, ‘pgCC’]

classmethod default_version(comp)The ‘-V’ option works for all the PGI compilers. Output looks like this:

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pgcc 15.10-0 64-bit target on x86-64 Linux -tp sandybridgeThe Portland Group - PGI Compilers and ToolsCopyright (c) 2015, NVIDIA CORPORATION. All rights reserved.

f77_names = [’pgfortran’, ‘pgf77’]

fc_names = [’pgfortran’, ‘pgf95’, ‘pgf90’]

link_paths = {‘cc’: ‘pgi/pgcc’, ‘cxx’: ‘pgi/pgc++’, ‘f77’: ‘pgi/pgfortran’, ‘fc’: ‘pgi/pgfortran’}

openmp_flag

spack.compilers.xl module

class spack.compilers.xl.Xl(cspec, operating_system, paths, modules=[], alias=None, **kwargs)Bases: spack.compiler.Compiler

cc_names = [’xlc’, ‘xlc_r’]

cxx11_flag

cxx_names = [’xlC’, ‘xlC_r’, ‘xlc++’, ‘xlc++_r’]

classmethod default_version(comp)The ‘-qversion’ is the standard option fo XL compilers. Output looks like this:

IBM XL C/C++ for Linux, V11.1 (5724-X14)Version: 11.01.0000.0000

or:

IBM XL Fortran for Linux, V13.1 (5724-X16)Version: 13.01.0000.0000

or:

IBM XL C/C++ for AIX, V11.1 (5724-X13)Version: 11.01.0000.0009

or:

IBM XL C/C++ Advanced Edition for Blue Gene/P, V9.0Version: 09.00.0000.0017

f77_names = [’xlf’, ‘xlf_r’]

classmethod f77_version(f77)

fc_names = [’xlf90’, ‘xlf90_r’, ‘xlf95’, ‘xlf95_r’, ‘xlf2003’, ‘xlf2003_r’, ‘xlf2008’, ‘xlf2008_r’]

classmethod fc_version(fc)The fortran and C/C++ versions of the XL compiler are always two units apart. By this we mean thatthe fortran release that goes with XL C/C++ 11.1 is 13.1. Having such a difference in version number isconfusing spack quite a lot. Most notably if you keep the versions as is the default xl compiler will onlyhave fortran and no C/C++. So we associate the Fortran compiler with the version associated to the C/C++compiler. One last stumble. Version numbers over 10 have at least a .1 those under 10 a .0. There is no xlf9.x or under currently available. BG/P and BG/L can such a compiler mix and possibly older version ofAIX and linux on power.

link_paths = {‘cc’: ‘xl/xlc’, ‘cxx’: ‘xl/xlc++’, ‘f77’: ‘xl/xlf’, ‘fc’: ‘xl/xlf90’}

openmp_flag

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Module contents

This module contains functions related to finding compilers on the system and configuring Spack to use multiplecompilers.

exception spack.compilers.CompilerSpecInsufficientlySpecificError(compiler_spec)Bases: spack.error.SpackError

exception spack.compilers.InvalidCompilerConfigurationError(compiler_spec)Bases: spack.error.SpackError

exception spack.compilers.NoCompilerForSpecError(compiler_spec, target)Bases: spack.error.SpackError

exception spack.compilers.NoCompilersErrorBases: spack.error.SpackError

spack.compilers.add_compilers_to_config(compilers, scope=None, init_config=True)Add compilers to the config for the specified architecture.

Arguments:

• compilers: a list of Compiler objects.

• scope: configuration scope to modify.

spack.compilers.all_compiler_types()

spack.compilers.all_compilers(scope=None, init_config=True)

spack.compilers.all_compilers_config(scope=None, init_config=True)Return a set of specs for all the compiler versions currently available to build with. These are instances ofCompilerSpec.

spack.compilers.all_os_classes()Return the list of classes for all operating systems available on this platform

spack.compilers.class_for_compiler_name(compiler_name)Given a compiler module name, get the corresponding Compiler class.

spack.compilers.compiler_for_spec(cspec_like, *args, **kwargs)

spack.compilers.compilers_for_spec(cspec_like, *args, **kwargs)

spack.compilers.default_compiler()

spack.compilers.find(cspec_like, *args, **kwargs)

spack.compilers.find_compilers(*paths)Return a list of compilers found in the suppied paths. This invokes the find_compilers() method for each oper-ating system associated with the host platform, and appends the compilers detected to a list.

spack.compilers.get_compiler_config(scope=None, init_config=True)Return the compiler configuration for the specified architecture.

spack.compilers.remove_compiler_from_config(cspec_like, *args, **kwargs)

spack.compilers.supported(cspec_like, *args, **kwargs)

spack.compilers.supported_compilers()Return a set of names of compilers supported by Spack.

See available_compilers() to get a list of all the available versions of supported compilers.

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spack.hooks package

Submodules

spack.hooks.dotkit module

spack.hooks.dotkit.post_install(pkg)

spack.hooks.dotkit.post_uninstall(pkg)

spack.hooks.extensions module

spack.hooks.extensions.pre_uninstall(pkg)

spack.hooks.licensing module

spack.hooks.licensing.post_install(pkg)This hook symlinks local licenses to the global license for licensed software.

spack.hooks.licensing.pre_install(pkg)This hook handles global license setup for licensed software.

spack.hooks.licensing.set_up_license(pkg)Prompt the user, letting them know that a license is required.

For packages that rely on license files, a global license file is created and opened for editing.

For packages that rely on environment variables to point to a license, a warning message is printed.

For all other packages, documentation on how to set up a license is printed.

spack.hooks.licensing.symlink_license(pkg)Create local symlinks that point to the global license file.

spack.hooks.licensing.write_license_file(pkg, license_path)Writes empty license file.

Comments give suggestions on alternative methods of installing a license.

spack.hooks.sbang module

spack.hooks.sbang.filter_shebang(path)Adds a second shebang line, using sbang, at the beginning of a file.

spack.hooks.sbang.filter_shebangs_in_directory(directory)

spack.hooks.sbang.post_install(pkg)This hook edits scripts so that they call /bin/bash $spack_prefix/bin/sbang instead of something longer than theshebang limit.

spack.hooks.sbang.shebang_too_long(path)Detects whether a file has a shebang line that is too long.

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spack.hooks.tclmodule module

spack.hooks.tclmodule.post_install(pkg)

spack.hooks.tclmodule.post_uninstall(pkg)

Module contents

This package contains modules with hooks for various stages in the Spack install process. You can add modules hereand they’ll be executaed by package at various times during the package lifecycle.

Each hook is just a function that takes a package as a parameter. Hooks are not executed in any particular order.

Currently the following hooks are supported:

• pre_install()

• post_install()

• pre_uninstall()

• post_uninstall()

This can be used to implement support for things like module systems (e.g. modules, dotkit, etc.) or to add othercustom features.

class spack.hooks.HookRunner(hook_name)Bases: object

spack.operating_systems package

Submodules

spack.operating_systems.cnl module

class spack.operating_systems.cnl.CnlBases: spack.architecture.OperatingSystem

Compute Node Linux (CNL) is the operating system used for the Cray XC series super computers. It is a verystripped down version of GNU/Linux. Any compilers found through this operating system will be used withmodules. If updated, user must make sure that version and name are updated to indicate that OS has beenupgraded (or downgraded)

find_compiler(cmp_cls, *paths)

find_compilers(*paths)

spack.operating_systems.linux_distro module

class spack.operating_systems.linux_distro.LinuxDistroBases: spack.architecture.OperatingSystem

This class will represent the autodetected operating system for a Linux System. Since there are many differentflavors of Linux, this class will attempt to encompass them all through autodetection using the python moduleplatform and the method platform.dist()

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spack.operating_systems.mac_os module

class spack.operating_systems.mac_os.MacOsBases: spack.architecture.OperatingSystem

This class represents the macOS operating system. This will be auto detected using the python plat-form.mac_ver. The macOS platform will be represented using the major version operating system name, i.eel capitan, yosemite...etc.

Module contents

spack.platforms package

Submodules

spack.platforms.bgq module

class spack.platforms.bgq.BgqBases: spack.architecture.Platform

back_end = ‘powerpc’

default = ‘powerpc’

classmethod detect()

front_end = ‘power7’

priority = 30

spack.platforms.cray module

class spack.platforms.cray.CrayBases: spack.architecture.Platform

classmethod detect()

priority = 10

classmethod setup_platform_environment(pkg, env)Change the linker to default dynamic to be more similar to linux/standard linker behavior

spack.platforms.darwin module

class spack.platforms.darwin.DarwinBases: spack.architecture.Platform

back_end = ‘x86_64’

default = ‘x86_64’

classmethod detect()

front_end = ‘x86_64’

priority = 89

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spack.platforms.linux module

class spack.platforms.linux.LinuxBases: spack.architecture.Platform

classmethod detect()

priority = 90

spack.platforms.test module

class spack.platforms.test.TestBases: spack.architecture.Platform

back_end = ‘x86_64’

back_os = ‘CNL10’

default = ‘x86_64’

default_os = ‘CNL10’

classmethod detect()

front_end = ‘x86_32’

priority = 1000000

Module contents

spack.schema package

Submodules

spack.schema.compilers module

Schema for compiler configuration files.

spack.schema.mirrors module

Schema for mirror configuration files.

spack.schema.modules module

Schema for mirror configuration files.

spack.schema.packages module

Schema for packages.yaml configuration files.

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spack.schema.repos module

Schema for repository configuration files.

spack.schema.targets module

Schema for target configuration files.

Module contents

This module contains jsonschema files for all of Spack’s YAML formats.

spack.test package

Subpackages

spack.test.cmd package

Submodules

spack.test.cmd.find moduleclass spack.test.cmd.find.FindTest(methodName=’runTest’)

Bases: unittest.case.TestCase

test_query_arguments()

spack.test.cmd.module moduleclass spack.test.cmd.module.TestModule(methodName=’runTest’)

Bases: spack.test.mock_database.MockDatabase

test_module_common_operations()

spack.test.cmd.test_compiler_cmd moduleclass spack.test.cmd.test_compiler_cmd.CompilerCmdTest(methodName=’runTest’)

Bases: spack.test.mock_packages_test.MockPackagesTest

Test compiler commands for add and remove

test_compiler_add()

test_compiler_remove()class spack.test.cmd.test_compiler_cmd.MockArgs(add_paths=[], scope=None, com-

piler_spec=None, all=None)Bases: object

spack.test.cmd.test_compiler_cmd.make_mock_compiler()Make a directory containing a fake, but detectable compiler.

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spack.test.cmd.test_install moduleclass spack.test.cmd.test_install.MockArgs(package)

Bases: objectclass spack.test.cmd.test_install.MockPackage(spec, buildLogPath)

Bases: object

do_install(*args, **kwargs)

class spack.test.cmd.test_install.MockPackageDb(init=None)Bases: object

get(spec)

class spack.test.cmd.test_install.MockSpec(name, version, hashStr=None)Bases: object

dag_hash()

dependencies(deptype=None)

dependents(deptype=None)

short_spec

traverse(order=None)

class spack.test.cmd.test_install.TestInstallTest(methodName=’runTest’)Bases: unittest.case.TestCase

Tests test-install where X->Y

setUp()

tearDown()

test_dependency_already_installed()

test_installing_both()

spack.test.cmd.test_install.mock_fetch_log(path)

spack.test.cmd.test_install.mock_open(*args, **kwds)

spack.test.cmd.uninstall moduleclass spack.test.cmd.uninstall.MockArgs(packages, all=False, force=False, dependents=False)

Bases: objectclass spack.test.cmd.uninstall.TestUninstall(methodName=’runTest’)

Bases: spack.test.mock_database.MockDatabase

test_uninstall()

Module contents

Submodules

spack.test.architecture module

Test checks if the architecture class is created correctly and also that the functions are looking for the correct architec-ture name

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class spack.test.architecture.ArchitectureTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

setUp()

tearDown()

test_boolness()

test_dict_functions_for_architecture()

test_platform()

test_user_back_end_input()Test when user inputs backend that both the backend target and backend operating system match

test_user_defaults()

test_user_front_end_input()Test when user inputs just frontend that both the frontend target and frontend operating system match

test_user_input_combination()

spack.test.build_system_guess module

class spack.test.build_system_guess.InstallTest(methodName=’runTest’)Bases: unittest.case.TestCase

Tests the build system guesser in spack create

check_archive(filename, system)

setUp()

tearDown()

test_R()

test_autotools()

test_cmake()

test_python()

test_scons()

test_unknown()

spack.test.cc module

This test checks that the Spack cc compiler wrapper is parsing arguments correctly.

class spack.test.cc.CompilerTest(methodName=’runTest’)Bases: unittest.case.TestCase

check_cc(command, args, expected)

check_cpp(command, args, expected)

check_cxx(command, args, expected)

check_fc(command, args, expected)

check_ld(command, args, expected)

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setUp()

tearDown()

test_all_deps()Ensure includes and RPATHs for all deps are added.

test_as_mode()

test_ccld_mode()

test_cpp_mode()

test_dep_include()Ensure a single dependency include directory is added.

test_dep_lib()Ensure a single dependency RPATH is added.

test_dep_rpath()Ensure RPATHs for root package are added.

test_flags()

test_ld_deps()Ensure no (extra) -I args or -Wl, are passed in ld mode.

test_ld_deps_reentrant()Make sure ld -r is handled correctly on OS’s where it doesn’t support rpaths.

test_ld_mode()

test_vcheck_mode()

spack.test.concretize module

class spack.test.concretize.ConcretizeTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

check_concretize(abstract_spec)

check_spec(abstract, concrete)

test_compiler_child()

test_compiler_inheritance()

test_concretize_dag()

test_concretize_no_deps()

test_concretize_preferred_version()

test_concretize_two_virtuals()Test a package with multiple virtual dependencies.

test_concretize_two_virtuals_with_dual_provider()Test a package with multiple virtual dependencies and force a provider that provides both.

test_concretize_two_virtuals_with_dual_provider_and_a_conflict()Test a package with multiple virtual dependencies and force a provider that provides both, and anotherconflicting package that provides one.

test_concretize_two_virtuals_with_one_bound()Test a package with multiple virtual dependencies and one preset.

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test_concretize_two_virtuals_with_two_bound()Test a package with multiple virtual deps and two of them preset.

test_concretize_variant()

test_concretize_with_provides_when()Make sure insufficient versions of MPI are not in providers list when we ask for some advanced version.

test_concretize_with_restricted_virtual()

test_concretize_with_virtual()

test_conretize_compiler_flags()

test_external_and_virtual()

test_external_package()

test_external_package_module()

test_find_spec_children()

test_find_spec_none()

test_find_spec_parents()Tests the spec finding logic used by concretization.

test_find_spec_self()

test_find_spec_sibling()

test_my_dep_depends_on_provider_of_my_virtual_dep()

test_nobuild_package()

test_virtual_is_fully_expanded_for_callpath()

test_virtual_is_fully_expanded_for_mpileaks()

spack.test.concretize_preferences module

class spack.test.concretize_preferences.ConcretizePreferencesTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

Test concretization preferences are being applied correctly.

assert_variant_values(spec, **variants)

concretize(abstract_spec)

setUp()Create config section to store concretization preferences

tearDown()

test_preferred_compilers()Test preferred compilers are applied correctly

test_preferred_providers()Test preferred providers of virtual packages are applied correctly

test_preferred_variants()Test preferred variants are applied correctly

test_preferred_versions()Test preferred package versions are applied correctly

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update_packages(pkgname, section, value)Update config and reread package list

spack.test.config module

class spack.test.config.ConfigTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

check_config(comps, *compiler_names)Check that named compilers in comps match Spack’s config.

setUp()

tearDown()

test_write_key_in_memory()

test_write_key_to_disk()

test_write_list_in_memory()

test_write_to_same_priority_file()

spack.test.database module

These tests check the database is functioning properly, both in memory and in its file

class spack.test.database.DatabaseTest(methodName=’runTest’)Bases: spack.test.mock_database.MockDatabase

test_005_db_exists()Make sure db cache file exists after creating.

test_010_all_install_sanity()Ensure that the install layout reflects what we think it does.

test_015_write_and_read()

test_020_db_sanity()Make sure query() returns what’s actually in the db.

test_030_db_sanity_from_another_process()

test_040_ref_counts()Ensure that we got ref counts right when we read the DB.

test_050_basic_query()Ensure querying database is consistent with what is installed.

test_060_remove_and_add_root_package()

test_070_remove_and_add_dependency_package()

test_080_root_ref_counts()

test_090_non_root_ref_counts()

test_100_no_write_with_exception_on_remove()

test_110_no_write_with_exception_on_install()

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spack.test.directory_layout module

This test verifies that the Spack directory layout works properly.

class spack.test.directory_layout.DirectoryLayoutTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

Tests that a directory layout works correctly and produces a consistent install path.

setUp()

tearDown()

test_find()Test that finding specs within an install layout works.

test_handle_unknown_package()This test ensures that spack can at least do some operations with packages that are installed but that it doesnot know about. This is actually not such an uncommon scenario with spack; it can happen when youswitch from a git branch where you’re working on a new package.

This test ensures that the directory layout stores enough information about installed packages’ specs touninstall or query them again if the package goes away.

test_read_and_write_spec()This goes through each package in spack and creates a directory for it. It then ensures that the spec for thedirectory’s installed package can be read back in consistently, and finally that the directory can be removedby the directory layout.

spack.test.environment module

class spack.test.environment.EnvironmentTest(methodName=’runTest’)Bases: unittest.case.TestCase

setUp()

tearDown()

test_extend()

test_extra_arguments()

test_path_manipulation()

test_set()

test_set_path()

test_source_files()

test_unset()

spack.test.file_cache module

Test Spack’s FileCache.

class spack.test.file_cache.FileCacheTest(methodName=’runTest’)Bases: unittest.case.TestCase

Ensure that a file cache can properly write to a file and recover its contents.

setUp()

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tearDown()

test_remove()Test removing an entry from the cache.

test_write_and_read_cache_file()Test writing then reading a cached file.

test_write_and_write_cache_file()Test two write transactions on a cached file.

spack.test.git_fetch module

class spack.test.git_fetch.GitFetchTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

Tests fetching from a dummy git repository.

assert_rev(rev)Check that the current git revision is equal to the supplied rev.

setUp()Create a git repository with master and two other branches, and one tag, so that we can experiment on it.

tearDown()Destroy the stage space used by this test.

test_fetch_branch()Test fetching a branch.

test_fetch_commit()Test fetching a particular commit.

test_fetch_master()Test a default git checkout with no commit or tag specified.

test_fetch_tag()Test fetching a tag.

try_fetch(rev, test_file, args)Tries to:

1.Fetch the repo using a fetch strategy constructed with supplied args.

2.Check if the test_file is in the checked out repository.

3.Assert that the repository is at the revision supplied.

4.Add and remove some files, then reset the repo, and ensure it’s all there again.

spack.test.hg_fetch module

class spack.test.hg_fetch.HgFetchTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

Tests fetching from a dummy hg repository.

setUp()Create a hg repository with master and two other branches, and one tag, so that we can experiment on it.

tearDown()Destroy the stage space used by this test.

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test_fetch_default()Test a default hg checkout with no commit or tag specified.

test_fetch_rev0()Test fetching a branch.

try_fetch(rev, test_file, args)Tries to:

1.Fetch the repo using a fetch strategy constructed with supplied args.

2.Check if the test_file is in the checked out repository.

3.Assert that the repository is at the revision supplied.

4.Add and remove some files, then reset the repo, and ensure it’s all there again.

spack.test.install module

class spack.test.install.InstallTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

Tests install and uninstall on a trivial package.

fake_fetchify(pkg)Fake the URL for a package so it downloads from a file.

setUp()

tearDown()

test_install_and_uninstall()

test_install_environment()

spack.test.link_tree module

class spack.test.link_tree.LinkTreeTest(methodName=’runTest’)Bases: unittest.case.TestCase

Tests Spack’s LinkTree class.

check_dir(filename)

check_file_link(filename)

setUp()

tearDown()

test_ignore()

test_merge_to_existing_directory()

test_merge_to_new_directory()

test_merge_with_empty_directories()

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spack.test.lock module

These tests ensure that our lock works correctly.

class spack.test.lock.LockTest(methodName=’runTest’)Bases: unittest.case.TestCase

acquire_read(barrier)

acquire_write(barrier)

multiproc_test(*functions)Order some processes using simple barrier synchronization.

setUp()

tearDown()

test_complex_acquire_and_release_chain()

test_read_lock_timeout_on_write()

test_read_lock_timeout_on_write_2()

test_read_lock_timeout_on_write_3()

test_transaction()

test_transaction_with_context_manager()

test_transaction_with_context_manager_and_exception()

test_transaction_with_exception()

test_write_lock_timeout_on_read()

test_write_lock_timeout_on_read_2()

test_write_lock_timeout_on_read_3()

test_write_lock_timeout_on_write()

test_write_lock_timeout_on_write_2()

test_write_lock_timeout_on_write_3()

test_write_lock_timeout_with_multiple_readers_2_1()

test_write_lock_timeout_with_multiple_readers_2_2()

test_write_lock_timeout_with_multiple_readers_3_1()

test_write_lock_timeout_with_multiple_readers_3_2()

timeout_read(barrier)

timeout_write(barrier)

spack.test.make_executable module

Tests for Spack’s built-in parallel make support.

This just tests whether the right args are getting passed to make.

class spack.test.make_executable.MakeExecutableTest(methodName=’runTest’)Bases: unittest.case.TestCase

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setUp()

tearDown()

test_make_explicit()

test_make_normal()

test_make_one_job()

test_make_parallel_disabled()

test_make_parallel_false()

test_make_parallel_precedence()

spack.test.mirror module

class spack.test.mirror.MirrorTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

check_mirror()

setUp()Sets up a mock package and a mock repo for each fetch strategy, to ensure that the mirror can createarchives for each of them.

set_up_package(name, MockRepoClass, url_attr)Set up a mock package to be mirrored. Each package needs us to:

1.Set up a mock repo/archive to fetch from.

2.Point the package’s version args at that repo.

tearDown()Destroy all the stages created by the repos in setup.

test_all_mirror()

test_git_mirror()

test_hg_mirror()

test_svn_mirror()

test_url_mirror()

spack.test.mock_database module

class spack.test.mock_database.MockDatabase(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

setUp()

tearDown()

spack.test.mock_packages_test module

class spack.test.mock_packages_test.MockPackagesTest(methodName=’runTest’)Bases: unittest.case.TestCase

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cleanmock()Restore the real packages path after any test.

initmock()

setUp()

set_pkg_dep(pkg_name, spec, deptypes=(‘build’, ‘link’, ‘run’))Alters dependence information for a package.

Adds a dependency on <spec> to pkg. Use this to mock up constraints.

tearDown()

spack.test.mock_repo module

class spack.test.mock_repo.MockArchiveBases: spack.test.mock_repo.MockRepo

Creates a very simple archive directory with a configure script and a makefile that installs to a prefix. Tars it upinto an archive.

class spack.test.mock_repo.MockGitRepoBases: spack.test.mock_repo.MockVCSRepo

rev_hash(rev)

class spack.test.mock_repo.MockHgRepoBases: spack.test.mock_repo.MockVCSRepo

get_rev()Get current mercurial revision.

class spack.test.mock_repo.MockRepo(stage_name, repo_name)Bases: object

destroy()Destroy resources associated with this mock repo.

class spack.test.mock_repo.MockSvnRepoBases: spack.test.mock_repo.MockVCSRepo

class spack.test.mock_repo.MockVCSRepo(stage_name, repo_name)Bases: spack.test.mock_repo.MockRepo

spack.test.modules module

class spack.test.modules.DotkitTests(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

get_modulefile_content(spec)

setUp()

tearDown()

test_dotkit()

class spack.test.modules.HelperFunctionsTests(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

test_inspect_path()

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test_update_dictionary_extending_list()

class spack.test.modules.TclTests(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

get_modulefile_content(spec)

setUp()

tearDown()

test_alter_environment()

test_autoload()

test_blacklist()

test_conflicts()

test_prerequisites()

test_simple_case()

test_suffixes()

spack.test.modules.mock_open(*args, **kwds)

spack.test.multimethod module

Test for multi_method dispatch.

class spack.test.multimethod.MultiMethodTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

test_default_works()

test_dependency_match()

test_mpi_version()

test_no_version_match()

test_one_version_match()

test_target_match()

test_undefined_mpi_version()

test_version_overlap()

test_virtual_dep_match()

spack.test.namespace_trie module

class spack.test.namespace_trie.NamespaceTrieTest(methodName=’runTest’)Bases: unittest.case.TestCase

setUp()

test_add_multiple()

test_add_none_multiple()

test_add_none_single()

test_add_single()

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test_add_three()

spack.test.optional_deps module

class spack.test.optional_deps.ConcretizeTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

check_normalize(spec_string, expected)

test_chained_mpi()

test_default_variant()

test_multiple_conditionals()

test_normalize_simple_conditionals()

test_transitive_chain()

spack.test.package_sanity module

This test does sanity checks on Spack’s builtin package database.

class spack.test.package_sanity.PackageSanityTest(methodName=’runTest’)Bases: unittest.case.TestCase

check_db()Get all packages in a DB to make sure they work.

test_get_all_mock_packages()Get the mock packages once each too.

test_get_all_packages()Get all packages once and make sure that works.

test_url_versions()Check URLs for regular packages, if they are explicitly defined.

spack.test.packages module

class spack.test.packages.PackagesTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

test_import_class_from_package()

test_import_module_from_package()

test_import_namespace_container_modules()

test_import_package()

test_import_package_as()

test_load_package()

test_nonexisting_package_filename()

test_package_class_names()

test_package_filename()

test_package_name()

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spack.test.pattern module

class spack.test.pattern.CompositeTest(methodName=’runTest’)Bases: unittest.case.TestCase

setUp()

test_composite_from_interface()

test_composite_from_method_list()

test_error_conditions()

spack.test.provider_index module

Tests for provider index cache files.

Tests assume that mock packages provide this:

{'blas': {blas: set([netlib-blas, openblas, openblas-with-lapack])},

'lapack': {lapack: set([netlib-lapack, openblas-with-lapack])},'mpi': {mpi@:1: set([mpich@:1]),

mpi@:2.0: set([mpich2]),mpi@:2.1: set([mpich2@1.1:]),mpi@:2.2: set([mpich2@1.2:]),mpi@:3: set([mpich@3:]),mpi@:10.0: set([zmpi])},

'stuff': {stuff: set([externalvirtual])}}

class spack.test.provider_index.ProviderIndexTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

test_copy()

test_equal()

test_mpi_providers()

test_providers_for_simple()

test_yaml_round_trip()

spack.test.python_version module

This test ensures that all Spack files are Python version 2.6 or less.

Spack was originally 2.7, but enough systems in 2014 are still using 2.6 on their frontend nodes that we need 2.6 toget adopted.

class spack.test.python_version.PythonVersionTest(methodName=’runTest’)Bases: unittest.case.TestCase

check_python_versions(*files)

package_py_files()

pyfiles(*search_paths)

test_core_module_compatibility()

test_package_module_compatibility()

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spack.test.sbang module

Test that Spack’s shebang filtering works correctly.

class spack.test.sbang.SbangTest(methodName=’runTest’)Bases: unittest.case.TestCase

setUp()

tearDown()

test_shebang_handles_non_writable_files()

test_shebang_handling()

spack.test.spec_dag module

These tests check Spec DAG operations using dummy packages. You can find the dummy packages here:

spack/lib/spack/spack/test/mock_packages

class spack.test.spec_dag.SpecDagTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

check_links(spec_to_check)

test_conflicting_package_constraints()

test_conflicting_spec_constraints()

test_contains()

test_copy_concretized()

test_copy_normalized()

test_copy_simple()

test_dependents_and_dependencies_are_correct()

test_deptype_traversal()

test_deptype_traversal_full()

test_deptype_traversal_run()

test_deptype_traversal_with_builddeps()

test_equal()

test_invalid_dep()

test_normalize_a_lot()

test_normalize_mpileaks()

test_normalize_twice()Make sure normalize can be run twice on the same spec, and that it is idempotent.

test_normalize_with_virtual_package()

test_normalize_with_virtual_spec()

test_postorder_edge_traversal()

test_postorder_node_traversal()

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test_postorder_path_traversal()

test_preorder_edge_traversal()

test_preorder_node_traversal()

test_preorder_path_traversal()

test_unsatisfiable_architecture()

test_unsatisfiable_compiler()

test_unsatisfiable_compiler_version()

test_unsatisfiable_version()

spack.test.spec_semantics module

class spack.test.spec_semantics.SpecSematicsTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

This tests satisfies(), constrain() and other semantic operations on specs.

check_constrain(expected, spec, constraint)

check_constrain_changed(spec, constraint)

check_constrain_not_changed(spec, constraint)

check_invalid_constraint(spec, constraint)

check_satisfies(spec, anon_spec, concrete=False)

check_unsatisfiable(spec, anon_spec, concrete=False)

test_constrain_architecture()

test_constrain_changed()

test_constrain_compiler()

test_constrain_compiler_flags()

test_constrain_dependency_changed()

test_constrain_dependency_not_changed()

test_constrain_not_changed()

test_constrain_variants()

test_dep_index()

test_invalid_constraint()

test_satisfies()

test_satisfies_architecture()

test_satisfies_compiler()

test_satisfies_compiler_version()

test_satisfies_dependencies()

test_satisfies_dependency_versions()

test_satisfies_matching_compiler_flag()

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test_satisfies_matching_variant()

test_satisfies_namespace()

test_satisfies_namespaced_dep()Ensure spec from same or unspecified namespace satisfies namespace constraint.

test_satisfies_unconstrained_compiler_flag()

test_satisfies_unconstrained_variant()

test_satisfies_virtual()

test_satisfies_virtual_dep_with_virtual_constraint()Ensure we can satisfy virtual constraints when there are multiple vdep providers in the specs.

test_satisfies_virtual_dependencies()

test_satisfies_virtual_dependency_versions()

test_self_index()

test_spec_contains_deps()

test_unsatisfiable_compiler_flag()

test_unsatisfiable_compiler_flag_mismatch()

test_unsatisfiable_variant_mismatch()

test_unsatisfiable_variants()

test_virtual_index()

spack.test.spec_syntax module

class spack.test.spec_syntax.SpecSyntaxTest(methodName=’runTest’)Bases: unittest.case.TestCase

check_lex(tokens, spec)Check that the provided spec parses to the provided token list.

check_parse(expected, spec=None, remove_arch=True)Assert that the provided spec is able to be parsed.

If this is called with one argument, it assumes that the string is canonical (i.e., no spaces and ~ instead of -for variants) and that it will convert back to the string it came from.

If this is called with two arguments, the first argument is the expected canonical form and the second is anon-canonical input to be parsed.

test_ambiguous()

test_canonicalize()

test_dependencies_with_versions()

test_duplicate_compiler()

test_duplicate_depdendence()

test_duplicate_variant()

test_full_specs()

test_minimal_spaces()

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test_package_names()

test_parse_errors()

test_simple_dependence()

test_spaces_between_dependences()

test_spaces_between_options()

test_way_too_many_spaces()

spack.test.spec_yaml module

Test YAML serialization for specs.

YAML format preserves DAG informatoin in the spec.

class spack.test.spec_yaml.SpecYamlTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

check_yaml_round_trip(spec)

test_ambiguous_version_spec()

test_concrete_spec()

test_normal_spec()

test_simple_spec()

test_yaml_subdag()

spack.test.stage module

Test that the Stage class works correctly.

class spack.test.stage.StageTest(methodName=’runTest’)Bases: unittest.case.TestCase

check_chdir(stage, stage_name)

check_chdir_to_source(stage, stage_name)

check_destroy(stage, stage_name)Figure out whether a stage was destroyed correctly.

check_expand_archive(stage, stage_name)

check_fetch(stage, stage_name)

check_setup(stage, stage_name)Figure out whether a stage was set up correctly.

get_stage_path(stage, stage_name)Figure out where a stage should be living. This depends on whether it’s named.

setUp()This sets up a mock archive to fetch, and a mock temp space for use by the Stage class. It doesn’t actuallycreate the Stage – that is done by individual tests.

tearDown()Blows away the test environment directory.

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test_chdir()

test_expand_archive()

test_expand_archive_with_chdir()

test_fetch()

test_keep_exceptions()

test_keep_without_exceptions()

test_no_keep_with_exceptions()

test_no_keep_without_exceptions()

test_restage()

test_setup_and_destroy_name_with_tmp()

test_setup_and_destroy_name_without_tmp()

test_setup_and_destroy_no_name_with_tmp()

test_setup_and_destroy_no_name_without_tmp()

spack.test.stage.use_tmp(*args, **kwds)Allow some test code to be executed with spack.use_tmp_stage set to a certain value. Context manager makessure it’s reset on failure.

spack.test.svn_fetch module

class spack.test.svn_fetch.SvnFetchTest(methodName=’runTest’)Bases: spack.test.mock_packages_test.MockPackagesTest

Tests fetching from a dummy git repository.

assert_rev(rev)Check that the current revision is equal to the supplied rev.

setUp()Create an svn repository with two revisions.

tearDown()Destroy the stage space used by this test.

test_fetch_default()Test a default checkout and make sure it’s on rev 1

test_fetch_r1()Test fetching an older revision (0).

try_fetch(rev, test_file, args)Tries to:

1.Fetch the repo using a fetch strategy constructed with supplied args.

2.Check if the test_file is in the checked out repository.

3.Assert that the repository is at the revision supplied.

4.Add and remove some files, then reset the repo, and ensure it’s all there again.

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spack.test.tally_plugin module

class spack.test.tally_plugin.TallyBases: nose.plugins.base.Plugin

addError(test, err)

addFailure(test, err)

addSuccess(test)

configure(options, conf)

finalize(result)

name = ‘tally’

numberOfTestsRunExcludes skipped tests

options(parser, env={‘LANG’: ‘C.UTF-8’, ‘READTHEDOCS_PROJECT’: ‘spack’,‘COLIFY_SIZE’: ‘25x80’, ‘READTHEDOCS’: ‘True’, ‘SPACK_ROOT’:‘../../..’, ‘APPDIR’: ‘/app’, ‘DEBIAN_FRONTEND’: ‘noninteractive’, ‘OLD-PWD’: ‘/’, ‘HOSTNAME’: ‘build-4354849-project-57069-spack’, ‘PWD’:‘/home/docs/checkouts/readthedocs.org/user_builds/spack/checkouts/bugfix-rtd-generation/lib/spack/docs’, ‘BIN_PATH’: ‘/home/docs/checkouts/readthedocs.org/user_builds/spack/envs/bugfix-rtd-generation/bin’, ‘READTHEDOCS_VERSION’: ‘bugfix-rtd-generation’,‘PATH’: ‘/home/docs/checkouts/readthedocs.org/user_builds/spack/envs/bugfix-rtd-generation/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:../../../bin’,‘HOME’: ‘/home/docs’})

spack.test.url_extrapolate module

Tests ability of spack to extrapolate URL versions from existing versions.

class spack.test.url_extrapolate.UrlExtrapolateTest(methodName=’runTest’)Bases: unittest.case.TestCase

check_url(base, version, new_url)

test_dyninst_version()

test_gcc()

test_github_raw()

test_libdwarf_version()

test_libelf_version()

test_mpileaks_version()

test_partial_version_prefix()

test_scalasca_partial_version()

spack.test.url_parse module

This file has a bunch of versions tests taken from the excellent version detection in Homebrew.

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class spack.test.url_parse.UrlParseTest(methodName=’runTest’)Bases: unittest.case.TestCase

assert_not_detected(string)

check(name, v, string, **kwargs)

test_angband_version_style()

test_another_erlang_version_style()

test_apache_version_style()

test_astyle_verson_style()

test_boost_version_style()

test_dash_rc_style()

test_dash_version_dash_style()

test_debian_style_1()

test_debian_style_2()

test_erlang_version_style()

test_fann_version()

test_gcc_version()

test_gcc_version_precedence()

test_github_raw_url()

test_gloox_beta_style()

test_haxe_version()

test_hdf5_version()

test_iges_version()

test_imagemagick_style()

test_imap_version()

test_jpeg_style()

test_lame_version_style()

test_mpileaks_version()

test_mvapich2_19_version()

test_mvapich2_20_version()

test_new_github_style()

test_no_version()

test_noseparator_single_digit()

test_omega_version_style()

test_openssl_version()

test_p7zip_version_style()

test_pypy_version()

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test_rc_style()

test_ruby_version_style()

test_scalasca_version()

test_sphinx_beta_style()

test_stable_suffix()

test_suite3270_version()

test_synergy_version()

test_version_all_dots()

test_version_developer_that_hates_us_format()

test_version_dos2unix()

test_version_github()

test_version_github_with_high_patch_number()

test_version_internal_dash()

test_version_regular()

test_version_single_digit()

test_version_sourceforge_download()

test_version_underscore_separator()

test_wwwoffle_version()

test_xaw3d_version()

test_yet_another_erlang_version_style()

test_yet_another_version()

spack.test.url_substitution module

This test does sanity checks on substituting new versions into URLs

class spack.test.url_substitution.PackageSanityTest(methodName=’runTest’)Bases: unittest.case.TestCase

test_hypre_url_substitution()

test_otf2_url_substitution()

spack.test.versions module

These version tests were taken from the RPM source code. We try to maintain compatibility with RPM’s versionsemantics where it makes sense.

class spack.test.versions.VersionsTest(methodName=’runTest’)Bases: unittest.case.TestCase

assert_canonical(canonical_list, version_list)

assert_does_not_satisfy(v1, v2)

assert_in(needle, haystack)

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assert_no_overlap(v1, v2)

assert_not_in(needle, haystack)

assert_overlaps(v1, v2)

assert_satisfies(v1, v2)

assert_ver_eq(a, b)

assert_ver_gt(a, b)

assert_ver_lt(a, b)

check_intersection(expected, a, b)

check_union(expected, a, b)

test_alpha()

test_alpha_beta()

test_alpha_with_dots()

test_basic_version_satisfaction()

test_basic_version_satisfaction_in_lists()

test_canonicalize_list()

test_close_numbers()

test_contains()

test_date_stamps()

test_double_alpha()

test_formatted_strings()

test_get_item()

test_in_list()

test_intersect_with_containment()

test_intersection()

test_lists_overlap()

test_num_alpha_with_no_separator()

test_nums_and_patch()

test_overlap_with_containment()

test_padded_numbers()

test_patch()

test_ranges_overlap()

test_rc_versions()

test_repr_and_str()

test_rpm_oddities()

test_satisfaction_with_lists()

test_three_segments()

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test_two_segments()

test_underscores()

test_union_with_containment()

test_version_range_satisfaction()

test_version_range_satisfaction_in_lists()

test_version_ranges()

spack.test.yaml module

Test Spack’s custom YAML format.

class spack.test.yaml.YamlTest(methodName=’runTest’)Bases: unittest.case.TestCase

setUp()

test_dict_order()

test_line_numbers()

test_parse()

Module contents

spack.test.list_tests()Return names of all tests that can be run for Spack.

spack.test.run(names, outputDir, verbose=False)Run tests with the supplied names. Names should be a list. If it’s empty, run ALL of Spack’s tests.

spack.util package

Submodules

spack.util.compression module

spack.util.compression.allowed_archive(path)

spack.util.compression.decompressor_for(path)Get the appropriate decompressor for a path.

spack.util.compression.extension(path)Get the archive extension for a path.

spack.util.compression.strip_extension(path)Get the part of a path that does not include its compressed type extension.

spack.util.crypto module

class spack.util.crypto.Checker(hexdigest, **kwargs)Bases: object

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A checker checks files against one particular hex digest. It will automatically determine what hashing algorithmto used based on the length of the digest it’s initialized with. e.g., if the digest is 32 hex characters long this willuse md5.

Example: know your tarball should hash to ‘abc123’. You want to check files against this. You would use thisclass like so:

hexdigest = 'abc123'checker = Checker(hexdigest)success = checker.check('downloaded.tar.gz')

After the call to check, the actual checksum is available in checker.sum, in case it’s needed for error output.

You can trade read performance and memory usage by adjusting the block_size optional arg. By default it’s a1MB (2**20 bytes) buffer.

check(filename)Read the file with the specified name and check its checksum against self.hexdigest. Return True if theymatch, False otherwise. Actual checksum is stored in self.sum.

hash_nameGet the name of the hash function this Checker is using.

spack.util.crypto.checksum(hashlib_algo, filename, **kwargs)Returns a hex digest of the filename generated using an algorithm from hashlib.

spack.util.debug module

Debug signal handler: prints a stack trace and enters interpreter.

register_interrupt_handler() enables a ctrl-C handler that prints a stack trace and drops the user into aninterpreter.

spack.util.debug.debug_handler(sig, frame)Interrupt running process, and provide a python prompt for interactive debugging.

spack.util.debug.register_interrupt_handler()Print traceback and enter an interpreter on Ctrl-C

spack.util.environment module

spack.util.environment.dump_environment(path)Dump the current environment out to a file.

spack.util.environment.env_flag(name)

spack.util.environment.get_path(name)

spack.util.environment.path_put_first(var_name, directories)Puts the provided directories first in the path, adding them if they’re not already there.

spack.util.environment.path_set(var_name, directories)

spack.util.executable module

class spack.util.executable.Executable(name)Bases: object

Class representing a program that can be run on the command line.

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add_default_arg(arg)

command

spack.util.executable.which(name, **kwargs)Finds an executable in the path like command-line which.

exception spack.util.executable.ProcessError(msg, long_message=None)Bases: spack.error.SpackError

long_message

spack.util.multiproc module

This implements a parallel map operation but it can accept more values than multiprocessing.Pool.apply() can. Forexample, apply() will fail to pickle functions if they’re passed indirectly as parameters.

spack.util.multiproc.spawn(f)

spack.util.multiproc.parmap(f, X)

class spack.util.multiproc.Barrier(n, timeout=None)Simple reusable semaphore barrier.

Python 2.6 doesn’t have multiprocessing barriers so we implement this.

See http://greenteapress.com/semaphores/downey08semaphores.pdf, p. 41.

wait()

spack.util.naming module

spack.util.naming.mod_to_class(mod_name)Convert a name from module style to class name style. Spack mostly follows PEP-8:

•Module and package names use lowercase_with_underscores.

•Class names use the CapWords convention.

Regular source code follows these convetions. Spack is a bit more liberal with its Package names nad Compilernames:

•They can contain ‘-‘ as well as ‘_’, but cannot start with ‘-‘.

•They can start with numbers, e.g. “3proxy”.

This function converts from the module convention to the class convention by removing _ and - and convertingsurrounding lowercase text to CapWords. If mod_name starts with a number, the class name returned will beprepended with ‘_’ to make a valid Python identifier.

spack.util.naming.spack_module_to_python_module(mod_name)Given a Spack module name, returns the name by which it can be imported in Python.

spack.util.naming.valid_module_name(mod_name)Return whether mod_name is valid for use in Spack.

spack.util.naming.valid_fully_qualified_module_name(mod_name)Return whether mod_name is a valid namespaced module name.

spack.util.naming.validate_fully_qualified_module_name(mod_name)Raise an exception if mod_name is not a valid namespaced module name.

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spack.util.naming.validate_module_name(mod_name)Raise an exception if mod_name is not valid.

spack.util.naming.possible_spack_module_names(python_mod_name)Given a Python module name, return a list of all possible spack module names that could correspond to it.

class spack.util.naming.NamespaceTrie(separator=’.’)Bases: object

class Element(value)Bases: object

NamespaceTrie.has_value(namespace)True if there is a value set for the given namespace.

NamespaceTrie.is_leaf(namespace)True if this namespace has no children in the trie.

NamespaceTrie.is_prefix(namespace)True if the namespace has a value, or if it’s the prefix of one that does.

spack.util.pattern module

class spack.util.pattern.Bunch(**kwargs)Bases: object

Carries a bunch of named attributes (from Alex Martelli bunch)

spack.util.pattern.composite(interface=None, method_list=None, container=<type ‘list’>)Returns a class decorator that patches a class adding all the methods it needs to be a composite for a giveninterface.

Parameters

• interface – class exposing the interface to which the composite object must conform.Only non-private and non-special methods will be taken into account

• method_list – names of methods that should be part of the composite

• container – container for the composite object (default = list). Must fulfill the Muta-bleSequence contract. The composite class will expose the container API to manage objectcomposition

Returns class decorator

spack.util.prefix module

This file contains utilities to help with installing packages.

class spack.util.prefix.PrefixBases: str

This class represents an installation prefix, but provides useful attributes for referring to directories inside theprefix.

For example, you can do something like this:

prefix = Prefix('/usr')print prefix.libprint prefix.lib64print prefix.bin

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print prefix.shareprint prefix.man4

This program would print:

/usr/lib /usr/lib64 /usr/bin /usr/share /usr/share/man/man4

Prefix objects behave identically to strings. In fact, they subclass str. So operators like + are legal:

print “foobar ” + prefix

This prints ‘foobar /usr”. All of this is meant to make custom installs easy.

spack.util.spack_yaml module

Enhanced YAML parsing for Spack.

• load() preserves YAML Marks on returned objects – this allows us to access file and line information later.

• Our load methods use ‘‘OrderedDict class instead of YAML’s default unorderd dict.

spack.util.spack_yaml.load(*args, **kwargs)Load but modify the loader instance so that it will add __line__ atrributes to the returned object.

spack.util.spack_yaml.dump(*args, **kwargs)

spack.util.string module

spack.util.string.comma_and(sequence)

spack.util.string.comma_list(sequence, article=’‘)

spack.util.string.comma_or(sequence)

spack.util.web module

class spack.util.web.LinkParserBases: HTMLParser.HTMLParser

This parser just takes an HTML page and strips out the hrefs on the links. Good enough for a really simplespider.

handle_starttag(tag, attrs)

spack.util.web.find_versions_of_archive(*archive_urls, **kwargs)Scrape web pages for new versions of a tarball.

Arguments:

archive_urls: URLs for different versions of a package. Typically these are just the tarballs from thepackage file itself. By default, this searches the parent directories of archives.

Keyword Arguments: list_url:

URL for a listing of archives. Spack wills scrape these pages for download links that look likethe archive URL.

list_depth: Max depth to follow links on list_url pages.

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spack.util.web.spider(root_url, **kwargs)Gets web pages from a root URL. If depth is specified (e.g., depth=2), then this will also fetches pages linkedfrom the root and its children up to depth.

This will spawn processes to fetch the children, for much improved performance over a sequential fetch.

Module contents

1.11.2 Submodules

1.11.3 spack.abi module

class spack.abi.ABIBases: object

This class provides methods to test ABI compatibility between specs. The current implementation is ratherrough and could be improved.

architecture_compatible(parent, child)Return true if parent and child have ABI compatible targets.

compatible(parent, child, **kwargs)Returns true iff a parent and child spec are ABI compatible

compiler_compatible(parent, child, **kwargs)Return true if compilers for parent and child are ABI compatible.

1.11.4 spack.architecture module

This module contains all the elements that are required to create an architecture object. These include, the targetprocessor, the operating system, and the architecture platform (i.e. cray, darwin, linux, bgq, etc) classes.

On a multiple architecture machine, the architecture spec field can be set to build a package against any target andoperating system that is present on the platform. On Cray platforms or any other architecture that has different frontand back end environments, the operating system will determine the method of compiler detection.

There are two different types of compiler detection:

1. Through the $PATH env variable (front-end detection)

2. Through the tcl module system. (back-end detection)

Depending on which operating system is specified, the compiler will be detected using one of those methods.

For platforms such as linux and darwin, the operating system is autodetected and the target is set to be x86_64.

The command line syntax for specifying an architecture is as follows:

target=<Target name> os=<OperatingSystem name>

If the user wishes to use the defaults, either target or os can be left out of the command line and Spack will concretizeusing the default. These defaults are set in the ‘platforms/’ directory which contains the different subclasses forplatforms. If the machine has multiple architectures, the user can also enter front-end, or fe or back-end or be. Thesesettings will concretize to their respective front-end and back-end targets and operating systems. Additional platformscan be added by creating a subclass of Platform and adding it inside the platform directory.

Platforms are an abstract class that are extended by subclasses. If the user wants to add a new type of platform (such ascray_xe), they can create a subclass and set all the class attributes such as priority, front_target, back_target, front_os,back_os. Platforms also contain a priority class attribute. A lower number signifies higher priority. These numbers

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are arbitrarily set and can be changed though often there isn’t much need unless a new platform is added and the userwants that to be detected first.

Targets are created inside the platform subclasses. Most architecture (like linux, and darwin) will have only one target(x86_64) but in the case of Cray machines, there is both a frontend and backend processor. The user can specify whichtargets are present on front-end and back-end architecture

Depending on the platform, operating systems are either auto-detected or are set. The user can set the front-end andback-end operating setting by the class attributes front_os and back_os. The operating system as described earlier, willbe responsible for compiler detection.

class spack.architecture.Arch(plat=None, os=None, target=None)Bases: object

Architecture is now a class to help with setting attributes.

TODO: refactor so that we don’t need this class.

concrete

to_dict()

exception spack.architecture.NoPlatformErrorBases: spack.error.SpackError

class spack.architecture.OperatingSystem(name, version)Bases: object

Operating System will be like a class similar to platform extended by subclasses for the specifics. OperatingSystem will contain the compiler finding logic. Instead of calling two separate methods to find compilers wecall find_compilers method for each operating system

find_compiler(cmp_cls, *path)Try to find the given type of compiler in the user’s environment. For each set of compilers found, thisreturns compiler objects with the cc, cxx, f77, fc paths and the version filled in.

This will search for compilers with the names in cc_names, cxx_names, etc. and it will group them if theyhave common prefixes, suffixes, and versions. e.g., gcc-mp-4.7 would be grouped with g++-mp-4.7 andgfortran-mp-4.7.

find_compilers(*paths)Return a list of compilers found in the suppied paths. This invokes the find() method for each Compilerclass, and appends the compilers detected to a list.

to_dict()

class spack.architecture.Platform(name)Bases: object

Abstract class that each type of Platform will subclass. Will return a instance of it once it is returned

add_operating_system(name, os_class)Add the operating_system class object into the platform.operating_sys dictionary

add_target(name, target)Used by the platform specific subclass to list available targets. Raises an error if the platform specifies aname that is reserved by spack as an alias.

back_end = None

back_os = None

default = None

default_os = None

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classmethod detect()Subclass is responsible for implementing this method. Returns True if the Platform class detects that it isthe current platform and False if it’s not.

front_end = None

front_os = None

operating_system(name)

priority = None

classmethod setup_platform_environment(pkg, env)Subclass can override this method if it requires any platform-specific build environment modifications.

target(name)This is a getter method for the target dictionary that handles defaulting based on the values provided bydefault, front-end, and back-end. This can be overwritten by a subclass for which we want to providefurther aliasing options.

class spack.architecture.Target(name, module_name=None)Bases: object

Target is the processor of the host machine. The host machine may have different front-end and back-end targets,especially if it is a Cray machine. The target will have a name and also the module_name (e.g craype-compiler).Targets will also recognize which platform they came from using the set_platform method. Targets will havecompiler finding strategies

spack.architecture.arch_from_dict(d)Uses _platform_from_dict, _operating_system_from_dict, _target_from_dict helper methods to recreate thearch tuple from the dictionary read from a yaml file

1.11.5 spack.build_environment module

This module contains all routines related to setting up the package build environment. All of this is set up by pack-age.py just before install() is called.

There are two parts to the build environment:

1. Python build environment (i.e. install() method)

This is how things are set up when install() is called. Spack takes advantage of each package being in itsown module by adding a bunch of command-like functions (like configure(), make(), etc.) in the package’smodule scope. Ths allows package writers to call them all directly in Package.install() without writing ‘self.’everywhere. No, this isn’t Pythonic. Yes, it makes the code more readable and more like the shell script fromwhich someone is likely porting.

2. Build execution environment

This is the set of environment variables, like PATH, CC, CXX, etc. that control the build. There are also a num-ber of environment variables used to pass information (like RPATHs and other information about dependencies)to Spack’s compiler wrappers. All of these env vars are also set up here.

Skimming this module is a nice way to get acquainted with the types of calls you can make from within the install()function.

exception spack.build_environment.InstallError(message, long_message=None)Bases: spack.error.SpackError

Raised when a package fails to install

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class spack.build_environment.MakeExecutable(name, jobs)Bases: spack.util.executable.Executable

Special callable executable object for make so the user can specify parallel or not on a per-invocation basis.Using ‘parallel’ as a kwarg will override whatever the package’s global setting is, so you can either default totrue or false and override particular calls.

Note that if the SPACK_NO_PARALLEL_MAKE env var is set it overrides everything.

spack.build_environment.fork(pkg, function, dirty=False)Fork a child process to do part of a spack build.

Parameters

• pkg – pkg whose environemnt we should set up the forked process for.

• function – arg-less function to run in the child process.

• dirty – If True, do NOT clean the environment before building.

Usage:

def child_fun():# do stuff

build_env.fork(pkg, child_fun)

Forked processes are run with the build environment set up by spack.build_environment. This allows packageauthors to have full control over the environment, etc. without affecting other builds that might be executed inthe same spack call.

If something goes wrong, the child process is expected to print the error and the parent process will exit witherror as well. If things go well, the child exits and the parent carries on.

spack.build_environment.get_path_from_module(mod)Inspects a TCL module for entries that indicate the absolute path at which the library supported by said modulecan be found.

spack.build_environment.get_rpaths(pkg)Get a list of all the rpaths for a package.

spack.build_environment.load_external_modules(pkg)traverse the spec list and find any specs that have external modules.

spack.build_environment.load_module(mod)Takes a module name and removes modules until it is possible to load that module. It then loads the providedmodule. Depends on the modulecmd implementation of modules used in cray and lmod.

spack.build_environment.parent_class_modules(cls)Get list of super class modules that are all descend from spack.Package

spack.build_environment.set_build_environment_variables(pkg, env, dirty=False)This ensures a clean install environment when we build packages.

Arguments: dirty – skip unsetting the user’s environment settings.

spack.build_environment.set_compiler_environment_variables(pkg, env)

spack.build_environment.set_module_variables_for_package(pkg, module)Populate the module scope of install() with some useful functions. This makes things easier for package writers.

spack.build_environment.setup_package(pkg, dirty=False)Execute all environment setup routines.

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1.11.6 spack.compiler module

class spack.compiler.Compiler(cspec, operating_system, paths, modules=[], alias=None, **kwargs)Bases: object

This class encapsulates a Spack “compiler”, which includes C, C++, and Fortran compilers. Subclasses shouldimplement support for specific compilers, their possible names, arguments, and how to identify the particulartype of compiler.

PrgEnv = None

PrgEnv_compiler = None

cc_names = []

cc_rpath_arg

classmethod cc_version(cc)

cxx11_flag

cxx14_flag

cxx_names = []

cxx_rpath_arg

classmethod cxx_version(cxx)

classmethod default_version(cc)Override just this to override all compiler version functions.

f77_names = []

f77_rpath_arg

classmethod f77_version(f77)

fc_names = []

fc_rpath_arg

classmethod fc_version(fc)

openmp_flag

prefixes = []

suffixes = [’-.*’]

version

spack.compiler.get_compiler_version(compiler_path, version_arg, regex=’(.*)’)

1.11.7 spack.concretize module

Functions here are used to take abstract specs and make them concrete. For example, if a spec asks for a versionbetween 1.8 and 1.9, these functions might take will take the most recent 1.9 version of the package available. Or,if the user didn’t specify a compiler for a spec, then this will assign a compiler to the spec based on defaults or userpreferences.

TODO: make this customizable and allow users to configure concretization policies.

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class spack.concretize.DefaultConcretizerBases: object

This class doesn’t have any state, it just provides some methods for concretization. You can subclass it tooverride just some of the default concretization strategies, or you can override all of them.

choose_virtual_or_external(spec)Given a list of candidate virtual and external packages, try to find one that is most ABI compatible.

concretize_architecture(spec)If the spec is empty provide the defaults of the platform. If the architecture is not a basestring, then checkif either the platform, target or operating system are concretized. If any of the fields are changed thenreturn True. If everything is concretized (i.e the architecture attribute is a namedtuple of classes) thenreturn False. If the target is a string type, then convert the string into a concretized architecture. If it hasno architecture and the root of the DAG has an architecture, then use the root otherwise use the defaults onthe platform.

concretize_compiler(spec)If the spec already has a compiler, we’re done. If not, then take the compiler used for the nearest ancestorwith a compiler spec and use that. If the ancestor’s compiler is not concrete, then used the preferredcompiler as specified in spackconfig.

Intuition: Use the spackconfig default if no package that depends on this one has a strict compiler re-quirement. Otherwise, try to build with the compiler that will be used by libraries that link to this one, tomaximize compatibility.

concretize_compiler_flags(spec)The compiler flags are updated to match those of the spec whose compiler is used, defaulting to no compilerflags in the spec. Default specs set at the compiler level will still be added later.

concretize_variants(spec)If the spec already has variants filled in, return. Otherwise, add the user preferences from packages.yamlor the default variants from the package specification.

concretize_version(spec)If the spec is already concrete, return. Otherwise take the preferred version from spackconfig, and defaultto the package’s version if there are no available versions.

TODO: In many cases we probably want to look for installed versions of each package and use an in-stalled version if we can link to it. The policy implemented here will tend to rebuild a lot of stuffbecasue it will prefer a compiler in the spec to any compiler already- installed things were built with.There is likely some better policy that finds some middle ground between these two extremes.

exception spack.concretize.NoBuildError(spec)Bases: spack.error.SpackError

Raised when a package is configured with the buildable option False, but no satisfactory external versions canbe found

exception spack.concretize.NoValidVersionError(spec)Bases: spack.error.SpackError

Raised when there is no way to have a concrete version for a particular spec.

exception spack.concretize.UnavailableCompilerVersionError(compiler_spec, operat-ing_system)

Bases: spack.error.SpackError

Raised when there is no available compiler that satisfies a compiler spec.

spack.concretize.cmp_specs(lhs, rhs)

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spack.concretize.find_spec(spec, condition)Searches the dag from spec in an intelligent order and looks for a spec that matches a condition

1.11.8 spack.config module

This module implements Spack’s configuration file handling.

Configuration file scopes

When Spack runs, it pulls configuration data from several config directories, each of which contains configurationfiles. In Spack, there are two configuration scopes:

1. site: Spack loads site-wide configuration options from $(prefix)/etc/spack/.

2. user: Spack next loads per-user configuration options from ~/.spack/.

Spack may read configuration files from both of these locations. When configurations conflict, the user config optionstake precedence over the site configurations. Each configuration directory may contain several configuration files,such as compilers.yaml or mirrors.yaml.

Configuration file format

Configuration files are formatted using YAML syntax. This format is implemented by libyaml (included with Spackas an external module), and it’s easy to read and versatile.

Config files are structured as trees, like this compiler section:

compilers:chaos_5_x86_64_ib:

gcc@4.4.7:cc: /usr/bin/gcccxx: /usr/bin/g++f77: /usr/bin/gfortranfc: /usr/bin/gfortran

bgqos_0:xlc@12.1:

cc: /usr/local/bin/mpixlc...

In this example, entries like “compilers” and “xlc@12.1” are used to categorize entries beneath them in the tree. Atthe root of the tree, entries like “cc” and “cxx” are specified as name/value pairs.

config.get_config() returns these trees as nested dicts, but it strips the first level off. So,config.get_config(’compilers’) would return something like this for the above example:

{ 'chaos_5_x86_64_ib' :{ 'gcc@4.4.7' :

{ 'cc' : '/usr/bin/gcc','cxx' : '/usr/bin/g++''f77' : '/usr/bin/gfortran''fc' : '/usr/bin/gfortran' }

}{ 'bgqos_0' :

{ 'cc' : '/usr/local/bin/mpixlc' } }

Likewise, the mirrors.yaml file’s first line must be mirrors:, but get_config() strips that off too.

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Precedence

config.py routines attempt to recursively merge configuration across scopes. So if there are compilers.py filesin both the site scope and the user scope, get_config(’compilers’) will return merged dictionaries of all thecompilers available. If a user compiler conflicts with a site compiler, Spack will overwrite the site configuration wtihthe user configuration. If both the user and site mirrors.yaml files contain lists of mirrors, then get_config()will return a concatenated list of mirrors, with the user config items first.

Sometimes, it is useful to completely override a site setting with a user one. To accomplish this, you can use two colonsat the end of a key in a configuration file. For example, this:

compilers::chaos_5_x86_64_ib:

gcc@4.4.7:cc: /usr/bin/gcccxx: /usr/bin/g++f77: /usr/bin/gfortranfc: /usr/bin/gfortran

bgqos_0:xlc@12.1:

cc: /usr/local/bin/mpixlc...

Will make Spack take compilers only from the user configuration, and the site configuration will be ignored.

exception spack.config.ConfigError(message, long_message=None)Bases: spack.error.SpackError

exception spack.config.ConfigFileError(message, long_message=None)Bases: spack.config.ConfigError

exception spack.config.ConfigFormatError(validation_error, data)Bases: spack.config.ConfigError

Raised when a configuration format does not match its schema.

exception spack.config.ConfigSanityError(validation_error, data)Bases: spack.config.ConfigFormatError

Same as ConfigFormatError, raised when config is written by Spack.

class spack.config.ConfigScope(name, path)Bases: object

This class represents a configuration scope.

A scope is one directory containing named configuration files. Each file is a config “section” (e.g., mirrors,compilers, etc).

clear()Empty cached config information.

get_section(section)

get_section_filename(section)

write_section(section)

spack.config.clear_config_caches()Clears the caches for configuration files, which will cause them to be re-read upon the next request

spack.config.extend_with_default(validator_class)Add support for the ‘default’ attr for properties and patternProperties.

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jsonschema does not handle this out of the box – it only validates. This allows us to set default values for configswhere certain fields are None b/c they’re deleted or commented out.

spack.config.get_config(section, scope=None)Get configuration settings for a section.

Strips off the top-level section name from the YAML dict.

spack.config.get_config_filename(scope, section)For some scope and section, get the name of the configuration file

spack.config.get_path(path, data)

spack.config.highest_precedence_scope()Get the scope with highest precedence (prefs will override others).

spack.config.is_spec_buildable(spec)Return true if the spec pkgspec is configured as buildable

spack.config.print_section(section)Print a configuration to stdout.

spack.config.section_schemas = {‘mirrors’: {‘additionalProperties’: False, ‘patternProperties’: {‘mirrors:?’: {‘default’: {}, ‘additionalProperties’: False, ‘patternProperties’: {‘\\w[\\w-]*’: {‘type’: ‘string’}}, ‘type’: ‘object’}}, ‘$schema’: ‘http://json-schema.org/schema#’, ‘type’: ‘object’, ‘title’: ‘Spack mirror configuration file schema’}, ‘repos’: {‘additionalProperties’: False, ‘patternProperties’: {‘repos:?’: {‘default’: [], ‘items’: {‘type’: ‘string’}, ‘type’: ‘array’}}, ‘$schema’: ‘http://json-schema.org/schema#’, ‘type’: ‘object’, ‘title’: ‘Spack repository configuration file schema’}, ‘modules’: {‘title’: ‘Spack module file configuration file schema’, ‘patternProperties’: {‘modules:?’: {‘default’: {}, ‘additionalProperties’: False, ‘type’: ‘object’, ‘properties’: {‘tcl’: {‘allOf’: [{‘$ref’: ‘#/definitions/module_type_configuration’}, {}]}, ‘enable’: {‘default’: [], ‘items’: {‘enum’: [’tcl’, ‘dotkit’], ‘type’: ‘string’}, ‘type’: ‘array’}, ‘dotkit’: {‘allOf’: [{‘$ref’: ‘#/definitions/module_type_configuration’}, {}]}, ‘prefix_inspections’: {‘patternProperties’: {‘\\w[\\w-]*’: {‘$ref’: ‘#/definitions/array_of_strings’}}, ‘type’: ‘object’}}}}, ‘additionalProperties’: False, ‘definitions’: {‘dependency_selection’: {‘enum’: [’none’, ‘direct’, ‘all’], ‘type’: ‘string’}, ‘array_of_strings’: {‘default’: [], ‘items’: {‘type’: ‘string’}, ‘type’: ‘array’}, ‘module_file_configuration’: {‘default’: {}, ‘additionalProperties’: False, ‘type’: ‘object’, ‘properties’: {‘load’: {‘$ref’: ‘#/definitions/array_of_strings’}, ‘environment’: {‘default’: {}, ‘additionalProperties’: False, ‘type’: ‘object’, ‘properties’: {‘append_path’: {‘$ref’: ‘#/definitions/dictionary_of_strings’}, ‘set’: {‘$ref’: ‘#/definitions/dictionary_of_strings’}, ‘prepend_path’: {‘$ref’: ‘#/definitions/dictionary_of_strings’}, ‘unset’: {‘$ref’: ‘#/definitions/array_of_strings’}}}, ‘prerequisites’: {‘$ref’: ‘#/definitions/dependency_selection’}, ‘autoload’: {‘$ref’: ‘#/definitions/dependency_selection’}, ‘filter’: {‘default’: {}, ‘additionalProperties’: False, ‘type’: ‘object’, ‘properties’: {‘environment_blacklist’: {‘default’: [], ‘items’: {‘type’: ‘string’}, ‘type’: ‘array’}}}, ‘conflict’: {‘$ref’: ‘#/definitions/array_of_strings’}, ‘suffixes’: {‘$ref’: ‘#/definitions/dictionary_of_strings’}}}, ‘dictionary_of_strings’: {‘patternProperties’: {‘\\w[\\w-]*’: {‘type’: ‘string’}}, ‘type’: ‘object’}, ‘module_type_configuration’: {‘default’: {}, ‘anyOf’: [{‘properties’: {‘blacklist’: {‘$ref’: ‘#/definitions/array_of_strings’}, ‘whitelist’: {‘$ref’: ‘#/definitions/array_of_strings’}, ‘hash_length’: {‘default’: 7, ‘minimum’: 0, ‘type’: ‘integer’}, ‘naming_scheme’: {‘type’: ‘string’}}}, {‘patternProperties’: {‘\\w[\\w-]*’: {‘$ref’: ‘#/definitions/module_file_configuration’}}}], ‘type’: ‘object’}}, ‘$schema’: ‘http://json-schema.org/schema#’, ‘type’: ‘object’}, ‘packages’: {‘additionalProperties’: False, ‘patternProperties’: {‘packages:?’: {‘default’: {}, ‘additionalProperties’: False, ‘patternProperties’: {‘\\w[\\w-]*’: {‘default’: {}, ‘additionalProperties’: False, ‘type’: ‘object’, ‘properties’: {‘paths’: {‘default’: {}, ‘type’: ‘object’}, ‘providers’: {‘default’: {}, ‘additionalProperties’: False, ‘patternProperties’: {‘\\w[\\w-]*’: {‘default’: [], ‘items’: {‘type’: ‘string’}, ‘type’: ‘array’}}, ‘type’: ‘object’}, ‘modules’: {‘default’: {}, ‘type’: ‘object’}, ‘buildable’: {‘default’: True, ‘type’: ‘boolean’}, ‘version’: {‘default’: [], ‘items’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘number’}]}, ‘type’: ‘array’}, ‘variants’: {‘oneOf’: [{‘type’: ‘string’}, {‘items’: {‘type’: ‘string’}, ‘type’: ‘array’}]}, ‘compiler’: {‘default’: [], ‘items’: {‘type’: ‘string’}, ‘type’: ‘array’}}}}, ‘type’: ‘object’}}, ‘$schema’: ‘http://json-schema.org/schema#’, ‘type’: ‘object’, ‘title’: ‘Spack package configuration file schema’}, ‘targets’: {‘additionalProperties’: False, ‘patternProperties’: {‘targets:?’: {‘default’: {}, ‘additionalProperties’: False, ‘patternProperties’: {‘\\w[\\w-]*’: {‘type’: ‘string’}}, ‘type’: ‘object’}}, ‘$schema’: ‘http://json-schema.org/schema#’, ‘type’: ‘object’, ‘title’: ‘Spack target configuration file schema’}, ‘compilers’: {‘additionalProperties’: False, ‘patternProperties’: {‘compilers:?’: {‘items’: {‘compiler’: {‘additionalProperties’: False, ‘required’: [’paths’, ‘spec’, ‘modules’, ‘operating_system’], ‘type’: ‘object’, ‘properties’: {‘paths’: {‘additionalProperties’: False, ‘required’: [’cc’, ‘cxx’, ‘f77’, ‘fc’], ‘type’: ‘object’, ‘properties’: {‘cxxflags’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘cxx’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘fc’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘cppflags’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘ldflags’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘cflags’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘cc’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘fflags’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘ldlibs’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}, ‘f77’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}}}, ‘operating_system’: {‘type’: ‘string’}, ‘modules’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}, {‘type’: ‘array’}]}, ‘spec’: {‘type’: ‘string’}, ‘alias’: {‘anyOf’: [{‘type’: ‘string’}, {‘type’: ‘null’}]}}}}, ‘type’: ‘array’}}, ‘$schema’: ‘http://json-schema.org/schema#’, ‘type’: ‘object’, ‘title’: ‘Spack compiler configuration file schema’}}OrderedDict of config scopes keyed by name. Later scopes will override earlier scopes.

spack.config.spec_externals(spec)Return a list of external specs (with external directory path filled in), one for each known external installation.

spack.config.update_config(section, update_data, scope=None)Update the configuration file for a particular scope.

Overwrites contents of a section in a scope with update_data, then writes out the config file.

update_data should have the top-level section name stripped off (it will be re-added). Data itself can be a list,dict, or any other yaml-ish structure.

spack.config.validate_scope(scope)Ensure that scope is valid, and return a valid scope if it is None.

This should be used by routines in config.py to validate scope name arguments, and to determine a defaultscope where no scope is specified.

spack.config.validate_section(data, schema)Validate data read in from a Spack YAML file.

This leverages the line information (start_mark, end_mark) stored on Spack YAML structures.

spack.config.validate_section_name(section)Exit if the section is not a valid section.

1.11.9 spack.database module

Spack’s installation tracking database.

The database serves two purposes:

1. It implements a cache on top of a potentially very large Spack directory hierarchy, speeding up many operationsthat would otherwise require filesystem access.

2. It will allow us to track external installations as well as lost packages and their dependencies.

Prior ot the implementation of this store, a direcotry layout served as the authoritative database of packages in Spack.This module provides a cache and a sanity checking mechanism for what is in the filesystem.

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exception spack.database.CorruptDatabaseError(path, msg=’‘)Bases: spack.error.SpackError

class spack.database.Database(root, db_dir=None)Bases: object

add(spec_like, *args, **kwargs)

get_record(spec_like, *args, **kwargs)

installed_extensions_for(spec_like, *args, **kwargs)

missing(spec)

query(query_spec=<built-in function any>, known=<built-in function any>, installed=True,explicit=<built-in function any>)

Run a query on the database.

query_spec Queries iterate through specs in the database and return those that satisfy the suppliedquery_spec. If query_spec is any, This will match all specs in the database. If it is a spec, we’llevaluate spec.satisfies(query_spec).

The query can be constrained by two additional attributes:

known Possible values: True, False, any

Specs that are “known” are those for which Spack can locate a package.py file – i.e., Spack“knows” how to install them. Specs that are unknown may represent packages that existed in a previ-ous version of Spack, but have since either changed their name or been removed.

installed Possible values: True, False, any

Specs for which a prefix exists are “installed”. A spec that is NOT installed will be in the database ifsome other spec depends on it but its installation has gone away since Spack installed it.

TODO: Specs are a lot like queries. Should there be a wildcard spec object, and should specs have at-tributes like installed and known that can be queried? Or are these really special cases that only belonghere?

query_one(query_spec, known=<built-in function any>, installed=True)Query for exactly one spec that matches the query spec.

Raises an assertion error if more than one spec matches the query. Returns None if no installed packagematches.

read_transaction(timeout=60)Get a read lock context manager for use in a with block.

reindex(directory_layout)Build database index from scratch based from a directory layout.

Locks the DB if it isn’t locked already.

remove(spec_like, *args, **kwargs)

write_transaction(timeout=60)Get a write lock context manager for use in a with block.

class spack.database.InstallRecord(spec, path, installed, ref_count=0, explicit=False)Bases: object

A record represents one installation in the DB.

The record keeps track of the spec for the installation, its install path, AND whether or not it is installed. Weneed the installed flag in case a user either:

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1.blew away a directory, or

2.used spack uninstall -f to get rid of it

If, in either case, the package was removed but others still depend on it, we still need to track its spec, so wedon’t actually remove from the database until a spec has no installed dependents left.

classmethod from_dict(spec, dictionary)

to_dict()

exception spack.database.InvalidDatabaseVersionError(expected, found)Bases: spack.error.SpackError

1.11.10 spack.directives module

This package contains directives that can be used within a package.

Directives are functions that can be called inside a package definition to modify the package, for example:

class OpenMpi(Package): depends_on(“hwloc”) provides(“mpi”) ...

provides and depends_on are spack directives.

The available directives are:

• version

• depends_on

• provides

• extends

• patch

• variant

• resource

spack.directives.depends_on(*args, **kwargs)Creates a dict of deps with specs defining when they apply.

spack.directives.extends(*args, **kwargs)Same as depends_on, but dependency is symlinked into parent prefix.

This is for Python and other language modules where the module needs to be installed into the prefix of thePython installation. Spack handles this by installing modules into their own prefix, but allowing ONE moduleversion to be symlinked into a parent Python install at a time.

keyword arguments can be passed to extends() so that extension packages can pass parameters to the extendee’sextension mechanism.

spack.directives.provides(*args, **kwargs)Allows packages to provide a virtual dependency. If a package provides ‘mpi’, other packages can declare thatthey depend on “mpi”, and spack can use the providing package to satisfy the dependency.

spack.directives.patch(*args, **kwargs)Packages can declare patches to apply to source. You can optionally provide a when spec to indicate that aparticular patch should only be applied when the package’s spec meets certain conditions (e.g. a particularversion).

spack.directives.version(*args, **kwargs)Adds a version and metadata describing how to fetch it. Metadata is just stored as a dict in the package’s versionsdictionary. Package must turn it into a valid fetch strategy later.

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spack.directives.variant(*args, **kwargs)Define a variant for the package. Packager can specify a default value (on or off) as well as a text description.

spack.directives.resource(*args, **kwargs)Define an external resource to be fetched and staged when building the package. Based on the keywords presentin the dictionary the appropriate FetchStrategy will be used for the resource. Resources are fetched and stagedin their own folder inside spack stage area, and then moved into the stage area of the package that needs them.

List of recognized keywords:

•‘when’ : (optional) represents the condition upon which the resource is needed

•‘destination’ : (optional) path where to move the resource. This path must be relative to the main packagestage area.

•‘placement’ : (optional) gives the possibility to fine tune how the resource is moved into the main packagestage area.

1.11.11 spack.directory_layout module

class spack.directory_layout.DirectoryLayout(root)Bases: object

A directory layout is used to associate unique paths with specs. Different installations are going to want differnetlayouts for their install, and they can use this to customize the nesting structure of spack installs.

add_extension(spec, ext_spec)Add to the list of currently installed extensions.

all_specs()To be implemented by subclasses to traverse all specs for which there is a directory within the root.

check_activated(spec, ext_spec)Ensure that ext_spec can be removed from spec.

If not, raise NoSuchExtensionError.

check_extension_conflict(spec, ext_spec)Ensure that ext_spec can be activated in spec.

If not, raise ExtensionAlreadyInstalledError or ExtensionConflictError.

check_installed(spec)Checks whether a spec is installed.

Return the spec’s prefix, if it is installed, None otherwise.

Raise an exception if the install is inconsistent or corrupt.

create_install_directory(spec)Creates the installation directory for a spec.

extension_map(spec)Get a dict of currently installed extension packages for a spec.

Dict maps { name : extension_spec } Modifying dict does not affect internals of this layout.

hidden_file_pathsReturn a list of hidden files used by the directory layout.

Paths are relative to the root of an install directory.

If the directory layout uses no hidden files to maintain state, this should return an empty container, e.g. []or (,).

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path_for_spec(spec)Return absolute path from the root to a directory for the spec.

relative_path_for_spec(spec)Implemented by subclasses to return a relative path from the install root to a unique location for theprovided spec.

remove_extension(spec, ext_spec)Remove from the list of currently installed extensions.

remove_install_directory(spec)Removes a prefix and any empty parent directories from the root. Raised RemoveFailedError if somethinggoes wrong.

exception spack.directory_layout.DirectoryLayoutError(message, long_msg=None)Bases: spack.error.SpackError

Superclass for directory layout errors.

exception spack.directory_layout.ExtensionAlreadyInstalledError(spec, ext_spec)Bases: spack.directory_layout.DirectoryLayoutError

Raised when an extension is added to a package that already has it.

exception spack.directory_layout.ExtensionConflictError(spec, ext_spec, conflict)Bases: spack.directory_layout.DirectoryLayoutError

Raised when an extension is added to a package that already has it.

exception spack.directory_layout.InconsistentInstallDirectoryError(message,long_msg=None)

Bases: spack.directory_layout.DirectoryLayoutError

Raised when a package seems to be installed to the wrong place.

exception spack.directory_layout.InstallDirectoryAlreadyExistsError(path)Bases: spack.directory_layout.DirectoryLayoutError

Raised when create_install_directory is called unnecessarily.

exception spack.directory_layout.InvalidExtensionSpecError(message,long_msg=None)

Bases: spack.directory_layout.DirectoryLayoutError

Raised when an extension file has a bad spec in it.

exception spack.directory_layout.NoSuchExtensionError(spec, ext_spec)Bases: spack.directory_layout.DirectoryLayoutError

Raised when an extension isn’t there on deactivate.

exception spack.directory_layout.RemoveFailedError(installed_spec, prefix, error)Bases: spack.directory_layout.DirectoryLayoutError

Raised when a DirectoryLayout cannot remove an install prefix.

exception spack.directory_layout.SpecHashCollisionError(installed_spec, new_spec)Bases: spack.directory_layout.DirectoryLayoutError

Raised when there is a hash collision in an install layout.

exception spack.directory_layout.SpecReadError(message, long_msg=None)Bases: spack.directory_layout.DirectoryLayoutError

Raised when directory layout can’t read a spec.

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class spack.directory_layout.YamlDirectoryLayout(root, **kwargs)Bases: spack.directory_layout.DirectoryLayout

Lays out installation directories like this::

<install root>/

<platform-os-target>/

<compiler>-<compiler version>/ <name>-<version>-<variants>-<hash>

The hash here is a SHA-1 hash for the full DAG plus the build spec. TODO: implement the build spec.

To avoid special characters (like ~) in the directory name, only enabled variants are included in the install path.Disabled variants are omitted.

add_extension(spec, ext_spec)

all_specs()

build_env_path(spec)

build_log_path(spec)

build_packages_path(spec)

check_activated(spec, ext_spec)

check_extension_conflict(spec, ext_spec)

check_installed(spec)

create_install_directory(spec)

extension_file_path(spec)Gets full path to an installed package’s extension file

extension_map(spec)Defensive copying version of _extension_map() for external API.

hidden_file_paths

metadata_path(spec)

read_spec(path)Read the contents of a file and parse them as a spec

relative_path_for_spec(spec)

remove_extension(spec, ext_spec)

spec_file_path(spec)Gets full path to spec file

specs_by_hash()

write_spec(spec, path)Write a spec out to a file.

1.11.12 spack.environment module

class spack.environment.AppendPath(name, value, **kwargs)Bases: spack.environment.NameValueModifier

execute()

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class spack.environment.EnvironmentModifications(other=None)Bases: object

Keeps track of requests to modify the current environment.

Each call to a method to modify the environment stores the extra information on the caller in the request:- ‘filename’ : filename of the module where the caller is defined - ‘lineno’: line number where the requestoccurred - ‘context’ : line of code that issued the request that failed

append_path(name, path, **kwargs)Stores in the current object a request to append a path to a path list

Args: name: name of the path list in the environment path: path to be appended

apply_modifications()Applies the modifications and clears the list

clear()Clears the current list of modifications

extend(other)

static from_sourcing_files(*args, **kwargs)Creates an instance of EnvironmentModifications that, if executed, has the same effect on the environmentas sourcing the files passed as parameters

Parameters *args – list of files to be sourced

Return type instance of EnvironmentModifications

group_by_name()Returns a dict of the modifications grouped by variable name

Returns: dict mapping the environment variable name to the modifications to be done on it

prepend_path(name, path, **kwargs)Same as append_path, but the path is pre-pended

Args: name: name of the path list in the environment path: path to be pre-pended

remove_path(name, path, **kwargs)Stores in the current object a request to remove a path from a path list

Args: name: name of the path list in the environment path: path to be removed

set(name, value, **kwargs)Stores in the current object a request to set an environment variable

Args: name: name of the environment variable to be set value: value of the environment variable

set_path(name, elts, **kwargs)Stores a request to set a path generated from a list.

Args: name: name o the environment variable to be set. elts: elements of the path to set.

unset(name, **kwargs)Stores in the current object a request to unset an environment variable

Args: name: name of the environment variable to be set

class spack.environment.NameModifier(name, **kwargs)Bases: object

update_args(**kwargs)

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class spack.environment.NameValueModifier(name, value, **kwargs)Bases: object

update_args(**kwargs)

class spack.environment.PrependPath(name, value, **kwargs)Bases: spack.environment.NameValueModifier

execute()

class spack.environment.RemovePath(name, value, **kwargs)Bases: spack.environment.NameValueModifier

execute()

class spack.environment.SetEnv(name, value, **kwargs)Bases: spack.environment.NameValueModifier

execute()

class spack.environment.SetPath(name, value, **kwargs)Bases: spack.environment.NameValueModifier

execute()

class spack.environment.UnsetEnv(name, **kwargs)Bases: spack.environment.NameModifier

execute()

spack.environment.concatenate_paths(paths, separator=’:’)Concatenates an iterable of paths into a string of paths separated by separator, defaulting to colon

Args: paths: iterable of paths separator: the separator to use, default ‘:’

Returns: string

spack.environment.filter_environment_blacklist(env, variables)Generator that filters out any change to environment variables present in the input list

Args: env: list of environment modifications variables: list of variable names to be filtered

Yields: items in env if they are not in variables

spack.environment.set_or_unset_not_first(variable, changes, errstream)Check if we are going to set or unset something after other modifications have already been requested

spack.environment.validate(env, errstream)Validates the environment modifications to check for the presence of suspicious patterns. Prompts a warning foreverything that was found

Current checks: - set or unset variables after other changes on the same variable

Args: env: list of environment modifications

1.11.13 spack.error module

exception spack.error.NoNetworkConnectionError(message, url)Bases: spack.error.SpackError

Raised when an operation needs an internet connection.

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exception spack.error.SpackError(message, long_message=None)Bases: exceptions.Exception

This is the superclass for all Spack errors. Subclasses can be found in the modules they have to do with.

die()

long_message

exception spack.error.UnsupportedPlatformError(message)Bases: spack.error.SpackError

Raised by packages when a platform is not supported

1.11.14 spack.fetch_strategy module

Fetch strategies are used to download source code into a staging area in order to build it. They need to define thefollowing methods:

• fetch() This should attempt to download/check out source from somewhere.

• check() Apply a checksum to the downloaded source code, e.g. for an archive. May not do anything if the fetchmethod was safe to begin with.

• expand() Expand (e.g., an archive) downloaded file to source.

• reset() Restore original state of downloaded code. Used by clean commands. This may just remove the ex-panded source and re-expand an archive, or it may run something like git reset –hard.

• archive() Archive a source directory, e.g. for creating a mirror.

class spack.fetch_strategy.CacheURLFetchStrategy(*args, **kwargs)Bases: spack.fetch_strategy.URLFetchStrategy

The resource associated with a cache URL may be out of date.

fetch(*args, **kwargs)

exception spack.fetch_strategy.ChecksumError(message, long_msg=None)Bases: spack.fetch_strategy.FetchError

Raised when archive fails to checksum.

exception spack.fetch_strategy.FailedDownloadError(url, msg=’‘)Bases: spack.fetch_strategy.FetchError

Raised wen a download fails.

exception spack.fetch_strategy.FetchError(msg, long_msg=None)Bases: spack.error.SpackError

class spack.fetch_strategy.FetchStrategyBases: object

Superclass of all fetch strategies.

archive(destination)

check()

enabled = False

expand()

fetch()

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classmethod matches(args)

required_attributes = None

reset()

set_stage(stage)This is called by Stage before any of the fetching methods are called on the stage.

class spack.fetch_strategy.FsCache(root)Bases: object

destroy()

fetcher(targetPath, digest)

store(fetcher, relativeDst)

class spack.fetch_strategy.GitFetchStrategy(**kwargs)Bases: spack.fetch_strategy.VCSFetchStrategy

Fetch strategy that gets source code from a git repository. Use like this in a package:

version(‘name’, git=’https://github.com/project/repo.git‘)

Optionally, you can provide a branch, or commit to check out, e.g.:

version(‘1.1’, git=’https://github.com/project/repo.git‘, tag=’v1.1’)

You can use these three optional attributes in addition to git:

•branch: Particular branch to build from (default is master)

•tag: Particular tag to check out

•commit: Particular commit hash in the repo

archive(destination)

enabled = True

fetch(*args, **kwargs)

git

git_version

required_attributes = (‘git’,)

reset(*args, **kwargs)

class spack.fetch_strategy.GoFetchStrategy(**kwargs)Bases: spack.fetch_strategy.VCSFetchStrategy

Fetch strategy that employs the go get infrastructure Use like this in a package:

version(‘name’, go=’github.com/monochromegane/the_platinum_searcher/...’)

Go get does not natively support versions, they can be faked with git

archive(destination)

enabled = True

fetch(*args, **kwargs)

go

go_version

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required_attributes = (‘go’,)

reset(*args, **kwargs)

class spack.fetch_strategy.HgFetchStrategy(**kwargs)Bases: spack.fetch_strategy.VCSFetchStrategy

Fetch strategy that gets source code from a Mercurial repository. Use like this in a package:

version(‘name’, hg=’https://jay.grs.rwth-aachen.de/hg/lwm2‘)

Optionally, you can provide a branch, or revision to check out, e.g.:

version(‘torus’, hg=’https://jay.grs.rwth-aachen.de/hg/lwm2‘, branch=’torus’)

You can use the optional ‘revision’ attribute to check out a branch, tag, or particular revision in hg. To preventnon-reproducible builds, using a moving target like a branch is discouraged.

•revision: Particular revision, branch, or tag.

archive(destination)

enabled = True

fetch(*args, **kwargs)

hg

required_attributes = [’hg’]

reset(*args, **kwargs)

exception spack.fetch_strategy.InvalidArgsError(pkg, version)Bases: spack.fetch_strategy.FetchError

exception spack.fetch_strategy.NoArchiveFileError(msg, long_msg)Bases: spack.fetch_strategy.FetchError

exception spack.fetch_strategy.NoDigestError(msg, long_msg=None)Bases: spack.fetch_strategy.FetchError

exception spack.fetch_strategy.NoStageError(method)Bases: spack.fetch_strategy.FetchError

Raised when fetch operations are called before set_stage().

class spack.fetch_strategy.SvnFetchStrategy(**kwargs)Bases: spack.fetch_strategy.VCSFetchStrategy

Fetch strategy that gets source code from a subversion repository. Use like this in a package:

version(‘name’, svn=’http://www.example.com/svn/trunk‘)

Optionally, you can provide a revision for the URL:

version(‘name’, svn=’http://www.example.com/svn/trunk‘, revision=‘1641’)

archive(destination)

enabled = True

fetch(*args, **kwargs)

required_attributes = [’svn’]

reset(*args, **kwargs)

svn

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class spack.fetch_strategy.URLFetchStrategy(url=None, digest=None, **kwargs)Bases: spack.fetch_strategy.FetchStrategy

FetchStrategy that pulls source code from a URL for an archive, checks the archive against a checksum,anddecompresses the archive.

archive(destination)Just moves this archive to the destination.

archive_filePath to the source archive within this stage directory.

check(*args, **kwargs)Check the downloaded archive against a checksum digest. No-op if this stage checks code out of a reposi-tory.

enabled = True

expand(*args, **kwargs)

fetch(*args, **kwargs)

required_attributes = [’url’]

reset(*args, **kwargs)Removes the source path if it exists, then re-expands the archive.

class spack.fetch_strategy.VCSFetchStrategy(name, *rev_types, **kwargs)Bases: spack.fetch_strategy.FetchStrategy

archive(*args, **kwargs)

check(*args, **kwargs)

expand(*args, **kwargs)

spack.fetch_strategy.args_are_for(args, fetcher)

spack.fetch_strategy.for_package_version(pkg, version)Determine a fetch strategy based on the arguments supplied to version() in the package description.

spack.fetch_strategy.from_kwargs(**kwargs)Construct the appropriate FetchStrategy from the given keyword arguments.

Parameters kwargs – dictionary of keyword arguments

Returns fetcher or raise a FetchError exception

spack.fetch_strategy.from_url(url)Given a URL, find an appropriate fetch strategy for it. Currently just gives you a URLFetchStrategy that usescurl.

TODO: make this return appropriate fetch strategies for other types of URLs.

1.11.15 spack.file_cache module

exception spack.file_cache.CacheError(message, long_message=None)Bases: spack.error.SpackError

class spack.file_cache.FileCache(root)Bases: object

This class manages cached data in the filesystem.

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•Cache files are fetched and stored by unique keys. Keys can be relative paths, so that thre can be somehierarchy in the cache.

•The FileCache handles locking cache files for reading and writing, so client code need not manage locksfor cache entries.

cache_path(key)Path to the file in the cache for a particular key.

destroy()Remove all files under the cache root.

init_entry(key)Ensure we can access a cache file. Create a lock for it if needed.

Return whether the cache file exists yet or not.

mtime(key)Return modification time of cache file, or 0 if it does not exist.

Time is in units returned by os.stat in the mtime field, which is platform-dependent.

read_transaction(key)Get a read transaction on a file cache item.

Returns a ReadTransaction context manager and opens the cache file for reading. You can use it like this:

with spack.user_cache.read_transaction(key) as cache_file: cache_file.read()

remove(key)

write_transaction(key)Get a write transaction on a file cache item.

Returns a WriteTransaction context manager that opens a temporary file for writing. Once the contextmanager finishes, if nothing went wrong, moves the file into place on top of the old file atomically.

1.11.16 spack.graph module

Functions for graphing DAGs of dependencies.

This file contains code for graphing DAGs of software packages (i.e. Spack specs). There are two main functions youprobably care about:

graph_ascii() will output a colored graph of a spec in ascii format, kind of like the graph git shows with “git log–graph”, e.g.:

o mpileaks| | | | o | callpath|/| || |\|| |\ | | |\ | | | | o adept-utils| |_|_|/||/| | | |o | | | | mpi/ / / /

| | o | dyninst| |/| ||/|/| || | |/| o | libdwarf|/ /

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o | libelf/

o boost

graph_dot() will output a graph of a spec (or multiple specs) in dot format.

Note that graph_ascii assumes a single spec while graph_dot can take a number of specs as input.

spack.graph.topological_sort(spec, **kwargs)Topological sort for specs.

Return a list of dependency specs sorted topologically. The spec argument is not modified in the process.

spack.graph.graph_ascii(spec, **kwargs)

class spack.graph.AsciiGraphBases: object

write(spec, **kwargs)Write out an ascii graph of the provided spec.

Arguments: spec – spec to graph. This only handles one spec at a time.

Optional arguments:

out – file object to write out to (default is sys.stdout)

color – whether to write in color. Default is to autodetect based on output file.

spack.graph.graph_dot(*specs, **kwargs)Generate a graph in dot format of all provided specs.

Print out a dot formatted graph of all the dependencies between package. Output can be passed to graphviz, e.g.:

spack graph –dot qt | dot -Tpdf > spack-graph.pdf

1.11.17 spack.mirror module

This file contains code for creating spack mirror directories. A mirror is an organized hierarchy containing speciallynamed archive files. This enabled spack to know where to find files in a mirror if the main server for a particularpackage is down. Or, if the computer where spack is run is not connected to the internet, it allows spack to downloadpackages directly from a mirror (e.g., on an intranet).

exception spack.mirror.MirrorError(msg, long_msg=None)Bases: spack.error.SpackError

Superclass of all mirror-creation related errors.

spack.mirror.add_single_spec(spec, mirror_root, categories, **kwargs)

spack.mirror.create(path, specs, **kwargs)Create a directory to be used as a spack mirror, and fill it with package archives.

Arguments: path: Path to create a mirror directory hierarchy in. specs: Any package versions matching thesespecs will be added to the mirror.

Keyword args: no_checksum: If True, do not checkpoint when fetching (default False) num_versions: Maxnumber of versions to fetch per spec, if spec is ambiguous (default is 0 for all of them)

Return Value: Returns a tuple of lists: (present, mirrored, error)

• present: Package specs that were already present.

• mirrored: Package specs that were successfully mirrored.

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• error: Package specs that failed to mirror due to some error.

This routine iterates through all known package versions, and it creates specs for those versions. If the versionsatisfies any spec in the specs list, it is downloaded and added to the mirror.

spack.mirror.get_matching_versions(specs, **kwargs)Get a spec for EACH known version matching any spec in the list.

spack.mirror.mirror_archive_filename(spec, fetcher)Get the name of the spec’s archive in the mirror.

spack.mirror.mirror_archive_path(spec, fetcher)Get the relative path to the spec’s archive within a mirror.

spack.mirror.suggest_archive_basename(resource)Return a tentative basename for an archive.

Raises an exception if the name is not an allowed archive type.

Parameters fetcher –

Returns

1.11.18 spack.modules module

This module contains code for creating environment modules, which can include dotkits, tcl modules, lmod, andothers.

The various types of modules are installed by post-install hooks and removed after an uninstall by post-uninstall hooks.This class consolidates the logic for creating an abstract description of the information that module systems need.

This module also includes logic for coming up with unique names for the module files so that they can be found bythe various shell-support files in $SPACK/share/spack/setup-env.*.

Each hook in hooks/ implements the logic for writing its specific type of module file.

class spack.modules.EnvModule(spec=None)Bases: object

autoload(spec)

blacklisted

category

file_nameSubclasses should implement this to return the name of the file where this module lives.

formats = {}

header

module_specific_content(configuration)

name = ‘env_module’

naming_scheme

prerequisite(spec)

process_environment_command(env)

remove()

tokensTokens that can be substituted in environment variable values and naming schemes

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upper_tokensTokens that can be substituted in environment variable names

use_nameSubclasses should implement this to return the name the module command uses to refer to the package.

write(overwrite=False)Writes out a module file for this object.

This method employs a template pattern and expects derived classes to: - override the header property -provide formats for autoload, prerequisites and environment changes

class spack.modules.Dotkit(spec=None)Bases: spack.modules.EnvModule

autoload_format = ‘dk_op {module_file}\n’

default_naming_format = ‘{name}-{version}-{compiler.name}-{compiler.version}’

environment_modifications_formats = {<class ‘spack.environment.RemovePath’>: ‘dk_unalter {name} {value}\n’, <class ‘spack.environment.PrependPath’>: ‘dk_alter {name} {value}\n’, <class ‘spack.environment.SetEnv’>: ‘dk_setenv {name} {value}\n’}

file_name

header

name = ‘dotkit’

path = ‘/home/docs/checkouts/readthedocs.org/user_builds/spack/checkouts/bugfix-rtd-generation/share/spack/dotkit’

prerequisite(spec)

class spack.modules.TclModule(spec=None)Bases: spack.modules.EnvModule

autoload_format = ‘if ![ is-loaded {module_file} ] {{\n puts stderr “Autoloading {module_file}”\n module load {module_file}\n}}\n\n’

default_naming_format = ‘{name}-{version}-{compiler.name}-{compiler.version}’

file_name

header

module_specific_content(configuration)

name = ‘tcl’

path = ‘/home/docs/checkouts/readthedocs.org/user_builds/spack/checkouts/bugfix-rtd-generation/share/spack/modules’

prerequisite_format = ‘prereq {module_file}\n’

process_environment_command(env)

1.11.19 spack.multimethod module

This module contains utilities for using multi-methods in spack. You can think of multi-methods like overloadedmethods – they’re methods with the same name, and we need to select a version of the method based on some criteria.e.g., for overloaded methods, you would select a version of the method to call based on the types of its arguments.

In spack, multi-methods are used to ease the life of package authors. They allow methods like install() (or othermethods called by install()) to declare multiple versions to be called when the package is instantiated with differentspecs. e.g., if the package is built with OpenMPI on x86_64„ you might want to call a different install method than ifit was built for mpich2 on BlueGene/Q. Likewise, you might want to do a different type of install for different versionsof the package.

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Multi-methods provide a simple decorator-based syntax for this that avoids overly complicated rat nests of if state-ments. Obviously, depending on the scenario, regular old conditionals might be clearer, so package authors should usetheir judgement.

exception spack.multimethod.MultiMethodError(message)Bases: spack.error.SpackError

Superclass for multimethod dispatch errors

exception spack.multimethod.NoSuchMethodError(cls, method_name, spec, possible_specs)Bases: spack.error.SpackError

Raised when we can’t find a version of a multi-method.

class spack.multimethod.SpecMultiMethod(default=None)Bases: object

This implements a multi-method for Spack specs. Packages are instantiated with a particular spec, and you maywant to execute different versions of methods based on what the spec looks like. For example, you might wantto call a different version of install() for one platform than you call on another.

The SpecMultiMethod class implements a callable object that handles method dispatch. When it is called, itlooks through registered methods and their associated specs, and it tries to find one that matches the package’sspec. If it finds one (and only one), it will call that method.

The package author is responsible for ensuring that only one condition on multi-methods ever evaluates to true.If multiple methods evaluate to true, this will raise an exception.

This is intended for use with decorators (see below). The decorator (see docs below) creates SpecMultiMethodsand registers method versions with them.

To register a method, you can do something like this: mm = SpecMultiMethod()mm.register(“^chaos_5_x86_64_ib”, some_method)

The object registered needs to be a Spec or some string that will parse to be a valid spec.

When the mm is actually called, it selects a version of the method to call based on the sys_type of the object itis called on.

See the docs for decorators below for more details.

register(spec, method)Register a version of a method for a particular sys_type.

class spack.multimethod.when(spec)Bases: object

This annotation lets packages declare multiple versions of methods like install() that depend on the package’sspec. For example:

class SomePackage(Package):...

def install(self, prefix):# Do default install

@when('arch=chaos_5_x86_64_ib')def install(self, prefix):

# This will be executed instead of the default install if# the package's platform() is chaos_5_x86_64_ib.

@when('arch=bgqos_0")

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def install(self, prefix):# This will be executed if the package's sys_type is bgqos_0

This allows each package to have a default version of install() AND specialized versions for particular platforms.The version that is called depends on the architecutre of the instantiated package.

Note that this works for methods other than install, as well. So, if you only have part of the install that is platformspecific, you could do this:

class SomePackage(Package):...# virtual dependence on MPI.# could resolve to mpich, mpich2, OpenMPIdepends_on('mpi')

def setup(self):# do nothing in the default casepass

@when('^openmpi')def setup(self):

# do something special when this is built with OpenMPI for# its MPI implementations.

def install(self, prefix):# Do common install stuffself.setup()# Do more common install stuff

There must be one (and only one) @when clause that matches the package’s spec. If there is more than one, orif none match, then the method will raise an exception when it’s called.

Note that the default version of decorated methods must always come first. Otherwise it will override all of theplatform-specific versions. There’s not much we can do to get around this because of the way decorators work.

1.11.20 spack.package module

This is where most of the action happens in Spack. See the Package docs for detailed instructions on how the classworks and on how to write your own packages.

The spack package structure is based strongly on Homebrew (http://wiki.github.com/mxcl/homebrew/), mainly be-cause Homebrew makes it very easy to create packages. For a complete rundown on spack and how it differs fromhomebrew, look at the README.

exception spack.package.ActivationError(msg, long_msg=None)Bases: spack.package.ExtensionError

class spack.package.CMakePackage(spec)Bases: spack.package.StagedPackage

configure_args()Returns package-specific arguments to be provided to the configure command.

configure_env()Returns package-specific environment under which the configure command should be run.

install_build()

install_configure()

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install_install()

install_setup()

make_make()

transitive_inc_path()

exception spack.package.DependencyConflictError(conflict)Bases: spack.error.SpackError

Raised when the dependencies cannot be flattened as asked for.

exception spack.package.ExtensionConflictError(path)Bases: spack.package.ExtensionError

exception spack.package.ExtensionError(message, long_msg=None)Bases: spack.package.PackageError

exception spack.package.ExternalPackageError(message, long_msg=None)Bases: spack.package.InstallError

Raised by install() when a package is only for external use.

exception spack.package.FetchError(message, long_msg=None)Bases: spack.error.SpackError

Raised when something goes wrong during fetch.

exception spack.package.InstallError(message, long_msg=None)Bases: spack.error.SpackError

Raised when something goes wrong during install or uninstall.

exception spack.package.NoURLError(cls)Bases: spack.package.PackageError

Raised when someone tries to build a URL for a package with no URLs.

class spack.package.Package(spec)Bases: object

This is the superclass for all spack packages.

*The Package class*

Package is where the bulk of the work of installing packages is done.

A package defines how to fetch, verfiy (via, e.g., md5), build, and install a piece of software. A Package alsodefines what other packages it depends on, so that dependencies can be installed along with the package itself.Packages are written in pure python.

Packages are all submodules of spack.packages. If spack is installed in $prefix, all of its pythonfiles are in $prefix/lib/spack. Most of them are in the spack module, so all the packages live in$prefix/lib/spack/spack/packages.

All you have to do to create a package is make a new subclass of Package in this directory. Spack automaticallyscans the python files there and figures out which one to import when you invoke it.

An example package

Let’s look at the cmake package to start with. This package lives in$prefix/var/spack/repos/builtin/packages/cmake/package.py:

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from spack import *class Cmake(Package):

homepage = 'https://www.cmake.org'url = 'http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz'md5 = '097278785da7182ec0aea8769d06860c'

def install(self, spec, prefix):configure('--prefix=%s' % prefix,

'--parallel=%s' % make_jobs)make()make('install')

Naming conventions

There are two names you should care about:

1.The module name, cmake.

•User will refers to this name, e.g. ‘spack install cmake’.

•It can include _, -, and numbers (it can even start with a number).

2.The class name, “Cmake”. This is formed by converting - or _ in the module name to camel case. If thename starts with a number, we prefix the class name with _. Examples:

Module Name Class Namefoo_bar FooBardocbook-xml DocbookXmlFooBar Foobar3proxy _3proxy

The class name is what spack looks for when it loads a package module.

Required Attributes

Aside from proper naming, here is the bare minimum set of things you need when you make a package:

homepage: informational URL, so that users know what they’re installing.

url or url_for_version(self, version): If url, then the URL of the source archive that spack will fetch. Ifurl_for_version(), then a method returning the URL required to fetch a particular version.

install(): This function tells spack how to build and install the software it downloaded.

Optional Attributes

You can also optionally add these attributes, if needed:

list_url: Webpage to scrape for available version strings. Default is the directory containing thetarball; use this if the default isn’t correct so that invoking ‘spack versions’ will work for thispackage.

url_version(self, version): When spack downloads packages at particular versions, it just convertsversion to string with str(version). Override this if your package needs special version formattingin its URL. boost is an example of a package that needs this.

*Creating Packages*

As a package creator, you can probably ignore most of the preceding information, because you can use the‘spack create’ command to do it all automatically.

You as the package creator generally only have to worry about writing your install function and specifyingdependencies.

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spack create

Most software comes in nicely packaged tarballs, like this one

http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz

Taking a page from homebrew, spack deduces pretty much everything it needs to know from the URL above. Ifyou simply type this:

spack create http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz

Spack will download the tarball, generate an md5 hash, figure out the version and the name of the package fromthe URL, and create a new package file for you with all the names and attributes set correctly.

Once this skeleton code is generated, spack pops up the new package in your $EDITOR so that you can modifythe parts that need changes.

Dependencies

If your package requires another in order to build, you can specify that like this:

class Stackwalker(Package):...depends_on("libdwarf")...

This tells spack that before it builds stackwalker, it needs to build the libdwarf package as well. Note that this isthe module name, not the class name (The class name is really only used by spack to find your package).

Spack will download an install each dependency before it installs your package. In addtion, it will add -L, -I,and rpath arguments to your compiler and linker for each dependency. In most cases, this allows you to avoidspecifying any dependencies in your configure or cmake line; you can just run configure or cmake without anyadditional arguments and it will find the dependencies automatically.

The Install Function

The install function is designed so that someone not too terribly familiar with Python could write a package in-staller. For example, we put a number of commands in install scope that you can use almost like shell commands.These include make, configure, cmake, rm, rmtree, mkdir, mkdirp, and others.

You can see above in the cmake script that these commands are used to run configure and make almost likethey’re used on the command line. The only difference is that they are python function calls and not shellcommands.

It may be puzzling to you where the commands and functions in install live. They are NOT instance variables onthe class; this would require us to type ‘self.’ all the time and it makes the install code unnecessarily long. Rather,spack puts these commands and variables in module scope for your Package subclass. Since each package hasits own module, this doesn’t pollute other namespaces, and it allows you to more easily implement an installfunction.

For a full list of commands and variables available in module scope, see the add_commands_to_module() func-tion in this class. This is where most of them are created and set on the module.

Parallel Builds

By default, Spack will run make in parallel when you run make() in your install function. Spack figures out howmany cores are available on your system and runs make with -j<cores>. If you do not want this behavior, youcan explicitly mark a package not to use parallel make:

class SomePackage(Package):...parallel = False...

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This changes thd default behavior so that make is sequential. If you still want to build some parts in parallel,you can do this in your install function:

make(parallel=True)

Likewise, if you do not supply parallel = True in your Package, you can keep the default parallel behavior andrun make like this when you want a sequential build:

make(parallel=False)

Package Lifecycle

This section is really only for developers of new spack commands.

A package’s lifecycle over a run of Spack looks something like this:

p = Package() # Done for you by spack

p.do_fetch() # downloads tarball from a URLp.do_stage() # expands tarball in a temp directoryp.do_patch() # applies patches to expanded sourcep.do_install() # calls package's install() functionp.do_uninstall() # removes install directory

There are also some other commands that clean the build area:

p.do_clean() # removes the stage directory entirelyp.do_restage() # removes the build directory and

# re-expands the archive.

The convention used here is that a do_* function is intended to be called internally by Spack commands (inspack.cmd). These aren’t for package writers to override, and doing so may break the functionality of thePackage class.

Package creators override functions like install() (all of them do this), clean() (some of them do this), and othersto provide custom behavior.

activate(extension, **kwargs)Symlinks all files from the extension into extendee’s install dir.

Package authors can override this method to support other extension mechanisms. Spack internals (com-mands, hooks, etc.) should call do_activate() method so that proper checks are always executed.

activated

all_urls

build_log_path

compilerGet the spack.compiler.Compiler object used to build this package

deactivate(extension, **kwargs)Unlinks all files from extension out of this package’s install dir.

Package authors can override this method to support other extension mechanisms. Spack internals (com-mands, hooks, etc.) should call do_deactivate() method so that proper checks are always executed.

dependencies_of_type(*deptypes)Get subset of the dependencies with certain types.

do_activate(force=False)Called on an extension to invoke the extendee’s activate method.

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Commands should call this routine, and should not call activate() directly.

do_clean()Removes the package’s build stage and source tarball.

do_deactivate(**kwargs)Called on the extension to invoke extendee’s deactivate() method.

do_fake_install()Make a fake install directory contaiing a ‘fake’ file in bin.

do_fetch(mirror_only=False)Creates a stage directory and downloads the tarball for this package. Working directory will be set to thestage directory.

do_install(keep_prefix=False, keep_stage=False, ignore_deps=False, skip_patch=False, ver-bose=False, make_jobs=None, run_tests=False, fake=False, explicit=False, dirty=False,install_phases=set([’provenance’, ‘configure’, ‘install’, ‘build’]))

Called by commands to install a package and its dependencies.

Package implementations should override install() to describe their build process.

Parameters

• keep_prefix – Keep install prefix on failure. By default, destroys it.

• keep_stage – By default, stage is destroyed only if there are no exceptions during build.Set to True to keep the stage even with exceptions.

• ignore_deps – Don’t install dependencies before installing this package

• fake – Don’t really build; install fake stub files instead.

• skip_patch – Skip patch stage of build if True.

• verbose – Display verbose build output (by default, suppresses it)

• dirty – Don’t clean the build environment before installing.

• make_jobs – Number of make jobs to use for install. Default is ncpus

• run_tests – Run tests within the package’s install()

do_install_dependencies(**kwargs)

do_patch()Calls do_stage(), then applied patches to the expanded tarball if they haven’t been applied already.

do_restage()Reverts expanded/checked out source to a pristine state.

do_stage(mirror_only=False)Unpacks the fetched tarball, then changes into the expanded tarball directory.

do_uninstall(force=False)

extendable = FalseList of prefix-relative file paths (or a single path). If these do not exist after install, or if they exist but arenot files, sanity checks fail.

extendee_argsSpec of the extendee of this package, or None if it is not an extension

extendee_specSpec of the extendee of this package, or None if it is not an extension

extends(spec)

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fetch_remote_versions()Try to find remote versions of this package using the list_url and any other URLs described in the packagefile.

fetcher

format_doc(**kwargs)Wrap doc string at 72 characters and format nicely

global_license_dirReturns the directory where global license files for all packages are stored.

global_license_fileReturns the path where a global license file for this particular package should be stored.

install(spec, prefix)Package implementations override this with their own configuration

install_phases = set([’provenance’, ‘configure’, ‘install’, ‘build’])

installed

installed_dependents

Return a list of the specs of all installed packages that depend on this one.

TODO: move this method to database.py?

is_extension

make_jobs = NoneBy default do not run tests within package’s install()

moduleUse this to add variables to the class’s module’s scope. This lets us use custom syntax in the install method.

namespace

nearest_url(version)Finds the URL for the next lowest version with a URL. If there is no lower version with a URL, uses thepackage url property. If that isn’t there, uses a higher URL, and if that isn’t there raises an error.

package_dirReturn the directory where the package.py file lives.

parallel = True# jobs to use for parallel make. If set, overrides default of ncpus.

prefixGet the prefix into which this package should be installed.

provides(vpkg_name)True if this package provides a virtual package with the specified name

remove_prefix()Removes the prefix for a package along with any empty parent directories

rpathGet the rpath this package links with, as a list of paths.

rpath_argsGet the rpath args as a string, with -Wl,-rpath, for each element

run_tests = FalseMost packages are NOT extendable. Set to True if you want extensions.

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sanity_check_is_dir = []

sanity_check_is_file = []List of prefix-relative directory paths (or a single path). If these do not exist after install, or if they existbut are not directories, sanity checks will fail.

sanity_check_prefix()This function checks whether install succeeded.

setup_dependent_environment(spack_env, run_env, dependent_spec)Set up the environment of packages that depend on this one.

This is similar to setup_environment, but it is used to modify the compile and runtime environmentsof packages that depend on this one. This gives packages like Python and others that follow the extensionmodel a way to implement common environment or compile-time settings for dependencies.

By default, this delegates to self.setup_environment()

Example:

1.Installing python modules generally requires PYTHONPATH to point to the lib/pythonX.Y/site-packages directory in the module’s install prefix. This could set that variable.

Args:

spack_env (EnvironmentModifications): list of modifications to be applied when the depen-dent package is bulit within Spack.

run_env (EnvironmentModifications): list of environment changes to be applied when thedependent package is run outside of Spack.

dependent_spec (Spec): The spec of the dependent package about to be built. This allows theextendee (self) to query the dependent’s state. Note that this package’s spec is available asself.spec.

This is useful if there are some common steps to installing all extensions for a certain package.

setup_dependent_package(module, dependent_spec)Set up Python module-scope variables for dependent packages.

Called before the install() method of dependents.

Default implementation does nothing, but this can be overridden by an extendable package to set up themodule of its extensions. This is useful if there are some common steps to installing all extensions for acertain package.

Example :

1.Extensions often need to invoke the python interpreter from the Python installation being extended.This routine can put a ‘python’ Executable object in the module scope for the extension package tosimplify extension installs.

2.MPI compilers could set some variables in the dependent’s scope that point to mpicc, mpicxx, etc.,allowing them to be called by common names regardless of which MPI is used.

3.BLAS/LAPACK implementations can set some variables indicating the path to their libraries, sincethese paths differ by BLAS/LAPACK implementation.

Args:

module (module): The Python module object of the dependent package. Packages can usethis to set module-scope variables for the dependent to use.

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dependent_spec (Spec): The spec of the dependent package about to be built. This allows theextendee (self) to query the dependent’s state. Note that this package’s spec is available asself.spec.

This is useful if there are some common steps to installing all extensions for a certain package.

setup_environment(spack_env, run_env)Set up the compile and runtime environments for a package.

spack_env and run_env are EnvironmentModifications objects. Package authors can call methods on themto alter the environment within Spack and at runtime.

Both spack_env and run_env are applied within the build process, before this package’s install() method iscalled.

Modifications in run_env will also be added to the generated environment modules for this package.

Default implementation does nothing, but this can be overridden if the package needs a particular environ-ment.

Examples:

1.Qt extensions need QTDIR set.

Args:

spack_env (EnvironmentModifications): list of modifications to be applied when this package isbuilt within Spack.

run_env (EnvironmentModifications): list of environment changes to be applied when this pack-age is run outside of Spack.

stage

url_for_version(version)Returns a URL that you can download a new version of this package from.

url_version(version)Given a version, this returns a string that should be substituted into the package’s URL to download thatversion.

By default, this just returns the version string. Subclasses may need to override this, e.g. for boost versionswhere you need to ensure that there are _’s in the download URL.

version

version_urls = <functools.partial object>

exception spack.package.PackageError(message, long_msg=None)Bases: spack.error.SpackError

Raised when something is wrong with a package definition.

exception spack.package.PackageStillNeededError(spec, dependents)Bases: spack.package.InstallError

Raised when package is still needed by another on uninstall.

exception spack.package.PackageVersionError(version)Bases: spack.package.PackageError

Raised when a version URL cannot automatically be determined.

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class spack.package.StagedPackage(spec)Bases: spack.package.Package

A Package subclass where the install() is split up into stages.

install(spec, prefix)

install_build()Runs the build process.

install_configure()Runs the configure process.

install_install()Runs the install process.

install_setup()Creates a spack_setup.py script to configure the package later.

exception spack.package.VersionFetchError(cls)Bases: spack.package.PackageError

Raised when a version URL cannot automatically be determined.

spack.package.dump_packages(spec, path)Dump all package information for a spec and its dependencies.

This creates a package repository within path for every namespace in the spec DAG, and fills the repos wtihpackage files and patch files for every node in the DAG.

spack.package.flatten_dependencies(spec, flat_dir)Make each dependency of spec present in dir via symlink.

spack.package.install_dependency_symlinks(pkg, spec, prefix)Execute a dummy install and flatten dependencies

spack.package.make_executable(path)

spack.package.print_pkg(message)Outputs a message with a package icon.

spack.package.use_cray_compiler_names()Compiler names for builds that rely on cray compiler names.

spack.package.validate_package_url(url_string)Determine whether spack can handle a particular URL or not.

1.11.21 spack.package_test module

spack.package_test.compare_output(current_output, blessed_output)Compare blessed and current output of executables.

spack.package_test.compare_output_file(current_output, blessed_output_file)Same as above, but when the blessed output is given as a file.

spack.package_test.compile_c_and_execute(source_file, include_flags, link_flags)Compile C @p source_file with @p include_flags and @p link_flags, run and return the output.

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1.11.22 spack.parse module

exception spack.parse.LexError(message, string, pos)Bases: spack.parse.ParseError

Raised when we don’t know how to lex something.

class spack.parse.Lexer(lexicon)Bases: object

Base class for Lexers that keep track of line numbers.

lex(text)

token(type, value=’‘)

exception spack.parse.ParseError(message, string, pos)Bases: spack.error.SpackError

Raised when we don’t hit an error while parsing.

class spack.parse.Parser(lexer)Bases: object

Base class for simple recursive descent parsers.

accept(id)Put the next symbol in self.token if accepted, then call gettok()

expect(id)Like accept(), but fails if we don’t like the next token.

gettok()Puts the next token in the input stream into self.next.

last_token_error(message)Raise an error about the previous token in the stream.

next_token_error(message)Raise an error about the next token in the stream.

parse(text)

push_tokens(iterable)Adds all tokens in some iterable to the token stream.

setup(text)

unexpected_token()

class spack.parse.Token(type, value=’‘, start=0, end=0)Represents tokens; generated from input by lexer and fed to parse().

is_a(type)

1.11.23 spack.patch module

exception spack.patch.NoSuchPatchFileError(package, path)Bases: spack.error.SpackError

Raised when user specifies a patch file that doesn’t exist.

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class spack.patch.Patch(pkg, path_or_url, level)Bases: object

This class describes a patch to be applied to some expanded source code.

apply(stage)Fetch this patch, if necessary, and apply it to the source code in the supplied stage.

1.11.24 spack.preferred_packages module

class spack.preferred_packages.PreferredPackagesBases: object

architecture_compare(pkgname, a, b)Return less-than-0, 0, or greater than 0 if architecture a of pkgname is respectively less-than, equal-to, orgreater-than architecture b of pkgname. One architecture is less-than another if it is preferred over theother.

compiler_compare(pkgname, a, b)Return less-than-0, 0, or greater than 0 if compiler a of pkgname is respecively less-than, equal-to, orgreater-than compiler b of pkgname. One compiler is less-than another if it is preferred over the other.

provider_compare(pkgname, provider_str, a, b)Return less-than-0, 0, or greater than 0 if a is respecively less-than, equal-to, or greater-than b. A and bare possible implementations of provider_str. One provider is less-than another if it is preferred over theother. For example, provider_compare(‘scorep’, ‘mpi’, ‘mvapich’, ‘openmpi’) would return -1 if mvapichshould be preferred over openmpi for scorep.

spec_has_preferred_provider(pkgname, provider_str)Return True iff the named package has a list of preferred providers

spec_preferred_variants(pkgname)Return a VariantMap of preferred variants and their values

variant_compare(pkgname, a, b)Return less-than-0, 0, or greater than 0 if variant a of pkgname is respectively less-than, equal-to, orgreater-than variant b of pkgname. One variant is less-than another if it is preferred over the other.

version_compare(pkgname, a, b)Return less-than-0, 0, or greater than 0 if version a of pkgname is respectively less-than, equal-to, orgreater-than version b of pkgname. One version is less-than another if it is preferred over the other.

1.11.25 spack.provider_index module

The virtual module contains utility classes for virtual dependencies.

class spack.provider_index.ProviderIndex(specs=None, restrict=False)Bases: object

This is a dict of dicts used for finding providers of particular virtual dependencies. The dict of dicts looks like:

{ vpkg name : { full vpkg spec : set(packages providing spec) } }

Callers can use this to first find which packages provide a vpkg, then find a matching full spec. e.g., in thisscenario:

{ ‘mpi’ :

{ mpi@:1.1 [set([mpich]),] mpi@:2.3 : set([mpich2@1.9:]) } }

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Calling providers_for(spec) will find specs that provide a matching implementation of MPI.

copy()Deep copy of this ProviderIndex.

static from_yaml(stream)

merge(other)Merge other ProviderIndex into this one.

providers_for(*vpkg_specs)Gives specs of all packages that provide virtual packages with the supplied specs.

remove_provider(pkg_name)Remove a provider from the ProviderIndex.

satisfies(other)Check that providers of virtual specs are compatible.

to_yaml(stream=None)

update(spec)

exception spack.provider_index.ProviderIndexError(message, long_message=None)Bases: spack.error.SpackError

Raised when there is a problem with a ProviderIndex.

1.11.26 spack.repository module

exception spack.repository.BadRepoError(message, long_message=None)Bases: spack.repository.RepoError

Raised when repo layout is invalid.

exception spack.repository.DuplicateRepoError(message, long_message=None)Bases: spack.repository.RepoError

Raised when duplicate repos are added to a RepoPath.

exception spack.repository.FailedConstructorError(name, exc_type, exc_obj, exc_tb)Bases: spack.repository.PackageLoadError

Raised when a package’s class constructor fails.

exception spack.repository.InvalidNamespaceError(message, long_message=None)Bases: spack.repository.RepoError

Raised when an invalid namespace is encountered.

exception spack.repository.NoRepoConfiguredError(message, long_message=None)Bases: spack.repository.RepoError

Raised when there are no repositories configured.

exception spack.repository.PackageLoadError(message, long_message=None)Bases: spack.error.SpackError

Superclass for errors related to loading packages.

class spack.repository.Repo(root, namespace=’spack.pkg’)Bases: object

Class representing a package repository in the filesystem.

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Each package repository must have a top-level configuration file called repo.yaml.

Currently, repo.yaml this must define:

namespace: A Python namespace where the repository’s packages should live.

all_package_names()Returns a sorted list of all package names in the Repo.

all_packages()Iterator over all packages in the repository.

Use this with care, because loading packages is slow.

dirname_for_package_name(spec_like, *args, **kwargs)

dump_provenance(spec_like, *args, **kwargs)

exists(pkg_name)Whether a package with the supplied name exists.

extensions_for(spec_like, *args, **kwargs)

filename_for_package_name(spec_like, *args, **kwargs)

find_module(fullname, path=None)Python find_module import hook.

Returns this Repo if it can load the module; None if not.

get(spec_like, *args, **kwargs)

get_pkg_class(pkg_name)Get the class for the package out of its module.

First loads (or fetches from cache) a module for the package. Then extracts the package class from themodule according to Spack’s naming convention.

is_prefix(fullname)True if fullname is a prefix of this Repo’s namespace.

load_module(fullname)Python importer load hook.

Tries to load the module; raises an ImportError if it can’t.

provider_indexA provider index with names specific to this repo.

providers_for(spec_like, *args, **kwargs)

purge()Clear entire package instance cache.

real_name(import_name)Allow users to import Spack packages using Python identifiers.

A python identifier might map to many different Spack package names due to hyphen/underscore ambigu-ity.

Easy example: num3proxy -> 3proxy

Ambiguous: foo_bar -> foo_bar, foo-bar

More ambiguous: foo_bar_baz -> foo_bar_baz, foo-bar-baz, foo_bar-baz, foo-bar_baz

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exception spack.repository.RepoError(message, long_message=None)Bases: spack.error.SpackError

Superclass for repository-related errors.

class spack.repository.RepoPath(*repo_dirs, **kwargs)Bases: object

A RepoPath is a list of repos that function as one.

It functions exactly like a Repo, but it operates on the combined results of the Repos in its list instead of on asingle package repository.

all_package_names()Return all unique package names in all repositories.

all_packages()

dirname_for_package_name(pkg_name)

dump_provenance(spec_like, *args, **kwargs)

exists(pkg_name)

extensions_for(spec_like, *args, **kwargs)

filename_for_package_name(pkg_name)

find_module(fullname, path=None)Implements precedence for overlaid namespaces.

Loop checks each namespace in self.repos for packages, and also handles loading empty containing names-paces.

first_repo()Get the first repo in precedence order.

get(spec_like, *args, **kwargs)

get_pkg_class(pkg_name)Find a class for the spec’s package and return the class object.

get_repo(namespace, default=<object object>)Get a repository by namespace.

Arguments:

namespace:

Look up this namespace in the RepoPath, and return it if found.

Optional Arguments:

default:

If default is provided, return it when the namespace isn’t found. If not, raise an Un-knownNamespaceError.

load_module(fullname)Handles loading container namespaces when necessary.

See Repo for how actual package modules are loaded.

provider_indexMerged ProviderIndex from all Repos in the RepoPath.

providers_for(spec_like, *args, **kwargs)

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put_first(repo)Add repo first in the search path.

put_last(repo)Add repo last in the search path.

remove(repo)Remove a repo from the search path.

repo_for_pkg(spec_like, *args, **kwargs)

swap(other)Convenience function to make swapping repostiories easier.

This is currently used by mock tests. TODO: Maybe there is a cleaner way.

class spack.repository.SpackNamespace(namespace)Bases: module

Allow lazy loading of modules.

exception spack.repository.UnknownNamespaceError(namespace)Bases: spack.repository.PackageLoadError

Raised when we encounter an unknown namespace

exception spack.repository.UnknownPackageError(name, repo=None)Bases: spack.repository.PackageLoadError

Raised when we encounter a package spack doesn’t have.

spack.repository.canonicalize_path(path)Substitute $spack, expand user home, take abspath.

spack.repository.create_repo(root, namespace=None)Create a new repository in root with the specified namespace.

If the namespace is not provided, use basename of root. Return the canonicalized path and namespace of thecreated repository.

spack.repository.substitute_spack_prefix(path)Replaces instances of $spack with Spack’s prefix.

1.11.27 spack.resource module

Describes an optional resource needed for a build.

Typically a bunch of sources that can be built in-tree within another package to enable optional features.

class spack.resource.Resource(name, fetcher, destination, placement)Bases: object

Represents an optional resource to be fetched by a package.

Aggregates a name, a fetcher, a destination and a placement.

1.11.28 spack.spec module

Spack allows very fine-grained control over how packages are installed and over how they are built and configured.To make this easy, it has its own syntax for declaring a dependence. We call a descriptor of a particular packageconfiguration a “spec”.

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The syntax looks like this:

$ spack install mpileaks ^openmpi @1.2:1.4 +debug %intel @12.1 =bgqos_00 1 2 3 4 5 6

The first part of this is the command, ‘spack install’. The rest of the line is a spec for a particular installation of thempileaks package.

0. The package to install

1. A dependency of the package, prefixed by ^

2. A version descriptor for the package. This can either be a specific version, like “1.2”, or it can be a range ofversions, e.g. “1.2:1.4”. If multiple specific versions or multiple ranges are acceptable, they can be separated bycommas, e.g. if a package will only build with versions 1.0, 1.2-1.4, and 1.6-1.8 of mavpich, you could say:

depends_on(“mvapich@1.0,1.2:1.4,1.6:1.8”)

3. A compile-time variant of the package. If you need openmpi to be built in debug mode for your package towork, you can require it by adding +debug to the openmpi spec when you depend on it. If you do NOT want thedebug option to be enabled, then replace this with -debug.

4. The name of the compiler to build with.

5. The versions of the compiler to build with. Note that the identifier for a compiler version is the same ‘@’ thatis used for a package version. A version list denoted by ‘@’ is associated with the compiler only if if it comesimmediately after the compiler name. Otherwise it will be associated with the current package spec.

6. The architecture to build with. This is needed on machines where cross-compilation is required

Here is the EBNF grammar for a spec:

spec-list = { spec [ dep-list ] }dep_list = { ^ spec }spec = id [ options ]options = { @version-list | +variant | -variant | ~variant |

%compiler | arch=architecture | [ flag ]=value}flag = { cflags | cxxflags | fcflags | fflags | cppflags |

ldflags | ldlibs }variant = idarchitecture = idcompiler = id [ version-list ]version-list = version [ { , version } ]version = id | id: | :id | id:idid = [A-Za-z0-9_][A-Za-z0-9_.-]*

Identifiers using the <name>=<value> command, such as architectures and compiler flags, require a space before thename.

There is one context-sensitive part: ids in versions may contain ‘.’, while other ids may not.

There is one ambiguity: since ‘-‘ is allowed in an id, you need to put whitespace space before -variant for it to betokenized properly. You can either use whitespace, or you can just use ~variant since it means the same thing. Spackuses ~variant in directory names and in the canonical form of specs to avoid ambiguity. Both are provided because ~can cause shell expansion when it is the first character in an id typed on the command line.

exception spack.spec.AmbiguousHashError(msg, *specs)Bases: spack.spec.SpecError

class spack.spec.CompilerSpec(*args)Bases: object

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The CompilerSpec field represents the compiler or range of compiler versions that a package should be builtwith. CompilerSpecs have a name and a version list.

concreteA CompilerSpec is concrete if its versions are concrete and there is an available compiler with the rightversion.

constrain(other)Intersect self’s versions with other.

Return whether the CompilerSpec changed.

copy()

static from_dict(d)

satisfies(other, strict=False)

to_dict()

version

class spack.spec.DependencyMapBases: llnl.util.lang.HashableMap

Each spec has a DependencyMap containing specs for its dependencies. The DependencyMap is keyed by name.

concrete

class spack.spec.DependencySpec(spec, deptypes)Bases: object

Dependencies can be one (or more) of several types:

•build: needs to be in the PATH at build time.

•link: is linked to and added to compiler flags.

•run: needs to be in the PATH for the package to run.

Fields: - spec: the spack.spec.Spec description of a dependency. - deptypes: strings representing the type ofdependency this is.

copy()

exception spack.spec.DuplicateArchitectureError(message)Bases: spack.spec.SpecError

Raised when the same architecture occurs in a spec twice.

exception spack.spec.DuplicateCompilerSpecError(message)Bases: spack.spec.SpecError

Raised when the same compiler occurs in a spec twice.

exception spack.spec.DuplicateDependencyError(message)Bases: spack.spec.SpecError

Raised when the same dependency occurs in a spec twice.

exception spack.spec.DuplicateVariantError(message)Bases: spack.spec.SpecError

Raised when the same variant occurs in a spec twice.

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class spack.spec.FlagMap(spec)Bases: llnl.util.lang.HashableMap

concrete

constrain(other)Add all flags in other that aren’t in self to self.

Return whether the spec changed.

copy()

satisfies(other, strict=False)

static valid_compiler_flags()

exception spack.spec.InconsistentSpecError(message)Bases: spack.spec.SpecError

Raised when two nodes in the same spec DAG have inconsistent constraints.

exception spack.spec.InvalidDependencyException(message)Bases: spack.spec.SpecError

Raised when a dependency in a spec is not actually a dependency of the package.

exception spack.spec.MultipleProviderError(vpkg, providers)Bases: spack.spec.SpecError

Raised when there is no package that provides a particular virtual dependency.

exception spack.spec.NoProviderError(vpkg)Bases: spack.spec.SpecError

Raised when there is no package that provides a particular virtual dependency.

exception spack.spec.SpackYAMLError(msg, yaml_error)Bases: spack.error.SpackError

class spack.spec.Spec(spec_like, *dep_like, **kwargs)Bases: object

colorized()

common_dependencies(other)Return names of dependencies that self an other have in common.

concreteA spec is concrete if it can describe only ONE build of a package. If any of the name, version, architecture,compiler, variants, or depdenencies are ambiguous,then it is not concrete.

concretize()A spec is concrete if it describes one build of a package uniquely. This will ensure that this spec is concrete.

If this spec could describe more than one version, variant, or build of a package, this will add constraintsto make it concrete.

Some rigorous validation and checks are also performed on the spec. Concretizing ensures that it is self-consistent and that it’s consistent with requirements of its pacakges. See flatten() and normalize() for moredetails on this.

concretized()This is a non-destructive version of concretize(). First clones, then returns a concrete version of thispackage without modifying this package.

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constrain(other, deps=True)Merge the constraints of other with self.

Returns True if the spec changed as a result, False if not.

constrained(other, deps=True)Return a constrained copy without modifying this spec.

copy(**kwargs)Return a copy of this spec. By default, returns a deep copy. Supply dependencies=False to get a shallowcopy.

cshort_specReturns a version of the spec with the dependencies hashed instead of completely enumerated.

dag_hash(length=None)Return a hash of the entire spec DAG, including connectivity.

dep_difference(other)Returns dependencies in self that are not in other.

dep_string()

dependencies(deptype=None)

dependencies_dict(deptype=None)

dependents(deptype=None)

dependents_dict(deptype=None)

eq_dag(other)True if the full dependency DAGs of specs are equal

eq_node(other)Equality with another spec, not including dependencies.

flat_dependencies(**kwargs)

flat_dependencies_with_deptype(**kwargs)Return a DependencyMap containing all of this spec’s dependencies with their constraints merged.

If copy is True, returns merged copies of its dependencies without modifying the spec it’s called on.

If copy is False, clears this spec’s dependencies and returns them.

format(format_string=’$_$@$%@+$+$=’, **kwargs)Prints out particular pieces of a spec, depending on what is in the format string. The format strings youcan provide are:

$_ Package name$. Full package name (with namespace)$@ Version with '@' prefix$% Compiler with '%' prefix$%@ Compiler with '%' prefix & compiler version with '@' prefix$%+ Compiler with '%' prefix & compiler flags prefixed by name$%@+ Compiler, compiler version, and compiler flags with same

prefixes as above$+ Options$= Architecture prefixed by 'arch='$# 7-char prefix of DAG hash with '-' prefix$$ $

You can also use full-string versions, which elide the prefixes:

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${PACKAGE} Package name${VERSION} Version${COMPILER} Full compiler string${COMPILERNAME} Compiler name${COMPILERVER} Compiler version${COMPILERFLAGS} Compiler flags${OPTIONS} Options${ARCHITECTURE} Architecture${SHA1} Dependencies 8-char sha1 prefix

${SPACK_ROOT} The spack root directory${SPACK_INSTALL} The default spack install directory,

${SPACK_PREFIX}/opt

Optionally you can provide a width, e.g. $20_ for a 20-wide name. Like printf, you can provide ‘-‘ forleft justification, e.g. $-20_ for a left-justified name.

Anything else is copied verbatim into the output stream.

Example: $_$@$+ translates to the name, version, and options of the package, but no dependencies, arch,or compiler.

TODO: allow, e.g., $6# to customize short hash length TODO: allow, e.g., $## for full hash.

static from_node_dict(node)

static from_yaml(stream)Construct a spec from YAML.

Parameters: stream – string or file object to read from.

TODO: currently discards hashes. Include hashes when they represent more than the DAG does.

fullname

get_dependency(name)

index()Return DependencyMap that points to all the dependencies in this spec.

static is_virtual(name)Test if a name is virtual without requiring a Spec.

ne_dag(other)True if the full dependency DAGs of specs are not equal

ne_node(other)Inequality with another spec, not including dependencies.

normalize(force=False)When specs are parsed, any dependencies specified are hanging off the root, and ONLY the ones that wereexplicitly provided are there. Normalization turns a partial flat spec into a DAG, where:

1.Known dependencies of the root package are in the DAG.

2.Each node’s dependencies dict only contains its known direct deps.

3.There is only ONE unique spec for each package in the DAG.

•This includes virtual packages. If there a non-virtual package that provides a virtual package thatis in the spec, then we replace the virtual package with the non-virtual one.

TODO: normalize should probably implement some form of cycle detection, to ensure that the spec isactually a DAG.

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normalized()Return a normalized copy of this spec without modifying this spec.

package

package_classInternal package call gets only the class object for a package. Use this to just get package metadata.

prefix

static read_yaml_dep_specs(dependency_dict)Read the DependencySpec portion of a YAML-formatted Spec.

This needs to be backward-compatible with older spack spec formats so that reindex will work on oldspecs/databases.

rootFollow dependent links and find the root of this spec’s DAG. In spack specs, there should be a single root(the package being installed). This will throw an assertion error if that is not the case.

satisfies(other, deps=True, strict=False)Determine if this spec satisfies all constraints of another.

There are two senses for satisfies:

•loose (default): the absence of a constraint in self implies that it could be satisfied by other, so weonly check that there are no conflicts with other for constraints that this spec actually has.

•strict: strict means that we must meet all the constraints specified on other.

satisfies_dependencies(other, strict=False)This checks constraints on common dependencies against each other.

short_specReturns a version of the spec with the dependencies hashed instead of completely enumerated.

sorted_deps()Return a list of all dependencies sorted by name.

to_node_dict()

to_yaml(stream=None)

traverse(visited=None, deptype=None, **kwargs)

traverse_with_deptype(visited=None, d=0, deptype=None, deptype_query=None,_self_deptype=None, **kwargs)

Generic traversal of the DAG represented by this spec. This will yield each node in the spec. Options:

order [=pre|post] Order to traverse spec nodes. Defaults to preorder traversal. Options are:

‘pre’: Pre-order traversal; each node is yielded before its children in the dependency DAG.

‘post’: Post-order traversal; each node is yielded after its children in the dependency DAG.

cover [=nodes|edges|paths] Determines how extensively to cover the dag. Possible vlaues:

‘nodes’: Visit each node in the dag only once. Every node yielded by this function will be unique.

‘edges’: If a node has been visited once but is reached along a new path from the root, yield it butdo not descend into it. This traverses each ‘edge’ in the DAG once.

‘paths’: Explore every unique path reachable from the root. This descends into visited subtreesand will yield nodes twice if they’re reachable by multiple paths.

depth [=False] Defaults to False. When True, yields not just nodes in the spec, but also their depth fromthe root in a (depth, node) tuple.

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key [=id] Allow a custom key function to track the identity of nodes in the traversal.

root [=True] If False, this won’t yield the root node, just its descendents.

direction [=children|parents] If ‘children’, does a traversal of this spec’s children. If ‘parents’, traversesupwards in the DAG towards the root.

tree(**kwargs)Prints out this spec and its dependencies, tree-formatted with indentation.

validate_names()This checks that names of packages and compilers in this spec are real. If they’re not, it will raise eitherUnknownPackageError or UnsupportedCompilerError.

version

virtualRight now, a spec is virtual if no package exists with its name.

TODO: revisit this – might need to use a separate namespace and be more explicit about this. Possibleidea: just use conventin and make virtual deps all caps, e.g., MPI vs mpi.

virtual_dependencies()Return list of any virtual deps in this spec.

exception spack.spec.SpecError(message)Bases: spack.error.SpackError

Superclass for all errors that occur while constructing specs.

class spack.spec.SpecLexerBases: spack.parse.Lexer

Parses tokens that make up spack specs.

exception spack.spec.SpecParseError(parse_error)Bases: spack.spec.SpecError

Wrapper for ParseError for when we’re parsing specs.

class spack.spec.SpecParserBases: spack.parse.Parser

check_identifier(id=None)The only identifiers that can contain ‘.’ are versions, but version ids are context-sensitive so we have tocheck on a case-by-case basis. Call this if we detect a version id where it shouldn’t be.

compiler()

do_parse()

parse_compiler(text)

spec(name, check_valid_token=False)Parse a spec out of the input. If a spec is supplied, then initialize and return it instead of creating a newone.

spec_by_hash()

variant(name=None)

version()

version_list()

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exception spack.spec.UnknownVariantError(pkg, variant)Bases: spack.spec.SpecError

Raised when the same variant occurs in a spec twice.

exception spack.spec.UnsatisfiableArchitectureSpecError(provided, required)Bases: spack.spec.UnsatisfiableSpecError

Raised when a spec architecture conflicts with package constraints.

exception spack.spec.UnsatisfiableCompilerFlagSpecError(provided, required)Bases: spack.spec.UnsatisfiableSpecError

Raised when a spec variant conflicts with package constraints.

exception spack.spec.UnsatisfiableCompilerSpecError(provided, required)Bases: spack.spec.UnsatisfiableSpecError

Raised when a spec comiler conflicts with package constraints.

exception spack.spec.UnsatisfiableDependencySpecError(provided, required)Bases: spack.spec.UnsatisfiableSpecError

Raised when some dependency of constrained specs are incompatible

exception spack.spec.UnsatisfiableProviderSpecError(provided, required)Bases: spack.spec.UnsatisfiableSpecError

Raised when a provider is supplied but constraints don’t match a vpkg requirement

exception spack.spec.UnsatisfiableSpecError(provided, required, constraint_type)Bases: spack.spec.SpecError

Raised when a spec conflicts with package constraints. Provide the requirement that was violated when raising.

exception spack.spec.UnsatisfiableSpecNameError(provided, required)Bases: spack.spec.UnsatisfiableSpecError

Raised when two specs aren’t even for the same package.

exception spack.spec.UnsatisfiableVariantSpecError(provided, required)Bases: spack.spec.UnsatisfiableSpecError

Raised when a spec variant conflicts with package constraints.

exception spack.spec.UnsatisfiableVersionSpecError(provided, required)Bases: spack.spec.UnsatisfiableSpecError

Raised when a spec version conflicts with package constraints.

exception spack.spec.UnsupportedCompilerError(compiler_name)Bases: spack.spec.SpecError

Raised when the user asks for a compiler spack doesn’t know about.

class spack.spec.VariantMap(spec)Bases: llnl.util.lang.HashableMap

concrete

constrain(other)Add all variants in other that aren’t in self to self.

Raises an error if any common variants don’t match. Return whether the spec changed.

copy()

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satisfies(other, strict=False)

class spack.spec.VariantSpec(name, value)Bases: object

Variants are named, build-time options for a package. Names depend on the particular package being built, andeach named variant can be enabled or disabled.

copy()

spack.spec.color_formats = {‘@’: ‘@c’, ‘#’: ‘@K’, ‘%’: ‘@g’, ‘+’: ‘@B’, ‘~’: ‘@r’, ‘=’: ‘@m’, ‘^’: ‘@.’}Regex used for splitting by spec field separators.

spack.spec.colorize_spec(spec)Returns a spec colorized according to the colors specified in color_formats.

spack.spec.hash_color = ‘@K’This map determines the coloring of specs when using color output. We make the fields different colors toenhance readability. See spack.color for descriptions of the color codes.

spack.spec.parse(string)Returns a list of specs from an input string. For creating one spec, see Spec() constructor.

spack.spec.parse_anonymous_spec(spec_like, pkg_name)Allow the user to omit the package name part of a spec if they know what it has to be already.

e.g., provides(‘mpi@2’, when=’@1.9:’) says that this package provides MPI-3 when its version is higher than1.9.

1.11.29 spack.stage module

exception spack.stage.ChdirError(message, long_message=None)Bases: spack.stage.StageError

Raised when Spack can’t change directories.

class spack.stage.DIYStage(path)Bases: object

Simple class that allows any directory to be a spack stage.

cache_local()

chdir()

chdir_to_source()

check()

destroy()

expand_archive()

fetch(mirror_only)

restage()

class spack.stage.ResourceStage(url_or_fetch_strategy, root, resource, **kwargs)Bases: spack.stage.Stage

expand_archive()

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exception spack.stage.RestageError(message, long_message=None)Bases: spack.stage.StageError

“Error encountered during restaging.

class spack.stage.Stage(url_or_fetch_strategy, name=None, mirror_path=None, keep=False,path=None)

Bases: object

Manages a temporary stage directory for building.

A Stage object is a context manager that handles a directory where some source code is downloaded and builtbefore being installed. It handles fetching the source code, either as an archive to be expanded or by checking itout of a repository. A stage’s lifecycle looks like this:

with Stage() as stage: # Context manager creates and destroys the# stage directory

stage.fetch() # Fetch a source archive into the stage.stage.expand_archive() # Expand the source archive.<install> # Build and install the archive.

# (handled by user of Stage)

When used as a context manager, the stage is automatically destroyed if no exception is raised by the context. Ifan excpetion is raised, the stage is left in the filesystem and NOT destroyed, for potential reuse later.

You can also use the stage’s create/destroy functions manually, like this:

stage = Stage()try:

stage.create() # Explicitly create the stage directory.stage.fetch() # Fetch a source archive into the stage.stage.expand_archive() # Expand the source archive.<install> # Build and install the archive.

# (handled by user of Stage)finally:

stage.destroy() # Explicitly destroy the stage directory.

If spack.use_tmp_stage is True, spack will attempt to create stages in a tmp directory. Otherwise, stages arecreated directly in spack.stage_path.

There are two kinds of stages: named and unnamed. Named stages can persist between runs of spack, e.g. ifyou fetched a tarball but didn’t finish building it, you won’t have to fetch it again.

Unnamed stages are created using standard mkdtemp mechanisms or similar, and are intended to persist for onlyone run of spack.

archive_filePath to the source archive within this stage directory.

cache_local()

chdir()Changes directory to the stage path. Or dies if it is not set up.

chdir_to_source()Changes directory to the expanded archive directory. Dies with an error if there was no expanded archive.

check()Check the downloaded archive against a checksum digest. No-op if this stage checks code out of a reposi-tory.

create()Creates the stage directory

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If self.tmp_root evaluates to False, the stage directory is created directly under spack.stage_path, otherwisethis will attempt to create a stage in a temporary directory and link it into spack.stage_path.

Spack will use the first writable location in spack.tmp_dirs to create a stage. If there is no valid location intmp_dirs, fall back to making the stage inside spack.stage_path.

destroy()Removes this stage directory.

expand_archive()Changes to the stage directory and attempt to expand the downloaded archive. Fail if the stage is not setup or if the archive is not yet downloaded.

expected_archive_filesPossible archive file paths.

fetch(mirror_only=False)Downloads an archive or checks out code from a repository.

restage()Removes the expanded archive path if it exists, then re-expands the archive.

source_pathReturns the path to the expanded/checked out source code.

To find the source code, this method searches for the first subdirectory of the stage that it can find, andreturns it. This assumes nothing besides the archive file will be in the stage path, but it has the advantagethat we don’t need to know the name of the archive or its contents.

If the fetch strategy is not supposed to expand the downloaded file, it will just return the stage path. If thearchive needs to be expanded, it will return None when no archive is found.

exception spack.stage.StageError(message, long_message=None)Bases: spack.error.SpackError

“Superclass for all errors encountered during staging.

spack.stage.ensure_access(file=’/home/docs/checkouts/readthedocs.org/user_builds/spack/checkouts/bugfix-rtd-generation/var/spack/stage’)

Ensure we can access a directory and die with an error if we can’t.

spack.stage.find_tmp_root()

spack.stage.purge()Remove all build directories in the top-level stage path.

1.11.30 spack.url module

This module has methods for parsing names and versions of packages from URLs. The idea is to allow package cre-ators to supply nothing more than the download location of the package, and figure out version and name informationfrom there.

Example: when spack is given the following URL:

ftp://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.1-p243.tar.gz

It can figure out that the package name is ruby, and that it is at version 1.9.1-p243. This is useful for making thecreation of packages simple: a user just supplies a URL and skeleton code is generated automatically.

Spack can also figure out that it can most likely download 1.8.1 at this URL:

ftp://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.8.1.tar.gz

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This is useful if a user asks for a package at a particular version number; spack doesn’t need anyone to tell it where toget the tarball even though it’s never been told about that version before.

exception spack.url.UndetectableNameError(path)Bases: spack.url.UrlParseError

Raised when we can’t parse a package name from a string.

exception spack.url.UndetectableVersionError(path)Bases: spack.url.UrlParseError

Raised when we can’t parse a version from a string.

exception spack.url.UrlParseError(msg, path)Bases: spack.error.SpackError

Raised when the URL module can’t parse something correctly.

spack.url.color_url(path, **kwargs)Color the parts of the url according to Spack’s parsing.

Colors are: Cyan: The version found by parse_version_offset(). Red: The name found by parse_name_offset().

Green: Instances of version string from substitute_version(). Magenta: Instances of the name (protectedfrom substitution).

Optional args: errors=True Append parse errors at end of string. subs=True Color substitutions as well asparsed name/version.

spack.url.cumsum(elts, init=0, fn=<function <lambda>>)Return cumulative sum of result of fn on each element in elts.

spack.url.downloaded_file_extension(path)This returns the type of archive a URL refers to. This is sometimes confusing because of URLs like:

1.https://github.com/petdance/ack/tarball/1.93_02

Where the URL doesn’t actually contain the filename. We need to know what type it is so that we can appropri-ately name files in mirrors.

spack.url.find_list_url(url)Finds a good list URL for the supplied URL. This depends on the site. By default, just assumes that a good listURL is the dirname of an archive path. For github URLs, this returns the URL of the project’s releases page.

spack.url.insensitize(string)Change upper and lowercase letters to be case insensitive in the provided string. e.g., ‘a’ because ‘[Aa]’, ‘B’becomes ‘[bB]’, etc. Use for building regexes.

spack.url.parse_name(path, ver=None)

spack.url.parse_name_and_version(path)

spack.url.parse_name_offset(path, v=None)

spack.url.parse_version(path)Given a URL or archive name, extract a version from it and return a version object.

spack.url.parse_version_offset(path)Try to extract a version string from a filename or URL. This is taken largely from Homebrew’s Version class.

spack.url.split_url_extension(path)Some URLs have a query string, e.g.:

1.https://github.com/losalamos/CLAMR/blob/packages/PowerParser_v2.0.7.tgz?raw=true

2.http://www.apache.org/dyn/closer.cgi?path=/cassandra/1.2.0/apache-cassandra-1.2.0-rc2-bin.tar.gz

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In (1), the query string needs to be stripped to get at the extension, but in (2), the filename is IN a single finalquery argument.

This strips the URL into three pieces: prefix, ext, and suffix. The suffix contains anything that was stripped offthe URL to get at the file extension. In (1), it will be ‘?raw=true’, but in (2), it will be empty. e.g.:

1.(‘https://github.com/losalamos/CLAMR/blob/packages/PowerParser_v2.0.7‘, ‘.tgz’, ‘?raw=true’)

2.(‘http://www.apache.org/dyn/closer.cgi?path=/cassandra/1.2.0/apache-cassandra-1.2.0-rc2-bin‘,‘.tar.gz’, None)

spack.url.strip_query_and_fragment(path)

spack.url.substitute_version(path, new_version)Given a URL or archive name, find the version in the path and substitute the new version for it. Replace alloccurrences of the version if they don’t overlap with the package name.

Simple example:: substitute_version(‘http://www.mr511.de/software/libelf-0.8.13.tar.gz‘, ‘2.9.3’) ->’http://www.mr511.de/software/libelf-2.9.3.tar.gz‘

Complex examples:: substitute_version(‘http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.0.tar.gz‘, 2.1) -> ‘http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz‘

# In this string, the “2” in mvapich2 is NOT replaced. substitute_version(‘http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.tar.gz‘, 2.1) -> ‘http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz‘

spack.url.substitution_offsets(path)This returns offsets for substituting versions and names in the provided path. It is a helper for substi-tute_version().

spack.url.wildcard_version(path)Find the version in the supplied path, and return a regular expression that will match this path with any versionin its place.

1.11.31 spack.variant module

Variant is a class describing flags on builds, or “variants”.

Could be generalized later to describe aribitrary parameters, but currently variants are just flags.

class spack.variant.Variant(default, description)Bases: object

Represents a variant on a build. Can be either on or off.

1.11.32 spack.version module

This module implements Version and version-ish objects. These are:

Version A single version of a package.

VersionRange A range of versions of a package.

VersionList A list of Versions and VersionRanges.

All of these types support the following operations, which can be called on any of the types:

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__eq__, __ne__, __lt__, __gt__, __ge__, __le__, __hash____contains__satisfiesoverlapsunionintersectionconcrete

class spack.version.Version(string)Bases: object

Class to represent versions

concrete

dashed

dotted

highest()

intersection(a, b, *args, **kwargs)

is_predecessor(other)True if the other version is the immediate predecessor of this one. That is, NO versions v exist such that:(self < v < other and v not in self).

is_successor(other)

lowest()

overlaps(a, b, *args, **kwargs)

satisfies(a, b, *args, **kwargs)A Version ‘satisfies’ another if it is at least as specific and has a common prefix. e.g., we want gcc@4.7.3to satisfy a request for gcc@4.7 so that when a user asks to build with gcc@4.7, we can find a suitablecompiler.

underscored

union(a, b, *args, **kwargs)

up_to(index)Return a version string up to the specified component, exclusive. e.g., if this is 10.8.2, self.up_to(2) willreturn ‘10.8’.

wildcard()Create a regex that will match variants of this version string.

class spack.version.VersionRange(start, end)Bases: object

concrete

highest()

intersection(a, b, *args, **kwargs)

lowest()

overlaps(a, b, *args, **kwargs)

satisfies(a, b, *args, **kwargs)A VersionRange satisfies another if some version in this range would satisfy some version in the otherrange. To do this it must either:

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1.Overlap with the other range

2.The start of this range satisfies the end of the other range.

This is essentially the same as overlaps(), but overlaps assumes that its arguments are specific. That is, 4.7is interpreted as 4.7.0.0.0.0... . This funciton assumes that 4.7 woudl be satisfied by 4.7.3.5, etc.

Rationale:

If a user asks for gcc@4.5:4.7, and a package is only compatible with gcc@4.7.3:4.8, then that packageshould be able to build under the constraints. Just using overlaps() would not work here.

Note that we don’t need to check whether the end of this range would satisfy the start of the other range,because overlaps() already covers that case.

Note further that overlaps() is a symmetric operation, while satisfies() is not.

union(a, b, *args, **kwargs)

class spack.version.VersionList(vlist=None)Bases: object

Sorted, non-redundant list of Versions and VersionRanges.

add(version)

concrete

copy()

static from_dict(dictionary)Parse dict from to_dict.

highest()Get the highest version in the list.

intersect(a, b, *args, **kwargs)Intersect this spec’s list with other.

Return True if the spec changed as a result; False otherwise

intersection(a, b, *args, **kwargs)

lowest()Get the lowest version in the list.

overlaps(a, b, *args, **kwargs)

satisfies(a, b, *args, **kwargs)A VersionList satisfies another if some version in the list would satisfy some version in the other list. Thisuses essentially the same algorithm as overlaps() does for VersionList, but it calls satisfies() on memberVersions and VersionRanges.

If strict is specified, this version list must lie entirely within the other in order to satisfy it.

to_dict()Generate human-readable dict for YAML.

union(a, b, *args, **kwargs)

update(a, b, *args, **kwargs)

spack.version.ver(obj)Parses a Version, VersionRange, or VersionList from a string or list of strings.

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1.11.33 spack.yaml_version_check module

Yaml Version Check is a module for ensuring that config file formats are compatible with the current version of Spack.

spack.yaml_version_check.check_compiler_yaml_version()

spack.yaml_version_check.check_yaml_versions()

1.11.34 Module contents

class spack.Package(spec)Bases: object

This is the superclass for all spack packages.

*The Package class*

Package is where the bulk of the work of installing packages is done.

A package defines how to fetch, verfiy (via, e.g., md5), build, and install a piece of software. A Package alsodefines what other packages it depends on, so that dependencies can be installed along with the package itself.Packages are written in pure python.

Packages are all submodules of spack.packages. If spack is installed in $prefix, all of its pythonfiles are in $prefix/lib/spack. Most of them are in the spack module, so all the packages live in$prefix/lib/spack/spack/packages.

All you have to do to create a package is make a new subclass of Package in this directory. Spack automaticallyscans the python files there and figures out which one to import when you invoke it.

An example package

Let’s look at the cmake package to start with. This package lives in$prefix/var/spack/repos/builtin/packages/cmake/package.py:

from spack import *class Cmake(Package):

homepage = 'https://www.cmake.org'url = 'http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz'md5 = '097278785da7182ec0aea8769d06860c'

def install(self, spec, prefix):configure('--prefix=%s' % prefix,

'--parallel=%s' % make_jobs)make()make('install')

Naming conventions

There are two names you should care about:

1.The module name, cmake.

•User will refers to this name, e.g. ‘spack install cmake’.

•It can include _, -, and numbers (it can even start with a number).

2.The class name, “Cmake”. This is formed by converting - or _ in the module name to camel case. If thename starts with a number, we prefix the class name with _. Examples:

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Module Name Class Namefoo_bar FooBardocbook-xml DocbookXmlFooBar Foobar3proxy _3proxy

The class name is what spack looks for when it loads a package module.

Required Attributes

Aside from proper naming, here is the bare minimum set of things you need when you make a package:

homepage: informational URL, so that users know what they’re installing.

url or url_for_version(self, version): If url, then the URL of the source archive that spack will fetch. Ifurl_for_version(), then a method returning the URL required to fetch a particular version.

install(): This function tells spack how to build and install the software it downloaded.

Optional Attributes

You can also optionally add these attributes, if needed:

list_url: Webpage to scrape for available version strings. Default is the directory containing thetarball; use this if the default isn’t correct so that invoking ‘spack versions’ will work for thispackage.

url_version(self, version): When spack downloads packages at particular versions, it just convertsversion to string with str(version). Override this if your package needs special version formattingin its URL. boost is an example of a package that needs this.

*Creating Packages*

As a package creator, you can probably ignore most of the preceding information, because you can use the‘spack create’ command to do it all automatically.

You as the package creator generally only have to worry about writing your install function and specifyingdependencies.

spack create

Most software comes in nicely packaged tarballs, like this one

http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz

Taking a page from homebrew, spack deduces pretty much everything it needs to know from the URL above. Ifyou simply type this:

spack create http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz

Spack will download the tarball, generate an md5 hash, figure out the version and the name of the package fromthe URL, and create a new package file for you with all the names and attributes set correctly.

Once this skeleton code is generated, spack pops up the new package in your $EDITOR so that you can modifythe parts that need changes.

Dependencies

If your package requires another in order to build, you can specify that like this:

class Stackwalker(Package):...depends_on("libdwarf")...

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This tells spack that before it builds stackwalker, it needs to build the libdwarf package as well. Note that this isthe module name, not the class name (The class name is really only used by spack to find your package).

Spack will download an install each dependency before it installs your package. In addtion, it will add -L, -I,and rpath arguments to your compiler and linker for each dependency. In most cases, this allows you to avoidspecifying any dependencies in your configure or cmake line; you can just run configure or cmake without anyadditional arguments and it will find the dependencies automatically.

The Install Function

The install function is designed so that someone not too terribly familiar with Python could write a package in-staller. For example, we put a number of commands in install scope that you can use almost like shell commands.These include make, configure, cmake, rm, rmtree, mkdir, mkdirp, and others.

You can see above in the cmake script that these commands are used to run configure and make almost likethey’re used on the command line. The only difference is that they are python function calls and not shellcommands.

It may be puzzling to you where the commands and functions in install live. They are NOT instance variables onthe class; this would require us to type ‘self.’ all the time and it makes the install code unnecessarily long. Rather,spack puts these commands and variables in module scope for your Package subclass. Since each package hasits own module, this doesn’t pollute other namespaces, and it allows you to more easily implement an installfunction.

For a full list of commands and variables available in module scope, see the add_commands_to_module() func-tion in this class. This is where most of them are created and set on the module.

Parallel Builds

By default, Spack will run make in parallel when you run make() in your install function. Spack figures out howmany cores are available on your system and runs make with -j<cores>. If you do not want this behavior, youcan explicitly mark a package not to use parallel make:

class SomePackage(Package):...parallel = False...

This changes thd default behavior so that make is sequential. If you still want to build some parts in parallel,you can do this in your install function:

make(parallel=True)

Likewise, if you do not supply parallel = True in your Package, you can keep the default parallel behavior andrun make like this when you want a sequential build:

make(parallel=False)

Package Lifecycle

This section is really only for developers of new spack commands.

A package’s lifecycle over a run of Spack looks something like this:

p = Package() # Done for you by spack

p.do_fetch() # downloads tarball from a URLp.do_stage() # expands tarball in a temp directoryp.do_patch() # applies patches to expanded sourcep.do_install() # calls package's install() functionp.do_uninstall() # removes install directory

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There are also some other commands that clean the build area:

p.do_clean() # removes the stage directory entirelyp.do_restage() # removes the build directory and

# re-expands the archive.

The convention used here is that a do_* function is intended to be called internally by Spack commands (inspack.cmd). These aren’t for package writers to override, and doing so may break the functionality of thePackage class.

Package creators override functions like install() (all of them do this), clean() (some of them do this), and othersto provide custom behavior.

activate(extension, **kwargs)Symlinks all files from the extension into extendee’s install dir.

Package authors can override this method to support other extension mechanisms. Spack internals (com-mands, hooks, etc.) should call do_activate() method so that proper checks are always executed.

activated

all_urls

build_log_path

compilerGet the spack.compiler.Compiler object used to build this package

deactivate(extension, **kwargs)Unlinks all files from extension out of this package’s install dir.

Package authors can override this method to support other extension mechanisms. Spack internals (com-mands, hooks, etc.) should call do_deactivate() method so that proper checks are always executed.

dependencies_of_type(*deptypes)Get subset of the dependencies with certain types.

do_activate(force=False)Called on an extension to invoke the extendee’s activate method.

Commands should call this routine, and should not call activate() directly.

do_clean()Removes the package’s build stage and source tarball.

do_deactivate(**kwargs)Called on the extension to invoke extendee’s deactivate() method.

do_fake_install()Make a fake install directory contaiing a ‘fake’ file in bin.

do_fetch(mirror_only=False)Creates a stage directory and downloads the tarball for this package. Working directory will be set to thestage directory.

do_install(keep_prefix=False, keep_stage=False, ignore_deps=False, skip_patch=False, ver-bose=False, make_jobs=None, run_tests=False, fake=False, explicit=False, dirty=False,install_phases=set([’provenance’, ‘configure’, ‘install’, ‘build’]))

Called by commands to install a package and its dependencies.

Package implementations should override install() to describe their build process.

Parameters

• keep_prefix – Keep install prefix on failure. By default, destroys it.

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• keep_stage – By default, stage is destroyed only if there are no exceptions during build.Set to True to keep the stage even with exceptions.

• ignore_deps – Don’t install dependencies before installing this package

• fake – Don’t really build; install fake stub files instead.

• skip_patch – Skip patch stage of build if True.

• verbose – Display verbose build output (by default, suppresses it)

• dirty – Don’t clean the build environment before installing.

• make_jobs – Number of make jobs to use for install. Default is ncpus

• run_tests – Run tests within the package’s install()

do_install_dependencies(**kwargs)

do_patch()Calls do_stage(), then applied patches to the expanded tarball if they haven’t been applied already.

do_restage()Reverts expanded/checked out source to a pristine state.

do_stage(mirror_only=False)Unpacks the fetched tarball, then changes into the expanded tarball directory.

do_uninstall(force=False)

extendable = False

extendee_argsSpec of the extendee of this package, or None if it is not an extension

extendee_specSpec of the extendee of this package, or None if it is not an extension

extends(spec)

fetch_remote_versions()Try to find remote versions of this package using the list_url and any other URLs described in the packagefile.

fetcher

format_doc(**kwargs)Wrap doc string at 72 characters and format nicely

global_license_dirReturns the directory where global license files for all packages are stored.

global_license_fileReturns the path where a global license file for this particular package should be stored.

install(spec, prefix)Package implementations override this with their own configuration

install_phases = set([’provenance’, ‘configure’, ‘install’, ‘build’])

installed

installed_dependents

Return a list of the specs of all installed packages that depend on this one.

TODO: move this method to database.py?

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is_extension

make_jobs = None

moduleUse this to add variables to the class’s module’s scope. This lets us use custom syntax in the install method.

namespace

nearest_url(version)Finds the URL for the next lowest version with a URL. If there is no lower version with a URL, uses thepackage url property. If that isn’t there, uses a higher URL, and if that isn’t there raises an error.

package_dirReturn the directory where the package.py file lives.

parallel = True

prefixGet the prefix into which this package should be installed.

provides(vpkg_name)True if this package provides a virtual package with the specified name

remove_prefix()Removes the prefix for a package along with any empty parent directories

rpathGet the rpath this package links with, as a list of paths.

rpath_argsGet the rpath args as a string, with -Wl,-rpath, for each element

run_tests = False

sanity_check_is_dir = []

sanity_check_is_file = []

sanity_check_prefix()This function checks whether install succeeded.

setup_dependent_environment(spack_env, run_env, dependent_spec)Set up the environment of packages that depend on this one.

This is similar to setup_environment, but it is used to modify the compile and runtime environmentsof packages that depend on this one. This gives packages like Python and others that follow the extensionmodel a way to implement common environment or compile-time settings for dependencies.

By default, this delegates to self.setup_environment()

Example:

1.Installing python modules generally requires PYTHONPATH to point to the lib/pythonX.Y/site-packages directory in the module’s install prefix. This could set that variable.

Args:

spack_env (EnvironmentModifications): list of modifications to be applied when the depen-dent package is bulit within Spack.

run_env (EnvironmentModifications): list of environment changes to be applied when thedependent package is run outside of Spack.

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dependent_spec (Spec): The spec of the dependent package about to be built. This allows theextendee (self) to query the dependent’s state. Note that this package’s spec is available asself.spec.

This is useful if there are some common steps to installing all extensions for a certain package.

setup_dependent_package(module, dependent_spec)Set up Python module-scope variables for dependent packages.

Called before the install() method of dependents.

Default implementation does nothing, but this can be overridden by an extendable package to set up themodule of its extensions. This is useful if there are some common steps to installing all extensions for acertain package.

Example :

1.Extensions often need to invoke the python interpreter from the Python installation being extended.This routine can put a ‘python’ Executable object in the module scope for the extension package tosimplify extension installs.

2.MPI compilers could set some variables in the dependent’s scope that point to mpicc, mpicxx, etc.,allowing them to be called by common names regardless of which MPI is used.

3.BLAS/LAPACK implementations can set some variables indicating the path to their libraries, sincethese paths differ by BLAS/LAPACK implementation.

Args:

module (module): The Python module object of the dependent package. Packages can usethis to set module-scope variables for the dependent to use.

dependent_spec (Spec): The spec of the dependent package about to be built. This allows theextendee (self) to query the dependent’s state. Note that this package’s spec is available asself.spec.

This is useful if there are some common steps to installing all extensions for a certain package.

setup_environment(spack_env, run_env)Set up the compile and runtime environments for a package.

spack_env and run_env are EnvironmentModifications objects. Package authors can call methods on themto alter the environment within Spack and at runtime.

Both spack_env and run_env are applied within the build process, before this package’s install() method iscalled.

Modifications in run_env will also be added to the generated environment modules for this package.

Default implementation does nothing, but this can be overridden if the package needs a particular environ-ment.

Examples:

1.Qt extensions need QTDIR set.

Args:

spack_env (EnvironmentModifications): list of modifications to be applied when this package isbuilt within Spack.

run_env (EnvironmentModifications): list of environment changes to be applied when this pack-age is run outside of Spack.

stage

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url_for_version(version)Returns a URL that you can download a new version of this package from.

url_version(version)Given a version, this returns a string that should be substituted into the package’s URL to download thatversion.

By default, this just returns the version string. Subclasses may need to override this, e.g. for boost versionswhere you need to ensure that there are _’s in the download URL.

version

version_urls = <functools.partial object>

class spack.StagedPackage(spec)Bases: spack.package.Package

A Package subclass where the install() is split up into stages.

install(spec, prefix)

install_build()Runs the build process.

install_configure()Runs the configure process.

install_install()Runs the install process.

install_setup()Creates a spack_setup.py script to configure the package later.

class spack.CMakePackage(spec)Bases: spack.package.StagedPackage

configure_args()Returns package-specific arguments to be provided to the configure command.

configure_env()Returns package-specific environment under which the configure command should be run.

install_build()

install_configure()

install_install()

install_setup()

make_make()

transitive_inc_path()

class spack.Version(string)Bases: object

Class to represent versions

concrete

dashed

dotted

highest()

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intersection(a, b, *args, **kwargs)

is_predecessor(other)True if the other version is the immediate predecessor of this one. That is, NO versions v exist such that:(self < v < other and v not in self).

is_successor(other)

lowest()

overlaps(a, b, *args, **kwargs)

satisfies(a, b, *args, **kwargs)A Version ‘satisfies’ another if it is at least as specific and has a common prefix. e.g., we want gcc@4.7.3to satisfy a request for gcc@4.7 so that when a user asks to build with gcc@4.7, we can find a suitablecompiler.

underscored

union(a, b, *args, **kwargs)

up_to(index)Return a version string up to the specified component, exclusive. e.g., if this is 10.8.2, self.up_to(2) willreturn ‘10.8’.

wildcard()Create a regex that will match variants of this version string.

class spack.when(spec)Bases: object

This annotation lets packages declare multiple versions of methods like install() that depend on the package’sspec. For example:

class SomePackage(Package):...

def install(self, prefix):# Do default install

@when('arch=chaos_5_x86_64_ib')def install(self, prefix):

# This will be executed instead of the default install if# the package's platform() is chaos_5_x86_64_ib.

@when('arch=bgqos_0")def install(self, prefix):

# This will be executed if the package's sys_type is bgqos_0

This allows each package to have a default version of install() AND specialized versions for particular platforms.The version that is called depends on the architecutre of the instantiated package.

Note that this works for methods other than install, as well. So, if you only have part of the install that is platformspecific, you could do this:

class SomePackage(Package):...# virtual dependence on MPI.# could resolve to mpich, mpich2, OpenMPIdepends_on('mpi')

def setup(self):

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# do nothing in the default casepass

@when('^openmpi')def setup(self):

# do something special when this is built with OpenMPI for# its MPI implementations.

def install(self, prefix):# Do common install stuffself.setup()# Do more common install stuff

There must be one (and only one) @when clause that matches the package’s spec. If there is more than one, orif none match, then the method will raise an exception when it’s called.

Note that the default version of decorated methods must always come first. Otherwise it will override all of theplatform-specific versions. There’s not much we can do to get around this because of the way decorators work.

spack.ver(obj)Parses a Version, VersionRange, or VersionList from a string or list of strings.

spack.set_install_permissions(path)Set appropriate permissions on the installed file.

spack.install(src, dest)Manually install a file to a particular location.

spack.install_tree(src, dest, **kwargs)Manually install a directory tree to a particular location.

spack.traverse_tree(source_root, dest_root, rel_path=’‘, **kwargs)Traverse two filesystem trees simultaneously.

Walks the LinkTree directory in pre or post order. Yields each file in the source directory with a matching pathfrom the dest directory, along with whether the file is a directory. e.g., for this tree:

root/a/

file1file2

b/file3

When called on dest, this yields:

('root', 'dest')('root/a', 'dest/a')('root/a/file1', 'dest/a/file1')('root/a/file2', 'dest/a/file2')('root/b', 'dest/b')('root/b/file3', 'dest/b/file3')

Optional args:

order=[pre|post] – Whether to do pre- or post-order traversal.

ignore=<predicate> – Predicate indicating which files to ignore.

follow_nonexisting – Whether to descend into directories in src that do not exit in dest. Default True.

follow_links – Whether to descend into symlinks in src.

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spack.expand_user(path)Find instances of ‘%u’ in a path and replace with the current user’s username.

spack.working_dir(*args, **kwds)

spack.touch(path)Creates an empty file at the specified path.

spack.touchp(path)Like touch, but creates any parent directories needed for the file.

spack.mkdirp(*paths)Creates a directory, as well as parent directories if needed.

spack.force_remove(*paths)Remove files without printing errors. Like rm -f, does NOT remove directories.

spack.join_path(prefix, *args)

spack.ancestor(dir, n=1)Get the nth ancestor of a directory.

spack.can_access(file_name)True if we have read/write access to the file.

spack.filter_file(regex, repl, *filenames, **kwargs)Like sed, but uses python regular expressions.

Filters every line of each file through regex and replaces the file with a filtered version. Preserves mode offiltered files.

As with re.sub, repl can be either a string or a callable. If it is a callable, it is passed the match object andshould return a suitable replacement string. If it is a string, it can contain , , etc. to represent back-substitutionas sed would allow.

Keyword Options: string[=False] If True, treat regex as a plain string. backup[=True] Make backup file(s)suffixed with ~ ignore_absent[=False] Ignore any files that don’t exist.

class spack.FileFilter(*filenames)Bases: object

Convenience class for calling filter_file a lot.

filter(regex, repl, **kwargs)

spack.change_sed_delimiter(old_delim, new_delim, *filenames)Find all sed search/replace commands and change the delimiter. e.g., if the file contains seds that look like ‘s///’,you can call change_sed_delimiter(‘/’, ‘@’, file) to change the delimiter to ‘@’.

NOTE that this routine will fail if the delimiter is ‘ or ”. Handling those is left for future work.

spack.is_exe(path)True if path is an executable file.

spack.force_symlink(src, dest)

spack.set_executable(path)

spack.copy_mode(src, dest)

spack.unset_executable_mode(path)

spack.remove_dead_links(root)Removes any dead link that is present in root

Args: root: path where to search for dead links

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spack.remove_linked_tree(path)Removes a directory and its contents. If the directory is a symlink, follows the link and removes the realdirectory before removing the link.

Args: path: directory to be removed

spack.find_library_path(libname, *paths)Searches for a file called <libname> in each path.

Return: directory where the library was found, if found. None otherwise.

spack.fix_darwin_install_name(path)Fix install name of dynamic libraries on Darwin to have full path. There are two parts of this task: (i) useinstall_name(‘-id’,...) to change install name of a single lib; (ii) use install_name(‘-change’,...) to change thecross linking between libs. The function assumes that all libraries are in one folder and currently won’t followsubfolders.

Args: path: directory in which .dylib files are located

spack.to_link_flags(library)Transforms a path to a <library> into linking flags -L<dir> -l<name>.

Return: A string of linking flags.

spack.to_lib_name(library)Transforms a path to the library /path/to/lib<name>.xyz into <name>

spack.depends_on(*args, **kwargs)Creates a dict of deps with specs defining when they apply.

spack.extends(*args, **kwargs)Same as depends_on, but dependency is symlinked into parent prefix.

This is for Python and other language modules where the module needs to be installed into the prefix of thePython installation. Spack handles this by installing modules into their own prefix, but allowing ONE moduleversion to be symlinked into a parent Python install at a time.

keyword arguments can be passed to extends() so that extension packages can pass parameters to the extendee’sextension mechanism.

spack.provides(*args, **kwargs)Allows packages to provide a virtual dependency. If a package provides ‘mpi’, other packages can declare thatthey depend on “mpi”, and spack can use the providing package to satisfy the dependency.

spack.patch(*args, **kwargs)Packages can declare patches to apply to source. You can optionally provide a when spec to indicate that aparticular patch should only be applied when the package’s spec meets certain conditions (e.g. a particularversion).

spack.version(*args, **kwargs)Adds a version and metadata describing how to fetch it. Metadata is just stored as a dict in the package’s versionsdictionary. Package must turn it into a valid fetch strategy later.

spack.variant(*args, **kwargs)Define a variant for the package. Packager can specify a default value (on or off) as well as a text description.

spack.resource(*args, **kwargs)Define an external resource to be fetched and staged when building the package. Based on the keywords presentin the dictionary the appropriate FetchStrategy will be used for the resource. Resources are fetched and stagedin their own folder inside spack stage area, and then moved into the stage area of the package that needs them.

List of recognized keywords:

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•‘when’ : (optional) represents the condition upon which the resource is needed

•‘destination’ : (optional) path where to move the resource. This path must be relative to the main packagestage area.

•‘placement’ : (optional) gives the possibility to fine tune how the resource is moved into the main packagestage area.

class spack.Executable(name)Bases: object

Class representing a program that can be run on the command line.

add_default_arg(arg)

command

spack.which(name, **kwargs)Finds an executable in the path like command-line which.

exception spack.ProcessError(msg, long_message=None)Bases: spack.error.SpackError

long_message

spack.install_dependency_symlinks(pkg, spec, prefix)Execute a dummy install and flatten dependencies

spack.flatten_dependencies(spec, flat_dir)Make each dependency of spec present in dir via symlink.

exception spack.DependencyConflictError(conflict)Bases: spack.error.SpackError

Raised when the dependencies cannot be flattened as asked for.

exception spack.InstallError(message, long_msg=None)Bases: spack.error.SpackError

Raised when something goes wrong during install or uninstall.

exception spack.ExternalPackageError(message, long_msg=None)Bases: spack.package.InstallError

Raised by install() when a package is only for external use.

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Indices and tables

• genindex

• modindex

• search

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Python Module Index

sspack.abi, 384spack.architecture, 384spack.build_environment, 386spack.cmd, 345spack.cmd.activate, 335spack.cmd.arch, 335spack.cmd.bootstrap, 335spack.cmd.cd, 335spack.cmd.checksum, 336spack.cmd.clean, 336spack.cmd.common, 335spack.cmd.common.arguments, 335spack.cmd.compiler, 336spack.cmd.compilers, 336spack.cmd.config, 336spack.cmd.create, 336spack.cmd.deactivate, 337spack.cmd.dependents, 337spack.cmd.diy, 337spack.cmd.doc, 337spack.cmd.edit, 337spack.cmd.env, 337spack.cmd.extensions, 337spack.cmd.fetch, 338spack.cmd.find, 338spack.cmd.graph, 338spack.cmd.help, 338spack.cmd.info, 338spack.cmd.install, 338spack.cmd.list, 338spack.cmd.load, 339spack.cmd.location, 339spack.cmd.md5, 339spack.cmd.mirror, 339spack.cmd.module, 339spack.cmd.package_list, 340spack.cmd.patch, 340spack.cmd.pkg, 340spack.cmd.providers, 341

spack.cmd.purge, 341spack.cmd.python, 341spack.cmd.reindex, 341spack.cmd.repo, 341spack.cmd.restage, 341spack.cmd.setup, 341spack.cmd.spec, 342spack.cmd.stage, 342spack.cmd.test, 342spack.cmd.test_install, 342spack.cmd.uninstall, 343spack.cmd.unload, 343spack.cmd.unuse, 343spack.cmd.url_parse, 343spack.cmd.urls, 344spack.cmd.use, 344spack.cmd.versions, 344spack.cmd.view, 344spack.compiler, 388spack.compilers, 350spack.compilers.cce, 346spack.compilers.clang, 346spack.compilers.gcc, 347spack.compilers.intel, 347spack.compilers.nag, 348spack.compilers.pgi, 348spack.compilers.xl, 349spack.concretize, 388spack.config, 390spack.database, 392spack.directives, 394spack.directory_layout, 395spack.environment, 397spack.error, 399spack.fetch_strategy, 400spack.file_cache, 403spack.graph, 404spack.hooks, 352spack.hooks.dotkit, 351spack.hooks.extensions, 351spack.hooks.licensing, 351

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spack.hooks.sbang, 351spack.hooks.tclmodule, 352spack.mirror, 405spack.modules, 406spack.multimethod, 407spack.operating_systems, 353spack.operating_systems.cnl, 352spack.operating_systems.linux_distro,

352spack.operating_systems.mac_os, 353spack.package, 409spack.package_test, 418spack.parse, 419spack.patch, 419spack.platforms, 354spack.platforms.bgq, 353spack.platforms.cray, 353spack.platforms.darwin, 353spack.platforms.linux, 354spack.platforms.test, 354spack.preferred_packages, 420spack.provider_index, 420spack.repository, 421spack.resource, 424spack.schema, 355spack.schema.compilers, 354spack.schema.mirrors, 354spack.schema.modules, 354spack.schema.packages, 354spack.schema.repos, 355spack.schema.targets, 355spack.spec, 424spack.stage, 433spack.test, 379spack.test.architecture, 356spack.test.build_system_guess, 357spack.test.cc, 357spack.test.cmd, 356spack.test.cmd.find, 355spack.test.cmd.module, 355spack.test.cmd.test_compiler_cmd, 355spack.test.cmd.test_install, 356spack.test.cmd.uninstall, 356spack.test.concretize, 358spack.test.concretize_preferences, 359spack.test.config, 360spack.test.database, 360spack.test.directory_layout, 361spack.test.environment, 361spack.test.file_cache, 361spack.test.git_fetch, 362spack.test.hg_fetch, 362spack.test.install, 363spack.test.link_tree, 363

spack.test.lock, 364spack.test.make_executable, 364spack.test.mirror, 365spack.test.mock_database, 365spack.test.mock_packages_test, 365spack.test.mock_repo, 366spack.test.modules, 366spack.test.multimethod, 367spack.test.namespace_trie, 367spack.test.optional_deps, 368spack.test.package_sanity, 368spack.test.packages, 368spack.test.pattern, 369spack.test.provider_index, 369spack.test.python_version, 369spack.test.sbang, 370spack.test.spec_dag, 370spack.test.spec_semantics, 371spack.test.spec_syntax, 372spack.test.spec_yaml, 373spack.test.stage, 373spack.test.svn_fetch, 374spack.test.tally_plugin, 375spack.test.url_extrapolate, 375spack.test.url_parse, 375spack.test.url_substitution, 377spack.test.versions, 377spack.test.yaml, 379spack.url, 435spack.util, 384spack.util.compression, 379spack.util.crypto, 379spack.util.debug, 380spack.util.environment, 380spack.util.executable, 380spack.util.multiproc, 381spack.util.naming, 381spack.util.pattern, 382spack.util.prefix, 382spack.util.spack_yaml, 383spack.util.string, 383spack.util.web, 383spack.variant, 437spack.version, 437spack.yaml_version_check, 440

456 Python Module Index

Index

AABI (class in spack.abi), 384accept() (spack.parse.Parser method), 419acquire_read() (spack.test.lock.LockTest method), 364acquire_write() (spack.test.lock.LockTest method), 364activate() (in module spack.cmd.activate), 335activate() (spack.package.Package method), 413activated (spack.package.Package attribute), 413ActivationError, 409add() (spack.database.Database method), 393add() (spack.version.VersionList method), 439add_common_arguments() (in module

spack.cmd.common.arguments), 335add_compilers_to_config() (in module spack.compilers),

350add_default_arg() (spack.util.executable.Executable

method), 380add_extension() (spack.directory_layout.DirectoryLayout

method), 395add_extension() (spack.directory_layout.YamlDirectoryLayout

method), 397add_operating_system() (spack.architecture.Platform

method), 385add_single_spec() (in module spack.mirror), 405add_target() (spack.architecture.Platform method), 385addError() (spack.test.tally_plugin.Tally method), 375addFailure() (spack.test.tally_plugin.Tally method), 375addSuccess() (spack.test.tally_plugin.Tally method), 375all_compiler_types() (in module spack.compilers), 350all_compilers() (in module spack.compilers), 350all_compilers_config() (in module spack.compilers), 350all_os_classes() (in module spack.compilers), 350all_package_names() (spack.repository.Repo method),

422all_package_names() (spack.repository.RepoPath

method), 423all_packages() (spack.repository.Repo method), 422all_packages() (spack.repository.RepoPath method), 423all_specs() (spack.directory_layout.DirectoryLayout

method), 395

all_specs() (spack.directory_layout.YamlDirectoryLayoutmethod), 397

all_urls (spack.package.Package attribute), 413allowed_archive() (in module spack.util.compression),

379AmbiguousHashError, 425append() (spack.cmd.test_install.TestSuite method), 342append_path() (spack.environment.EnvironmentModifications

method), 398AppendPath (class in spack.environment), 397apply() (spack.patch.Patch method), 420apply_modifications() (spack.environment.EnvironmentModifications

method), 398Arch (class in spack.architecture), 385arch() (in module spack.cmd.arch), 335arch_from_dict() (in module spack.architecture), 386architecture_compare() (spack.preferred_packages.PreferredPackages

method), 420architecture_compatible() (spack.abi.ABI method), 384ArchitectureTest (class in spack.test.architecture), 356archive() (spack.fetch_strategy.FetchStrategy method),

400archive() (spack.fetch_strategy.GitFetchStrategy

method), 401archive() (spack.fetch_strategy.GoFetchStrategy

method), 401archive() (spack.fetch_strategy.HgFetchStrategy

method), 402archive() (spack.fetch_strategy.SvnFetchStrategy

method), 402archive() (spack.fetch_strategy.URLFetchStrategy

method), 403archive() (spack.fetch_strategy.VCSFetchStrategy

method), 403archive_file (spack.fetch_strategy.URLFetchStrategy at-

tribute), 403archive_file (spack.stage.Stage attribute), 434args_are_for() (in module spack.fetch_strategy), 403AsciiGraph (class in spack.graph), 405ask_for_confirmation() (in module spack.cmd), 345

457

Spack Documentation, Release 0.9

assert_canonical() (spack.test.versions.VersionsTestmethod), 377

assert_does_not_satisfy()(spack.test.versions.VersionsTest method),377

assert_in() (spack.test.versions.VersionsTest method),377

assert_no_overlap() (spack.test.versions.VersionsTestmethod), 378

assert_not_detected() (spack.test.url_parse.UrlParseTestmethod), 376

assert_not_in() (spack.test.versions.VersionsTestmethod), 378

assert_overlaps() (spack.test.versions.VersionsTestmethod), 378

assert_rev() (spack.test.git_fetch.GitFetchTest method),362

assert_rev() (spack.test.svn_fetch.SvnFetchTest method),374

assert_satisfies() (spack.test.versions.VersionsTestmethod), 378

assert_variant_values() (spack.test.concretize_preferences.ConcretizePreferencesTestmethod), 359

assert_ver_eq() (spack.test.versions.VersionsTestmethod), 378

assert_ver_gt() (spack.test.versions.VersionsTestmethod), 378

assert_ver_lt() (spack.test.versions.VersionsTest method),378

assuredir() (in module spack.cmd.view), 344autoload() (spack.modules.EnvModule method), 406autoload_format (spack.modules.Dotkit attribute), 407autoload_format (spack.modules.TclModule attribute),

407

Bback_end (spack.architecture.Platform attribute), 385back_end (spack.platforms.bgq.Bgq attribute), 353back_end (spack.platforms.darwin.Darwin attribute), 353back_end (spack.platforms.test.Test attribute), 354back_os (spack.architecture.Platform attribute), 385back_os (spack.platforms.test.Test attribute), 354BadRepoError, 421Barrier (class in spack.util.multiproc), 381Bgq (class in spack.platforms.bgq), 353blacklisted (spack.modules.EnvModule attribute), 406bootstrap() (in module spack.cmd.bootstrap), 335build_env_path() (spack.directory_layout.YamlDirectoryLayout

method), 397build_log_path (spack.package.Package attribute), 413build_log_path() (spack.directory_layout.YamlDirectoryLayout

method), 397build_packages_path() (spack.directory_layout.YamlDirectoryLayout

method), 397

BuildSystemGuesser (class in spack.cmd.create), 336Bunch (class in spack.util.pattern), 382

Ccache_local() (spack.stage.DIYStage method), 433cache_local() (spack.stage.Stage method), 434cache_path() (spack.file_cache.FileCache method), 404CacheError, 403CacheURLFetchStrategy (class in spack.fetch_strategy),

400canonicalize_path() (in module spack.repository), 424category (spack.modules.EnvModule attribute), 406cc_names (spack.compiler.Compiler attribute), 388cc_names (spack.compilers.cce.Cce attribute), 346cc_names (spack.compilers.clang.Clang attribute), 346cc_names (spack.compilers.gcc.Gcc attribute), 347cc_names (spack.compilers.intel.Intel attribute), 347cc_names (spack.compilers.nag.Nag attribute), 348cc_names (spack.compilers.pgi.Pgi attribute), 348cc_names (spack.compilers.xl.Xl attribute), 349cc_rpath_arg (spack.compiler.Compiler attribute), 388cc_version() (spack.compiler.Compiler class method),

388Cce (class in spack.compilers.cce), 346cd() (in module spack.cmd.cd), 335chdir() (spack.stage.DIYStage method), 433chdir() (spack.stage.Stage method), 434chdir_to_source() (spack.stage.DIYStage method), 433chdir_to_source() (spack.stage.Stage method), 434ChdirError, 433check() (spack.fetch_strategy.FetchStrategy method), 400check() (spack.fetch_strategy.URLFetchStrategy

method), 403check() (spack.fetch_strategy.VCSFetchStrategy

method), 403check() (spack.stage.DIYStage method), 433check() (spack.stage.Stage method), 434check() (spack.test.url_parse.UrlParseTest method), 376check() (spack.util.crypto.Checker method), 380check_activated() (spack.directory_layout.DirectoryLayout

method), 395check_activated() (spack.directory_layout.YamlDirectoryLayout

method), 397check_archive() (spack.test.build_system_guess.InstallTest

method), 357check_cc() (spack.test.cc.CompilerTest method), 357check_chdir() (spack.test.stage.StageTest method), 373check_chdir_to_source() (spack.test.stage.StageTest

method), 373check_compiler_yaml_version() (in module

spack.yaml_version_check), 440check_concretize() (spack.test.concretize.ConcretizeTest

method), 358

458 Index

Spack Documentation, Release 0.9

check_config() (spack.test.config.ConfigTest method),360

check_constrain() (spack.test.spec_semantics.SpecSematicsTestmethod), 371

check_constrain_changed()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

check_constrain_not_changed()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

check_cpp() (spack.test.cc.CompilerTest method), 357check_cxx() (spack.test.cc.CompilerTest method), 357check_db() (spack.test.package_sanity.PackageSanityTest

method), 368check_destroy() (spack.test.stage.StageTest method), 373check_dir() (spack.test.link_tree.LinkTreeTest method),

363check_expand_archive() (spack.test.stage.StageTest

method), 373check_extension_conflict()

(spack.directory_layout.DirectoryLayoutmethod), 395

check_extension_conflict()(spack.directory_layout.YamlDirectoryLayoutmethod), 397

check_fc() (spack.test.cc.CompilerTest method), 357check_fetch() (spack.test.stage.StageTest method), 373check_file_link() (spack.test.link_tree.LinkTreeTest

method), 363check_identifier() (spack.spec.SpecParser method), 431check_installed() (spack.directory_layout.DirectoryLayout

method), 395check_installed() (spack.directory_layout.YamlDirectoryLayout

method), 397check_intersection() (spack.test.versions.VersionsTest

method), 378check_invalid_constraint()

(spack.test.spec_semantics.SpecSematicsTestmethod), 371

check_ld() (spack.test.cc.CompilerTest method), 357check_lex() (spack.test.spec_syntax.SpecSyntaxTest

method), 372check_links() (spack.test.spec_dag.SpecDagTest

method), 370check_mirror() (spack.test.mirror.MirrorTest method),

365check_normalize() (spack.test.optional_deps.ConcretizeTest

method), 368check_one() (in module spack.cmd.view), 344check_parse() (spack.test.spec_syntax.SpecSyntaxTest

method), 372check_python_versions()

(spack.test.python_version.PythonVersionTestmethod), 369

check_satisfies() (spack.test.spec_semantics.SpecSematicsTestmethod), 371

check_setup() (spack.test.stage.StageTest method), 373check_spec() (spack.test.concretize.ConcretizeTest

method), 358check_union() (spack.test.versions.VersionsTest method),

378check_unsatisfiable() (spack.test.spec_semantics.SpecSematicsTest

method), 371check_url() (spack.test.url_extrapolate.UrlExtrapolateTest

method), 375check_yaml_round_trip()

(spack.test.spec_yaml.SpecYamlTest method),373

check_yaml_versions() (in modulespack.yaml_version_check), 440

Checker (class in spack.util.crypto), 379checksum() (in module spack.cmd.checksum), 336checksum() (in module spack.util.crypto), 380ChecksumError, 400choose_virtual_or_external()

(spack.concretize.DefaultConcretizer method),389

Clang (class in spack.compilers.clang), 346class_for_compiler_name() (in module spack.compilers),

350clean() (in module spack.cmd.clean), 336cleanmock() (spack.test.mock_packages_test.MockPackagesTest

method), 365clear() (spack.config.ConfigScope method), 391clear() (spack.environment.EnvironmentModifications

method), 398clear_config_caches() (in module spack.config), 391CMakePackage (class in spack.package), 409cmp_specs() (in module spack.concretize), 389Cnl (class in spack.operating_systems.cnl), 352color_formats (in module spack.spec), 433color_url() (in module spack.url), 436colorize_spec() (in module spack.spec), 433colorized() (spack.spec.Spec method), 427comma_and() (in module spack.util.string), 383comma_list() (in module spack.util.string), 383comma_or() (in module spack.util.string), 383command (spack.util.executable.Executable attribute),

381common_dependencies() (spack.spec.Spec method), 427compare_output() (in module spack.package_test), 418compare_output_file() (in module spack.package_test),

418compatible() (spack.abi.ABI method), 384compile_c_and_execute() (in module

spack.package_test), 418Compiler (class in spack.compiler), 388compiler (spack.package.Package attribute), 413

Index 459

Spack Documentation, Release 0.9

compiler() (in module spack.cmd.compiler), 336compiler() (spack.spec.SpecParser method), 431compiler_compare() (spack.preferred_packages.PreferredPackages

method), 420compiler_compatible() (spack.abi.ABI method), 384compiler_find() (in module spack.cmd.compiler), 336compiler_for_spec() (in module spack.compilers), 350compiler_info() (in module spack.cmd.compiler), 336compiler_list() (in module spack.cmd.compiler), 336compiler_remove() (in module spack.cmd.compiler), 336CompilerCmdTest (class in

spack.test.cmd.test_compiler_cmd), 355compilers() (in module spack.cmd.compilers), 336compilers_for_spec() (in module spack.compilers), 350CompilerSpec (class in spack.spec), 425CompilerSpecInsufficientlySpecificError, 350CompilerTest (class in spack.test.cc), 357composite() (in module spack.util.pattern), 382CompositeTest (class in spack.test.pattern), 369compute_md5_checksum() (in module spack.cmd.md5),

339concatenate_paths() (in module spack.environment), 399concrete (spack.architecture.Arch attribute), 385concrete (spack.spec.CompilerSpec attribute), 426concrete (spack.spec.DependencyMap attribute), 426concrete (spack.spec.FlagMap attribute), 427concrete (spack.spec.Spec attribute), 427concrete (spack.spec.VariantMap attribute), 432concrete (spack.version.Version attribute), 438concrete (spack.version.VersionList attribute), 439concrete (spack.version.VersionRange attribute), 438concretize() (spack.spec.Spec method), 427concretize() (spack.test.concretize_preferences.ConcretizePreferencesTest

method), 359concretize_architecture()

(spack.concretize.DefaultConcretizer method),389

concretize_compiler() (spack.concretize.DefaultConcretizermethod), 389

concretize_compiler_flags()(spack.concretize.DefaultConcretizer method),389

concretize_specs() (in module spack.cmd.uninstall), 343concretize_variants() (spack.concretize.DefaultConcretizer

method), 389concretize_version() (spack.concretize.DefaultConcretizer

method), 389concretized() (spack.spec.Spec method), 427ConcretizePreferencesTest (class in

spack.test.concretize_preferences), 359ConcretizeTest (class in spack.test.concretize), 358ConcretizeTest (class in spack.test.optional_deps), 368config() (in module spack.cmd.config), 336config_edit() (in module spack.cmd.config), 336

config_get() (in module spack.cmd.config), 336ConfigError, 391ConfigFileError, 391ConfigFormatError, 391ConfigSanityError, 391ConfigScope (class in spack.config), 391ConfigTest (class in spack.test.config), 360configure() (spack.test.tally_plugin.Tally method), 375configure_args() (spack.package.CMakePackage

method), 409configure_env() (spack.package.CMakePackage method),

409constrain() (spack.spec.CompilerSpec method), 426constrain() (spack.spec.FlagMap method), 427constrain() (spack.spec.Spec method), 427constrain() (spack.spec.VariantMap method), 432constrained() (spack.spec.Spec method), 428copy() (spack.provider_index.ProviderIndex method),

421copy() (spack.spec.CompilerSpec method), 426copy() (spack.spec.DependencySpec method), 426copy() (spack.spec.FlagMap method), 427copy() (spack.spec.Spec method), 428copy() (spack.spec.VariantMap method), 432copy() (spack.spec.VariantSpec method), 433copy() (spack.version.VersionList method), 439CorruptDatabaseError, 392Cray (class in spack.platforms.cray), 353create() (in module spack.cmd.create), 336create() (in module spack.mirror), 405create() (spack.stage.Stage method), 434create_install_directory()

(spack.directory_layout.DirectoryLayoutmethod), 395

create_install_directory()(spack.directory_layout.YamlDirectoryLayoutmethod), 397

create_repo() (in module spack.repository), 424cshort_spec (spack.spec.Spec attribute), 428cumsum() (in module spack.url), 436cxx11_flag (spack.compiler.Compiler attribute), 388cxx11_flag (spack.compilers.clang.Clang attribute), 346cxx11_flag (spack.compilers.gcc.Gcc attribute), 347cxx11_flag (spack.compilers.intel.Intel attribute), 347cxx11_flag (spack.compilers.nag.Nag attribute), 348cxx11_flag (spack.compilers.pgi.Pgi attribute), 348cxx11_flag (spack.compilers.xl.Xl attribute), 349cxx14_flag (spack.compiler.Compiler attribute), 388cxx14_flag (spack.compilers.gcc.Gcc attribute), 347cxx_names (spack.compiler.Compiler attribute), 388cxx_names (spack.compilers.cce.Cce attribute), 346cxx_names (spack.compilers.clang.Clang attribute), 346cxx_names (spack.compilers.gcc.Gcc attribute), 347cxx_names (spack.compilers.intel.Intel attribute), 347

460 Index

Spack Documentation, Release 0.9

cxx_names (spack.compilers.nag.Nag attribute), 348cxx_names (spack.compilers.pgi.Pgi attribute), 348cxx_names (spack.compilers.xl.Xl attribute), 349cxx_rpath_arg (spack.compiler.Compiler attribute), 388cxx_version() (spack.compiler.Compiler class method),

388

Ddag_hash() (spack.spec.Spec method), 428dag_hash() (spack.test.cmd.test_install.MockSpec

method), 356Darwin (class in spack.platforms.darwin), 353dashed (spack.version.Version attribute), 438Database (class in spack.database), 393DatabaseTest (class in spack.test.database), 360deactivate() (in module spack.cmd.deactivate), 337deactivate() (spack.package.Package method), 413debug_handler() (in module spack.util.debug), 380decompressor_for() (in module spack.util.compression),

379default (spack.architecture.Platform attribute), 385default (spack.platforms.bgq.Bgq attribute), 353default (spack.platforms.darwin.Darwin attribute), 353default (spack.platforms.test.Test attribute), 354default_compiler() (in module spack.compilers), 350default_naming_format (spack.modules.Dotkit attribute),

407default_naming_format (spack.modules.TclModule at-

tribute), 407default_os (spack.architecture.Platform attribute), 385default_os (spack.platforms.test.Test attribute), 354default_version() (spack.compiler.Compiler class

method), 388default_version() (spack.compilers.cce.Cce class

method), 346default_version() (spack.compilers.clang.Clang class

method), 346default_version() (spack.compilers.intel.Intel class

method), 347default_version() (spack.compilers.nag.Nag class

method), 348default_version() (spack.compilers.pgi.Pgi class method),

348default_version() (spack.compilers.xl.Xl class method),

349DefaultConcretizer (class in spack.concretize), 388dep_difference() (spack.spec.Spec method), 428dep_string() (spack.spec.Spec method), 428dependencies() (spack.spec.Spec method), 428dependencies() (spack.test.cmd.test_install.MockSpec

method), 356dependencies_dict() (spack.spec.Spec method), 428dependencies_of_type() (spack.package.Package

method), 413

DependencyConflictError, 410DependencyMap (class in spack.spec), 426DependencySpec (class in spack.spec), 426dependents() (in module spack.cmd.dependents), 337dependents() (spack.spec.Spec method), 428dependents() (spack.test.cmd.test_install.MockSpec

method), 356dependents_dict() (spack.spec.Spec method), 428depends_on() (in module spack.directives), 394destroy() (spack.fetch_strategy.FsCache method), 401destroy() (spack.file_cache.FileCache method), 404destroy() (spack.stage.DIYStage method), 433destroy() (spack.stage.Stage method), 435destroy() (spack.test.mock_repo.MockRepo method), 366detect() (spack.architecture.Platform class method), 385detect() (spack.platforms.bgq.Bgq class method), 353detect() (spack.platforms.cray.Cray class method), 353detect() (spack.platforms.darwin.Darwin class method),

353detect() (spack.platforms.linux.Linux class method), 354detect() (spack.platforms.test.Test class method), 354die() (spack.error.SpackError method), 400diff_packages() (in module spack.cmd.pkg), 340DirectoryLayout (class in spack.directory_layout), 395DirectoryLayoutError, 396DirectoryLayoutTest (class in

spack.test.directory_layout), 361dirname_for_package_name() (spack.repository.Repo

method), 422dirname_for_package_name()

(spack.repository.RepoPath method), 423disambiguate_spec() (in module spack.cmd), 345display_specs() (in module spack.cmd), 345diy() (in module spack.cmd.diy), 337DIYStage (class in spack.stage), 433do_activate() (spack.package.Package method), 413do_clean() (spack.package.Package method), 414do_deactivate() (spack.package.Package method), 414do_fake_install() (spack.package.Package method), 414do_fetch() (spack.package.Package method), 414do_install() (spack.package.Package method), 414do_install() (spack.test.cmd.test_install.MockPackage

method), 356do_install_dependencies() (spack.package.Package

method), 414do_parse() (spack.spec.SpecParser method), 431do_patch() (spack.package.Package method), 414do_restage() (spack.package.Package method), 414do_stage() (spack.package.Package method), 414do_uninstall() (in module spack.cmd.uninstall), 343do_uninstall() (spack.package.Package method), 414doc() (in module spack.cmd.doc), 337Dotkit (class in spack.modules), 407DotkitTests (class in spack.test.modules), 366

Index 461

Spack Documentation, Release 0.9

dotted (spack.version.Version attribute), 438downloaded_file_extension() (in module spack.url), 436dump() (in module spack.util.spack_yaml), 383dump_environment() (in module spack.util.environment),

380dump_packages() (in module spack.package), 418dump_provenance() (spack.repository.Repo method), 422dump_provenance() (spack.repository.RepoPath method),

423DuplicateArchitectureError, 426DuplicateCompilerSpecError, 426DuplicateDependencyError, 426DuplicateRepoError, 421DuplicateVariantError, 426

Eedit() (in module spack.cmd.edit), 337edit_package() (in module spack.cmd.edit), 337elide_list() (in module spack.cmd), 345enabled (spack.fetch_strategy.FetchStrategy attribute),

400enabled (spack.fetch_strategy.GitFetchStrategy attribute),

401enabled (spack.fetch_strategy.GoFetchStrategy attribute),

401enabled (spack.fetch_strategy.HgFetchStrategy attribute),

402enabled (spack.fetch_strategy.SvnFetchStrategy at-

tribute), 402enabled (spack.fetch_strategy.URLFetchStrategy at-

tribute), 403ensure_access() (in module spack.stage), 435env() (in module spack.cmd.env), 337env_flag() (in module spack.util.environment), 380environment_modifications_formats

(spack.modules.Dotkit attribute), 407EnvironmentModifications (class in spack.environment),

397EnvironmentTest (class in spack.test.environment), 361EnvModule (class in spack.modules), 406eq_dag() (spack.spec.Spec method), 428eq_node() (spack.spec.Spec method), 428ERRORED (spack.cmd.test_install.TestResult attribute),

342Executable (class in spack.util.executable), 380execute() (spack.environment.AppendPath method), 397execute() (spack.environment.PrependPath method), 399execute() (spack.environment.RemovePath method), 399execute() (spack.environment.SetEnv method), 399execute() (spack.environment.SetPath method), 399execute() (spack.environment.UnsetEnv method), 399exists() (spack.repository.Repo method), 422exists() (spack.repository.RepoPath method), 423

expand() (spack.fetch_strategy.FetchStrategy method),400

expand() (spack.fetch_strategy.URLFetchStrategymethod), 403

expand() (spack.fetch_strategy.VCSFetchStrategymethod), 403

expand_archive() (spack.stage.DIYStage method), 433expand_archive() (spack.stage.ResourceStage method),

433expand_archive() (spack.stage.Stage method), 435expect() (spack.parse.Parser method), 419expected_archive_files (spack.stage.Stage attribute), 435extend() (spack.environment.EnvironmentModifications

method), 398extend_with_default() (in module spack.config), 391extendable (spack.package.Package attribute), 414extendee_args (spack.package.Package attribute), 414extendee_spec (spack.package.Package attribute), 414extends() (in module spack.directives), 394extends() (spack.package.Package method), 414extension() (in module spack.util.compression), 379extension_file_path() (spack.directory_layout.YamlDirectoryLayout

method), 397extension_map() (spack.directory_layout.DirectoryLayout

method), 395extension_map() (spack.directory_layout.YamlDirectoryLayout

method), 397ExtensionAlreadyInstalledError, 396ExtensionConflictError, 396, 410ExtensionError, 410extensions() (in module spack.cmd.extensions), 337extensions_for() (spack.repository.Repo method), 422extensions_for() (spack.repository.RepoPath method),

423ExternalPackageError, 410

Ff77_names (spack.compiler.Compiler attribute), 388f77_names (spack.compilers.cce.Cce attribute), 346f77_names (spack.compilers.clang.Clang attribute), 347f77_names (spack.compilers.gcc.Gcc attribute), 347f77_names (spack.compilers.intel.Intel attribute), 348f77_names (spack.compilers.nag.Nag attribute), 348f77_names (spack.compilers.pgi.Pgi attribute), 349f77_names (spack.compilers.xl.Xl attribute), 349f77_rpath_arg (spack.compiler.Compiler attribute), 388f77_rpath_arg (spack.compilers.nag.Nag attribute), 348f77_version() (spack.compiler.Compiler class method),

388f77_version() (spack.compilers.gcc.Gcc class method),

347f77_version() (spack.compilers.xl.Xl class method), 349FAILED (spack.cmd.test_install.TestResult attribute),

342

462 Index

Spack Documentation, Release 0.9

failed_dependencies() (in module spack.cmd.test_install),342

FailedConstructorError, 421FailedDownloadError, 400fake_fetchify() (spack.test.install.InstallTest method), 363fc_names (spack.compiler.Compiler attribute), 388fc_names (spack.compilers.cce.Cce attribute), 346fc_names (spack.compilers.clang.Clang attribute), 347fc_names (spack.compilers.gcc.Gcc attribute), 347fc_names (spack.compilers.intel.Intel attribute), 348fc_names (spack.compilers.nag.Nag attribute), 348fc_names (spack.compilers.pgi.Pgi attribute), 349fc_names (spack.compilers.xl.Xl attribute), 349fc_rpath_arg (spack.compiler.Compiler attribute), 388fc_rpath_arg (spack.compilers.nag.Nag attribute), 348fc_version() (spack.compiler.Compiler class method),

388fc_version() (spack.compilers.gcc.Gcc class method), 347fc_version() (spack.compilers.xl.Xl class method), 349fetch() (in module spack.cmd.fetch), 338fetch() (spack.cmd.test.MockCacheFetcher method), 342fetch() (spack.fetch_strategy.CacheURLFetchStrategy

method), 400fetch() (spack.fetch_strategy.FetchStrategy method), 400fetch() (spack.fetch_strategy.GitFetchStrategy method),

401fetch() (spack.fetch_strategy.GoFetchStrategy method),

401fetch() (spack.fetch_strategy.HgFetchStrategy method),

402fetch() (spack.fetch_strategy.SvnFetchStrategy method),

402fetch() (spack.fetch_strategy.URLFetchStrategy method),

403fetch() (spack.stage.DIYStage method), 433fetch() (spack.stage.Stage method), 435fetch_log() (in module spack.cmd.test_install), 342fetch_remote_versions() (spack.package.Package

method), 415fetch_tarballs() (in module spack.cmd.create), 336fetcher (spack.package.Package attribute), 415fetcher() (spack.cmd.test.MockCache method), 342fetcher() (spack.fetch_strategy.FsCache method), 401FetchError, 400, 410FetchStrategy (class in spack.fetch_strategy), 400file_name (spack.modules.Dotkit attribute), 407file_name (spack.modules.EnvModule attribute), 406file_name (spack.modules.TclModule attribute), 407FileCache (class in spack.file_cache), 403FileCacheTest (class in spack.test.file_cache), 361filename_for_package_name() (spack.repository.Repo

method), 422filename_for_package_name()

(spack.repository.RepoPath method), 423

filter_environment_blacklist() (in modulespack.environment), 399

filter_exclude() (in module spack.cmd.view), 344filter_shebang() (in module spack.hooks.sbang), 351filter_shebangs_in_directory() (in module

spack.hooks.sbang), 351finalize() (spack.test.tally_plugin.Tally method), 375find() (in module spack.cmd.find), 338find() (in module spack.cmd.module), 339find() (in module spack.compilers), 350find_compiler() (spack.architecture.OperatingSystem

method), 385find_compiler() (spack.operating_systems.cnl.Cnl

method), 352find_compilers() (in module spack.compilers), 350find_compilers() (spack.architecture.OperatingSystem

method), 385find_compilers() (spack.operating_systems.cnl.Cnl

method), 352find_list_url() (in module spack.url), 436find_module() (spack.repository.Repo method), 422find_module() (spack.repository.RepoPath method), 423find_repository() (in module spack.cmd.create), 336find_spec() (in module spack.concretize), 389find_tmp_root() (in module spack.stage), 435find_versions_of_archive() (in module spack.util.web),

383FindTest (class in spack.test.cmd.find), 355first_repo() (spack.repository.RepoPath method), 423FlagMap (class in spack.spec), 426flat_dependencies() (spack.spec.Spec method), 428flat_dependencies_with_deptype() (spack.spec.Spec

method), 428flatten() (in module spack.cmd.view), 344flatten_dependencies() (in module spack.package), 418for_package_version() (in module spack.fetch_strategy),

403fork() (in module spack.build_environment), 387format() (spack.spec.Spec method), 428format_doc() (spack.package.Package method), 415formats (spack.modules.EnvModule attribute), 406from_dict() (spack.database.InstallRecord class method),

394from_dict() (spack.spec.CompilerSpec static method),

426from_dict() (spack.version.VersionList static method),

439from_kwargs() (in module spack.fetch_strategy), 403from_node_dict() (spack.spec.Spec static method), 429from_sourcing_files() (spack.environment.EnvironmentModifications

static method), 398from_url() (in module spack.fetch_strategy), 403from_yaml() (spack.provider_index.ProviderIndex static

method), 421

Index 463

Spack Documentation, Release 0.9

from_yaml() (spack.spec.Spec static method), 429front_end (spack.architecture.Platform attribute), 386front_end (spack.platforms.bgq.Bgq attribute), 353front_end (spack.platforms.darwin.Darwin attribute), 353front_end (spack.platforms.test.Test attribute), 354front_os (spack.architecture.Platform attribute), 386FsCache (class in spack.fetch_strategy), 401fullname (spack.spec.Spec attribute), 429

GGcc (class in spack.compilers.gcc), 347get() (spack.repository.Repo method), 422get() (spack.repository.RepoPath method), 423get() (spack.test.cmd.test_install.MockPackageDb

method), 356get_checksums() (in module spack.cmd.checksum), 336get_cmd_function_name() (in module spack.cmd), 345get_command() (in module spack.cmd), 345get_compiler_config() (in module spack.compilers), 350get_compiler_version() (in module spack.compiler), 388get_config() (in module spack.config), 392get_config_filename() (in module spack.config), 392get_dependency() (spack.spec.Spec method), 429get_filename() (in module spack.cmd.test_install), 342get_git() (in module spack.cmd.pkg), 340get_matching_versions() (in module spack.mirror), 406get_module() (in module spack.cmd), 346get_modulefile_content()

(spack.test.modules.DotkitTests method),366

get_modulefile_content() (spack.test.modules.TclTestsmethod), 367

get_origin_info() (in module spack.cmd.bootstrap), 335get_path() (in module spack.config), 392get_path() (in module spack.util.environment), 380get_path_from_module() (in module

spack.build_environment), 387get_pkg_class() (spack.repository.Repo method), 422get_pkg_class() (spack.repository.RepoPath method), 423get_record() (spack.database.Database method), 393get_repo() (spack.repository.RepoPath method), 423get_rev() (spack.test.mock_repo.MockHgRepo method),

366get_rpaths() (in module spack.build_environment), 387get_section() (spack.config.ConfigScope method), 391get_section_filename() (spack.config.ConfigScope

method), 391get_stage_path() (spack.test.stage.StageTest method),

373get_top_spec_or_die() (in module

spack.cmd.test_install), 343gettok() (spack.parse.Parser method), 419git (spack.fetch_strategy.GitFetchStrategy attribute), 401

git_version (spack.fetch_strategy.GitFetchStrategyattribute), 401

GitFetchStrategy (class in spack.fetch_strategy), 401GitFetchTest (class in spack.test.git_fetch), 362github_url() (in module spack.cmd.package_list), 340global_license_dir (spack.package.Package attribute),

415global_license_file (spack.package.Package attribute),

415go (spack.fetch_strategy.GoFetchStrategy attribute), 401go_version (spack.fetch_strategy.GoFetchStrategy

attribute), 401GoFetchStrategy (class in spack.fetch_strategy), 401graph() (in module spack.cmd.graph), 338graph_ascii() (in module spack.graph), 405graph_dot() (in module spack.graph), 405gray_hash() (in module spack.cmd), 346group_by_name() (spack.environment.EnvironmentModifications

method), 398guess_name_and_version() (in module

spack.cmd.create), 337

Hhandle_starttag() (spack.util.web.LinkParser method),

383has_value() (spack.util.naming.NamespaceTrie method),

382hash_color (in module spack.spec), 433hash_name (spack.util.crypto.Checker attribute), 380header (spack.modules.Dotkit attribute), 407header (spack.modules.EnvModule attribute), 406header (spack.modules.TclModule attribute), 407help() (in module spack.cmd.help), 338HelperFunctionsTests (class in spack.test.modules), 366hg (spack.fetch_strategy.HgFetchStrategy attribute), 402HgFetchStrategy (class in spack.fetch_strategy), 402HgFetchTest (class in spack.test.hg_fetch), 362hidden_file_paths (spack.directory_layout.DirectoryLayout

attribute), 395hidden_file_paths (spack.directory_layout.YamlDirectoryLayout

attribute), 397highest() (spack.version.Version method), 438highest() (spack.version.VersionList method), 439highest() (spack.version.VersionRange method), 438highest_precedence_scope() (in module spack.config),

392HookRunner (class in spack.hooks), 352

IInconsistentInstallDirectoryError, 396InconsistentSpecError, 427index() (spack.spec.Spec method), 429info() (in module spack.cmd.info), 338init_entry() (spack.file_cache.FileCache method), 404

464 Index

Spack Documentation, Release 0.9

initmock() (spack.test.mock_packages_test.MockPackagesTestmethod), 366

insensitize() (in module spack.url), 436install() (in module spack.cmd.install), 338install() (spack.package.Package method), 415install() (spack.package.StagedPackage method), 418install_build() (spack.package.CMakePackage method),

409install_build() (spack.package.StagedPackage method),

418install_configure() (spack.package.CMakePackage

method), 409install_configure() (spack.package.StagedPackage

method), 418install_dependency_symlinks() (in module

spack.package), 418install_install() (spack.package.CMakePackage method),

409install_install() (spack.package.StagedPackage method),

418install_phases (spack.package.Package attribute), 415install_setup() (spack.package.CMakePackage method),

410install_setup() (spack.package.StagedPackage method),

418install_single_spec() (in module spack.cmd.test_install),

343InstallDirectoryAlreadyExistsError, 396installed (spack.package.Package attribute), 415installed_dependents (spack.package.Package attribute),

415installed_dependents() (in module spack.cmd.uninstall),

343installed_extensions_for() (spack.database.Database

method), 393InstallError, 386, 410InstallRecord (class in spack.database), 393InstallTest (class in spack.test.build_system_guess), 357InstallTest (class in spack.test.install), 363Intel (class in spack.compilers.intel), 347intersect() (spack.version.VersionList method), 439intersection() (spack.version.Version method), 438intersection() (spack.version.VersionList method), 439intersection() (spack.version.VersionRange method), 438InvalidArgsError, 402InvalidCompilerConfigurationError, 350InvalidDatabaseVersionError, 394InvalidDependencyException, 427InvalidExtensionSpecError, 396InvalidNamespaceError, 421is_a() (spack.parse.Token method), 419is_apple (spack.compilers.clang.Clang attribute), 347is_extension (spack.package.Package attribute), 415is_leaf() (spack.util.naming.NamespaceTrie method), 382

is_predecessor() (spack.version.Version method), 438is_prefix() (spack.repository.Repo method), 422is_prefix() (spack.util.naming.NamespaceTrie method),

382is_spec_buildable() (in module spack.config), 392is_successor() (spack.version.Version method), 438is_virtual() (spack.spec.Spec static method), 429

Llast_token_error() (spack.parse.Parser method), 419lex() (spack.parse.Lexer method), 419Lexer (class in spack.parse), 419LexError, 419link_one() (in module spack.cmd.view), 344link_paths (spack.compilers.cce.Cce attribute), 346link_paths (spack.compilers.clang.Clang attribute), 347link_paths (spack.compilers.gcc.Gcc attribute), 347link_paths (spack.compilers.intel.Intel attribute), 348link_paths (spack.compilers.nag.Nag attribute), 348link_paths (spack.compilers.pgi.Pgi attribute), 349link_paths (spack.compilers.xl.Xl attribute), 349LinkParser (class in spack.util.web), 383LinkTreeTest (class in spack.test.link_tree), 363Linux (class in spack.platforms.linux), 354LinuxDistro (class in spack.operating_systems.linux_distro),

352list() (in module spack.cmd.list), 338list_packages() (in module spack.cmd.pkg), 340list_tests() (in module spack.test), 379load() (in module spack.cmd.load), 339load() (in module spack.util.spack_yaml), 383load_external_modules() (in module

spack.build_environment), 387load_module() (in module spack.build_environment), 387load_module() (spack.repository.Repo method), 422load_module() (spack.repository.RepoPath method), 423loads() (in module spack.cmd.module), 339location() (in module spack.cmd.location), 339LockTest (class in spack.test.lock), 364long_message (spack.error.SpackError attribute), 400long_message (spack.util.executable.ProcessError at-

tribute), 381lowest() (spack.version.Version method), 438lowest() (spack.version.VersionList method), 439lowest() (spack.version.VersionRange method), 438

MMacOs (class in spack.operating_systems.mac_os), 353make_executable() (in module spack.package), 418make_jobs (spack.package.Package attribute), 415make_make() (spack.package.CMakePackage method),

410make_mock_compiler() (in module

spack.test.cmd.test_compiler_cmd), 355

Index 465

Spack Documentation, Release 0.9

make_version_calls() (in module spack.cmd.create), 337MakeExecutable (class in spack.build_environment), 386MakeExecutableTest (class in

spack.test.make_executable), 364matches() (spack.fetch_strategy.FetchStrategy class

method), 400md5() (in module spack.cmd.md5), 339merge() (spack.provider_index.ProviderIndex method),

421metadata_path() (spack.directory_layout.YamlDirectoryLayout

method), 397mirror() (in module spack.cmd.mirror), 339mirror_add() (in module spack.cmd.mirror), 339mirror_archive_filename() (in module spack.mirror), 406mirror_archive_path() (in module spack.mirror), 406mirror_create() (in module spack.cmd.mirror), 339mirror_list() (in module spack.cmd.mirror), 339mirror_remove() (in module spack.cmd.mirror), 339MirrorError, 405MirrorTest (class in spack.test.mirror), 365missing() (spack.database.Database method), 393mock_fetch_log() (in module spack.test.cmd.test_install),

356mock_open() (in module spack.test.cmd.test_install), 356mock_open() (in module spack.test.modules), 367MockArchive (class in spack.test.mock_repo), 366MockArgs (class in spack.test.cmd.test_compiler_cmd),

355MockArgs (class in spack.test.cmd.test_install), 356MockArgs (class in spack.test.cmd.uninstall), 356MockCache (class in spack.cmd.test), 342MockCacheFetcher (class in spack.cmd.test), 342MockDatabase (class in spack.test.mock_database), 365MockGitRepo (class in spack.test.mock_repo), 366MockHgRepo (class in spack.test.mock_repo), 366MockPackage (class in spack.test.cmd.test_install), 356MockPackageDb (class in spack.test.cmd.test_install),

356MockPackagesTest (class in

spack.test.mock_packages_test), 365MockRepo (class in spack.test.mock_repo), 366MockSpec (class in spack.test.cmd.test_install), 356MockSvnRepo (class in spack.test.mock_repo), 366MockVCSRepo (class in spack.test.mock_repo), 366mod_to_class() (in module spack.util.naming), 381module (spack.package.Package attribute), 415module() (in module spack.cmd.module), 339module_specific_content() (spack.modules.EnvModule

method), 406module_specific_content() (spack.modules.TclModule

method), 407mtime() (spack.file_cache.FileCache method), 404MultiMethodError, 408MultiMethodTest (class in spack.test.multimethod), 367

MultipleMatches, 339MultipleProviderError, 427multiproc_test() (spack.test.lock.LockTest method), 364

NNag (class in spack.compilers.nag), 348name (spack.modules.Dotkit attribute), 407name (spack.modules.EnvModule attribute), 406name (spack.modules.TclModule attribute), 407name (spack.test.tally_plugin.Tally attribute), 375NameModifier (class in spack.environment), 398namespace (spack.package.Package attribute), 415NamespaceTrie (class in spack.util.naming), 382NamespaceTrie.Element (class in spack.util.naming), 382NamespaceTrieTest (class in spack.test.namespace_trie),

367NameValueModifier (class in spack.environment), 398naming_scheme (spack.modules.EnvModule attribute),

406ne_dag() (spack.spec.Spec method), 429ne_node() (spack.spec.Spec method), 429nearest_url() (spack.package.Package method), 415next_token_error() (spack.parse.Parser method), 419NoArchiveFileError, 402NoBuildError, 389NoCompilerForSpecError, 350NoCompilersError, 350NoDigestError, 402NoMatch, 339NoNetworkConnectionError, 399NoPlatformError, 385NoProviderError, 427NoRepoConfiguredError, 421normalize() (spack.spec.Spec method), 429normalized() (spack.spec.Spec method), 429NoStageError, 402NoSuchExtensionError, 396NoSuchMethodError, 408NoSuchPatchFileError, 419NoURLError, 410NoValidVersionError, 389numberOfTestsRun (spack.test.tally_plugin.Tally at-

tribute), 375

Oopenmp_flag (spack.compiler.Compiler attribute), 388openmp_flag (spack.compilers.clang.Clang attribute),

347openmp_flag (spack.compilers.gcc.Gcc attribute), 347openmp_flag (spack.compilers.intel.Intel attribute), 348openmp_flag (spack.compilers.nag.Nag attribute), 348openmp_flag (spack.compilers.pgi.Pgi attribute), 349openmp_flag (spack.compilers.xl.Xl attribute), 349

466 Index

Spack Documentation, Release 0.9

operating_system() (spack.architecture.Platformmethod), 386

OperatingSystem (class in spack.architecture), 385options() (spack.test.tally_plugin.Tally method), 375overlaps() (spack.version.Version method), 438overlaps() (spack.version.VersionList method), 439overlaps() (spack.version.VersionRange method), 438

PPackage (class in spack.package), 410package (spack.spec.Spec attribute), 430package_class (spack.spec.Spec attribute), 430package_dir (spack.package.Package attribute), 415package_list() (in module spack.cmd.package_list), 340package_py_files() (spack.test.python_version.PythonVersionTest

method), 369PackageError, 417PackageLoadError, 421PackageSanityTest (class in spack.test.package_sanity),

368PackageSanityTest (class in spack.test.url_substitution),

377PackagesTest (class in spack.test.packages), 368PackageStillNeededError, 417PackageVersionError, 417padder() (in module spack.cmd.info), 338parallel (spack.package.Package attribute), 415parent_class_modules() (in module

spack.build_environment), 387parmap() (in module spack.util.multiproc), 381parse() (in module spack.spec), 433parse() (spack.parse.Parser method), 419parse_anonymous_spec() (in module spack.spec), 433parse_compiler() (spack.spec.SpecParser method), 431parse_name() (in module spack.url), 436parse_name_and_version() (in module spack.url), 436parse_name_offset() (in module spack.url), 436parse_specs() (in module spack.cmd), 346parse_version() (in module spack.url), 436parse_version_offset() (in module spack.url), 436ParseError, 419Parser (class in spack.parse), 419PASSED (spack.cmd.test_install.TestResult attribute),

342Patch (class in spack.patch), 419patch() (in module spack.cmd.patch), 340patch() (in module spack.directives), 394path (spack.modules.Dotkit attribute), 407path (spack.modules.TclModule attribute), 407path_for_spec() (spack.directory_layout.DirectoryLayout

method), 396path_put_first() (in module spack.util.environment), 380path_set() (in module spack.util.environment), 380Pgi (class in spack.compilers.pgi), 348

pkg() (in module spack.cmd.pkg), 340pkg_add() (in module spack.cmd.pkg), 340pkg_added() (in module spack.cmd.pkg), 340pkg_diff() (in module spack.cmd.pkg), 340pkg_list() (in module spack.cmd.pkg), 340pkg_removed() (in module spack.cmd.pkg), 340Platform (class in spack.architecture), 385possible_spack_module_names() (in module

spack.util.naming), 382post_install() (in module spack.hooks.dotkit), 351post_install() (in module spack.hooks.licensing), 351post_install() (in module spack.hooks.sbang), 351post_install() (in module spack.hooks.tclmodule), 352post_uninstall() (in module spack.hooks.dotkit), 351post_uninstall() (in module spack.hooks.tclmodule), 352pre_install() (in module spack.hooks.licensing), 351pre_uninstall() (in module spack.hooks.extensions), 351PreferredPackages (class in spack.preferred_packages),

420Prefix (class in spack.util.prefix), 382prefix (spack.package.Package attribute), 415prefix (spack.spec.Spec attribute), 430prefixes (spack.compiler.Compiler attribute), 388prepend_path() (spack.environment.EnvironmentModifications

method), 398PrependPath (class in spack.environment), 399prerequisite() (spack.modules.Dotkit method), 407prerequisite() (spack.modules.EnvModule method), 406prerequisite_format (spack.modules.TclModule at-

tribute), 407PrgEnv (spack.compiler.Compiler attribute), 388PrgEnv (spack.compilers.cce.Cce attribute), 346PrgEnv (spack.compilers.gcc.Gcc attribute), 347PrgEnv (spack.compilers.intel.Intel attribute), 347PrgEnv (spack.compilers.pgi.Pgi attribute), 348PrgEnv_compiler (spack.compiler.Compiler attribute),

388PrgEnv_compiler (spack.compilers.cce.Cce attribute),

346PrgEnv_compiler (spack.compilers.gcc.Gcc attribute),

347PrgEnv_compiler (spack.compilers.intel.Intel attribute),

347PrgEnv_compiler (spack.compilers.pgi.Pgi attribute), 348print_name_and_version() (in module

spack.cmd.url_parse), 343print_pkg() (in module spack.package), 418print_rst_package_list() (in module

spack.cmd.package_list), 340print_section() (in module spack.config), 392print_text_info() (in module spack.cmd.info), 338priority (spack.architecture.Platform attribute), 386priority (spack.platforms.bgq.Bgq attribute), 353priority (spack.platforms.cray.Cray attribute), 353

Index 467

Spack Documentation, Release 0.9

priority (spack.platforms.darwin.Darwin attribute), 353priority (spack.platforms.linux.Linux attribute), 354priority (spack.platforms.test.Test attribute), 354process_environment_command()

(spack.modules.EnvModule method), 406process_environment_command()

(spack.modules.TclModule method), 407ProcessError, 381provider_compare() (spack.preferred_packages.PreferredPackages

method), 420provider_index (spack.repository.Repo attribute), 422provider_index (spack.repository.RepoPath attribute),

423ProviderIndex (class in spack.provider_index), 420ProviderIndexError, 421ProviderIndexTest (class in spack.test.provider_index),

369providers() (in module spack.cmd.providers), 341providers_for() (spack.provider_index.ProviderIndex

method), 421providers_for() (spack.repository.Repo method), 422providers_for() (spack.repository.RepoPath method), 423provides() (in module spack.directives), 394provides() (spack.package.Package method), 415purge() (in module spack.cmd.purge), 341purge() (in module spack.stage), 435purge() (spack.repository.Repo method), 422purge_empty_directories() (in module spack.cmd.view),

344push_tokens() (spack.parse.Parser method), 419put_first() (spack.repository.RepoPath method), 423put_last() (spack.repository.RepoPath method), 424pyfiles() (spack.test.python_version.PythonVersionTest

method), 369python() (in module spack.cmd.python), 341PythonVersionTest (class in spack.test.python_version),

369

Qquery() (spack.database.Database method), 393query_arguments() (in module spack.cmd.find), 338query_one() (spack.database.Database method), 393

Rread_spec() (spack.directory_layout.YamlDirectoryLayout

method), 397read_transaction() (spack.database.Database method),

393read_transaction() (spack.file_cache.FileCache method),

404read_yaml_dep_specs() (spack.spec.Spec static method),

430real_name() (spack.repository.Repo method), 422refresh() (in module spack.cmd.module), 339

register() (spack.multimethod.SpecMultiMethodmethod), 408

register_interrupt_handler() (in module spack.util.debug),380

reindex() (in module spack.cmd.reindex), 341reindex() (spack.database.Database method), 393relative_path_for_spec() (spack.directory_layout.DirectoryLayout

method), 396relative_path_for_spec() (spack.directory_layout.YamlDirectoryLayout

method), 397relative_to() (in module spack.cmd.view), 344remove() (spack.database.Database method), 393remove() (spack.file_cache.FileCache method), 404remove() (spack.modules.EnvModule method), 406remove() (spack.repository.RepoPath method), 424remove_compiler_from_config() (in module

spack.compilers), 350remove_extension() (spack.directory_layout.DirectoryLayout

method), 396remove_extension() (spack.directory_layout.YamlDirectoryLayout

method), 397remove_install_directory()

(spack.directory_layout.DirectoryLayoutmethod), 396

remove_one() (in module spack.cmd.view), 345remove_path() (spack.environment.EnvironmentModifications

method), 398remove_prefix() (spack.package.Package method), 415remove_provider() (spack.provider_index.ProviderIndex

method), 421RemoveFailedError, 396RemovePath (class in spack.environment), 399Repo (class in spack.repository), 421repo() (in module spack.cmd.repo), 341repo_add() (in module spack.cmd.repo), 341repo_create() (in module spack.cmd.repo), 341repo_for_pkg() (spack.repository.RepoPath method), 424repo_list() (in module spack.cmd.repo), 341repo_remove() (in module spack.cmd.repo), 341RepoError, 422RepoPath (class in spack.repository), 423required_attributes (spack.fetch_strategy.FetchStrategy

attribute), 401required_attributes (spack.fetch_strategy.GitFetchStrategy

attribute), 401required_attributes (spack.fetch_strategy.GoFetchStrategy

attribute), 401required_attributes (spack.fetch_strategy.HgFetchStrategy

attribute), 402required_attributes (spack.fetch_strategy.SvnFetchStrategy

attribute), 402required_attributes (spack.fetch_strategy.URLFetchStrategy

attribute), 403reset() (spack.fetch_strategy.FetchStrategy method), 401

468 Index

Spack Documentation, Release 0.9

reset() (spack.fetch_strategy.GitFetchStrategy method),401

reset() (spack.fetch_strategy.GoFetchStrategy method),402

reset() (spack.fetch_strategy.HgFetchStrategy method),402

reset() (spack.fetch_strategy.SvnFetchStrategy method),402

reset() (spack.fetch_strategy.URLFetchStrategy method),403

Resource (class in spack.resource), 424resource() (in module spack.directives), 395ResourceStage (class in spack.stage), 433restage() (in module spack.cmd.restage), 341restage() (spack.stage.DIYStage method), 433restage() (spack.stage.Stage method), 435RestageError, 433results (spack.cmd.test_install.TestCase attribute), 342rev_hash() (spack.test.mock_repo.MockGitRepo

method), 366rm() (in module spack.cmd.module), 340root (spack.spec.Spec attribute), 430rpath (spack.package.Package attribute), 415rpath_args (spack.package.Package attribute), 415rst_table() (in module spack.cmd.package_list), 340run() (in module spack.test), 379run_tests (spack.package.Package attribute), 415

Ssanity_check_is_dir (spack.package.Package attribute),

415sanity_check_is_file (spack.package.Package attribute),

416sanity_check_prefix() (spack.package.Package method),

416satisfies() (spack.provider_index.ProviderIndex method),

421satisfies() (spack.spec.CompilerSpec method), 426satisfies() (spack.spec.FlagMap method), 427satisfies() (spack.spec.Spec method), 430satisfies() (spack.spec.VariantMap method), 432satisfies() (spack.version.Version method), 438satisfies() (spack.version.VersionList method), 439satisfies() (spack.version.VersionRange method), 438satisfies_dependencies() (spack.spec.Spec method), 430SbangTest (class in spack.test.sbang), 370section_schemas (in module spack.config), 392set() (spack.environment.EnvironmentModifications

method), 398set_build_environment_variables() (in module

spack.build_environment), 387set_compiler_environment_variables() (in module

spack.build_environment), 387

set_module_variables_for_package() (in modulespack.build_environment), 387

set_or_unset_not_first() (in module spack.environment),399

set_path() (spack.environment.EnvironmentModificationsmethod), 398

set_pkg_dep() (spack.test.mock_packages_test.MockPackagesTestmethod), 366

set_result() (spack.cmd.test_install.TestCase method),342

set_stage() (spack.cmd.test.MockCacheFetcher method),342

set_stage() (spack.fetch_strategy.FetchStrategy method),401

set_up_license() (in module spack.hooks.licensing), 351set_up_package() (spack.test.mirror.MirrorTest method),

365SetEnv (class in spack.environment), 399SetPath (class in spack.environment), 399setup() (in module spack.cmd.setup), 341setup() (spack.parse.Parser method), 419setUp() (spack.test.architecture.ArchitectureTest

method), 357setUp() (spack.test.build_system_guess.InstallTest

method), 357setUp() (spack.test.cc.CompilerTest method), 357setUp() (spack.test.cmd.test_install.TestInstallTest

method), 356setUp() (spack.test.concretize_preferences.ConcretizePreferencesTest

method), 359setUp() (spack.test.config.ConfigTest method), 360setUp() (spack.test.directory_layout.DirectoryLayoutTest

method), 361setUp() (spack.test.environment.EnvironmentTest

method), 361setUp() (spack.test.file_cache.FileCacheTest method),

361setUp() (spack.test.git_fetch.GitFetchTest method), 362setUp() (spack.test.hg_fetch.HgFetchTest method), 362setUp() (spack.test.install.InstallTest method), 363setUp() (spack.test.link_tree.LinkTreeTest method), 363setUp() (spack.test.lock.LockTest method), 364setUp() (spack.test.make_executable.MakeExecutableTest

method), 364setUp() (spack.test.mirror.MirrorTest method), 365setUp() (spack.test.mock_database.MockDatabase

method), 365setUp() (spack.test.mock_packages_test.MockPackagesTest

method), 366setUp() (spack.test.modules.DotkitTests method), 366setUp() (spack.test.modules.TclTests method), 367setUp() (spack.test.namespace_trie.NamespaceTrieTest

method), 367setUp() (spack.test.pattern.CompositeTest method), 369

Index 469

Spack Documentation, Release 0.9

setUp() (spack.test.sbang.SbangTest method), 370setUp() (spack.test.stage.StageTest method), 373setUp() (spack.test.svn_fetch.SvnFetchTest method), 374setUp() (spack.test.yaml.YamlTest method), 379setup_dependent_environment() (spack.package.Package

method), 416setup_dependent_package() (spack.package.Package

method), 416setup_environment() (spack.package.Package method),

417setup_package() (in module spack.build_environment),

387setup_parser() (in module spack.cmd.activate), 335setup_parser() (in module spack.cmd.bootstrap), 335setup_parser() (in module spack.cmd.cd), 335setup_parser() (in module spack.cmd.checksum), 336setup_parser() (in module spack.cmd.clean), 336setup_parser() (in module spack.cmd.compiler), 336setup_parser() (in module spack.cmd.compilers), 336setup_parser() (in module spack.cmd.config), 336setup_parser() (in module spack.cmd.create), 337setup_parser() (in module spack.cmd.deactivate), 337setup_parser() (in module spack.cmd.dependents), 337setup_parser() (in module spack.cmd.diy), 337setup_parser() (in module spack.cmd.doc), 337setup_parser() (in module spack.cmd.edit), 337setup_parser() (in module spack.cmd.env), 337setup_parser() (in module spack.cmd.extensions), 337setup_parser() (in module spack.cmd.fetch), 338setup_parser() (in module spack.cmd.find), 338setup_parser() (in module spack.cmd.graph), 338setup_parser() (in module spack.cmd.help), 338setup_parser() (in module spack.cmd.info), 338setup_parser() (in module spack.cmd.install), 338setup_parser() (in module spack.cmd.list), 338setup_parser() (in module spack.cmd.load), 339setup_parser() (in module spack.cmd.location), 339setup_parser() (in module spack.cmd.md5), 339setup_parser() (in module spack.cmd.mirror), 339setup_parser() (in module spack.cmd.module), 340setup_parser() (in module spack.cmd.patch), 340setup_parser() (in module spack.cmd.pkg), 340setup_parser() (in module spack.cmd.providers), 341setup_parser() (in module spack.cmd.purge), 341setup_parser() (in module spack.cmd.python), 341setup_parser() (in module spack.cmd.repo), 341setup_parser() (in module spack.cmd.restage), 341setup_parser() (in module spack.cmd.setup), 341setup_parser() (in module spack.cmd.spec), 342setup_parser() (in module spack.cmd.stage), 342setup_parser() (in module spack.cmd.test), 342setup_parser() (in module spack.cmd.test_install), 343setup_parser() (in module spack.cmd.uninstall), 343setup_parser() (in module spack.cmd.unload), 343

setup_parser() (in module spack.cmd.unuse), 343setup_parser() (in module spack.cmd.url_parse), 343setup_parser() (in module spack.cmd.urls), 344setup_parser() (in module spack.cmd.use), 344setup_parser() (in module spack.cmd.versions), 344setup_parser() (in module spack.cmd.view), 345setup_platform_environment()

(spack.architecture.Platform class method),386

setup_platform_environment()(spack.platforms.cray.Cray class method),353

shebang_too_long() (in module spack.hooks.sbang), 351short_spec (spack.spec.Spec attribute), 430short_spec (spack.test.cmd.test_install.MockSpec at-

tribute), 356SKIPPED (spack.cmd.test_install.TestResult attribute),

342sorted_deps() (spack.spec.Spec method), 430source_path (spack.stage.Stage attribute), 435spack.abi (module), 384spack.architecture (module), 384spack.build_environment (module), 386spack.cmd (module), 345spack.cmd.activate (module), 335spack.cmd.arch (module), 335spack.cmd.bootstrap (module), 335spack.cmd.cd (module), 335spack.cmd.checksum (module), 336spack.cmd.clean (module), 336spack.cmd.common (module), 335spack.cmd.common.arguments (module), 335spack.cmd.compiler (module), 336spack.cmd.compilers (module), 336spack.cmd.config (module), 336spack.cmd.create (module), 336spack.cmd.deactivate (module), 337spack.cmd.dependents (module), 337spack.cmd.diy (module), 337spack.cmd.doc (module), 337spack.cmd.edit (module), 337spack.cmd.env (module), 337spack.cmd.extensions (module), 337spack.cmd.fetch (module), 338spack.cmd.find (module), 338spack.cmd.graph (module), 338spack.cmd.help (module), 338spack.cmd.info (module), 338spack.cmd.install (module), 338spack.cmd.list (module), 338spack.cmd.load (module), 339spack.cmd.location (module), 339spack.cmd.md5 (module), 339spack.cmd.mirror (module), 339

470 Index

Spack Documentation, Release 0.9

spack.cmd.module (module), 339spack.cmd.package_list (module), 340spack.cmd.patch (module), 340spack.cmd.pkg (module), 340spack.cmd.providers (module), 341spack.cmd.purge (module), 341spack.cmd.python (module), 341spack.cmd.reindex (module), 341spack.cmd.repo (module), 341spack.cmd.restage (module), 341spack.cmd.setup (module), 341spack.cmd.spec (module), 342spack.cmd.stage (module), 342spack.cmd.test (module), 342spack.cmd.test_install (module), 342spack.cmd.uninstall (module), 343spack.cmd.unload (module), 343spack.cmd.unuse (module), 343spack.cmd.url_parse (module), 343spack.cmd.urls (module), 344spack.cmd.use (module), 344spack.cmd.versions (module), 344spack.cmd.view (module), 344spack.compiler (module), 388spack.compilers (module), 350spack.compilers.cce (module), 346spack.compilers.clang (module), 346spack.compilers.gcc (module), 347spack.compilers.intel (module), 347spack.compilers.nag (module), 348spack.compilers.pgi (module), 348spack.compilers.xl (module), 349spack.concretize (module), 388spack.config (module), 390spack.database (module), 392spack.directives (module), 394spack.directory_layout (module), 395spack.environment (module), 397spack.error (module), 399spack.fetch_strategy (module), 400spack.file_cache (module), 403spack.graph (module), 404spack.hooks (module), 352spack.hooks.dotkit (module), 351spack.hooks.extensions (module), 351spack.hooks.licensing (module), 351spack.hooks.sbang (module), 351spack.hooks.tclmodule (module), 352spack.mirror (module), 405spack.modules (module), 406spack.multimethod (module), 407spack.operating_systems (module), 353spack.operating_systems.cnl (module), 352spack.operating_systems.linux_distro (module), 352

spack.operating_systems.mac_os (module), 353spack.package (module), 409spack.package_test (module), 418spack.parse (module), 419spack.patch (module), 419spack.platforms (module), 354spack.platforms.bgq (module), 353spack.platforms.cray (module), 353spack.platforms.darwin (module), 353spack.platforms.linux (module), 354spack.platforms.test (module), 354spack.preferred_packages (module), 420spack.provider_index (module), 420spack.repository (module), 421spack.resource (module), 424spack.schema (module), 355spack.schema.compilers (module), 354spack.schema.mirrors (module), 354spack.schema.modules (module), 354spack.schema.packages (module), 354spack.schema.repos (module), 355spack.schema.targets (module), 355spack.spec (module), 424spack.stage (module), 433spack.test (module), 379spack.test.architecture (module), 356spack.test.build_system_guess (module), 357spack.test.cc (module), 357spack.test.cmd (module), 356spack.test.cmd.find (module), 355spack.test.cmd.module (module), 355spack.test.cmd.test_compiler_cmd (module), 355spack.test.cmd.test_install (module), 356spack.test.cmd.uninstall (module), 356spack.test.concretize (module), 358spack.test.concretize_preferences (module), 359spack.test.config (module), 360spack.test.database (module), 360spack.test.directory_layout (module), 361spack.test.environment (module), 361spack.test.file_cache (module), 361spack.test.git_fetch (module), 362spack.test.hg_fetch (module), 362spack.test.install (module), 363spack.test.link_tree (module), 363spack.test.lock (module), 364spack.test.make_executable (module), 364spack.test.mirror (module), 365spack.test.mock_database (module), 365spack.test.mock_packages_test (module), 365spack.test.mock_repo (module), 366spack.test.modules (module), 366spack.test.multimethod (module), 367spack.test.namespace_trie (module), 367

Index 471

Spack Documentation, Release 0.9

spack.test.optional_deps (module), 368spack.test.package_sanity (module), 368spack.test.packages (module), 368spack.test.pattern (module), 369spack.test.provider_index (module), 369spack.test.python_version (module), 369spack.test.sbang (module), 370spack.test.spec_dag (module), 370spack.test.spec_semantics (module), 371spack.test.spec_syntax (module), 372spack.test.spec_yaml (module), 373spack.test.stage (module), 373spack.test.svn_fetch (module), 374spack.test.tally_plugin (module), 375spack.test.url_extrapolate (module), 375spack.test.url_parse (module), 375spack.test.url_substitution (module), 377spack.test.versions (module), 377spack.test.yaml (module), 379spack.url (module), 435spack.util (module), 384spack.util.compression (module), 379spack.util.crypto (module), 379spack.util.debug (module), 380spack.util.environment (module), 380spack.util.executable (module), 380spack.util.multiproc (module), 381spack.util.naming (module), 381spack.util.pattern (module), 382spack.util.prefix (module), 382spack.util.spack_yaml (module), 383spack.util.string (module), 383spack.util.web (module), 383spack.variant (module), 437spack.version (module), 437spack.yaml_version_check (module), 440spack_module_to_python_module() (in module

spack.util.naming), 381SpackError, 399SpackNamespace (class in spack.repository), 424SpackYAMLError, 427spawn() (in module spack.util.multiproc), 381Spec (class in spack.spec), 427spec() (in module spack.cmd.spec), 342spec() (spack.spec.SpecParser method), 431spec_by_hash() (spack.spec.SpecParser method), 431spec_externals() (in module spack.config), 392spec_file_path() (spack.directory_layout.YamlDirectoryLayout

method), 397spec_has_preferred_provider()

(spack.preferred_packages.PreferredPackagesmethod), 420

spec_preferred_variants()(spack.preferred_packages.PreferredPackages

method), 420SpecDagTest (class in spack.test.spec_dag), 370SpecError, 431SpecHashCollisionError, 396SpecLexer (class in spack.spec), 431SpecMultiMethod (class in spack.multimethod), 408SpecParseError, 431SpecParser (class in spack.spec), 431SpecReadError, 396specs_by_hash() (spack.directory_layout.YamlDirectoryLayout

method), 397SpecSematicsTest (class in spack.test.spec_semantics),

371SpecSyntaxTest (class in spack.test.spec_syntax), 372SpecYamlTest (class in spack.test.spec_yaml), 373spider() (in module spack.util.web), 383split_url_extension() (in module spack.url), 436Stage (class in spack.stage), 434stage (spack.package.Package attribute), 417stage() (in module spack.cmd.stage), 342StagedPackage (class in spack.package), 417StageError, 435StageTest (class in spack.test.stage), 373store() (spack.cmd.test.MockCache method), 342store() (spack.fetch_strategy.FsCache method), 401strip_extension() (in module spack.util.compression), 379strip_query_and_fragment() (in module spack.url), 437subcommand() (in module spack.cmd.module), 340substitute_spack_prefix() (in module spack.repository),

424substitute_version() (in module spack.url), 437substitution_offsets() (in module spack.url), 437suffixes (spack.compiler.Compiler attribute), 388suffixes (spack.compilers.cce.Cce attribute), 346suffixes (spack.compilers.gcc.Gcc attribute), 347suggest_archive_basename() (in module spack.mirror),

406supported() (in module spack.compilers), 350supported_compilers() (in module spack.compilers), 350svn (spack.fetch_strategy.SvnFetchStrategy attribute),

402SvnFetchStrategy (class in spack.fetch_strategy), 402SvnFetchTest (class in spack.test.svn_fetch), 374swap() (spack.repository.RepoPath method), 424symlink_license() (in module spack.hooks.licensing), 351

TTally (class in spack.test.tally_plugin), 375Target (class in spack.architecture), 386target() (spack.architecture.Platform method), 386TclModule (class in spack.modules), 407TclTests (class in spack.test.modules), 367tearDown() (spack.test.architecture.ArchitectureTest

method), 357

472 Index

Spack Documentation, Release 0.9

tearDown() (spack.test.build_system_guess.InstallTestmethod), 357

tearDown() (spack.test.cc.CompilerTest method), 358tearDown() (spack.test.cmd.test_install.TestInstallTest

method), 356tearDown() (spack.test.concretize_preferences.ConcretizePreferencesTest

method), 359tearDown() (spack.test.config.ConfigTest method), 360tearDown() (spack.test.directory_layout.DirectoryLayoutTest

method), 361tearDown() (spack.test.environment.EnvironmentTest

method), 361tearDown() (spack.test.file_cache.FileCacheTest

method), 361tearDown() (spack.test.git_fetch.GitFetchTest method),

362tearDown() (spack.test.hg_fetch.HgFetchTest method),

362tearDown() (spack.test.install.InstallTest method), 363tearDown() (spack.test.link_tree.LinkTreeTest method),

363tearDown() (spack.test.lock.LockTest method), 364tearDown() (spack.test.make_executable.MakeExecutableTest

method), 365tearDown() (spack.test.mirror.MirrorTest method), 365tearDown() (spack.test.mock_database.MockDatabase

method), 365tearDown() (spack.test.mock_packages_test.MockPackagesTest

method), 366tearDown() (spack.test.modules.DotkitTests method), 366tearDown() (spack.test.modules.TclTests method), 367tearDown() (spack.test.sbang.SbangTest method), 370tearDown() (spack.test.stage.StageTest method), 373tearDown() (spack.test.svn_fetch.SvnFetchTest method),

374Test (class in spack.platforms.test), 354test() (in module spack.cmd.test), 342test_005_db_exists() (spack.test.database.DatabaseTest

method), 360test_010_all_install_sanity()

(spack.test.database.DatabaseTest method),360

test_015_write_and_read()(spack.test.database.DatabaseTest method),360

test_020_db_sanity() (spack.test.database.DatabaseTestmethod), 360

test_030_db_sanity_from_another_process()(spack.test.database.DatabaseTest method),360

test_040_ref_counts() (spack.test.database.DatabaseTestmethod), 360

test_050_basic_query() (spack.test.database.DatabaseTestmethod), 360

test_060_remove_and_add_root_package()(spack.test.database.DatabaseTest method),360

test_070_remove_and_add_dependency_package()(spack.test.database.DatabaseTest method),360

test_080_root_ref_counts()(spack.test.database.DatabaseTest method),360

test_090_non_root_ref_counts()(spack.test.database.DatabaseTest method),360

test_100_no_write_with_exception_on_remove()(spack.test.database.DatabaseTest method),360

test_110_no_write_with_exception_on_install()(spack.test.database.DatabaseTest method),360

test_add_multiple() (spack.test.namespace_trie.NamespaceTrieTestmethod), 367

test_add_none_multiple()(spack.test.namespace_trie.NamespaceTrieTestmethod), 367

test_add_none_single() (spack.test.namespace_trie.NamespaceTrieTestmethod), 367

test_add_single() (spack.test.namespace_trie.NamespaceTrieTestmethod), 367

test_add_three() (spack.test.namespace_trie.NamespaceTrieTestmethod), 368

test_all_deps() (spack.test.cc.CompilerTest method), 358test_all_mirror() (spack.test.mirror.MirrorTest method),

365test_alpha() (spack.test.versions.VersionsTest method),

378test_alpha_beta() (spack.test.versions.VersionsTest

method), 378test_alpha_with_dots() (spack.test.versions.VersionsTest

method), 378test_alter_environment() (spack.test.modules.TclTests

method), 367test_ambiguous() (spack.test.spec_syntax.SpecSyntaxTest

method), 372test_ambiguous_version_spec()

(spack.test.spec_yaml.SpecYamlTest method),373

test_angband_version_style()(spack.test.url_parse.UrlParseTest method),376

test_another_erlang_version_style()(spack.test.url_parse.UrlParseTest method),376

test_apache_version_style()(spack.test.url_parse.UrlParseTest method),376

Index 473

Spack Documentation, Release 0.9

test_as_mode() (spack.test.cc.CompilerTest method), 358test_astyle_verson_style()

(spack.test.url_parse.UrlParseTest method),376

test_autoload() (spack.test.modules.TclTests method),367

test_autotools() (spack.test.build_system_guess.InstallTestmethod), 357

test_basic_version_satisfaction()(spack.test.versions.VersionsTest method),378

test_basic_version_satisfaction_in_lists()(spack.test.versions.VersionsTest method),378

test_blacklist() (spack.test.modules.TclTests method),367

test_boolness() (spack.test.architecture.ArchitectureTestmethod), 357

test_boost_version_style()(spack.test.url_parse.UrlParseTest method),376

test_canonicalize() (spack.test.spec_syntax.SpecSyntaxTestmethod), 372

test_canonicalize_list() (spack.test.versions.VersionsTestmethod), 378

test_ccld_mode() (spack.test.cc.CompilerTest method),358

test_chained_mpi() (spack.test.optional_deps.ConcretizeTestmethod), 368

test_chdir() (spack.test.stage.StageTest method), 373test_close_numbers() (spack.test.versions.VersionsTest

method), 378test_cmake() (spack.test.build_system_guess.InstallTest

method), 357test_compiler_add() (spack.test.cmd.test_compiler_cmd.CompilerCmdTest

method), 355test_compiler_child() (spack.test.concretize.ConcretizeTest

method), 358test_compiler_inheritance()

(spack.test.concretize.ConcretizeTest method),358

test_compiler_remove() (spack.test.cmd.test_compiler_cmd.CompilerCmdTestmethod), 355

test_complex_acquire_and_release_chain()(spack.test.lock.LockTest method), 364

test_composite_from_interface()(spack.test.pattern.CompositeTest method),369

test_composite_from_method_list()(spack.test.pattern.CompositeTest method),369

test_concrete_spec() (spack.test.spec_yaml.SpecYamlTestmethod), 373

test_concretize_dag() (spack.test.concretize.ConcretizeTestmethod), 358

test_concretize_no_deps()(spack.test.concretize.ConcretizeTest method),358

test_concretize_preferred_version()(spack.test.concretize.ConcretizeTest method),358

test_concretize_two_virtuals()(spack.test.concretize.ConcretizeTest method),358

test_concretize_two_virtuals_with_dual_provider()(spack.test.concretize.ConcretizeTest method),358

test_concretize_two_virtuals_with_dual_provider_and_a_conflict()(spack.test.concretize.ConcretizeTest method),358

test_concretize_two_virtuals_with_one_bound()(spack.test.concretize.ConcretizeTest method),358

test_concretize_two_virtuals_with_two_bound()(spack.test.concretize.ConcretizeTest method),358

test_concretize_variant() (spack.test.concretize.ConcretizeTestmethod), 359

test_concretize_with_provides_when()(spack.test.concretize.ConcretizeTest method),359

test_concretize_with_restricted_virtual()(spack.test.concretize.ConcretizeTest method),359

test_concretize_with_virtual()(spack.test.concretize.ConcretizeTest method),359

test_conflicting_package_constraints()(spack.test.spec_dag.SpecDagTest method),370

test_conflicting_spec_constraints()(spack.test.spec_dag.SpecDagTest method),370

test_conflicts() (spack.test.modules.TclTests method),367

test_conretize_compiler_flags()(spack.test.concretize.ConcretizeTest method),359

test_constrain_architecture()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_constrain_changed()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_constrain_compiler()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

474 Index

Spack Documentation, Release 0.9

test_constrain_compiler_flags()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_constrain_dependency_changed()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_constrain_dependency_not_changed()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_constrain_not_changed()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_constrain_variants() (spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_contains() (spack.test.spec_dag.SpecDagTestmethod), 370

test_contains() (spack.test.versions.VersionsTestmethod), 378

test_copy() (spack.test.provider_index.ProviderIndexTestmethod), 369

test_copy_concretized() (spack.test.spec_dag.SpecDagTestmethod), 370

test_copy_normalized() (spack.test.spec_dag.SpecDagTestmethod), 370

test_copy_simple() (spack.test.spec_dag.SpecDagTestmethod), 370

test_core_module_compatibility()(spack.test.python_version.PythonVersionTestmethod), 369

test_cpp_mode() (spack.test.cc.CompilerTest method),358

test_dash_rc_style() (spack.test.url_parse.UrlParseTestmethod), 376

test_dash_version_dash_style()(spack.test.url_parse.UrlParseTest method),376

test_date_stamps() (spack.test.versions.VersionsTestmethod), 378

test_debian_style_1() (spack.test.url_parse.UrlParseTestmethod), 376

test_debian_style_2() (spack.test.url_parse.UrlParseTestmethod), 376

test_default_variant() (spack.test.optional_deps.ConcretizeTestmethod), 368

test_default_works() (spack.test.multimethod.MultiMethodTestmethod), 367

test_dep_include() (spack.test.cc.CompilerTest method),358

test_dep_index() (spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_dep_lib() (spack.test.cc.CompilerTest method), 358test_dep_rpath() (spack.test.cc.CompilerTest method),

358

test_dependencies_with_versions()(spack.test.spec_syntax.SpecSyntaxTestmethod), 372

test_dependency_already_installed()(spack.test.cmd.test_install.TestInstallTestmethod), 356

test_dependency_match()(spack.test.multimethod.MultiMethodTestmethod), 367

test_dependents_and_dependencies_are_correct()(spack.test.spec_dag.SpecDagTest method),370

test_deptype_traversal() (spack.test.spec_dag.SpecDagTestmethod), 370

test_deptype_traversal_full()(spack.test.spec_dag.SpecDagTest method),370

test_deptype_traversal_run()(spack.test.spec_dag.SpecDagTest method),370

test_deptype_traversal_with_builddeps()(spack.test.spec_dag.SpecDagTest method),370

test_dict_functions_for_architecture()(spack.test.architecture.ArchitectureTestmethod), 357

test_dict_order() (spack.test.yaml.YamlTest method), 379test_dotkit() (spack.test.modules.DotkitTests method),

366test_double_alpha() (spack.test.versions.VersionsTest

method), 378test_duplicate_compiler()

(spack.test.spec_syntax.SpecSyntaxTestmethod), 372

test_duplicate_depdendence()(spack.test.spec_syntax.SpecSyntaxTestmethod), 372

test_duplicate_variant() (spack.test.spec_syntax.SpecSyntaxTestmethod), 372

test_dyninst_version() (spack.test.url_extrapolate.UrlExtrapolateTestmethod), 375

test_equal() (spack.test.provider_index.ProviderIndexTestmethod), 369

test_equal() (spack.test.spec_dag.SpecDagTest method),370

test_erlang_version_style()(spack.test.url_parse.UrlParseTest method),376

test_error_conditions() (spack.test.pattern.CompositeTestmethod), 369

test_expand_archive() (spack.test.stage.StageTestmethod), 374

test_expand_archive_with_chdir()(spack.test.stage.StageTest method), 374

Index 475

Spack Documentation, Release 0.9

test_extend() (spack.test.environment.EnvironmentTestmethod), 361

test_external_and_virtual()(spack.test.concretize.ConcretizeTest method),359

test_external_package() (spack.test.concretize.ConcretizeTestmethod), 359

test_external_package_module()(spack.test.concretize.ConcretizeTest method),359

test_extra_arguments() (spack.test.environment.EnvironmentTestmethod), 361

test_fann_version() (spack.test.url_parse.UrlParseTestmethod), 376

test_fetch() (spack.test.stage.StageTest method), 374test_fetch_branch() (spack.test.git_fetch.GitFetchTest

method), 362test_fetch_commit() (spack.test.git_fetch.GitFetchTest

method), 362test_fetch_default() (spack.test.hg_fetch.HgFetchTest

method), 363test_fetch_default() (spack.test.svn_fetch.SvnFetchTest

method), 374test_fetch_master() (spack.test.git_fetch.GitFetchTest

method), 362test_fetch_r1() (spack.test.svn_fetch.SvnFetchTest

method), 374test_fetch_rev0() (spack.test.hg_fetch.HgFetchTest

method), 363test_fetch_tag() (spack.test.git_fetch.GitFetchTest

method), 362test_find() (spack.test.directory_layout.DirectoryLayoutTest

method), 361test_find_spec_children()

(spack.test.concretize.ConcretizeTest method),359

test_find_spec_none() (spack.test.concretize.ConcretizeTestmethod), 359

test_find_spec_parents() (spack.test.concretize.ConcretizeTestmethod), 359

test_find_spec_self() (spack.test.concretize.ConcretizeTestmethod), 359

test_find_spec_sibling() (spack.test.concretize.ConcretizeTestmethod), 359

test_flags() (spack.test.cc.CompilerTest method), 358test_formatted_strings() (spack.test.versions.VersionsTest

method), 378test_full_specs() (spack.test.spec_syntax.SpecSyntaxTest

method), 372test_gcc() (spack.test.url_extrapolate.UrlExtrapolateTest

method), 375test_gcc_version() (spack.test.url_parse.UrlParseTest

method), 376

test_gcc_version_precedence()(spack.test.url_parse.UrlParseTest method),376

test_get_all_mock_packages()(spack.test.package_sanity.PackageSanityTestmethod), 368

test_get_all_packages() (spack.test.package_sanity.PackageSanityTestmethod), 368

test_get_item() (spack.test.versions.VersionsTestmethod), 378

test_git_mirror() (spack.test.mirror.MirrorTest method),365

test_github_raw() (spack.test.url_extrapolate.UrlExtrapolateTestmethod), 375

test_github_raw_url() (spack.test.url_parse.UrlParseTestmethod), 376

test_gloox_beta_style() (spack.test.url_parse.UrlParseTestmethod), 376

test_handle_unknown_package()(spack.test.directory_layout.DirectoryLayoutTestmethod), 361

test_haxe_version() (spack.test.url_parse.UrlParseTestmethod), 376

test_hdf5_version() (spack.test.url_parse.UrlParseTestmethod), 376

test_hg_mirror() (spack.test.mirror.MirrorTest method),365

test_hypre_url_substitution()(spack.test.url_substitution.PackageSanityTestmethod), 377

test_iges_version() (spack.test.url_parse.UrlParseTestmethod), 376

test_ignore() (spack.test.link_tree.LinkTreeTest method),363

test_imagemagick_style()(spack.test.url_parse.UrlParseTest method),376

test_imap_version() (spack.test.url_parse.UrlParseTestmethod), 376

test_import_class_from_package()(spack.test.packages.PackagesTest method),368

test_import_module_from_package()(spack.test.packages.PackagesTest method),368

test_import_namespace_container_modules()(spack.test.packages.PackagesTest method),368

test_import_package() (spack.test.packages.PackagesTestmethod), 368

test_import_package_as()(spack.test.packages.PackagesTest method),368

476 Index

Spack Documentation, Release 0.9

test_in_list() (spack.test.versions.VersionsTest method),378

test_inspect_path() (spack.test.modules.HelperFunctionsTestsmethod), 366

test_install() (in module spack.cmd.test_install), 343test_install_and_uninstall() (spack.test.install.InstallTest

method), 363test_install_environment() (spack.test.install.InstallTest

method), 363test_installing_both() (spack.test.cmd.test_install.TestInstallTest

method), 356test_intersect_with_containment()

(spack.test.versions.VersionsTest method),378

test_intersection() (spack.test.versions.VersionsTestmethod), 378

test_invalid_constraint() (spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_invalid_dep() (spack.test.spec_dag.SpecDagTestmethod), 370

test_jpeg_style() (spack.test.url_parse.UrlParseTestmethod), 376

test_keep_exceptions() (spack.test.stage.StageTestmethod), 374

test_keep_without_exceptions()(spack.test.stage.StageTest method), 374

test_lame_version_style()(spack.test.url_parse.UrlParseTest method),376

test_ld_deps() (spack.test.cc.CompilerTest method), 358test_ld_deps_reentrant() (spack.test.cc.CompilerTest

method), 358test_ld_mode() (spack.test.cc.CompilerTest method), 358test_libdwarf_version() (spack.test.url_extrapolate.UrlExtrapolateTest

method), 375test_libelf_version() (spack.test.url_extrapolate.UrlExtrapolateTest

method), 375test_line_numbers() (spack.test.yaml.YamlTest method),

379test_lists_overlap() (spack.test.versions.VersionsTest

method), 378test_load_package() (spack.test.packages.PackagesTest

method), 368test_make_explicit() (spack.test.make_executable.MakeExecutableTest

method), 365test_make_normal() (spack.test.make_executable.MakeExecutableTest

method), 365test_make_one_job() (spack.test.make_executable.MakeExecutableTest

method), 365test_make_parallel_disabled()

(spack.test.make_executable.MakeExecutableTestmethod), 365

test_make_parallel_false()(spack.test.make_executable.MakeExecutableTest

method), 365test_make_parallel_precedence()

(spack.test.make_executable.MakeExecutableTestmethod), 365

test_merge_to_existing_directory()(spack.test.link_tree.LinkTreeTest method),363

test_merge_to_new_directory()(spack.test.link_tree.LinkTreeTest method),363

test_merge_with_empty_directories()(spack.test.link_tree.LinkTreeTest method),363

test_minimal_spaces() (spack.test.spec_syntax.SpecSyntaxTestmethod), 372

test_module_common_operations()(spack.test.cmd.module.TestModule method),355

test_mpi_providers() (spack.test.provider_index.ProviderIndexTestmethod), 369

test_mpi_version() (spack.test.multimethod.MultiMethodTestmethod), 367

test_mpileaks_version() (spack.test.url_extrapolate.UrlExtrapolateTestmethod), 375

test_mpileaks_version() (spack.test.url_parse.UrlParseTestmethod), 376

test_multiple_conditionals()(spack.test.optional_deps.ConcretizeTestmethod), 368

test_mvapich2_19_version()(spack.test.url_parse.UrlParseTest method),376

test_mvapich2_20_version()(spack.test.url_parse.UrlParseTest method),376

test_my_dep_depends_on_provider_of_my_virtual_dep()(spack.test.concretize.ConcretizeTest method),359

test_new_github_style() (spack.test.url_parse.UrlParseTestmethod), 376

test_no_keep_with_exceptions()(spack.test.stage.StageTest method), 374

test_no_keep_without_exceptions()(spack.test.stage.StageTest method), 374

test_no_version() (spack.test.url_parse.UrlParseTestmethod), 376

test_no_version_match() (spack.test.multimethod.MultiMethodTestmethod), 367

test_nobuild_package() (spack.test.concretize.ConcretizeTestmethod), 359

test_nonexisting_package_filename()(spack.test.packages.PackagesTest method),368

Index 477

Spack Documentation, Release 0.9

test_normal_spec() (spack.test.spec_yaml.SpecYamlTestmethod), 373

test_normalize_a_lot() (spack.test.spec_dag.SpecDagTestmethod), 370

test_normalize_mpileaks()(spack.test.spec_dag.SpecDagTest method),370

test_normalize_simple_conditionals()(spack.test.optional_deps.ConcretizeTestmethod), 368

test_normalize_twice() (spack.test.spec_dag.SpecDagTestmethod), 370

test_normalize_with_virtual_package()(spack.test.spec_dag.SpecDagTest method),370

test_normalize_with_virtual_spec()(spack.test.spec_dag.SpecDagTest method),370

test_noseparator_single_digit()(spack.test.url_parse.UrlParseTest method),376

test_num_alpha_with_no_separator()(spack.test.versions.VersionsTest method),378

test_nums_and_patch() (spack.test.versions.VersionsTestmethod), 378

test_omega_version_style()(spack.test.url_parse.UrlParseTest method),376

test_one_version_match()(spack.test.multimethod.MultiMethodTestmethod), 367

test_openssl_version() (spack.test.url_parse.UrlParseTestmethod), 376

test_otf2_url_substitution()(spack.test.url_substitution.PackageSanityTestmethod), 377

test_overlap_with_containment()(spack.test.versions.VersionsTest method),378

test_p7zip_version_style()(spack.test.url_parse.UrlParseTest method),376

test_package_class_names()(spack.test.packages.PackagesTest method),368

test_package_filename() (spack.test.packages.PackagesTestmethod), 368

test_package_module_compatibility()(spack.test.python_version.PythonVersionTestmethod), 369

test_package_name() (spack.test.packages.PackagesTestmethod), 368

test_package_names() (spack.test.spec_syntax.SpecSyntaxTestmethod), 372

test_padded_numbers() (spack.test.versions.VersionsTestmethod), 378

test_parse() (spack.test.yaml.YamlTest method), 379test_parse_errors() (spack.test.spec_syntax.SpecSyntaxTest

method), 373test_partial_version_prefix()

(spack.test.url_extrapolate.UrlExtrapolateTestmethod), 375

test_patch() (spack.test.versions.VersionsTest method),378

test_path_manipulation()(spack.test.environment.EnvironmentTestmethod), 361

test_platform() (spack.test.architecture.ArchitectureTestmethod), 357

test_postorder_edge_traversal()(spack.test.spec_dag.SpecDagTest method),370

test_postorder_node_traversal()(spack.test.spec_dag.SpecDagTest method),370

test_postorder_path_traversal()(spack.test.spec_dag.SpecDagTest method),370

test_preferred_compilers()(spack.test.concretize_preferences.ConcretizePreferencesTestmethod), 359

test_preferred_providers()(spack.test.concretize_preferences.ConcretizePreferencesTestmethod), 359

test_preferred_variants() (spack.test.concretize_preferences.ConcretizePreferencesTestmethod), 359

test_preferred_versions()(spack.test.concretize_preferences.ConcretizePreferencesTestmethod), 359

test_preorder_edge_traversal()(spack.test.spec_dag.SpecDagTest method),371

test_preorder_node_traversal()(spack.test.spec_dag.SpecDagTest method),371

test_preorder_path_traversal()(spack.test.spec_dag.SpecDagTest method),371

test_prerequisites() (spack.test.modules.TclTestsmethod), 367

test_providers_for_simple()(spack.test.provider_index.ProviderIndexTestmethod), 369

test_pypy_version() (spack.test.url_parse.UrlParseTestmethod), 376

478 Index

Spack Documentation, Release 0.9

test_python() (spack.test.build_system_guess.InstallTestmethod), 357

test_query_arguments() (spack.test.cmd.find.FindTestmethod), 355

test_R() (spack.test.build_system_guess.InstallTestmethod), 357

test_ranges_overlap() (spack.test.versions.VersionsTestmethod), 378

test_rc_style() (spack.test.url_parse.UrlParseTestmethod), 376

test_rc_versions() (spack.test.versions.VersionsTestmethod), 378

test_read_and_write_spec()(spack.test.directory_layout.DirectoryLayoutTestmethod), 361

test_read_lock_timeout_on_write()(spack.test.lock.LockTest method), 364

test_read_lock_timeout_on_write_2()(spack.test.lock.LockTest method), 364

test_read_lock_timeout_on_write_3()(spack.test.lock.LockTest method), 364

test_remove() (spack.test.file_cache.FileCacheTestmethod), 362

test_repr_and_str() (spack.test.versions.VersionsTestmethod), 378

test_restage() (spack.test.stage.StageTest method), 374test_rpm_oddities() (spack.test.versions.VersionsTest

method), 378test_ruby_version_style()

(spack.test.url_parse.UrlParseTest method),377

test_satisfaction_with_lists()(spack.test.versions.VersionsTest method),378

test_satisfies() (spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_satisfies_architecture()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_satisfies_compiler() (spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_satisfies_compiler_version()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_satisfies_dependencies()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_satisfies_dependency_versions()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_satisfies_matching_compiler_flag()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_satisfies_matching_variant()(spack.test.spec_semantics.SpecSematicsTestmethod), 371

test_satisfies_namespace()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_satisfies_namespaced_dep()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_satisfies_unconstrained_compiler_flag()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_satisfies_unconstrained_variant()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_satisfies_virtual() (spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_satisfies_virtual_dep_with_virtual_constraint()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_satisfies_virtual_dependencies()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_satisfies_virtual_dependency_versions()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_scalasca_partial_version()(spack.test.url_extrapolate.UrlExtrapolateTestmethod), 375

test_scalasca_version() (spack.test.url_parse.UrlParseTestmethod), 377

test_scons() (spack.test.build_system_guess.InstallTestmethod), 357

test_self_index() (spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_set() (spack.test.environment.EnvironmentTestmethod), 361

test_set_path() (spack.test.environment.EnvironmentTestmethod), 361

test_setup_and_destroy_name_with_tmp()(spack.test.stage.StageTest method), 374

test_setup_and_destroy_name_without_tmp()(spack.test.stage.StageTest method), 374

test_setup_and_destroy_no_name_with_tmp()(spack.test.stage.StageTest method), 374

test_setup_and_destroy_no_name_without_tmp()(spack.test.stage.StageTest method), 374

test_shebang_handles_non_writable_files()(spack.test.sbang.SbangTest method), 370

test_shebang_handling() (spack.test.sbang.SbangTestmethod), 370

test_simple_case() (spack.test.modules.TclTests method),367

Index 479

Spack Documentation, Release 0.9

test_simple_dependence()(spack.test.spec_syntax.SpecSyntaxTestmethod), 373

test_simple_spec() (spack.test.spec_yaml.SpecYamlTestmethod), 373

test_source_files() (spack.test.environment.EnvironmentTestmethod), 361

test_spaces_between_dependences()(spack.test.spec_syntax.SpecSyntaxTestmethod), 373

test_spaces_between_options()(spack.test.spec_syntax.SpecSyntaxTestmethod), 373

test_spec_contains_deps()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_sphinx_beta_style() (spack.test.url_parse.UrlParseTestmethod), 377

test_stable_suffix() (spack.test.url_parse.UrlParseTestmethod), 377

test_suffixes() (spack.test.modules.TclTests method), 367test_suite3270_version() (spack.test.url_parse.UrlParseTest

method), 377test_svn_mirror() (spack.test.mirror.MirrorTest method),

365test_synergy_version() (spack.test.url_parse.UrlParseTest

method), 377test_target_match() (spack.test.multimethod.MultiMethodTest

method), 367test_three_segments() (spack.test.versions.VersionsTest

method), 378test_transaction() (spack.test.lock.LockTest method), 364test_transaction_with_context_manager()

(spack.test.lock.LockTest method), 364test_transaction_with_context_manager_and_exception()

(spack.test.lock.LockTest method), 364test_transaction_with_exception()

(spack.test.lock.LockTest method), 364test_transitive_chain() (spack.test.optional_deps.ConcretizeTest

method), 368test_two_segments() (spack.test.versions.VersionsTest

method), 378test_undefined_mpi_version()

(spack.test.multimethod.MultiMethodTestmethod), 367

test_underscores() (spack.test.versions.VersionsTestmethod), 379

test_uninstall() (spack.test.cmd.uninstall.TestUninstallmethod), 356

test_union_with_containment()(spack.test.versions.VersionsTest method),379

test_unknown() (spack.test.build_system_guess.InstallTestmethod), 357

test_unsatisfiable_architecture()(spack.test.spec_dag.SpecDagTest method),371

test_unsatisfiable_compiler()(spack.test.spec_dag.SpecDagTest method),371

test_unsatisfiable_compiler_flag()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_unsatisfiable_compiler_flag_mismatch()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_unsatisfiable_compiler_version()(spack.test.spec_dag.SpecDagTest method),371

test_unsatisfiable_variant_mismatch()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_unsatisfiable_variants()(spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_unsatisfiable_version()(spack.test.spec_dag.SpecDagTest method),371

test_unset() (spack.test.environment.EnvironmentTestmethod), 361

test_update_dictionary_extending_list()(spack.test.modules.HelperFunctionsTestsmethod), 366

test_url_mirror() (spack.test.mirror.MirrorTest method),365

test_url_versions() (spack.test.package_sanity.PackageSanityTestmethod), 368

test_user_back_end_input()(spack.test.architecture.ArchitectureTestmethod), 357

test_user_defaults() (spack.test.architecture.ArchitectureTestmethod), 357

test_user_front_end_input()(spack.test.architecture.ArchitectureTestmethod), 357

test_user_input_combination()(spack.test.architecture.ArchitectureTestmethod), 357

test_vcheck_mode() (spack.test.cc.CompilerTestmethod), 358

test_version_all_dots() (spack.test.url_parse.UrlParseTestmethod), 377

test_version_developer_that_hates_us_format()(spack.test.url_parse.UrlParseTest method),377

test_version_dos2unix() (spack.test.url_parse.UrlParseTestmethod), 377

480 Index

Spack Documentation, Release 0.9

test_version_github() (spack.test.url_parse.UrlParseTestmethod), 377

test_version_github_with_high_patch_number()(spack.test.url_parse.UrlParseTest method),377

test_version_internal_dash()(spack.test.url_parse.UrlParseTest method),377

test_version_overlap() (spack.test.multimethod.MultiMethodTestmethod), 367

test_version_range_satisfaction()(spack.test.versions.VersionsTest method),379

test_version_range_satisfaction_in_lists()(spack.test.versions.VersionsTest method),379

test_version_ranges() (spack.test.versions.VersionsTestmethod), 379

test_version_regular() (spack.test.url_parse.UrlParseTestmethod), 377

test_version_single_digit()(spack.test.url_parse.UrlParseTest method),377

test_version_sourceforge_download()(spack.test.url_parse.UrlParseTest method),377

test_version_underscore_separator()(spack.test.url_parse.UrlParseTest method),377

test_virtual_dep_match()(spack.test.multimethod.MultiMethodTestmethod), 367

test_virtual_index() (spack.test.spec_semantics.SpecSematicsTestmethod), 372

test_virtual_is_fully_expanded_for_callpath()(spack.test.concretize.ConcretizeTest method),359

test_virtual_is_fully_expanded_for_mpileaks()(spack.test.concretize.ConcretizeTest method),359

test_way_too_many_spaces()(spack.test.spec_syntax.SpecSyntaxTestmethod), 373

test_write_and_read_cache_file()(spack.test.file_cache.FileCacheTest method),362

test_write_and_write_cache_file()(spack.test.file_cache.FileCacheTest method),362

test_write_key_in_memory()(spack.test.config.ConfigTest method), 360

test_write_key_to_disk() (spack.test.config.ConfigTestmethod), 360

test_write_list_in_memory()(spack.test.config.ConfigTest method), 360

test_write_lock_timeout_on_read()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_on_read_2()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_on_read_3()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_on_write()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_on_write_2()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_on_write_3()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_with_multiple_readers_2_1()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_with_multiple_readers_2_2()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_with_multiple_readers_3_1()(spack.test.lock.LockTest method), 364

test_write_lock_timeout_with_multiple_readers_3_2()(spack.test.lock.LockTest method), 364

test_write_to_same_priority_file()(spack.test.config.ConfigTest method), 360

test_wwwoffle_version() (spack.test.url_parse.UrlParseTestmethod), 377

test_xaw3d_version() (spack.test.url_parse.UrlParseTestmethod), 377

test_yaml_round_trip() (spack.test.provider_index.ProviderIndexTestmethod), 369

test_yaml_subdag() (spack.test.spec_yaml.SpecYamlTestmethod), 373

test_yet_another_erlang_version_style()(spack.test.url_parse.UrlParseTest method),377

test_yet_another_version()(spack.test.url_parse.UrlParseTest method),377

TestCase (class in spack.cmd.test_install), 342TestInstallTest (class in spack.test.cmd.test_install), 356TestModule (class in spack.test.cmd.module), 355TestResult (class in spack.cmd.test_install), 342TestSuite (class in spack.cmd.test_install), 342TestUninstall (class in spack.test.cmd.uninstall), 356timeout_read() (spack.test.lock.LockTest method), 364timeout_write() (spack.test.lock.LockTest method), 364to_dict() (spack.architecture.Arch method), 385to_dict() (spack.architecture.OperatingSystem method),

385to_dict() (spack.database.InstallRecord method), 394to_dict() (spack.spec.CompilerSpec method), 426to_dict() (spack.version.VersionList method), 439to_node_dict() (spack.spec.Spec method), 430

Index 481

Spack Documentation, Release 0.9

to_yaml() (spack.provider_index.ProviderIndex method),421

to_yaml() (spack.spec.Spec method), 430Token (class in spack.parse), 419token() (spack.parse.Lexer method), 419tokens (spack.modules.EnvModule attribute), 406topological_sort() (in module spack.graph), 405transform_path() (in module spack.cmd.view), 345transitive_inc_path() (spack.package.CMakePackage

method), 410traverse() (spack.spec.Spec method), 430traverse() (spack.test.cmd.test_install.MockSpec

method), 356traverse_with_deptype() (spack.spec.Spec method), 430tree() (spack.spec.Spec method), 431try_fetch() (spack.test.git_fetch.GitFetchTest method),

362try_fetch() (spack.test.hg_fetch.HgFetchTest method),

363try_fetch() (spack.test.svn_fetch.SvnFetchTest method),

374

UUnavailableCompilerVersionError, 389underscored (spack.version.Version attribute), 438UndetectableNameError, 436UndetectableVersionError, 436unexpected_token() (spack.parse.Parser method), 419uninstall() (in module spack.cmd.uninstall), 343union() (spack.version.Version method), 438union() (spack.version.VersionList method), 439union() (spack.version.VersionRange method), 439UnknownNamespaceError, 424UnknownPackageError, 424UnknownVariantError, 431unload() (in module spack.cmd.unload), 343UnsatisfiableArchitectureSpecError, 432UnsatisfiableCompilerFlagSpecError, 432UnsatisfiableCompilerSpecError, 432UnsatisfiableDependencySpecError, 432UnsatisfiableProviderSpecError, 432UnsatisfiableSpecError, 432UnsatisfiableSpecNameError, 432UnsatisfiableVariantSpecError, 432UnsatisfiableVersionSpecError, 432unset() (spack.environment.EnvironmentModifications

method), 398UnsetEnv (class in spack.environment), 399UnsupportedCompilerError, 432UnsupportedPlatformError, 400unuse() (in module spack.cmd.unuse), 343up_to() (spack.version.Version method), 438update() (spack.provider_index.ProviderIndex method),

421

update() (spack.version.VersionList method), 439update_args() (spack.environment.NameModifier

method), 398update_args() (spack.environment.NameValueModifier

method), 399update_config() (in module spack.config), 392update_packages() (spack.test.concretize_preferences.ConcretizePreferencesTest

method), 359upper_tokens (spack.modules.EnvModule attribute), 407url_for_version() (spack.package.Package method), 417url_parse() (in module spack.cmd.url_parse), 343url_version() (spack.package.Package method), 417UrlExtrapolateTest (class in spack.test.url_extrapolate),

375URLFetchStrategy (class in spack.fetch_strategy), 402UrlParseError, 436UrlParseTest (class in spack.test.url_parse), 375urls() (in module spack.cmd.urls), 344use() (in module spack.cmd.use), 344use_cray_compiler_names() (in module spack.package),

418use_name (spack.modules.EnvModule attribute), 407use_tmp() (in module spack.test.stage), 374

Vvalid_compiler_flags() (spack.spec.FlagMap static

method), 427valid_fully_qualified_module_name() (in module

spack.util.naming), 381valid_module_name() (in module spack.util.naming), 381validate() (in module spack.environment), 399validate_fully_qualified_module_name() (in module

spack.util.naming), 381validate_module_name() (in module spack.util.naming),

381validate_names() (spack.spec.Spec method), 431validate_package_url() (in module spack.package), 418validate_scope() (in module spack.config), 392validate_section() (in module spack.config), 392validate_section_name() (in module spack.config), 392Variant (class in spack.variant), 437variant() (in module spack.directives), 395variant() (spack.spec.SpecParser method), 431variant_compare() (spack.preferred_packages.PreferredPackages

method), 420VariantMap (class in spack.spec), 432VariantSpec (class in spack.spec), 433VCSFetchStrategy (class in spack.fetch_strategy), 403ver() (in module spack.version), 439Version (class in spack.version), 438version (spack.compiler.Compiler attribute), 388version (spack.package.Package attribute), 417version (spack.spec.CompilerSpec attribute), 426version (spack.spec.Spec attribute), 431

482 Index

Spack Documentation, Release 0.9

version() (in module spack.directives), 394version() (spack.spec.SpecParser method), 431version_compare() (spack.preferred_packages.PreferredPackages

method), 420version_list() (spack.spec.SpecParser method), 431version_urls (spack.package.Package attribute), 417VersionFetchError, 418VersionList (class in spack.version), 439VersionRange (class in spack.version), 438versions() (in module spack.cmd.versions), 344VersionsTest (class in spack.test.versions), 377view() (in module spack.cmd.view), 345virtual (spack.spec.Spec attribute), 431virtual_dependencies() (spack.spec.Spec method), 431visitor_add() (in module spack.cmd.view), 345visitor_check() (in module spack.cmd.view), 345visitor_hard() (in module spack.cmd.view), 345visitor_hardlink() (in module spack.cmd.view), 345visitor_remove() (in module spack.cmd.view), 345visitor_rm() (in module spack.cmd.view), 345visitor_soft() (in module spack.cmd.view), 345visitor_statlink() (in module spack.cmd.view), 345visitor_status() (in module spack.cmd.view), 345visitor_symlink() (in module spack.cmd.view), 345

Wwait() (spack.util.multiproc.Barrier method), 381when (class in spack.multimethod), 408which() (in module spack.util.executable), 381wildcard() (spack.version.Version method), 438wildcard_version() (in module spack.url), 437write() (spack.graph.AsciiGraph method), 405write() (spack.modules.EnvModule method), 407write_license_file() (in module spack.hooks.licensing),

351write_section() (spack.config.ConfigScope method), 391write_spec() (spack.directory_layout.YamlDirectoryLayout

method), 397write_transaction() (spack.database.Database method),

393write_transaction() (spack.file_cache.FileCache method),

404

XXl (class in spack.compilers.xl), 349

YYamlDirectoryLayout (class in spack.directory_layout),

396YamlTest (class in spack.test.yaml), 379

Index 483