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Abaqus

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

Usage

Abaqus versions 2018, 2017-ga, 2017 or 6.14-2 can be activated using the module files:

module load apps/abaqus/2018/binary
module load apps/abaqus/2017-ga/binary
module load apps/abaqus/2017/binary
module load apps/abaqus/6.14-2/binary

Type abaqus cae to launch the Abaqus GUI from an interactive session with X Window support (e.g. an interactive qsh session). Please see usage note below for graphics support options. Type abaqus for the command line interface. Typing abaqus -help will display a list of usage options.

Abaqus 2017-ga (module apps/abaqus/2017-ga/binary) has the Tosca component installed and is equivalent to Abaqus 2017 (‘ga’ is an accronym for ‘general availabilty’).

The PDF viewer foxit can be launched to view the PDF documentation for Abaqus 6.14-2 located at /usr/local/packages/apps/abaqus/6.14-2/binary/Documentation/docs/v6.14/pdf_books.

Abaqus 2017 documentation in HTML format is located at /usr/local/packages/apps/abaqus/2017/binary/Documentation/DSSIMULIA_Established_homepage_English.htm.

Abaqus 2017-ga documentation in HTML format is located at /usr/local/packages/apps/abaqus/2017-ga/binary/SIMULIA2017doc/DSSIMULIA_Established_homepage_English.htm.

Abaqus 2018 documentation in HTML format is located at /usr/local/packages/apps/abaqus/2018/binary/SIMULIA2018doc/DSSIMULIA_Established_homepage_English.htm.

Note: When using hardware-accelerated graphics rendering for Abaqus 6.14-2 on ShARC, i.e., during a qsh-vis interactive session, please run abq6142 cae to launch the GUI. When using a general compute node for Abaqus 2017, 2017-ga or 2018 on ShARC, please run abaqus cae -mesa or abq2017 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 easiest way of running a batch job for a particular version of Abaqus (e.g. 6.14-2) is:

module load apps/abaqus/6.14-2/binary
runabaqus

The runabaqus command submits an Abaqus input file into the batch queuing system and can take a number of different parameters according to your requirements. Typing runabaqus will display information about its usage. Note: runabaqus is not setup for use with Abaqus 2017, 2017-ga and 2018.

Users are encouraged to write their own batch submission scripts. The following is an example batch submission script, my_job.sh, to run the executable abq6142 and which is submitted to the queue by typing qsub my_job.sh:

#!/bin/bash
#$ -cwd
#$ -l h_rt=00:30:00
#$ -l rmem=2G
#$ -pe smp 4

module load apps/abaqus/6.14-2/binary

abq6142 job=my_job input=s4d.inp scratch=$TMPDIR memory="2gb" interactive mp_mode=threads cpus=$NSLOTS

The above script requests 4 cores using the OpenMP parallel environment smp with a runtime of 30 mins and 2 GB of real memory per core. The Abaqus input file is s4d.inp.

User subroutines: 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
#$ -cwd
#$ -l h_rt=00:30:00
#$ -l rmem=8G

module load apps/abaqus/6.14-2/binary

abq6142 job=my_user_job input=umatmst3.inp user=umatmst3.f scratch=$TMPDIR memory="8gb" interactive

The input file umatmst3.inp and the Fortran user subroutine umatmst3.f are obtained by typing abaqus fetch job=umatmst3*. Note that the module dev/intel-compilers/15.0.7, required for user subroutines, is automatically loaded when the module for Abaqus is loaded.

Important information: Please note that at present Abaqus will not run on more than one node when using MPI on ShARC. The SGE option -l excl=true can be used to request that an MPI job runs on one compute node only. The recommended way to run Abaqus in parallel on ShARC is to use OpenMP.

Using /fastdata as your Abaqus working directory

If you want to run Abaqus from a directory on /fastdata then you need to have the following line in your batch job submission script just before the main abaqus command:

export BAS_DISABLE_FILE_LOCKING=1

Otherwise your Abaqus job will fail and you will see errors like the following in your my_job_name.dat output file:

***ERROR: An error occurred during a write access to
          <rank=0,arg_name=outdir>my_user_job.stt file. Check the disk space
          on your system.

This is a lie; Abaqus is failing to write the .stt file as it tries to use file locking which is not enabled on the /fastdata filesystem at present for performance reasons. Setting the BAS_DISABLE_FILE_LOCKING environment variable to 1 is a Dassault Systems-approved workaround for this.

Licensed options

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

$ module load apps/abaqus/2017/binary
$ abaqus licensing r

Feature                         Version     #licenses    Expires      Vendor
_______                         _________   _________    __________   ______
abaqus_extended                 61.9         19          31-dec-2018  ABAQUSLM
abaqus                          61.9         250         31-dec-2018  ABAQUSLM
ams                             61.9         1           31-dec-2018  ABAQUSLM
aqua                            61.9         250         31-dec-2018  ABAQUSLM
cosim_acusolve                  61.9         1           31-dec-2018  ABAQUSLM
cosim_direct                    61.9         1           31-dec-2018  ABAQUSLM
cse                             61.9         1           31-dec-2018  ABAQUSLM
design                          61.9         250         31-dec-2018  ABAQUSLM
euler_lagrange                  61.9         1           31-dec-2018  ABAQUSLM
gpgpu                           61.9         1           31-dec-2018  ABAQUSLM
multiphysics                    61.9         1           31-dec-2018  ABAQUSLM
parallel                        61.9         16384       31-dec-2018  ABAQUSLM
sw_assoc_import                 61.9         1           31-dec-2018  ABAQUSLM
catiav5_assoc_import            61.9         1           31-dec-2018  ABAQUSLM
catiav5_import                  61.9         1           31-dec-2018  ABAQUSLM
catiav6_assoc_import            61.9         1           31-dec-2018  ABAQUSLM
tomee                           61.9         1           31-dec-2018  ABAQUSLM
pydriver                        61.9         1           31-dec-2018  ABAQUSLM
cae                             61.9         19          31-dec-2018  ABAQUSLM
rtgateway                       61.9         19          31-dec-2018  ABAQUSLM
gateway                         61.9         19          31-dec-2018  ABAQUSLM
safe_ex_gui                     61.9         19          31-dec-2018  ABAQUSLM
cfd                             61.9         250         31-dec-2018  ABAQUSLM
explicit                        61.9         250         31-dec-2018  ABAQUSLM
foundation                      61.9         250         31-dec-2018  ABAQUSLM
simflow                         61.9         250         31-dec-2018  ABAQUSLM
standard                        61.9         250         31-dec-2018  ABAQUSLM
cse_token                       61.9         250         31-dec-2018  ABAQUSLM
safe_ex_engine                  61.9         250         31-dec-2018  ABAQUSLM
tosca_topo                      61.9         250         31-dec-2018  ABAQUSLM
tosca_shape                     61.9         250         31-dec-2018  ABAQUSLM
tosca_bead                      61.9         250         31-dec-2018  ABAQUSLM
tosca_sizing                    61.9         250         31-dec-2018  ABAQUSLM
tosca_int_abaqus                61.9         250         31-dec-2018  ABAQUSLM
tosca_int_ansys                 61.9         250         31-dec-2018  ABAQUSLM
tosca_int_nastran               61.9         250         31-dec-2018  ABAQUSLM
tosca_adv_nonlinear             61.9         250         31-dec-2018  ABAQUSLM
tosca_adv_durability            61.9         250         31-dec-2018  ABAQUSLM
tosca_adv_morph                 61.9         250         31-dec-2018  ABAQUSLM
tosca_smooth                    61.9         250         31-dec-2018  ABAQUSLM
tosca_report                    61.9         250         31-dec-2018  ABAQUSLM
tfluid_topo                     61.9         250         31-dec-2018  ABAQUSLM
tfluid_smooth                   61.9         250         31-dec-2018  ABAQUSLM
tfluid_parallel                 61.9         250         31-dec-2018  ABAQUSLM
tfluid_int_ccmp                 61.9         250         31-dec-2018  ABAQUSLM
tfluid_int_fluent               61.9         250         31-dec-2018  ABAQUSLM

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

Installation notes

Abaqus 2018 was installed using the install_abaqus_2018.sh script; the module file is /usr/local/modulefiles/apps/abaqus/2018/binary.

Abaqus 2017-ga was installed using the install_abaqus_2017-ga.sh script; the module file is /usr/local/modulefiles/apps/abaqus/2017-ga/binary.

Abaqus 2017 was installed using the install_abaqus_2017.sh script; the module file is /usr/local/modulefiles/apps/abaqus/2017/binary.

Abaqus 6.14-2 was installed using the install_abaqus.sh script; the module file is /usr/local/modulefiles/apps/abaqus/6.14-2/binary.

The binary installations were tested by launching abaqus cae and by using the above batch submission scripts. Abaqus at present does not run on more than one node when using MPI due to password-less ssh being disabled across nodes on ShARC.