(→4cpu SMP Job) |
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==8cpu MPI Job== | ==8cpu MPI Job== | ||
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<pre>sqsub -r 1h -q mpi -o ofile.%J -n 8 --mpp=2G lsdyna_d i=airbag.deploy.k</pre> | <pre>sqsub -r 1h -q mpi -o ofile.%J -n 8 --mpp=2G lsdyna_d i=airbag.deploy.k</pre> | ||
| − | + | Optionally, though not currently recommended, one may specify memory setting(s) on the command line when submitting the job. Doing so is not beneficial on sharcnet since the queue reserves the same memory per core for all mpi processes. Therefore a decomposition processor cannot be allocated larger system memory. It would therefore be sufficient to only specify memory=464898 if there is some special reason to do so but none is known at this time: | |
<pre> | <pre> | ||
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</pre> | </pre> | ||
| − | where memory is the number of 8byte words allocated per processor in double precession found | + | where memory is the number of 8byte words allocated per processor in double precession found by running job interactively on a orca compute node(s) for example: <i>Memory required to begin solution (memory= 464898 memory2= 158794 )</i> |
| − | <i>Memory required to begin solution (memory= 464898 memory2= 158794 )</i> | + | |
=Example Job= | =Example Job= | ||
Revision as of 20:23, 9 September 2015
| LSDYNA |
|---|
| Description: Suite of programs for transient dynamic finite element program |
| SHARCNET Package information: see LSDYNA software page in web portal |
| Full list of SHARCNET supported software |
Contents
Introduction
Before a research group can use LSDYNA on sharcnet, a license must be purchased directly from LSTC for the sharcnet license server. Alternately, if a research group resides at a institution that has sharcnet computing hardware (mac, uwo, guelph, waterloo) it maybe possible to use a pre-existing site license hosted on an accessible institutional license server. To access and use this software you must open a ticket and request to be added to the sharcnet lsdyna group.
Version Selection
License
Once a license configuration is established, the research group will be given a 5 digit port number. The value should then be inserted into the appropriate departmental export statement before loading the module file as follows:
o UofT Mechanical Engineering Dept
export LSTC_LICENSE_SERVER='Port-Number'@license1.uwo.sharcnet
o McGill Mechanical Engineering Department
export LSTC_LICENSE_SERVER='Port-Number'@license2.uwo.sharcnet
o UW Mechanical and Mechatronics Engineering Dept
export LSTC_LICENSE_SERVER='Port-Number'@license3.uwo.sharcnet
Module
The next step is to load the sharcnet lsdyna module for the version you want to use. First check which modules are available by running the module avail command then load one the modules as shown:
[roberpj@saw-login2:~] module avail lsdyna lsdyna/mpp/r611.79036 lsdyna/mpp/r611.80542 lsdyna/smp/r711.88920 lsdyna/mpp/r711.88920 lsdyna/hyb/r711.88920 lsdyna/ls980smpB1 lsdyna/ls980mppB1 lsdyna/ls980mppB2
r8.0.0 versions
o For serial or threaded jobs:
module load lsdyna/smp/r800.95359
o For mpi jobs:
module unload intel openmpi lsdyna module load intel/12.1.3 openmpi/intel/1.8.3 lsdyna/mpp/r800.95359
r7.1.1 versions
o For serial or threaded jobs:
module load lsdyna/smp/r711.88920
o For mpi jobs:
module load lsdyna/mpp/r711.88920
r6.1.1 versions
o For mpi jobs:
module unload intel openmpi lsdyna module load intel/11.1.069 openmpi/intel/1.6.4 lsdyna/mpp/r611.79036 or module load intel/11.1.069 openmpi/intel/1.6.4 lsdyna/mpp/r611.80542
where r611.80542 provides lsdyna_s only.
ls980 versions
o For serial or threaded jobs:
module load lsdyna/smp/ls980B1.78258
o For mpi jobs:
module unload intel openmpi lsdyna module load intel/12.1.3 openmpi/intel/1.4.5 lsdyna/mpp/ls980B1.011113 or module load intel/12.1.3 openmpi/intel/1.6.2 lsdyna/smp/ls980B1.78258
Note1) restart capability for ls980smpB1 and ls980mppB1 is not supported Note2) the module using legacy openmpi/intel/1.4.5 will run extremely slow
Job Submission
To run the single or double precision solvers specify lsdyna_s or lsdyna_d respectively in the following sqsub commands:
1cpu SERIAL Job
sqsub -r 1h -q serial -o ofile.%J --mpp=2G lsdyna_d i=airbag.deploy.k ncpu=1
4cpu SMP Job
sqsub -r 1h -q threaded -n 4 -o ofile.%J --mpp=1G lsdyna_s i=airbag.deploy.k ncpu=4
where memory is the number of 4 bytes words shared by all processors in single precision. Optionally, though not currently recommended, one may specify an initial memory setting on the command line when submitting the job as follows:
export LSTC_MEMORY=auto sqsub -r 1h -q threaded -n 4 -o ofile.%J --mpp=2G lsdyna_d i=airbag.deploy.k ncpu=4 memory=754414
where memory is the minimum number of 8 bytes words shared by all processors in double precision determined by running the simulation interactively on a orca development node to get the following output: Memory required to begin solution : 754414
8cpu MPI Job
sqsub -r 1h -q mpi -o ofile.%J -n 8 --mpp=2G lsdyna_d i=airbag.deploy.k
Optionally, though not currently recommended, one may specify memory setting(s) on the command line when submitting the job. Doing so is not beneficial on sharcnet since the queue reserves the same memory per core for all mpi processes. Therefore a decomposition processor cannot be allocated larger system memory. It would therefore be sufficient to only specify memory=464898 if there is some special reason to do so but none is known at this time:
export LSTC_MEMORY=AUTO sqsub -r 1h -q mpi -o ofile.%J -n 8 --mpp=2G lsdyna_d i=airbag.deploy.k memory=464898 memory2=158794
where memory is the number of 8byte words allocated per processor in double precession found by running job interactively on a orca compute node(s) for example: Memory required to begin solution (memory= 464898 memory2= 158794 )
Example Job
STEP1) The following shows sqsub submission of the airbag example to the mpi queue. Its recommended to first edit airbag.deploy.k and change endtim to 3.000E-00 so the job runs long enough to perform the restart in steps 2 and 3 below:
cp -a /opt/sharcnet/lsdyna/r611.79036/examples /work/$USER/test-lsdyna cd /work/$USER/test-lsdyna/misc/airbag gunzip airbag.deploy.k.gz cp airbag.deploy.k airbag.deploy.restart.k nano deploy.restart.k (reduce plot file creation frequency) *DATABASE_BINARY_D3PLOT $ dt lcdtdeploy.restart.k 1.000E-01 <--- change from 5.000E-04 export LSTC_LICENSE_SERVER=#####@license#.uwo.sharcnet module unload intel openmpi lsdyna module load intel/11.1.069 openmpi/intel/1.6.4 lsdyna/mpp/r611.79036 sqsub -r 10m -q mpi --mpp=2G -n 8 -o ofile.%J lsdyna_d i=airbag.deploy.k
STEP2) With the job still running, use the echo command as follows to create a file called "D3KIL" that will trigger generation of restart files at which point the file D3KIL itself will be erased. Do this once a day if data loss is critical to you OR once or twice just before the sqsub -r time limit is reached. Further information can be found here http://www.dynasupport.com/tutorial/ls-dyna-users-guide/sense-switch-control:
echo "sw3" > D3KIL sqkill job#
STEP3) Before the job can be restarted, the following two lines must be added to the airbag.deploy.restart.k file:
*CHANGE_CURVE_DEFINITION
1
STEP4) Now resubmit the job as follows using "r=" to specify the restart file:
sqsub -r 1h -q mpi --mpp=2G -n 8 -o ofile.%J lsdyna_d i=airbag.deploy.restart.k r=d3dump01
General Notes
Command Line Use
Parallel lsdyna jobs can be run interactively on the command line (outside the queue) for short run testing purposes as follows:
o Orca Development Node MPP (mpi) Example
ssh orca.sharcnet.ca ssh orc-dev1 (or dev2,3,4) module unload intel openmpi lsdyna module load intel/12.1.3 openmpi/intel/1.6.2 lsdyna/mpp/r711.88920 mpirun -np 8 lsdyna_d i=airbag.deploy.k
o Orca Development Node SMP (threaded) Example
ssh orca.sharcnet.ca ssh orc-dev1 (or dev2,3,4) module unload intel openmpi lsdyna module load lsdyna/smp/r711.88920 lsdyna_d i=airbag.deploy.k ncpu=8
Memory Issues
A minumum of mpp=2G is recommended although the memory requirement of a job may suggest much less is required. For instance setting mpp=1G for the airbag test job above will result in the following error when running a job in the queue:
-------------------------------------------------------------------------- An attempt to set processor affinity has failed - please check to ensure that your system supports such functionality. If so, then this is probably something that should be reported to the OMPI developers. --------------------------------------------------------------------------
To get an idea of the amount of memory a job used run grep on the output file:
[roberpj@orc-login1:~/samples/lsdyna/airbag] cat ofile.2063302.orc-admin2.orca.sharcnet | grep Memory
| Distributed Memory Parallel |
Memory size from command line: 500000, 500000
Memory for the head node
Memory installed (MB) : 32237
Memory free (MB) : 11259
Memory required (MB) : 0
Memory required to process keyword : 458120
Memory required for decomposition : 458120
Memory required to begin solution (memory= 458120 memory2= 230721)
Max. Memory reqd for implicit sol: max used 0
Max. Memory reqd for implicit sol: incore 0
Max. Memory reqd for implicit sol: oocore 0
Memory required to complete solution (memory= 458120 memory2= 230721)
Version and Revision
Again run grep on the output file to extract the major and minor revision:
[roberpj@orc-login1:~/samples/lsdyna/airbag] cat ofile.2063302.orc-admin2.orca.sharcnet | grep 'Revision\|Version'
| Version : mpp s R6.1.1 Date: 01/02/2013 |
| Revision: 78769 Time: 07:43:30 |
| SVN Version: 80542 |
Check License Status
To get a summary of running and/or queued jobs use the lstc_qrun command as follows, where queued means the job has started running according to the sqsub command but its actually sitting waiting for license resources to come available. Once these are acquired the job will start running on the cluster and appear as a Running Program according to lstc_qrun ie)
[roberpj@hnd19:~] lstc_qrun Defaulting to server 1 specified by LSTC_LICENSE_SERVER variable Running Programs User Host Program Started # procs ----------------------------------------------------------------------------- dgierczy 20277@saw61.saw.sharcn LS-DYNA_971 Mon Apr 8 17:44 1 dgierczy 8570@saw32.saw.sharcn LS-DYNA_971 Mon Apr 8 17:44 1 dscronin 25486@hnd6 MPPDYNA_971 Tue Apr 9 20:19 6 dscronin 14897@hnd18 MPPDYNA_971 Tue Apr 9 21:48 6 dscronin 14971@hnd18 MPPDYNA_971 Tue Apr 9 21:48 6 dscronin 15046@hnd18 MPPDYNA_971 Tue Apr 9 21:48 6 dscronin 31237@hnd16 MPPDYNA_971 Tue Apr 9 21:53 6 dscronin 31313@hnd16 MPPDYNA_971 Tue Apr 9 21:54 6 dscronin 6396@hnd15 MPPDYNA_971 Tue Apr 9 21:54 6 csharson 28890@saw175.saw.sharc MPPDYNA_971 Wed Apr 10 16:48 6 No programs queued
To additionally show license file expiration details, append "-R" to the command:
[roberpj@hnd19:~] lstc_qrun -R Defaulting to server 1 specified by LSTC_LICENSE_SERVER variable **** LICENSE INFORMATION **** PROGRAM EXPIRATION CPUS USED FREE MAX | QUEUE ---------------- ---------- ----- ------ ------ | ----- LS-DYNA_971 12/31/2013 - 966 1024 | 0 dgierczy 20277@saw61.saw.sharcnet 1 dgierczy 8570@saw32.saw.sharcnet 1 MPPDYNA_971 12/31/2013 - 966 1024 | 0 dscronin 25486@hnd6 6 dscronin 14897@hnd18 6 dscronin 14971@hnd18 6 dscronin 15046@hnd18 6 dscronin 31237@hnd16 6 dscronin 31313@hnd16 6 dscronin 6396@hnd15 6 csharson 28890@saw175.saw.sharcnet 6 LICENSE GROUP 58 966 1024 | 0 PROGRAM EXPIRATION CPUS USED FREE MAX | QUEUE ---------------- ---------- ----- ------ ------ | ----- LS-OPT 12/31/2013 0 1024 1024 | 0 LICENSE GROUP 0 1024 1024 | 0
Legacy Instructions
The following binaries remain available on saw and orca for backward compatibility testing:
[roberpj@orc-login2:~] cd /opt/sharcnet/local/lsdyna [roberpj@orc129:/opt/sharcnet/local/lsdyna] ls ls971* ls971_d_R3_1 ls971_d_R4_2_1 ls971_s_R3_1 ls971_s_R4_2_1 ls971_s_R5_1_1 ls971_d_R4_2_0 ls971_d_R5_0 ls971_s_R4_2_0 ls971_s_R5_0
There are currently no sharcnet modules for these versions, hence jobs should be submitted as follows:
module load lsdyna export PATH=/opt/sharcnet/local/lsdyna:$PATH export LSTC_LICENSE_SERVER=XXXXX@license3.uwo.sharcnet cp /opt/sharcnet/local/lsdyna/examples/airbag.deploy.k airbag.deploy.k SERIAL JOB: sqsub -q serial -r 1d -o ofile.%J ls971_d_R4_2_1 i=airbag.deploy.k THREADED JOB: sqsub -q threaded -n 4 -r 1d -o ofile.%J ls971_d_R4_2_1 ncpu=4 para=2 i=airbag.deploy.k
Note! the ls971_s_R3_1 and ls971_d_R3_1 binaries do not work, a fix is being looked for.
References
o LSTC Release Notes
http://www.dynasupport.com/search?Subject%3Alist=release%20note
o LSTC LS-DYNA Homepage
http://www.lstc.com/products/ls-dyna
o LSTC LS-DYNA Support (Tutorials, HowTos, Faq, Manuals, Release Notes, News, Links)
http://www.dynasupport.com/
o LS-DYNA and d3VIEW Blog
http://blog2.d3view.com/a-few-words-on-memory-settings-in-ls-dyna/
o Convert Words to GB ie) memory=500MW (3.73GB) choose -mpp=4G
http://deviceanalytics.com/memcalc.php
o LS-DYNA Support Environment variables
http://www.dynasupport.com/howtos/general/environment-variables
o http://www.dynasupport.com/release-notes http://www.dynasupport.com/release-notes