Difference between revisions of "Abaqus Guide"

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Revision as of 10:22, 8 January 2020

Abaqus
Author 3DS
Website http://www.3ds.com/
Source Proprietary Closed Source
Category Finite-Element Analyzer
Help Simulia Learning Community
simulia.east.support@3ds.com


The Abaqus FEA is a software suite for finite element analysis and computer-aided engineering, originally released in 1978 [1].

Unlike other modules, Abaqus FEA has been directly integrated with SLURM and one uses an abq* command instead of using sbatch.

Loading Modules

Abaqus

To use Abaqus 2017 on the cluster you will need first load the abaqus/2017 module using this command:

module avail abaqus 
module load abaqus/2017

FORTRAN

If you need to use FORTRAN subroutine with your simulation, load FORTRAN compiler as well:

 module avail intelics
 module load intelics/2015.3

Auto-load on log-in

If you wish Abaqus 2017 and FORTRAN modulus to be loaded every time you log in:

 module initadd abaqus/2017
 module initadd intelics/2015.3

You can undo this by removing those lines from your ~/.bashrc file.

Running Abaqus

Abaqus jobs are managed by SLURM. To submit a job to Abaqus, transfer your model input file to the cluster and run this command:

abq2017 job=FILE que=general:fslocal

where

abq2017
Is the command (case sensitive) to invoke Abaqus 2017.
FILE
The name of your input (.inp) file without the file extension.
que=general:fslocal
Runs the Abaqus simulation on a local file system using the general partition (you can use any of the partitions from sinfo -o %P)
The simulation will run on another compute node and copy the result files upon completion.
To run ABAQUS in a shared file system, use que=general:fsshared instead.

Adding a user subroutine

If a user subroutine is adopted in the Abaqus model, run the command with "user" option.

abq2017 job=job-1 user=CODE.f que=general:fslocal

where

CODE.f
Is the file name of the user subroutine written in FORTRAN.

CPU parallel analysis

If parallel computing is needed, run the command with "cpus" option.

abq2017 job=file cpus=5 que=general:fslocal

where

cpus=5
Will request five CPUs to run the job. More CPUs will require more Abaqus license tokens to run.

Unexpected end of file error

When submitting an abaqus job, you will see:

sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
Submitted batch job 12345

These sh warnings are harmless, and you can ignore them.

Checking job status

Run this command:

 tail -f FILE.sta

where

FILE.sta
Is the name of the status file.
If you are running your job in a local file system, then you have to change the directory the specific folder and specific node to check the status of your job.
Normally when the simulation is finished, the HPC will send you an email showing the simulation is completed successfully or exited with error.

Terminating an Abaqus Analysis

If an analysis job needs to be terminated before completion, find the Job ID with this command.

 sjobs

which will list all the jobs are running. Then run this command to kill a specific job.

 scancel SLURM_JOB_ID

where

SLURM_JOB_ID
Is the SLURM ID number of the job you want to kill.

Bash Script

As an extra note, if you would like your Abaqus jobs to email you or for job status tracking, a normal Slurm bash script can be made to call the Abaqus commands as well.

Here is an example

#!/bin/bash 
#SBATCH -p general # Name of partition
#SBATCH -n 1 # submit using 1 core
#SBATCH -N 1 # submit using 1 node
#SBATCH --mail-user=first.lastname@uconn.edu # Destination email address
#SBATCH --mail-type=ALL # Event(s) that triggers email notification (BEGIN,END,FAIL,ALL)
module load abaqus/2017 
abq2017 job=jobnamehere input=./yourinputfile.inp cpus=1 que=general:fslocal

Notes

At this time, the Abaqus script and subroutines written in C++ have not been tested.

Abaqus CAE/Viewer

To be able to launch the CAE or Viewer for Abaqus 2017, a X session would need to be set up when logging into the cluster. Once a terminal session has been loaded with X enabled (either through X2Go or ssh -X), a fisbatch job would need to be submitted to the cluster.

Example fisbatch command to submit to the general partition:

fisbatch -N 1 -n 24 -p general

Once the job has been submitted and a node has been allocated, the abaqus/2017 module would need to be loaded.

module load abaqus/2017

After the abaqus/2017 module has been loaded in the fisbatch session, the GUI can be launched by using either of the following commands:

abq2017cae cae -mesa

or

abq2017cae viewer -mesa

Abaqus License Info

License Type License Server Tokens of Abaqus Tokens of Abaqus Viewer(cae -mesa)
Abaqus 2019 RESEARCH 27008@engr-license2.grove.ad.uconn.edu 58 10
Abaqus 2017 RESEARCH 27008@engr-license2.grove.ad.uconn.edu 58 10
Abaqus 6.13 RESEARCH 27008@ecs-license2.engr.uconn.edu 58 10