How do I run "Abaqus" on the workup node?

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 a test job of Abaqus on the login node sfnode0. 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 a 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 (using enivronment variable ABAQUS_HOME:

export ABAQUS_HOME=/opt/abaqus-6.5/Commands 
$ABAQUS_HOME/abaqus job=test001 inp=testsys.inp scratch=/scratch/hpcXXXX

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.

Note that 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.

Note that 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 (XXXX being the numbers in your userid). This can be done in one of two ways:

• Either include the option "scratch=/opt/hpcXXXX" (not including the double quotes) in your command line.
• Or put a file called abaqus_v6.env into your home directory ($HOME) that contains the line:
  scratch="/opt/hpcXXXX" (including the double quotes).

The second option is probably preferable. Note that the scratch directory has to be creaed manually, for instance for user hpc1005, type:

mkdir /scratch/hpc1005
chmod 700 /scratch/hpc1005

Also, do not forget to occasionally check the contents of this scratch directory by typing (sticking with the hpc1005 example):

ls -lt /scratch/hpc1005

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.

The abaqus_v6.env file in the home directory can also be used to "fix" a memory problem that sometimes arises when large jobs are run. If the .msg file of an Abaqus run shows errors because of not enough "Standard Memory", you can reset this by including the line

standard_memory="512 mb" 

(including the quotes) to reset it to 512 MB. The default is 256 MB.

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.