Updated 2019-04-22

Batch Mode: Run Abaqus on the Cluster

Overview

  • Abaqus is a licensed simulation software that provides for "both the modeling and analysis of mechanical components and assemblies (pre-processing) and visualizing the finite element analysis result" Source: Wiki.
  • This guide will focus on two parts of Abaqus:
    • Submitting a simulation in batch mode
    • Opening the results in Abaqus (interactively)
  • This guide focuses on the batch (non-interactive) part, for the interactive part see the Abaqus interactive guide

Important

Running Abaqus uses up licenses

  • In the PBS script, load Abaqaus with module load <abaqus version>. Find available versions with module avail abaqus
  • Make sure you use the interactive option in the computation portion of the PBS script. For example, to run Abaqus on an input file called abaqus_demo.inp, use the line:
  • abaqus job=abaqus_demo input=abaqus_demo.inp cpus=<#ofCpus> interactive
  • Running in Parallel: if using multiple cores, add the option cpus=x, and make sure x is the number of total cores you requested in the top (directives) part of the PBS script

Walkthrough: Run Abaqus on the Cluster

  • This walkthrough will use a simple abaqus input file, abaqus_demo.inp. Credit for the input script goes to Tennessee Tech.
  • Input Script (abaqus_demo.inp) can be found here
  • PBS Script (abaqus.pbs) can be found here
  • After logging in, You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.

Part 1: The PBS Script

#PBS -N abaqusTest
#PBS -l nodes=1:ppn=4
#PBS -l pmem=2gb
#PBS -l walltime=30:00
#PBS -q force-6
#PBS -j oe
#PBS -o abaqusTest.out

cd $PBS_O_WORKDIR
module load abaqus/6.16
abaqus job=abaqus_demo input=abaqus_demo.inp  cpus=4 interactive

  • The #PBS directives are standard, requesting just 30 minutes of walltime and 1 node with 4 cores. More on #PBS directives can be found in the PBS guide
    • $PBS_O_WORKDIR is simply a variable that represents the directory you submit the PBS script from. Make sure the .inp abaqus script you want to run (in this case, abaqus_demo.inp) is in the same directory you put the PBS script.
  • module load abaqus/6.16 loads the 6.16 version of Abaqus. To see what Abaqus versions are available, run module avail abaqus
  • The last line runs abaqus. Make sure you include the interactive option
  • For multiple cpus (parallel) use the cpus= flag. Make sure it is equal to the number of cores you requested in the #PBS directives part of the script.

Part 2: Submit Job and Check Status

  • Be sure to change to the directory that contains the PBS Script
  • qsub abaqus.pbs
  • Check job status with qstat -t <jobid>, replacing the number with the job id returned after running qsub
  • You can delete the job with qdel <jobid> , again replacing the number with the jobid returned after running qsub

Part 3: Collecting Results

  • In the directory where you submitted the PBS script, you should see all the generated output files, such as the abaqus_demo.dat and abaqus_demo.odb files. Use cat abaqus_demo.out to view information on the completed job, which should like:
Job name:   abaqusTest
Queue:      force-6
End PBS Prologue Tue Sep 11 16:53:43 EDT 2018
---------------------------------------
Analysis initiated from SIMULIA established products
Abaqus JOB abaqus_demo
Abaqus 3DEXPERIENCE R2016x
Abaqus License Manager checked out the following licenses:
Abaqus/Foundation checked out 5 tokens from Flexnet server abaquslic.ecs.gatech.edu.
<828 out of 1631 licenses remain available>.
Begin Analysis Input File Processor
Tue 11 Sep 2018 04:54:02 PM EDT
Run pre
Tue 11 Sep 2018 05:03:04 PM EDT
End Analysis Input File Processor
Begin Abaqus/Standard Analysis
Tue 11 Sep 2018 05:03:04 PM EDT
Run standard
Tue 11 Sep 2018 05:08:05 PM EDT
End Abaqus/Standard Analysis
Begin MFS->SFS and SIM cleanup
Tue 11 Sep 2018 05:08:05 PM EDT
Run SMASimUtility
Tue 11 Sep 2018 05:08:06 PM EDT
End MFS->SFS and SIM cleanup
Abaqus JOB abaqus_demo COMPLETED
---------------------------------------
Begin PBS Epilogue Tue Sep 11 17:08:06 EDT 2018
Job ID:     22318563.shared-sched.pace.gatech.edu

  • After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
  • Congratulations! You successfully ran an abaqus input file on the cluster.

Running Abaqus CAE Python

Users that need to run Python scripts that use import abaqus using Abaqus CAE can do it using the following template:

#!/bin/bash
#PBS -N abaqus_python       # job name
#PBS -l nodes=1:ppn=8       # number of nodes and cores per node required
#PBS -l pmem=2gb            # memory per task
#PBS -l walltime=10:00:00   # duration of the job
#PBS -q iw-shared-6         # queue name (where job is submitted)
#PBS -j oe                  # combine output and error messages into 1 file
#PBS -o abaqus_python..out  # output file name
#PBS -m abe                 # event notification, set to email on start, end, or fail

cd $PBS_O_WORKDIR
echo "Started on `/bin/hostname`"
module load abaqus/6.16
# user supplies their own script
abaqus cae noGUI=user_python_script.py