Revision as of 17:06, 10 April 2013

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.

Usage

These usage instructions apply to the module based installation of lsdyna found under directory /opt/sharcnet/lsdyna on licensed clusters shown in the above Availability Table. To access and use this software you must be a member of the lsdyna group. Users who belong to a licensed department 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 UWO Civil and Environmental Engineering Dept

export LSTC_LICENSE_SERVER='PortNumber'@license1.uwo.sharcnet

o McGill Mechanical Engineering Department

export LSTC_LICENSE_SERVER='PortNumber'@license2.uwo.sharcnet

o UW Mechanical and Mechatronics Engineering Dept

export LSTC_LICENSE_SERVER='PortNumber'@license3.uwo.sharcnet

Module Selection

[roberpj@orc-login1:~] module avail lsdyna
 
-------------------------------------- /opt/sharcnet/modules ---------------------------------------
lsdyna/ls971mpp6.0.0 lsdyna/ls971mpp6.1.1 lsdyna/ls971smp6.1.0 lsdyna/ls980mppB1
lsdyna/ls971mpp6.1.0 lsdyna/ls971smp6.0.0 lsdyna/ls971smp6.1.1 lsdyna/ls980smpB1

o For serial or threaded jobs, using ls971 do:

module load lsdyna/ls971smp6.1.1

o For mpi jobs, using ls971 do:

module unload intel openmpi lsdyna
module load intel/11.1.069 openmpi/intel/1.5.4 lsdyna/ls971mpp6.1.1

o For serial or threaded jobs, using version ls980 do:

module load lsdyna/ls980smpB1

o For mpi jobs, using version ls980 do:

module unload intel openmpi lsdyna
module load intel/12.1.3 openmpi/intel/1.4.5 lsdyna/ls980mppB1

Job Submission

To run the single or double precision solvers specify lsdyna_s or lsdyna_d respectively:

o SUBMIT 1CPU SERIAL JOB

sqsub -r 7d -q serial -o ofile.%J --mpp=2G lsdyna_d i=airbag.deploy.k ncpu=1 

o SUBMIT 4CPU SMP JOB

sqsub -r 7d -q threaded -n 4 -o ofile.%J --mpp=2G lsdyna_d i=airbag.deploy.k ncpu=4

o SUBMIT 4CPU MPI JOB

sqsub -r 7d -q mpi -n 4 -o ofile.%J --mpp=1G lsdyna_d i=airbag.deploy.k

Example Job

STEP1) The following shows a sample sqsub jobs submission for the airbag example to the mpi queue shown in this link http://www.dynaexamples.com/examples-manual/misc/airbag where you I suggest first changing endtim to 3.000E-00 in airbag.deploy.k to the job runs long enough to perform all steps in this section:

cp -a /opt/sharcnet/lsdyna/ls971smp6.1.1/examples /work/$USER/test-lsdyna
cd /work/$USER/test-lsdyna/misc/airbag
gunzip airbag.deploy.k.gz
module unload intel openmpi lsdyna
module load intel/11.1.069 openmpi/intel/1.5.4 lsdyna/ls971mpp6.1.1
export LSTC_LICENSE_SERVER=#####@license#.uwo.sharcnet
cp airbag.deploy.k airbag.deploy.restart.k
sqsub -r 1h -q mpi --mpp=4G -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 after which manually kill the job or wait until it exceeds the sqsub -r time limit 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=4G -n 8 -o ofile.%J lsdyna_d i=airbag.deploy.restart.k r=d3dump01

General Notes

Checking Job Status

To check the status of your job in the queue use the sqjobs command. On x86_64 systems you can check whether any of your jobs are queued on the license server use lstc_qrun. Its possible that sqsub will start your job but it will sit idle until enough license are available on the license server and the lstc_qrun command will reveal this:

[roberpj@hnd19:~/samples/lsdyna] lstc_qrun
Defaulting to server 1 specified by LSTC_LICENSE_SERVER variable
 
                     Running Programs
 
    User             Host          Program              Started       # procs
-----------------------------------------------------------------------------
hsnmoham    12208@orc271.orca.shar MPPDYNA          Mon Jan  7 18:17    24
 roberpj     9767@hnd15            LS-DYNA_971      Mon Jan  7 19:42     4
No programs queued

Checking License Details

At the time of this writing UWO is running on a 4cpu demo license as follows:

[roberpj@hnd19:~/samples/lsdyna]  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      05/31/2013          -    172    200 |     0
 roberpj     9767@hnd15              4
MPPDYNA_971      05/31/2013          0    172    200 |     0
LS-DYNA          05/31/2013          0    172    200 |     0
MPPDYNA          05/31/2013          -    172    200 |     0
 hsnmoham   12208@orc271.orca.sharcnet  24
                   LICENSE GROUP    28    172    200 |     0
 
PROGRAM          EXPIRATION CPUS  USED   FREE    MAX | QUEUE
---------------- ----------      ----- ------ ------ | -----
LS-OPT           05/31/2013          0    200    200 |     0
                   LICENSE GROUP     0    200    200 |     0

Legacy Version 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/lsdyna.htm