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(Threaded Job)
(Mpi Job)
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srun ls-dyna_d i=airbag.deploy.k memory=125M
 
srun ls-dyna_d i=airbag.deploy.k memory=125M
 
</pre>
 
</pre>
 +
 +
where memory = 1000M / 8 (bytes/word) = 125M words
  
 
==New Orca==
 
==New Orca==

Revision as of 16:45, 15 November 2018

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

Graham Cluster

License

Create and customize this file for your license server, where XXXXX should be replaced with your port number and Y with your server number:

[roberpj@gra1:~] cat .licenses/ls-dyna.lic 
#LICENSE_TYPE: network
#LICENSE_SERVER: XXXXX@licenseY.uwo.sharcnet

Module

The modules are loaded automatically in the testomp.sh and testmpi.sh script shown below in the example section:

For single node smp jobs the available versions can be found by doing:

[roberpj@gra-login2:~] module spider ls-dyna
       ls-dyna/7.1.2
       ls-dyna/7.1.3
       ls-dyna/8.1
       ls-dyna/9.1
       ls-dyna/9.2
       ls-dyna/10.0

To load any version do for example:

module load ls-dyna/9.1

For multi node mpp jobs the available versions can be found by doing:

[roberpj@gra-login2:~] module spider ls-dyna-mpi
       ls-dyna-mpi/7.1.2
       ls-dyna-mpi/7.1.3
       ls-dyna-mpi/8.1
       ls-dyna-mpi/9.1
       ls-dyna-mpi/9.2
       ls-dyna-mpi/10.0

To load the 7.1.X modules do the following:

module load openmpi/1.6.5 ls-dyna-mpi/7.1.3

To load the 8.X or 9.X modules do:

module load openmpi/1.8.8 ls-dyna-mpi/9.2

To load the 10.X modules do:

module load openmpi/1.10.7 ls-dyna-mpi/10.0

Legacy Clusters

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@license1.uwo.sharcnet

o McGill Mechanical Engineering Department

export LSTC_LICENSE_SERVER=Port@license2.uwo.sharcnet

o UW Mechanical and Mechatronics Engineering Dept

export LSTC_LICENSE_SERVER=Port@license3.uwo.sharcnet

o Laurentian University Bharti School of Engineering

export LSTC_LICENSE_SERVER=Port@license4.uwo.sharcnet

o Fictitious Example:

export LSTC_LICENSE_SERVER=12345@license1.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/r711.88920     lsdyna/smp/r611.79036
lsdyna/mpp/ls971.r85718   lsdyna/mpp/r712.95028     lsdyna/smp/r711.88920
lsdyna/mpp/ls980B1.011113 lsdyna/mpp/r800.95359     lsdyna/smp/r712.95028
lsdyna/mpp/r611.79036     lsdyna/mpp/r901.109912    lsdyna/smp/r800.95359
lsdyna/mpp/r611.80542     lsdyna/smp/ls980B1.78258  lsdyna/smp/r901.109912

r9.0.1 versions

o For serial or threaded jobs:

module load lsdyna/smp/r901.109912

o For mpi jobs:

module unload intel openmpi lsdyna mkl
module load intel/15.0.3 openmpi/intel1503-std/1.8.7 lsdyna/mpp/r901.109912

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

Graham Cluster

The submission scripts myompjob.sh and mympijob.sh for the airbag problem are shown in the example section below. Note that you should specify your own username if submitting to a def account (not roberpj). Alternatively you could specify your resource allocation account:

Sample threaded job submit script:

sbatch myompjob.sh

Sample mpi job submit script:

sbatch  mympijob.sh

Legacy Clusters

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 can be 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.

8cpu MPI Job

sqsub -r 1h -q mpi -o ofile.%J -n 8 --mpp=2G lsdyna_d i=airbag.deploy.k

Optionally one can specify initial memory settings on the sqsub command line: "memory=" for the first master processor to decompose the problem and "memory2=" used on all processors including the master to solves the decomposed problem, where the values are specified as 4 bytes per word in single precision and 8 bytes per word in double precision. The number of words can be specified as memory=260M instead of memory=260000000, for further details see https://www.d3view.com/2006/10/a-few-words-on-memory-settings-in-ls-dyna/.

The values can be found by running simulation interactively on a orca compute node and checking the output for a line such as: Memory required to begin solution (memory= 464898 memory2= 158794 ) which could then be implemented for a job run in the queue by doing:

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

However note that specifying memory2 on sharcnet is not beneficial since the queue reserves the same memory per core for all nodes hence the decomposition master node cannot be allocated larger system memory. Therefore its sufficient to only the memory paramemter such as:

export LSTC_MEMORY=auto 
sqsub -r 1h -q mpi -o ofile.%J -n 8 --mpp=2G lsdyna_d i=airbag.deploy.k memory=464898

Example Job

Copy the airbag example to your account:

rsync -av orca.sharcnet.ca:/opt/sharcnet/lsdyna/r901.109912/examples r901.109912_examples
cd r901.109912_examples/examples/misc/airbag
gunzip airbag.deploy.k.gz

Graham Cluster

Threaded Job

Sample submission script mysmpjob8.sh for 8 core smp job:

#!/bin/bash
# Submit job:  sbatch myompjob.sh
# https://docs.computecanada.ca/wiki/Running_jobs
#SBATCH --account=def-username 
#SBATCH --nodes=1                           # use one node
#SBATCH --cpus-per-task=8                   # number threads 
#SBATCH --mem=4000M                         # total memory
#SBATCH --time=00:30:00                     # hrs:min:sec
#SBATCH --job-name=testomp                  # %x = jobname
#SBATCH --output=slurm-%x-%N-%j.out
echo "SLURM_CPUS_PER_TASK= "$SLURM_CPUS_PER_TASK
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
# ----------------------------------------------------------
# IMPORTANT:  to set license server do either:
# 1) export LSTC_LICENSE_SERVER=port@some.license.server
# 2) create  ~/.licenses/ls-dyna.lic as shown above
# ----------------------------------------------------------
module load ls-dyna/9.1
srun ls-dyna_d i=airbag.deploy.k memory=500M ncpu=8

where memory = 4000M / 8 (bytes/word) = 500M words

Mpi Job

Sample submission script mympijob8.sh for 8 core mpp job:

#!/bin/bash
# Submit job: sbatch mympijob.sh
# https://docs.computecanada.ca/wiki/Running_jobs
#SBATCH --account=def-roberpj
#SBATCH --ntasks=8                     # number of ranks
#SBATCH --mem-per-cpu=1000M            # memory per rank 
#SBATCH --time=00:30:00                # hrs:min:sec
#SBATCH --job-name=test-mpi            # %x = jobname
#SBATCH --output=slurm-%x-%N-%j.out
# ----------------------------------------------------------
# IMPORTANT:  to set license server do either:
# 1) export LSTC_LICENSE_SERVER=port@some.license.server
# 2) create  ~/.licenses/ls-dyna.lic as shown above
# ----------------------------------------------------------
module load openmpi/1.8.8 ls-dyna-mpi/9.1
srun ls-dyna_d i=airbag.deploy.k memory=125M

where memory = 1000M / 8 (bytes/word) = 125M words

New Orca

Sample submission script mysmpjob4.sh for 4 core smp job using legacy sharcnet lsdyna modules:

#!/bin/bash
# Submit job:  sbatch myompjob.sh
# https://docs.computecanada.ca/wiki/Running_jobs
#SBATCH --account=def-username 
#SBATCH --nodes=1                           # use one node
#SBATCH --cpus-per-task=4                   # number threads 
#SBATCH --mem=2000M                         # total memory
#SBATCH --time=00:30:00                     # hrs:min:sec
#SBATCH --job-name=testomp                  # %x = jobname
#SBATCH --output=slurm-%x-%N-%j.out
echo "SLURM_CPUS_PER_TASK= "$SLURM_CPUS_PER_TASK
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
# ----------------------------------------------------------
# IMPORTANT:  to set license server must do:
export LSTC_LICENSE_SERVER=port@some.license.server
# ~/.licenses/ls-dyna.lic does not work with legacy modules
# ----------------------------------------------------------
module load ls-dyna/9.1
srun ls-dyna_d i=airbag.deploy.k memory=500M ncpu=8

Sample submission script mympijob4.sh for 4 core mpp job using legacy sharcnet lsdyna modules:

#!/bin/bash
#SBATCH --account=def-username
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=2G
#SBATCH --time=00:30:00
#SBATCH --job-name=testmpi
module purge --force
export MODULEPATH=/opt/sharcnet/modules
# ----------------------------------------------------------
# IMPORTANT:  to set license server must do:
export LSTC_LICENSE_SERVER=port@some.license.server
# ~/.licenses/ls-dyna.lic does not work with legacy modules
# ----------------------------------------------------------
module load intel/12.1.3 openmpi/intel/1.6.5 lsdyna/mpp/r712.95028
lsdyna_s i=01_Master.k  memory=100M

Legacy Clusters

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

Graham Cluster

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:~] export LSTC_LICENSE_SERVER=#####@license#.uwo.sharcnet
 
[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 show license file expiration details, append "-R" to the command:

[roberpj@hnd19:~] export LSTC_LICENSE_SERVER=#####@license#.uwo.sharcnet
 
[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