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CAE utilities

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Revision as of 14:26, 16 October 2008 by Hpcbern (talk | contribs) (→‎qgen)
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A collection of small helper scripts.

module load cae

will you take care that these are found when called through the commandline or e.g. a job script.


qgen will generate a job script based on a template.

qgen -h

will print some help and

qgen -l

will list all available templates found in the QGEN_TEMPLATE_PATH One of these templates is "test", which doesn't need any further arguments.

qgen test

A job file will be printed. Save this job file to "test.pbs" and compare it with the template:

qgen -o test.pbs test
tkdiff test.pbs /app/rus/struct/bin/qgen_templates/test

(If there's no X avaiable, replace tkdiff with e.g. sdiff)

qgen just replaces some placeholders within the template. Everyone can expand the system writing own templates. The default path for these files is ~/qgen_templates

Now the job script could be submitted with "qsub test.pbs", but... (approx.) the same (for 2 requested nodes) can also be achieved with:

qgen -n 2 --submit test

However, omitting the -o option, the executed job script will not be saved for the user.

In general, templates require additional options. The help might give you a hint at the end, e.g.

qgen -h abaqus
qgen    a tool to generate(&submit) pbs jobfiles        (author: Martin Bernreuther <bernreuther@hlrs.de>)
usage: qgen [-n|--nodes <nodes>] [-t|--walltime <walltime>] [-N|--jobname <jobname>] [-w|--workdir <workdir>] [-o <jobfile>] [--submit|--submitq <queue>|--execute] [-] [<template>] [<template_opt1> <template_opt2>...]
      -n|--nodes <nodes>       [default: 1]    number of nodes
      -t|--walltime <walltime> [default: 12:00:00]      walltime
      -N|--jobname <jobname>   [default: <template><datetime>] job name
      -w|--workdir <workdir>   [default: /scratch2/ws/hpcbern-dynatest-0]       working directory
      -o <jobfile>     [default: <stdout>]      jobfile output
      --submit         submit immediately (to standard queue)
      --submitq <queue>        submit immediately to queue
      --execute        execute on current host immediately
      -l               list system templates
      -h|--help                print help and exit
      <template>               template to use
      <template_options>       additional options depending on the template
qgen will create a pbs jobscript based on a template, substituting
$QGEN_NODES, $QGEN_WALLTIME, $QGEN_NAME, $QGEN_WORKDIR and $* (latter with template options)
Instead of setting the values with command line arguments,"
       echo "environment variables might be used (except for template options)
These environment variables might be also set in the configuration file
~/.qgenrc, which is sourced at the beginning.
Templates are searched for in $QGEN_TEMPLATE_PATH, actually set to:
~/qgen_templates /app/rus/struct/bin/qgen_templates

abaqus template_options: options for abaqus, e.g. job=<jobname>

Submitting an ABAQUS job on 4 nodes is as easy as executing

qgen -n 4 --submit abaqus job=<jobname>

with <jobname> as ABAQUS inputfile (absolute path or relative path to the current directory). Typically a workspace is used here. As mentioned before, more control is gained, if the PBS jobfile is generated first and submitted afterwards, like with this LS-Dyna example:

qgen -o lsdyna.pbs -n 8 dyna i=<inputfile>
qsub lsdyna.pbs

Before the submission with qsub, the jobfile might be changed/tuned.

There's also a simple template to execute a single command:

qgen -N cmdtoptest --submit cmd top -b -n 1

The -N option sets the jobname and affects the names of the stdout/stderr files. The output of the command "top -b -n 1" can thus be found in the cmdtoptest.o* file. The error output cmdtoptest.e* is hopefully empty...