HowTo:abaqus

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Abaqus

This is a short help file on using the Finite-Element Analysis (FEA) code "Abaqus" on our machines. This software is only licensed for academic researchers who work at a university that is already covered by an Abaqus license. The software is only made available to persons who belong to a specific Unix group. See details below.

This file documents the usage of the software on both the "old" SW cluster and the "new" Frontenac cluster. Please make sure you consult the sections for the right platform

What is Abaqus ?

The ABAQUS suite of software for finite element analysis (FEA) has the ability to solve a wide variety of simulations. The ABAQUS suite consists of three core products - ABAQUS/Standard, ABAQUS/Explicit and ABAQUS/CAE.

  • ABAQUS/Standard is designed to solve traditional implicit finite element analyses, such as static, dynamics, and thermal. It is equipped with a wide range of contact and nonlinear material options. ABAQUS/Standard also has optional add-on and interface products, as well as integration with third party software.
  • ABAQUS/Explicit is focused on transient dynamics and quasi-static analyses using an explicit approach appropriate in many applications such as drop test, crushing and many manufacturing processes.
  • ABAQUS/CAE provides a modeling and visualization environment for ABAQUS analysis products. It offers access to CAD models, advanced meshing and visualization, and an exclusive view towards ABAQUS analysis products. ABAQUS/CAE is used mainly for pre- and post-processing. Note that this part of the ABAQUS software is not running on our machines, but on a user client machine.

Version

The most recent version of Abaqus on our systems is Abaqus 2017. Earlier versions are available.

Location

All versions of the Abaqus package are located in the directory /opt/abaqus (on SW cluster, swlogin1) or /global/software/abaqus (on Frontenac, caclogin01).

Access and Licensing

This software is only available to our users working at a university that is already covered by a license. Since our license does count as a license for Queen's University, this software can be used by our Queen's users without stipulation. To use it, you are required to read through the Abaqus Licensing Policy, and sign a statement. Then you will be added to a Unix group "abaqus", which enables you to run the software. Contact us if you are in doubt of whether you will be able to run Abaqus on our system.

The Abaqus license is "token limited". At present, there are the following licensing limits on our systems. Different components of the software different numbers of tokens for execution. The number of tokens is approximately equal to the number of processors employed. Currently our license supports

150 process tokens

Running Abaqus

Setup

On SW cluster

Setup through the "usepackage" command:

use abaqus

will add the proper directories to the PATH and enable using the software. This needs to be done on the Linux workup node swlogin1. The version this is currently setting up is 6.11 (for compatibility). To setup for the latest version (2017) use

use abaqus-2017

On Frontenac

Setup through the "module" command:

module load abaqus

will add the proper directories to the PATH and enable using the software. The version this is currently setting up is the current "2017".

Interactive runs

The following instructions assume that you are a member of the Unix group "abaqus". They pertain only to the Standard and Explicit components of the software. The instructions in this section are only useful if you want to run an interactive test job of Abaqus on the workup node. If you want to run a production job, please refer to to instructions on how to start a Abaqus batch job (see next section).

The Abaqus program uses a sophisticated syntax to set up a job run. Instructions to the program are written into an input file which is specified when the program is evoked. While an input file can be written "from scratch", it is also possible to use the ABAQUS/CAE component to generate such a file. Both techniques are outside the scope of this FAQ. You also can have a look at a simple example input file here . Documentation for Abaqus is extensive, and available both electronically and in print. There is no substitute to consulting it.

Assuming that we have an input file called testsys.inp, we can initiate a run:

abaqus job=test001 inp=testsys.inp scratch=/scratch/hpcXXXX  (on SW)
abaqus job=test001 inp=testsys.inp scratch=/global/scratch/hpcXXXX  (on Frontenac)

The job= option specified what the output files are to be called. They have various different "filename extensions" but share the name specified here (in our case test001). With the inp= option, we specify which input file to use. There are more options, such as cpus= and mp_mode= for running parallel jobs, but the two used above should get a simple serial job running.

The above sequence starts the job in the background, i.e. after an initial setup phase, your terminal returns although the job is still running. If you want to avoid this, you can include the interactive option in the command line.

The Abaqus software uses a directory in /tmp (which is local to the nodes on which the software is executing) as scratch space. This is the default setting and causes some Abaqus jobs to fail. It must therefore be changed to the standard scratch space /scratch/hpcXXXX on SW or /global/scratch/hpcXXXX on Frontenac, where XXXX being the numbers in your username. This can be done by including the option scratch=/opt/hpcXXXX or scratch=/global/scrach/hpcXXXX in your command line.

Also, do not forget to occasionally check the contents of this scratch directory by typing (replacing XXXX with the proper numbers for your username):

ls -lt /scratch/hpcXXXX (SW)
ls -lt /global/scratch/hpcXXXX (Frontenac)

and removing any files that might be left over from old Abaqus runs. This is necessary because Abaqus will not remove these files if a job was terminated before it ran to completion.

More about changing the Abaqus environment may be learned from the "Installation and Licensing Guide" (chapter 4) of the Abaqus documentation. Please contact us if you need assistance.

Parallel production (batch) runs

In most cases, you will run Abaqus in batch mode. Most interactive work can be done elsewhere, whereas the computationally intensive runs are executed on the cluster. Production jobs are submitted on the systems via a scheduler.

Note that the usage of the scheduler for all production jobs is mandatory. Production jobs that are submitted outside of the load balancing software will be terminated by the system administrator.

The Abaqus jobs that you will want to run on our machines are likely to be quite large. To utilize parallelism, Abaqus offers to execute the solver on several CPU's simultaneously.

The Abaqus software achieves a certain degree of parallel scaling using either shared- or distributed memory machines. Here is a list of operations with the corresponding parallel mode that Abaqus supports:

  • Element operations - MPI only
  • Iterative solver - MPI or threads
  • Direct solver - Threads only
  • Lanczos solver - Threads only

Note that only the shared-memory parallelism is in use on our clusters. It is necessary to decide before a parallel Abaqus run how many processes are to be started.

On SW cluster

To obtain details about the scheduler, read our Gridengine help file. For an Abaqus batch job, this means that rather than issuing the above commands directly, you wrap them into a Grid Engine batch script. Production jobs must be submitted via the Grid Engine scheduling software. Here is an example script for a parallel submission:

#!/bin/bash
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -m be
#$ -M {email address}
#$ -o {output file}
#$ -e {error file}
#$ -pe shm.pe {number of processors}
export PATH="/opt/abaqus/6.11/Commands":$PATH
export PATH="/bin":$PATH
source /opt/ics/bin/compilervars.sh intel64
abaqus job={job_name} input={input file} scratch=/scratch/{username} cpus=$NSLOTS mp_mode=threads -interactive

This script needs to be altered by replacing all the relevant items in curly brackets by the right values. The -interactive option is necessary; without it the program will not start properly. The -m and -M option set up email notification at the beginning and end of a run. -o and -e redirect the screen output (standard output and standard error) to a specified file. -V and -cwd instruct the scheduler to inherit shell settings and work from the current directory, respectively.

The -pe line sets up a parallel run. It is used to specify the number of processors, and asks for the corresponding number of free cores from the scheduler. It also sets the variable NSLOTS which is used on the "abaqus" command line to execute the software with that number of processors. This way you have to set it only once in the -pe line. Grid Engine allocates all processors on a single node.

Note that Abaqus needs to be set up correctly before submitting this script, as it inherits the settings of the submitting shell.

After altering the script (let's call it adf.sh) by substituting the items enclosed in curly brackets, it is submitted by

qsub abaqus_test.sh

On Frontenac

Production jobs must be submitted via the SLURM scheduler. To obtain details about the scheduler, read our SLURM help file. For an Abaqus batch job, this means that rather than issuing the commands directly, you wrap them into a batch script that looks similar to this:

#!/bin/bash
#SBATCH --job-name=Abaqus_Test
#SBATCH --mail-type=ALL
#SBATCH --mail-user=myEmail@whatever.com
#SBATCH -o STD.out
#SBATCH -e STD.err
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH -t 05:00
#SBATCH --mem=1000
module load abaqus
abaqus job=test input=testsys.inp cpus=$SLURM_CPUS_PER_TASK mp_mode=threads scratch=/global/scratch/hpcXXXX  -interactive

The script (let's call it ababus_test.sh) needs to be altered to fit the specifics.

The --mail-type and --mail-user lines set up for email notification at beginning and end of a run. -o and -e are meant to specify a file name to capture "standard output" and "standard error", i.e. the information that would be sent to the screen in an interactive run.

The -t option indicates a time limit. Choose it such that the job will have time to finish as it will be terminated when the time limit is reached. Note that this must be specified as it otherwise set to a (likely too short) default value. Don't set it too long either, as that will make the job hard to schedule. The same hold for the --mem option specifying an upper limit for memory usage. Jobs that use more than this limit will terminate. Choose it such that the job "fits" but don't high-ball it too much, as this will make the job hard or impossible to schedule.

Keep the "-n" and "-N" options at 1 to indicate that one main process is running on a single node.

The -c option specifies the number of processors (cores) that are requested. The value of the variable SLURM_CPUS_PER_TASK is set to the value specified in this line. "mp_mode=threads" enables shared-memory parallel execution. Note that all processors are allocated on a single node.

After altering the script appropriately, it is submitted by

sbatch ababus_test.sh

Because of the limited scaling capabilities, only 12-processor jobs should be run. Also, the total memory of each node is limited, meaning that jobs with large memory requirements should request memory up-front to avoid getting scheduled on too small a node. Please contact us if you need help with this.

Migration SW -> Frontenac

The following is a list of differences concerning Abaqus usage on the SW cluster vs the new Frontenac cluster. The main impact comes from the different scheduler.

Changes when migrating from SW cluster (SGE) to Frontenac (SLURM)
SW (swlogin1) Frontenac (caclogin01)
default Version 6.11 (2017 available) 2017
Scheduler Sun Grid Engine (SGE) SLURM
GUI available yes yes
Queue specification
in submit script
none none
Login node for
submission
swlogin1 caclogin01
Setup command use abaqus module load abaqus











For Queen's Users : Installing Abaqus on your local PC

Our Abaqus license counts as a floating site license for Queen's University. As a result, our users can access the license from other locations on Queen's Campus. This only works for fixed machines on the Queen's network. Here are instructions on how to install Abaqus on a Queen's PC. Note that we will make the software available only to our Queen's users and that the license server is being monitored. Usage falling outside of the licensing terms is prohibited and will be investigated if detected.

  1. Download files
    2017.AM_SIM_Abaqus_Extend.AllOS.X-6.tar (X=1…6)
    [contact us about location]
  2. Unpack the files using a tool such as 7z (http://www.7-zip.org/download.html) into a directory close to root (c:) to avoid overly long file names. Make sure all 6 are unpacked into the same directory
  3. Find the file "hosts" in /Windows/System32/drivers/etc and open it as administgrator. Insert the line
    130.15.59.6   license08.cac.queensu.ca
    and save the file. This is crucial.
  4. Go into AM_SIM_Abaqus_Extend.AllOS/1 of the unpacking directory and execute the file "setup.exe"
  5. Install the following products in that order and one-by-one, i.e. only highlight one at a time and hit next:
    Abaqus Simulation Services, Abaqus Simulation Services CAA API, Abaqus/CAE
  6. When installing Abaqus/CAE it will ask you for various directories etc. When possible, go for the default. When asked for the licensing, select "Flexnet" and enter
    28525@license08.cac.queensu.ca
    into the box. If this works after you press "Next", you're in business. This will only work if you have done Step 3 properly. At some point it will ask about documentation, but handle that later, i.e. opt out of it for now.
  7. Once these three components are installed, the software should work.

Further Help

Abaqus is a very complex software package, and requires some practice to be used efficiently. We can't explain it use in any detail here.

  • Online documentation for the program is available on machines where Abaqus is installed.
  • On the login node, it can be accessed by a web browser:
/opt/abaqus/2017/SIMULIA2017doc/English/DSSIMULIA_Established.htm (SW cluster)
/global/software/abaqus/2017/SIMULIA2017doc/English/DSSIMULIA_Established.htm (Frontenac) 

Start firefox locally. For security, we do not have a web server running on the cluster.

  • A pdf version of the Abaqus documentation can be found in /opt/abaqus (SW cluster, swlogin1) or /global/software/abaqus (Frontenac, caclogin01)
  • We provide user support. Please send email to cac.help@queensu.ca.