Abaqus

Abaqus

Versions:

6.14.2 (see Addendum section), 2018, 2021

Dependencies:

User subroutines need the Intel FORTRAN compiler 2019 (auto loaded via Abaqus modules).

URL:

http://www.3ds.com/products-services/simulia/products/abaqus/

Documentation:

https://help.3ds.com/ (note: register for an account to access.)

Abaqus is a software suite for Finite Element Analysis (FEA) developed by Dassault Systèmes.

Interactive usage

After connecting to Bessemer (see Establishing a SSH connection), start an interactive graphical session.

Abaqus can be activated using one of the following module files:

module load ABAQUS/6.14.2/binary
module load ABAQUS/2018
module load ABAQUS/2021/binary

and launched using:

abaqus cae -mesa

Note

Users must unset the SLURM environment variable SLURM_GTIDS. Failure to do so will cause Abaqus to get stuck due to the MPI that Abaqus ships with not supporting the SLURM scheduler. SLURM_GTIDS should be unset for both interactive/GUI and batch jobs:

unset SLURM_GTIDS

When using a general compute node for Abaqus 2018 or 2021 on Bessemer, please run abaqus cae -mesa (or abq2018 cae -mesa) to launch the GUI without support for hardware-accelerated graphics rendering. The option -mesa disables hardware-accelerated graphics rendering within Abaqus’s GUI.

---

Abaqus example problems

Abaqus contains a large number of example problems which can be used to become familiar with Abaqus on the system. These example problems are described in the Abaqus documentation and can be obtained using the Abaqus fetch command. For example, after loading the Abaqus module enter the following at the command line to extract the input file for test problem s4d:

abaqus fetch job=s4d

This will extract the input file s4d.inp to run the computation defined by the commands and batch submission script below.

---

Batch jobs

The following is an example batch submission script, my_job.sh, to run the executable abaqus with input file is s4d.inp. The script requests 4 cores using the OpenMP parallel environment smp with a runtime of 30 mins and 2 GB of real memory per core.

#!/bin/bash
#SBATCH --job-name=abaqus_smp_test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem=8000
#SBATCH --output=output_abaqus_smp_4
#SBATCH --time=00:30:00
#SBATCH --mail-user=a.person@sheffield.ac.uk
#SBATCH --mail-type=ALL
module load ABAQUS/2018
unset SLURM_GTIDS
abaqus job=my_job input=s4d.inp mp_mode=threads cpus=$SLURM_NTASKS scratch=$TMPDIR memory="8gb" interactive

The job is submitted to the queue by typing:

sbatch my_job.sh

User subroutines: The umatmst3 model has a user defined subroutine umatmst3.f. The model files are obtained using

abaqus fetch job=umatst3*

The script below is an example of a batch submission script for a single core job with a runtime of 30 mins, 8 GB of real memory and with user subroutine umatmst3.f and input file umatmst3.inp.

#!/bin/bash
#SBATCH --job-name=abaqus_subroutine_test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=8000
#SBATCH --output=output_abaqus_subroutine
#SBATCH --time=00:30:00
#SBATCH --mail-user=a.person@sheffield.ac.uk
#SBATCH --mail-type=ALL
module load ABAQUS/2018
module load ifort/2019.1.144-GCC-8.2.0-2.31.1
unset SLURM_GTIDS
abaqus job=my_job input=umatmst3.inp user=umatmst3.f scratch=$TMPDIR memory="8gb" interactive

Note that the module ifort/2019.1.144-GCC-8.2.0-2.31.1, required for compiling the user subroutines, may not be automatically loaded when the module for Abaqus is loaded.

---

Licensed options

All available Abaqus licenses can be viewed using abaqus licensing r e.g.

$ module load ABAQUS/2018
$ abaqus licensing r

Run abaqus licensing for usage info for the Abaqus licensing sub-command. Run abaqus licensing ru to see current licence usage.

---

Checkpointing your work

Abaqus has a built-in checkpoint and restart feature.

Add the following to the input file (refer to official Abaqus documentation for detail):

*RESTART, WRITE, OVERLAY, FREQUENCY=10

OVERLAY saves only one state, i.e. overwrites the restart file every time new restart information is written

FREQUENCY=N writes restart information every N timesteps

And, to restart the job, create a new input file newJobName with only a single line:

*RESTART, READ

Then run Abaqus specifying both the new and old job names:

abaqus jobname=newJobName oldjob=oldJobName

---

Installation notes

Addendum: Abaqus 2021 (non-EasyBuild install):

Abaqus 6.14.2 was installed using the standard Abaqus interactive GUI installer (StartGUI.sh).

The module file is /usr/local/modulefiles/live/noeb/ABAQUS/2021/binary.

Addendum: Abaqus 6.14.2 (non-EasyBuild install):

Abaqus 6.14.2 was installed using the standard Abaqus installer due to issues using EasyBuild.

It can be activated using the following module commands:

module load ABAQUS/6.14.2/binary

and launched using:

abaqus cae

The following is an example batch submission script, my_job.sh, to run the executable abaqus with input file is s4d.inp. The script requests 4 cores using the OpenMP parallel environment smp with a runtime of 30 mins and 2 GB of real memory per core.

#!/bin/bash
#SBATCH --job-name=abaqus_smp_test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem=8000
#SBATCH --output=output_abaqus_smp_4
#SBATCH --time=00:30:00
#SBATCH --mail-user=a.person@sheffield.ac.uk
#SBATCH --mail-type=ALL
module use /usr/local/modulefiles/live/apps
module load ABAQUS/6.14.2/binary
unset SLURM_GTIDS
abaqus job=my_job input=s4d.inp mp_mode=threads cpus=$SLURM_NTASKS scratch=$TMPDIR memory="8gb" interactive