free & open source software for engineers and...

Faculty of Mechanical EngineeringEngineering Computing Panel

Free & Open Source Software

for

Engineers and Scientists

January 2014

(noone�dev.null) FOSS for Engineers and Scientists January 2014 1 / 48

Overview

Definitions

Free Software

Open Source Software

Tools

CAD/DGraphics

Data AnalysisStatisticsCAE–CFD & CSM

SDK

Challenges

ShortfallsQuotes

Uber-FOSS: Linux

DistrosServices and Apps for Linux

ServersApps for Linux WorkstationsRemote Computing


DefinitionsFree Software

“Free software” is a matter of liberty, not price. To understand the concept,you should think of “free” as in “free speech,” not as in “free lunch.”

Free software is a matter of the users’ freedom to run, copy, distribute,study, change and improve the software.

More precisely, “free software” means that the program’s users have thefour essential freedoms:

Freedom 0: The freedom to run the program, for any purpose.Freedom 1: The freedom to study how the program works, and change it tomake it do what you wish. Access to the source code is a precondition for

this.Freedom 2: The freedom to redistribute copies so you can help yourneighbor.

Freedom 3: The freedom to improve the program, and release yourimprovements (and modified versions in general) to the public, so that thewhole community benefits. Access to the source code is a precondition for

this.


DefinitionsFree & Open Source Software

Open source is an approach tothe design, development, anddistribution of software,offering practical accessibility toa software’s source code.

Free and Open Source Software(FOSS) is software which isliberally licensed to grant theright of users to study, change,and improve its design throughthe availability of its sourcecode.

Guarded, but not trademarked,by the Open Source Initiativehttp://www.opensour e.org/ Figure 1: Free & Open Source Software.


ToolsComputer Aided Design/Drafting

QCAD is a free, open sourceapplication for computer aideddrafting (CAD) in twodimensions (2D). With QCADyou can create technicaldrawings such as plans forbuildings, interiors, mechanicalparts or schematics anddiagrams. QCAD works onWindows, Mac OS X and Linux.The source code of QCAD isreleased under the GPL version3 (GPLv3), a popular OpenSource license.http://www.q ad.org/en/ Figure 2: QCAD.



FreeCAD is a parametric 3Dmodeler. Parametric modelingallows you to easily modify yourdesign by going back into yourmodel history and changing itsparameters. FreeCAD is opensource (LGPL license) andcompletely modular, allowingfor very advanced extension andcustomization.

FreeCAD is multiplatfom, andreads and writes many open fileformats such as STEP, IGES, STLand others.http://www.free adweb.org/ Figure 3: FreeCAD.



BRL-CAD is a powerfulcross-platform open source solidmodeling system that includesinteractive geometry editing,high-performance ray-tracingfor rendering and geometricanalysis, image andsignal-processing tools, a systemperformance analysisbenchmark suite, libraries forrobust geometricrepresentation, with more than20 years of active development.http://brl ad.org/

Figure 4: BRL-CAD.


ToolsGraphics

Blender is the free open source3D content creation suite,available for all major operatingsystems under the GNU GeneralPublic License. It models,shades, animates, renders, doescomposite interactive 3Dgraphics.

http://www.blender.org/ Figure 5: Blender.


ToolsGraphics

Inkscape is an Open Sourcevector graphics editor, withcapabilities similar to Illustrator,CorelDraw, or Xara X, using theW3C standard Scalable VectorGraphics (SVG) file format.

http://www.inks ape.org/ Figure 6: Inkscape.


ToolsGraphics

GIMP is the GNU ImageManipulation Program. It is afreely distributed piece ofsoftware for such tasks as photoretouching, image compositionand image authoring. It workson many operating systems, inmany languages.

http://www.gimp.org/Figure 7: GIMP.


ToolsData Analysis

g3data is used for extractingdata from graphs. Inpublications graphs often areincluded, but the actual data ismissing. g3data makes theextracting process much easier.

http://www.frantz.fi/software/g3data.php Figure 8: g3data.


ToolsData Analysis

GNUplot is a portablecommand-line driven interactivedata and function plottingutility for UNIX, IBM OS/2, MSWindows, DOS, Macintosh,VMS, Atari and many otherplatforms.

It supports many types of plotsin either 2D and 3D. It can drawusing lines, points, boxes,contours, vector fields, surfaces,and various associated text. Italso supports variousspecialized plot types.http://www.gnuplot.info/ Figure 9: GNUplot.


ToolsData Analysis

LabPlot is an open source dataanalysis and visualisationprogram, written for KDE. It issimilar to Origin and is able toimport Origin’s data files.

http://labplot.sour eforge.net/ Figure 10: LabPlot.


ToolsData Analysis

GRACE, for GRaphing,Advanced Computation andExploration of data, is a freeWYSIWYG 2D graph plottingtool, for Unix-like operatingsystems.

http://plasma-gate.weizmann.a .il/Gra e/ Figure 11: GRACE.


ToolsData Analysis

MRIcroGL is a programdesigned to display 3D medicalimaging. By using yourcomputer’s graphics card, it canallow real-time interactiverendering.

http://www.m ausland enter.s .edu/CRNL/tools Figure 12: MRIcroGL.


ToolsData Analysis

MRIcronx is a medical imagevisualization and analysispackage. It provides tools fordrawing volumes of interest andvolume rendering.

In addition, it includesnon-parametric statisticalmapping (npm) and conversionof images from DICOM formatto NIfTI format (dcm2nii).

http://www.m ausland enter.s .edu/CRNL/tools Figure 13: MRIcronx.


ToolsData Analysis

GNU Octave is a high-levellanguage, primarily intended fornumerical computations.

It provides a convenientcommand line interface forsolving linear and nonlinearproblems numerically, and forperforming other numericalexperiments using a languagethat is mostly compatible withMatlab. It may also be used as abatch-oriented language.http://www.gnu.org/software/o tave/ Figure 14: GNU Octave.


ToolsData Analysis

Scilab is a scientific softwarepackage for numericalcomputations providing apowerful open computingenvironment for engineeringand scientific applications.

It’s almost similar to Matlab, butnot quite!

http://www.s ilab.org/ Figure 15: Scilab.


ToolsData Analysis

Maxima is system for themanipulation of symbolic andnumerical expressions,including differentiation,integration, Taylor series,Laplace transforms, ordinarydifferential equations, systemsof linear equations,polynomials, and sets, lists,vectors, matrices, and tensors.

http://maxima.sour eforge.net/ Figure 16: Maxima.


ToolsStatistics

R is a programming languageand software environment forstatistical computing andgraphics.

It is an implementation of the Sprogramming language withlexical scoping semanticsinspired by Scheme.

http://www.r-proje t.org/ Figure 17: R.


ToolsStatistics

RStudio is a powerful andproductive IntegratedDevelopment Environment(IDE) for R. It’s free and opensource, and works great onWindows, Mac, and Linux.

http://www.rstudio. om/ Figure 18: RStudio.


ToolsCAE–CFD & CSM

Code_Aster is an Open Sourcesoftware package for Civil andStructural Engineering finiteelement analysis and numericsimulation in structuralmechanics originally developedas an in-house application bythe French company EDF.

It was released as free softwareunder the terms of the GNUGeneral Public License, inOctober 2001.http://www. ode-aster.org/V2/spip.php?rubrique2 Figure 19: Code_Aster.



Code_Saturne solves theNavier-Stokes equations for 2D,2D-axisymmetric and 3D flows,steady or unsteady, laminar orturbulent, incompressible orweakly dilatable, isothermal ornot, with scalars transport ifrequired. Several turbulencemodels are available, fromReynolds-Averaged models(a.k.a. RANS models) toLarge-Eddy Simulation models.

It was released under the termsof the GNU General PublicLicense in 2001.http://www. ode-saturne.org/ Figure 20: Code_Saturne GUI.



Salome provides a genericplatform for Pre- andPost-Processing for numericalsimulation. It is based on anopen and flexible architecturemade of reusable components.Numerical simulation solverslike Code_Aster andCode_Saturne can be easilyintegrated into this platform.

http://www.salome-platform.org/ Figure 21: Salome.



Elmer is an open sourcemultiphysical simulationsoftware developed by CSC.Elmer development was started1995 in collaboration withFinnish Universities, researchinstitutes and industry.

Elmer includes physical modelsof fluid dynamics, structuralmechanics, electromagnetics,heat transfer and acoustics, forexample. These are describedby partial differential equationswhich Elmer solves by the finiteelement method.http://www. s .fi/english/pages/elmer Figure 22: Elmer.



Z88Aurora is a free finiteelement software package forstatic calculation in MechanicalEngineering. Beside linear staticanalysis you can use it for largedisplacement analysis, stadystate thermal analysis andnatural frequency analysis.

Z88Aurora is made up of threecomponents:

FE-Preprocessor,FE-Solver and

FE-Postprocessor.http://www.z88.uni-bayreuth.de/z88aurora/wasistz88_e.htmFigure 23: Z88 Aurora.



Dolfyn is an open source CFDcode initiative originated inNoord-Brabant, theNetherlands. The goal of dolfynis to promote, introduce andteach the use of modernnumerical simulation techniquesin general and the use of CFD inparticular.

http://www.dolfyn.net/ Figure 24: Dolfyn.



OpenFOAM (Open FieldOperation And Manipulation)is a C++ toolbox for thecustomisation and extension ofnumerical solvers for continuummechanics problems, includingCFD. Standard Solvers include:basic CFD, incompressible flows,compressible flows, multiphaseflows, particle-tracking flows,combustion, heat transfer,molecular dynamics, directsimulation Monte Carlo,electro-magnetics, soliddynamics, etc.http://www.openfoam. om/ Figure 25: OpenFOAM.



OpenFVM was developed tosimulate the flow in complex 3Dgeometries using the finitevolume method. Its mesh can beunstructured and containcontrol volumes with arbitraryshape. The code has twoimplementations:

serial (using LASpack), and

parallel (using PETSc).

Both implementations use theopen source tool gmsh for pre-and post-processing.http://openfvm.sour eforge.net/ Figure 26: OpenFVM.



gmsh is an automatic 3D finiteelement grid generator with abuilt-in CAD engine andpost-processor. gmsh is builtaround four modules:

geometry,

mesh,solver andpost-processing.

The specification of any input tothese modules is done eitherinteractively using GUI or inASCII text files using gmsh’sown scripting language.http://www.geuz.org/gmsh/ Figure 27: Gmsh.



Netgen is a multi-platformautomatic mesh generation toolwritten in C++ capable ofgenerating meshes in 2- and3-D. It generates triangular orquadrilateral meshes in 2D, andtetrahedral meshes in 3D. Theinput for 2D is described byspline curves, and the input for3D problems can be defined byConstructive Solid Geometry(CSG), the standard STL fileformat, or BRep/IGES/STEPwhen compiled withOpenCascade support.http://sour eforge.net/apps/mediawiki/netgen-mesher/index.php?title=Main_PageFigure 28: Netgen.



enGrid is a mesh generationsoftware with CFD applicationsin mind. It supports automaticprismatic boundary layer gridsfor CFD simulations and has aQt-based GUI. enGrid uses theNetgen library for tetrahedralgrid generation and an in-housedevelopment for prismaticboundary layer grids. Internally,enGrid uses the VTK datastructures as well as the .vtu fileformat. To create grids forOpenFOAM, the gmsh formatcan be used.http://sour eforge.net/proje ts/engrid

Figure 29: enGrid.



ParaView is an open-source,multi-platform data analysisand visualization application.ParaView users can quicklybuild visualizations to analyzetheir data using qualitative andquantitative techniques.

The data exploration can bedone interactively in 3D orprogrammatically usingParaView’s batch processingcapabilities.http://www.paraview.org/

Figure 30: ParaView.



VisIt is a free interactive parallelvisualization and graphicalanalysis tool for viewingscientific data. It can be used tovisualize scalar and vector fieldsdefined on 2- and 3-Dstructured and unstructuredmeshes.

VisIt was designed to handlevery large data set sizes in theterascale range and yet can alsohandle small data sets in thekilobyte range.https://w i.llnl.gov/ odes/visit/ Figure 31: VisIt.


ToolsSoftware Development Kits

GNU Compilers Collection(GCC) includes front ends for C,C++, Objective-C, Fortran,Java, and Ada, as well aslibraries for these languages(libstdc++, libgcj, . . . ).

GCC was originally written asthe compiler for the GNUoperating system. The GNUsystem was developed to be100% free software, free in thesense that it respects the user’sfreedom.http://g .gnu.org/http://en.wikipedia.org/wiki/GNU_Compiler_Colle tion



Cygwin is a Linux-likeenvironment for Windows. Itconsists of two parts:

a DLL ( ygwin1.dll) whichacts as a Linux API emulationlayer providing substantial

Linux API functionality, anda collection of tools whichprovide Linux look and feel.

http://www. ygwin. om/http://www.redhat. om/servi es/ ustom/ ygwin/Figure 32: Cygwin on Windows.



Cygwin/X is a port of the XWindow System to theMicrosoft Windows family ofoperating systems. It consists ofan X Server, X libraries, andnearly all of the standard Xclients, such as xterm, xhost,xdpyinfo, xclock, and xeyes.Cygwin/X, as the name implies,uses the Cygwin project whichprovides a UNIX-like API to Xliband X clients, thus minimizingthe amount of porting required.http://x. ygwin. om/

Figure 33: Cygwin/X on Windows.


ToolsSoftware Development Kits: Libraries

If you are developing software, these are some of the major repositories ofhighly efficient codes you might want to pay a visit:

StatLib is a system for distributing statistical software, datasets, andinformation by electronic mail, FTP and WWW.Visit http://lib.stat. mu.edu/.

TOMS (Transactions on Mathematical Software) is part of the family ofjournals produced by the Association for Computing Machinery (ACM). Italso publishes machine-readable computer software which is incorporatedinto the Collected Algorithms of the ACM.Visit http://toms.a m.org/.

GAMS (General Algebraic Modeling System) is a high-level modelingsystem for mathematical programming and optimization. It is tailored forcomplex, large scale modeling applications, and allows you to build largemaintainable models that can be adapted quickly to new situations.Visit http://www.gams. om/.



Netlib is a collection of mathematical software, papers, and databases.Visit http://www.netlib.org.

PETSc PETSc, pronounced PET-see (the S is silent), is a suite of datastructures and routines for the scalable (parallel) solution of scientificapplications modeled by partial differential equations. It employs the MPIstandard for parallelism.Visit http://www.m s.anl.gov/pets /pets -as/.

SciPy & NumPy: SciPy is open-source software for mathematics, science,and engineering. The SciPy library depends on NumPy, which providesconvenient and fast N-dimensional array manipulation.Visit http://www.s ipy.org/.

Dislin: A high-level plotting library for displaying data as curves, polarplots, bar graphs, pie charts, 3D-color plots, surfaces, contours and maps.Visit http://www.mps.mpg.de/dislin/.



PLplot A cross-platform software package for creating scientific plots. Tohelp accomplish that task it is organized as a core C library, languagebindings for that library, and device drivers which control how the plotsare presented in non-interactive and interactive plotting contexts.Visit http://plplot.sour eforge.net/.

VTK (Visualization ToolKit): is an open-source, freely available softwaresystem for 3D computer graphics, image processing and visualization.VTK consists of a C++ class library and several interpreted interfacelayers including Tcl/Tk, Java, and Python.Visit http://www.vtk.org/.


ChallengesShortfalls of FOSS

Where do I get started?

Time consuming

More difficult to use

Limited or no support

Commercial codes have broader range of models for industrialapplications


ChallengesQuotes from FOSS USers

“The best part of using FOSS is there are lot of freeware in FOSS,

and if you have an inhouse FOSS developer or tweaker, it works out

cheaper than Licensing.”

“We use Blender. It’s a powerful 3D modeling/rendering app. We

use it in many of the corporate videos we produce. The best part

about this kind of software is that there are thousands of people

working on tools for it. Every time we turn around someone else

has developed some kind of plug in or something that helps thingsmove along. When it comes down to it OSS is really what the

internet is about. Communities working to make things faster and

better.”


ChallengesQuotes from FOSS USers

“FOSS is highly integrable to lots of licensed software and devices

too.”

“For those of us that directly use OSS, the advantages of using it

have to be weighed against the costs of using it. If you have thetechnical expertise in house to support a project, the cost savings

can be significant. If you don’t have that in house talent, the cost of

ownership can approach or exceed commercially supported systems.

In my opinion, convincing people that Open Source is not free can

be difficult. In the end, you have to weigh all the options and pick

the best solution. Sometimes it is going to be Open Source

Software, sometimes it is going to be commercial off-the-shelf

software. The real trick is knowing the difference.”


Linux: The Uber-FOSSDistros

When Linus Torvalds first developed Linux back in August of 1991, theoperating system basically consisted of his kernel and some GNU tools.With the help of others Linus added more and more tools andapplications.

With time, individuals, university students and companies begandistributing Linux with their own choice of packages bound around Linus’kernel. This is where the concept of the distribution, or distro, was born.Sample distros include

RedHat, CentOS, Scientific Linux, Mandriva, SuSe: (rpm, Unix Sys V)Debian, Ubuntu/Kubuntu, CAELinux: (deb, Unix Sys V)Slackware: (tgz, BSD)

Go visit http://distrowat h. om/ for all the distros available out there!!

Check out the various distros available at our local repository athttp://ossm.utm.my/(noone�dev.null) FOSS for Engineers and Scientists January 2014 44 / 48

Linux: The Uber-FOSSCommon Services running on Linux Servers

Linux running on servers are capable of offering these services:

Mail Service: sendmail, postfix

File Service: NFS, SambaDNS Service: BINDFTP Service: vsftp, ProFTPWWW Service: Apache

Database Service: MariaDB, PostgreSQLCaching Proxy Server: Squid, Squidguard, DansguardianFirewall: NetFilter/iptables

NIDS: Snort, Snortsam, Ethereal, Etherape, Nessus, Arpwatch, EttercapLAMP Server: Linux+Apache+MariaDB+PHP


Linux: The Uber-FOSSCommon Apps running on Linux Workstations

For desktop/laptop workstations, most Linux distros readily come (oreasily installable) with the following applications:

Office Suite: LibreOffice, ScribusSoftware Development Kits: GNU Compilers, GSL, Lapack, BLASMultimedia Tools: K3B, MPlayer, VLC, Audacious, XMMSInternet Tools: Firefox, Opera, Konqueror, Thunderbird, Kmail, IRC

Graphics Tools: Blender, GIMP, ImageMagickCAE Tools: OpenFOAM, Code_Aster, Code_Saturne, Gerris, z88 Aurora,GNUplot, FreeCAD, gmsh, Netgen, Octave, Scilab, Maxima, Paraview, VisIt,

DolfynUtilities: Ghostscript, Evince, Calibre, GSview, GV, PDFCreator


Linux: The Uber-FOSSRemote Computing

Linux Apps Server: Serves useraccounts, SSH, VNC services forremote access; CAE applicationslike Code_Aster, Code_Saturne,Salome, OpenFOAM from FOSScollection and commercial oneslike Ansys, Abaqus, Comsol,Matlab etc.

Linux Workstation: Needsclient apps to acces Linux AppsServer: SSH client, VNC viewerand/or nx client.

Windows 7 Workstation:Needs client apps to acces LinuxApps Server: PuTTY, VNCviewer and/or nx client.

Figure 34: Remote computing concept.


Thank you

. . . and may the FOSS be with you.


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