Updated 2023-04-28

Abaqus

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)

  • In the SBATCH 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 SBATCH 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 SBATCH 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
  • After logging in, You can transfer the files to your account on the cluster to follow along.

Part 1: The SBATCH Script

#SBATCH -J abaqus_demo
#SBATCH -A <charge-account>   # starts with "p-" or "GT-"
#SBATCH -q inferno
#SBATCH -N 1 --ntasks-per-node=4
#SBATCH --mem-per-cpu=2G
#SBATCH -t 30
#SBATCH -j oe
#SBATCH -o Report-%j.out
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=gburdell3@gatech.edu

cd $SLURM_SUBMIT_DIR

module load abaqus/2023

abaqus job=abaqus_demo input=abaqus_demo.inp cpus=4 interactive
  • The #SBATCH directives are standard, requesting just 30 minutes of walltime and 1 node with 4 cores.
    • $SLURM_SUBMIT_DIR is simply a variable that represents the directory you submit the SBATCH 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 SBATCH script.
  • module load abaqus/2023 loads the 2023 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 #SBATCH directives part of the script.

Part 2: Submit Job and Check Status

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

Part 3: Collecting Results

  • In the directory where you submitted the SBATCH 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:
---------------------------------------
Begin SBATCH Prologue Wed Nov 23 15:47:13 EDT 2022
Job ID:     4650913.sched-torque.pace.gatech.edu
User ID:    gburdell3
Job name:   abaqus_demo
Queue:      inferno
End SBATCH Prologue Thu Nov 10 15:47:13 EDT 2022
---------------------------------------
Unloading mvapich2 module to avoid internal conflict with Abaqus.
Please report Abaqus license server issues to coe-software@coe.gatech.edu.
OIT-ART PACE does not maintain this license server directly.
For software issues not related to the license server, please contact PACE
support at pace-support@oit.gatech.edu
Analysis initiated from SIMULIA established products
Abaqus JOB abaqus_demo
Abaqus 2021
Abaqus License Manager checked out the following licenses:
Abaqus/Foundation checked out 5 tokens from Flexnet server abaquslic.ecs.gatech.edu.
<1425 out of 1631 licenses remain available>.
Begin Analysis Input File Processor
Thu 10 Nov 2022 03:47:16 PM EDT
Run pre
Thu 10 Nov 2022 03:47:17 PM EDT
End Analysis Input File Processor
Begin Abaqus/Standard Analysis
Thu 10 Nov 2022 03:47:17 PM EDT
Run standard
Thu 10 Nov 2022 03:47:18 PM EDT
End Abaqus/Standard Analysis
Begin SIM Wrap-up
Thu 10 Nov 2022 03:47:18 PM EDT
Run SMASimUtility
Thu 10 Nov 2022 03:47:18 PM EDT
End SIM Wrap-up
Abaqus JOB abaqus_demo COMPLETED
---------------------------------------
Begin SBATCH Epilogue Thu Nov 10 15:47:18 EDT 2022
Job ID:     4650913.sched-torque.pace.gatech.edu
User ID:    gburdell3
Job name:   abaqus_demo
Resources:  1 --ntasks-pernode=4,--mem-per-cpu=2G,-t30
Rsrc Used:  cput=00:00:03,vmem=0kb,-t0.5,--mem-per-cpu=1G,energy_used=0
Queue:      inferno
Nodes:
atl1-1-02-010-17-r.pace.gatech.edu
End SBATCH Epilogue Thu Nov 10 15:47:18 EDT 2022
---------------------------------------
  • After the result files are produced, you can move the files off the cluster.
  • 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
#SBATCH -abaqus_python                          # job name
#SBATCH --account=hive-gburdell3                # Tracking account
#SBATCH -n4                                     # Number of cores required
#SBATCH --mem-per-cpu=1G                        # Memory per core
#SBATCH -t15                                    # Duration of the job (Ex: 15 mins)
#SBATCH -phive                                  # Queue name (where job is submitted)
#SBATCH -oReport-%j.out                         # Combined output and error messages file
#SBATCH --mail-type=BEGIN,END,FAIL              # Mail preferences
#SBATCH --mail-user=gburdell3@gatech.edu        # E-mail address for notifications
cd $SLURM_SUBMIT_DIR                            # Change to working directory

echo "Started on `/bin/hostname`"
module load abaqus/2021                         # Load module dependencies
# user supplies their own script
srun python test.py                             # Example Process

Run Abaqus Interactively

Overview

  • After you have run the above abaqus solver on an input file, you can view the results interactively.
  • This guide will focus on running this interactive side of Abaqus on the cluster

Set up Interactive (Open OnDemand) Session

  • Open the Open OnDemand Guide and select the version of Open OnDemand you want to use. Note: You must be connected to the Georgia Tech VPN to access Open OnDemand
  • Open the link and navigate to the top of the page and select Slurm Interactive Apps > Interactive Desktop
  • Enter your username and choose whether you want to use inferno (paid) or embers
  • Adjust the rest of the settings to your needs and then click Launch

Start Abaqus on Open OnDemand

  • Open Terminal in the Open OnDemand Virutal Desktop
  • All commands here on will be typed in terminal in Open OnDemand
  • To see available versions of Abaqus run
module avail abaqus
  • Load abaqus module and start abaqus
module load <version of abaqus>  #example: module load abaqus/2023
  • To start abaqus, run abaqus cae -mesa

Opening Output Files

  • Simply click File --> open to open whatever files you wish.