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August 10, 2018 By jedicker

Abaqus

Abaqus is part of the SIMULIA suite of tools from 3DS.

Abaqus can be used to perform a variety of analyses in solid and structural mechanics as well as some types of fluid dynamics.

Abaqus is available on the HPC Clusters.   A sample sbatch script for an Abaqus job is shown below.  This sample job assumes you have an input file for Abaqus called my-sample.inp, and a Fortran module stored in the file my-sample.for.  The work directory is /work/my_group/ABAQUS/my-sample-folder.   The job requests a total of 32 processors on two nodes.

#!/bin/bash
#SBATCH -J my-sample
#SBATCH -D /work/my_group/ABAQUS/my-sample-folder
#SBATCH -N 2
#SBATCH -n 32
#SBATCH --partition=medium
#SBATCH --ntasks-per-node=16
# it's a good idea to tell SLURM to use a large amount of memory. 120000 = 120GB.
#SBATCH --mem=120000
#SBATCH --time=168:00:00
#SBATCH -C compute
#SBATCH --error=my-sample.%j.error
#SBATCH --output=my-sample.%j.output
#SBATCH --mail-type=BEGIN,FAIL,END,TIMELMIT_50,TIMELIMIT_80
#SBATCH --mail-user=username@iastate.edu
# Use this to setup the job to run after another so
# you consume excessive abaqus tokens
#SBATCH --depend=afterany:247211

cd /work/my_group/ABAQUS/my-sample-folder

# Load the Intel compiler and Abaqus software.
module load intel/17.4
module load abaqus/2017

# Abaqus doesn't support SLURM natively. So, the script below gets the list of
# allocated hosts from SLURM and uses it to construct the mp_host_list[] variable.
# It copies the global custom_v6.env file from the global Abaqus "site" directory and
# adds the mp_host_list[] line to the bottom of the abaqus_v6.env file in the current folder.

create_abaqus_mp_host_list.sh

unset SLURM_GTIDS

export I_MPI_HYDRA_BOOTSTRAP=ssh

export PBS_NODEFILE=$( /shared/bin/generate_pbs_nodefile )

abaqus interactive analysis job=my-sample input=/work/my_group/ABAQUS/my-sample-folder/my-sample.inp cpus=32 mp_mode=mpi memory="80 %" user=/work/my_group/ABAQUS/my-sample-folder/my-sample.for scratch=/work/my_group/ABAQUS/my-sample-folder

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