Difference between revisions of "LSDYNA"

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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

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 load the desired sharcnet lsdyna module version. Check which modules are available by running the module avail command then load one the modules as shown:

[roberpj@orc-login2:~] module avail lsdyna
--------------------------------- /opt/sharcnet/modules ----------------------------------
lsdyna/hyb/r711.88920     lsdyna/mpp/r611.80542     lsdyna/smp/ls980B1.78258
lsdyna/mpp/ls971.r85718   lsdyna/mpp/r711.88920     lsdyna/smp/r711.88920
lsdyna/mpp/ls980B1.011113 lsdyna/mpp/r712.95028     lsdyna/smp/r712.95028
lsdyna/mpp/r611.79036     lsdyna/mpp/r800.95359     lsdyna/smp/r800.95359

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 mkl
module load intel/15.0.3 openmpi/intel1503-std/1.8.7 lsdyna/mpp/r800.95359

r7.1.2 versions

o For serial or threaded jobs:

module load lsdyna/smp/r712.95028

o For mpi jobs:

module unload intel openmpi lsdyna
module load intel/12.1.3 openmpi/intel/1.6.5 lsdyna/mpp/r712.95028

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 serial or threaded jobs:

module load lsdyna/smp/r611.79036

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

Optionally one may specify an initial memory setting on the command line when submitting a 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. The initial value maybe determined by running the simulation interactively on a orca development node and locating the output:

 Memory required to begin solution      :      754414

When using the single precision solver memory would be the number of 4 bytes words shared by all processors in single precision. Further details regarding the memory command line setting maybe found in the memory related links provided in the Reference section at bottom.

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 known special reason to do so:

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 /scratch/$USER/test-lsdyna
cd /scratch/$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.
--------------------------------------------------------------------------

Another error message which can occur after a job runs for a while if mpp is chosen to small is:

>>>>> Process 45 <<<<<
>>>>> Signal 11 : Segmentation Violation <<<<<

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 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 Release Notes
http://www.dynasupport.com/release-notes

o LS-PrePost Online Documentation FAQ
http://www.lstc.com/lspp/content/faq.shtml

o LSTC Download/Install Overview Page
Provides links to binaries for LS-DYNA SMP/MPP, LS-OPT, LS-PREPOST, LS-TASC.
http://www.lstc.com/download

Memory Links

o Implicit: Memory notes
http://www.dynasupport.com/howtos/implicit/implicit-memory-notes

o LS-DYNA Support Environment variables
http://www.dynasupport.com/howtos/general/environment-variables

o LS-DYNA and d3VIEW Blog (a few words on memory settings)
http://blog2.d3view.com/a-few-words-on-memory-settings-in-ls-dyna/

o Convert Words to GB ie) memory=500MW (3.73GB)
http://deviceanalytics.com/memcalc.php

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