ABAQUS on Sweetgum at UM/MCSR 

See also Abaqus on Redwood at MCSR

1.        How can I run an Abaqus job on sweetgum using PBS?

2.        What version(s) of Abaqus are installed?

3.        Can I run Abaqus interactively?

4.        What is the largest Abaqus file I can create with Abaqus on sweetgum?

5.        How long does it take to create 17 gigabytes file?

6.        What will happen if I reach the limit?

7.        What should I do not to reach the limit and run my job?

8.        Does the command line changes other than the first run in the PBS script?

9.        How do I reach the manuals on sweetgum?

10.     link to Abaqus official site

11.     link to PBS official site

How can I run an Abaqus job on sweetgum using PBS?

When you login to your sweetgum account, you will see the command line as below:

sweetgum%

Then type vi [filename] to the command line to edit a PBS file.

Example:

sweetgum% vi run.pbs

Instead of vi editor, you may use pico editor by typing pico instead of vi to the command line. Then type the lines as shown in the format below to the PBS file you have created:

#PBS -l ncpus=[number of processors],mem=[memory in terms of gigabyte]

#PBS -m abe

limit coredumpsize 10 kbytes

cd [directory your abaqus file is in]

module add ab58

ab58 job=[filename{no extension}] interactive

Example:

#PBS -l ncpus=1,mem=1gb

#PBS -m abe

limit coredumpsize 10 kbytes

cd /ptmp/ccsam/abaqus

module add ab58

ab58 job=run1 Interactive

After you have saved and exit from the PBS file, which is called run.pbs in our example, type the command qsub [filename] to the command line.

Example:

sweetgum% qsub run.pbs

This command will run the file you have specified at the last line of the PBS file.

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What version(s) of Abaqus are installed?

Abaqus version 6.5-5 is currently installed on sweetgum. To activate Abaqus6.5-5 on sweetgum enter:

/usr/local/appl/bin/ab655

after the above command is entered, user should enter my.inp, where my.inp is the input file.

Below is the command to run a job under Abaqus6.41:

ab641 job=my.inp, where “my.inp” is the user’s input file.

                Table 1. Command table for versions of ABAQUS

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Can I run Abaqus interactively?

You can run Abaqus interactively if the cpu time of run is not more than 30 minutes out of 24 hours. In other words I-limit is 30 minutes.

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What is the largest Abaqus file I can create with Abaqus on sweetgum?

The largest Abaqus restart file you can create is 17 gigabytes. The output file is achieved from the restart file.

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How long does it take to create 17 gigabytes file?

The approximate period to create a 17-gigabyte file is 30 hours. Do not forget PBS script should be used to run a job, the run size of which is more than 30 minutes.

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What will happen if I reach the limit?

If you reach the limit, which means you have created 17GB restart file, the job submitted will just hang. It will not stop or kill itself. You have to kill it manually.

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What should I do not to reach the limit and run my job?

To prevent the job to create a file above the limit file, you should create a restart file (.res) usually every 2 GB and run the job step by step by using the previous restart file as an input to the next run that forms another restart file. Then you will have lots of 2 GB files but not one file above the limit.

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Does the command line changes other than the first run in the PBS script?

The command line in the PBS script as shown below will change because PBS doesn’t accept standard input of the name of the oldfile (previous run).

ab611 job=[filename{no extension}] interactive

In other words, PBS will not recognize the input from terminal. Thus, this leaves us one solution; enter the name of the previous run from the command line by typing oldjob parameter.

ab611 job=[filename{no extension}] oldjob=[filename of previous run{no extension}] interactive

Example (PBS script for second run):

#PBS -l ncpus=1,mem=1gb

#PBS -m abe

limit coredumpsize 10 kbytes

cd /ptmp/ccsam/abaqus

module add ab58

ab58 job=run2 oldjob=run1 Interactive

If the Abaqus command cannot be executed by simply the command, this means the command is not specified in your account’s binary path. So try to specify the directory of abaqus binary file in the last line of script by typing /usr/local//appl/bin/[command syntax].

/usr/local/appl/bin/ab641 job=run2 oldjob=run1 Interactive

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How do I reach the manuals on sweetgum?

The manual commands on sweetgum are as shown in Table 2. below.

                Table 2. Commands to run various ABAQUS versions

Example:

sweetgum% abaqus doc

If you are working with a computer running other than Unix or Linux operating systems, you should be running X-Win software package to be able to open the manuals.

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