Abaqus#

Abaqus is an application that is used for solving structural simulation of multi-physics problems.

There are two main modes of running Abaqus on Octopus:

batch mode (using the command line or scripts)

graphical user interface mode (using desktop sessions)

To use any of these two the abaqus module should be loaded:

module load abaqus

Graphical user interface mode#

To launch the Abaqus GUI after connecting to a desktop environment, to launch CAE (Complete Abaqus Environment) the following command can be executed in a terminal:

module load abaqus
abaqus cae

Template Abaqus job (batch mode)#

The following job script can be used as a template to run abaqus batch jobs on one compute node.

#!/bin/bash

## specify the job and project name
#SBATCH --job-name=abaqus
#SBATCH --account=ab123

## specify the required resources
#SBATCH --partition=normal
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64000
#SBATCH --time=1-00:00:00

source ~/.bashrc
module load abaqus/2020
# module load intel/2021   # uncomment to load the intel compiler to build user subroutines
abaqus job=my_abaqus_sim_name input=my_sim.inp cpus=`nproc` mp_mode=threads interactive

Multi-node parallel Abaqus jobs#

The following job script below can be used to run a parallel Abaqus job using multiple compute nodes in batch mode. The script below can be downloaded by clicking here

If a graphica user interface job is used then the following script should be executed in the same folder where the command abaqus cae -mesa is executed:

module load abaqus
chmod +x slurm_abaqus_mpi_env_gen.sh
./slurm_abaqus_mpi_env_gen.sh
abaqus cae -mesa

After the job is executed MPI must be selected in the the ABAQUS job in the GUI.

script for running a multi-node parallel job in batch mode

#!/bin/bash

## specify the job and project name
#SBATCH --job-name=abaqus
#SBATCH --account=ab123

## specify the required resources
#SBATCH --partition=large
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --mem=64000
#SBATCH --time=1-00:00:00

source ~/.bashrc
module load abaqus/2020

##############################################################
# DO NOT MODIFY BEYOND THIS UNLESS YOU KNOW WHAT YOU ARE DOING
##############################################################

# dump the hosts to a text file
SLURM_HOSTS_FILE=slurm-hosts-${SLURM_JOBID}.out

#
# generate the mp_host_list environment variable
#
srun hostname > ${SLURM_HOSTS_FILE}

mp_host_list="["
for HOST in `sort ${SLURM_HOSTS_FILE} | uniq`; do
    echo ${HOST}
    mp_host_list="${mp_host_list}""['${HOST}',`grep ${HOST} ${SLURM_HOSTS_FILE} | wc -l`]"
done

mp_host_list=`echo ${mp_host_list} | sed 's/\]\[/\]\,\[/g'`"]"

echo $mp_host_list

#
# write the abaqus environment file
#
ABAQUS_ENV_FILE="abaqus_v6.env"
cat > ${ABAQUS_ENV_FILE} << EOF
import os
os.environ['ABA_BATCH_OVERRIDE'] = '1'
verbose=3
mp_host_list=${mp_host_list}
if 'SLURM_PROCID' in os.environ:
    del os.environ['SLURM_PROCID']
EOF

abaqus job=my_input_file.inp cpus=$SLURM_NPROCS` -verbose 3 standard_parallel=all mp_mode=mpi interactive

User defined subroutines and functions in Abaqus#

To define user subroutines and functions in Abaqus the following steps should be followed:

Create the subroutine file (e.g. my_custom_constants.f)

Compile it to build a library

Run the simulation using the compiled library

The .inp and the .f file should be in the same folder. It is possible to organize them into different folders but the paths should be specified with care (check the abaqus help and documentation for more information).

The following should exist in the directory of the simulation:

job.sh

my_simulation.inp

my_custom_constants.f

libstandardU.so # this is generated in step-2 below

Step-1: Create the subroutine file#

The following example shows how to create a subroutine file (disclamer, this subroutine does not do anything useful, please make sure to replace the content with your own):

 SUBROUTINE CREEP(DECRA,DESWA,STATEV,SERD,EC,ESW,P,QTILD,
1 TEMP,DTEMP,PREDEF,DPRED,TIME,DTIME,CMNAME,LEXIMP,LEND,
2 COORDS,NSTATV,NOEL,NPT,LAYER,KSPT,KSTEP,KINC)

 INCLUDE 'aba_param.inc'

 CHARACTER*80 CMNAME
 DIMENSION DECRA(*)

 DECRA(1) = 0.001 * DTIME

 RETURN
 END

Step-2: Compile the subroutine file#

The Intel compiler environment should be loaded since abaqus relies on Intel’s fortran compiler to build the libraries. The following command can be used to

module load intel/2021
$ abaqus make library=my_custom_constants.f

[john@node ~]$ abaqus make library=foo.f
Abaqus JOB foo.f
Begin Compiling Abaqus/Standard User Subroutines
Mon 13 May 2024 05:28:07 AM EEST
Intel(R) Fortran Intel(R) 64 Compiler Classic for applications running on Intel(R) 64, Version 2021.2.0 Build 20210228_000000
Copyright (C) 1985-2021 Intel Corporation.  All rights reserved.

 Intel(R) Fortran 2021.2.0-2262
End Compiling Abaqus/Standard User Subroutines
Begin Linking Abaqus/Standard User Subroutines
Intel(R) Fortran Intel(R) 64 Compiler Classic for applications running on Intel(R) 64, Version 2021.2.0 Build 20210228_000000
Copyright (C) 1985-2021 Intel Corporation.  All rights reserved.

GNU ld version 2.27-34.base.el7
End Linking Abaqus/Standard User Subroutines
Mon 13 May 2024 05:28:13 AM EEST
Abaqus JOB foo.f COMPLETED

```

The following file will be generated libstandardU.so that is automatically picked up by abaqus when running the simulation.