Batch Mode: Run Abaqus on the Cluster¶
- 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
Running Abaqus uses up licenses
- In the
PBSscript, load Abaqaus with
module load <abaqus version>. Find available versions with
module avail abaqus
- Make sure you use the
interactiveoption in the computation portion of the
PBSscript. 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
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
#PBSdirectives are standard, requesting just 30 minutes of walltime and 1 node with 4 cores. More on
#PBSdirectives can be found in the PBS guide
$PBS_O_WORKDIRis simply a variable that represents the directory you submit the PBS script from. Make sure the
.inpabaqus script you want to run (in this case,
abaqus_demo.inp) is in the same directory you put the PBS script.
module load abaqus/6.16loads 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
- For multiple cpus (parallel) use the
cpus=flag. Make sure it is equal to the number of cores you requested in the
#PBSdirectives part of the script.
Part 2: Submit Job and Check Status¶
- Be sure to change to the directory that contains the
- 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
PBSscript, you should see all the generated output files, such as the
cat abaqus_demo.outto 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