getting started on emerald
DESCRIPTION
Getting Started on Emerald. Research Computing Group. Course Outline. What is Emerald? Logging into Emerald File manipulation on Emerald Submitting jobs on Emerald Interactive programs on Emerald. Help Documentation. Getting Started on Emerald http://help.unc.edu/6020 - PowerPoint PPT PresentationTRANSCRIPT
Getting Started on Emerald
Getting Started on Emerald
Research Computing Group
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What is Emerald?
Logging into Emerald
File manipulation on Emerald
Submitting jobs on Emerald
Interactive programs on Emerald
Course OutlineCourse Outline
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Help DocumentationHelp Documentation
Getting Started on Emerald•http://help.unc.edu/6020
•General overview of Emerald for range of users
Short Course – Getting Started on Emerald•http://help.unc.edu/6479
•Detailed notes for beginning Emerald users
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What is Emerald?What is Emerald?
352-processor Linux Cluster•Maintained by Research Computing Group
Appropriate for all users regardless of expertise level
Other Servers:•Cedar/Cypress (128-processor SGI/Altix)
•Topsail (4160-processor Dell Linux Cluster)
Mass Storage•Account access
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Advantages of Using Emerald
Advantages of Using Emerald
High performance
Large capacity
Parallel processing
Many available software packages
Variety of compiling options
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Emerald Linux ClusterEmerald Linux Cluster
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Distributed vs. Shared MemoryDistributed vs.
Shared Memory
Shared memory - single address space. All processors have access to a pool of shared memory. (examples: Yatta, Cedar/Cypress) Methods of memory access : Bus and Crossbar
Distributed memory - each processorhas it’s own local memory. Must do message passing to exchange data between processors. (examples: Emerald, Topsail)
MEMORY
BUS
CPU CPU CPU CPUCPU CPU CPU CPU
MMMM
NETWORK
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Logging Into EmeraldLogging Into Emerald
UNIX/Linux/OSX
•ssh [email protected]
Windows: SSH Secure Shell
•Setting up a Profile for Emerald
•Forwarding X11 packets
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Home and Work Directories on
Emerald
Home and Work Directories on
Emerald Home Directory
• /afs/isis/home/m/y/my_onyen/•250MB quota•~/private/•Files backed up daily [ ~/OldFiles ]•Space quota/usage in Home Directory:
fs lq
Work Directory• /netscr/my_onyen/•No space limit but periodically cleaned
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File Manipulation Commands
File Manipulation Commands
SSH Secure File Transfer Copy files
• cp command
cp /afs/isis/depts/atn/rcg/example_code/Gaussian/water.com /netscr/my_onyen/.
cp /afs/isis/depts/atn/rcg/example_code/sas/test.sas /netscr/my_onyen/.
• cp -r cp -r ~/private/TestDirectory .
Move files• mv commands
mv ~/private/testfile.txt .
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File Manipulation Commands
File Manipulation Commands
Tar archive
•To create a tar filetar –cvzf TestDirectory.tgz ./
•To see a tar file’s table of contenttar –tvzf TestDirectory.tgz
•To untar a tar file tar –xvzf TestDirectory.tgz
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Submitting Jobs: LSF and Packages
Submitting Jobs: LSF and Packages
LSF (Load Sharing Facility)•Fairly distribute compute nodes among
users•60 processor per user limit
Packages• ipm commands
ipm add (ipm a) ipm remove (ipm r) ipm query (ipm q)
•Available packageshttp://www.renci.org/unc/computing/resources/
applications.php
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Details of LSFDetails of LSF
Submission host
LIM
Batch API
Master host
MLIM
MBD
Execution host
SBD
Child SBD
LIM
RES
User jobLIM – Load Information ManagerMLIM – Master LIMMBD – Master Batch DaemonSBD – Slave Batch DaemonRES – Remote Execution Server
queue1
2
3
45
6 7
89
10
11
12
13
Loadinformation
otherhosts
otherhosts
bsub app
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Submitting Jobs: bsub Command
Submitting Jobs: bsub Command
bsub command All files must be in /netscr/my_onyen/ bsub [- bsub_opts] executable [-exec_opts]
Queues – bqueues command
•week
•idle
bsub –o
•bsub –o out.%J
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Submitting Jobs: Following Job
Progress
Submitting Jobs: Following Job
Progress bjobs
•bjobs –l JobID
•Shows current status of job
bhist•bhist –l JobID
bkill•bkill JobID
•Ends job prematurely
bfree
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Submitting Jobs: Specialty ScriptsSubmitting Jobs: Specialty Scripts
bsas•bsub -q week -R blade sas program.sas
•bsas test.sas
bmatlab•bsub -q week -R blade matlab -nodisplay
-nojvm -nosplash program.m -logfile program.log
•bmatlab test.m
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Compiling on EmeraldCompiling on Emerald
• Compilers
– FORTRAN 77/90/95
– C/C++
• Parallel Computing – OpenMP
– MPI (MPICH, LAM/MPI, MPICH-GM)
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Compiling Details on Emerald
Compiling Details on Emerald
Compiler Package name Command
Intel intel_fortran, intel_CC ifort, icc
Portland Group pgi pgf77, pgf90,pgcc,pgCC
Absoft profortran f77, f90
GNU gcc g77,gcc, g++
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Compiling Details on Emerald
Compiling Details on Emerald
Add a compiler into your working environment
•ipm add package_name
Compile a code
•command code.f –o executable
Run executable on a compute node using the bsub command
•bsub –q week –R blade executable
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Submitting Jobs: Job Output
Submitting Jobs: Job Output
Output sent to email
bsub –o
•Output saved in working directory
bsub –u email@address
•Output sent to specified email address
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Interactive Jobs: Setup
Interactive Jobs: Setup
X-Windows
•Linux/OSXX11 client
•WindowsX-Win32
Offered on UNC Software Acquisition sitePort forwarding on SSH Secure Shell
Setting up a session on X-Win32
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Interactive Jobs: Submission
Interactive Jobs: Submission
–Ip
•bsub –q int –R blade –Ip sas
•bsub –q int –R blade –Ip gv
Specialty Scripts
•xsas
•xstata
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Contacting Research Computing
Contacting Research Computing
For assistance with Emerald, please contact the Research Computing Group:
•Email: [email protected]
•Phone: 919-962-HELP
•Submit help ticket at http://help.unc.edu