ABAQUS is a Finite Element Analysis software used for engineering simulations. Currently, ABAQUS versions 6.10, 6.13, 6.14 are available on Palmetto cluster as modules.

$ module avail abaqus

abaqus/6.10 abaqus/6.13 abaqus/6.14

To see license usage of ABAQUS-related packages, you can use the lmstat command:

/software/USR_LOCAL/flexlm/lmstat -a -c /software/USR_LOCAL/flexlm/licenses/abaqus.dat

Running ABAQUS interactive viewer

To run the interactive viewer, you must log-in with tunneling enabled, and then ask for an interactive session:

$ qsub -I -X -l select=1:ncpus=8:mpiprocs=8:mem=6gb:interconnect=mx,walltime=00:15:00

Once logged-in to an interactive compute node, to launch the interactive viewer, load the abaqus module, and run the abaqus executable with the viewer and -mesa options:

$ module add abaqus/6.14
$ abaqus viewer -mesa

Similarly, to launch the ABAQUS CAE graphical interface:

$ abaqus cae -mesa

Running ABAQUS in batch mode

To run ABAQUS in batch mode on Palmetto cluster, you can use the job script in the following example as a template. This example shows how to run ABAQUS in parallel using MPI. This demonstration runs the “Axisymmetric analysis of bolted pipe flange connections” example provided in the ABAQUS documentation here. Please see the documentation for the physics and simulation details. You can obtain the files required to run this example using the following commands:

$ cd /scratch2/username
$ module add examples
$ example get ABAQUS
$ cd ABAQUS && ls

abaqus_v6.env  boltpipeflange_axi_element.inp  boltpipeflange_axi_node.inp  boltpipeflange_axi_solidgask.inp  job.sh

The .inp files describe the model and simulation to be performed - see the documentation for details. The batch script job.sh submits the job to the cluster. The .env file is a configuration file that must be included in all ABAQUS job submission folders on Palmetto.

#!/bin/bash
#PBS -N AbaqusDemo
#PBS -l select=2:ncpus=8:mpiprocs=8:mem=6gb:interconnect=mx,walltime=00:15:00
#PBS -j oe

module purge
module add abaqus/6.14

pbsdsh sleep 20

NCORES=`wc -l $PBS_NODEFILE | gawk '{print $1}'`
cd $PBS_O_WORKDIR

SCRATCH=$TMPDIR

# copy all input files into the scratch directory
for node in `uniq $PBS_NODEFILE`
do
    ssh $node "cp $PBS_O_WORKDIR/*.inp $SCRATCH"
done

cd $SCRATCH

# run the abaqus program, providing the .inp file as input
abaqus job=abdemo double input=$SCRATCH/boltpipeflange_axi_solidgask.inp scratch=$SCRATCH cpus=$NCORES mp_mode=mpi interactive 

# copy results back from scratch directory to $PBS_O_WORKDIR
for node in `uniq $PBS_NODEFILE`
do
    ssh $node "cp -r $SCRATCH/* $PBS_O_WORKDIR"
done

In the batch script job.sh:

  1. The following line extracts the total number of CPU cores available across all the nodes requested by the job:

    NCORES=`wc -l $PBS_NODEFILE | gawk '{print $1}'`
    
  2. The following line runs the ABAQUS program, specifying various options such as the path to the .inp file, the scratch directory to use, etc.,

    abaqus job=abdemo double input=/scratch2/$USER/ABAQUS/boltpipeflange_axi_solidgask.inp scratch=$SCRATCH cpus=$NCORES mp_mode=mpi interactive
    

To submit the job:

$ qsub job.sh
9668628

After job completion, you will see the job submission directory (/scratch2/username/ABAQUS) populated with various files:

$ ls

AbaqusDemo.o9668628  abdemo.dat  abdemo.msg  abdemo.res  abdemo.stt                      boltpipeflange_axi_solidgask.inp
abaqus_v6.env        abdemo.fil  abdemo.odb  abdemo.sim  boltpipeflange_axi_element.inp  job.sh
abdemo.com           abdemo.mdl  abdemo.prt  abdemo.sta  boltpipeflange_axi_node.inp

If everything went well, the job output file (AbaqusDemo.o9668628) should look like this:

[atrikut@login001 ABAQUS]$ cat AbaqusDemo.o9668628
Abaqus JOB abdemo
Abaqus 6.14-1
Abaqus License Manager checked out the following licenses:
Abaqus/Standard checked out 16 tokens from Flexnet server licensevm4.clemson.edu.
<567 out of 602 licenses remain available>.
Begin Analysis Input File Processor
Mon 13 Feb 2017 12:35:29 PM EST
Run pre
Mon 13 Feb 2017 12:35:31 PM EST
End Analysis Input File Processor
Begin Abaqus/Standard Analysis
Mon 13 Feb 2017 12:35:31 PM EST
Run standard
Mon 13 Feb 2017 12:35:35 PM EST
End Abaqus/Standard Analysis
Abaqus JOB abdemo COMPLETED


+------------------------------------------+
| PALMETTO CLUSTER PBS RESOURCES REQUESTED |
+------------------------------------------+

mem=12gb,ncpus=16,walltime=00:15:00


+-------------------------------------+
| PALMETTO CLUSTER PBS RESOURCES USED |
+-------------------------------------+

cpupercent=90,cput=00:00:10,mem=636kb,ncpus=16,vmem=12612kb,walltime=00:00:13

The output database (.odb) file contains the results of the simulation which can be viewed using the ABAQUS viewer: