UQ HPC Web Pages - How should I run compute jobs on VisAC workstations?

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How should I run compute jobs on VisAC workstations?

The short answer is to make use of the Sun Grid Engine batch system that has been deployed in the VisAC workstation lab.

Please the batch system whenever you wish to run computations on the lab machines that will take longer than on hour to finish.

The details of how are as follows:

1. Before you can use N1 Sun Grid engine you need to set up the environment.

This is most easily done by adding lines to your personal .bashrc file.

So, edit $HOME/.bashrc and add the lines:

#
#Settings for SunGridEngine
source /opt/sge/ViSAC/common/settings.sh

2. Manually source the settings file or logout and log back in again.

source /opt/sge/ViSAC/common/settings.sh

3. Next create a submission script file.

This contains what you want to have done, and also some special instructions to SGE about run time environment. The submit script looks like a shell script and can be tested at the command line if you wish. I name my submission script something.sge but you can call it anything you like.

The following example will submit a job to the mathematica queue that will run only on nodes that are licensed for Mathematica.

#!/bin/sh
#
#
# (c) 2007 Sun Microsystems, Inc. All rights reserved. Use is subject to license terms.  

# This is a simple example of a SGE batch script
# request Bourne shell as shell for job
#$ -S /bin/sh
#$ -N Mathe_RRR
#$ -cwd
#$ -q mathematica
#
# print date and time
/bin/date
echo
echo WorkDir is $SGE_O_WORKDIR
echo StdOut  is $SGE_STDOUT_PATH
echo StdErr  is $SGE_STDERR_PATH
echo
/bin/hostname
# Sleep for 20 seconds
sleep 1
# print date and time again
/bin/date

RUN=RRR
/usr/local/Wolfram/Mathematica/5.1/Executables/math < ${RUN}.m 1> ${RUN}.out 2> ${RUN}.err


4. Submit your job

qsub  something.sge

5. Verify that it was queued

qstat -f

The output will look like this:

-bash-3.1$ qstat -f

queuename                      qtype used/tot. load_avg arch          states

----------------------------------------------------------------------------

all.q@ws01.visac.uq.edu.au     BIP   0/2       1.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws02.visac.uq.edu.au     BIP   0/2       1.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws03.visac.uq.edu.au     BIP   0/2       1.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws04.visac.uq.edu.au     BIP   0/2       1.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws05.visac.uq.edu.au     BIP   0/2       1.02     lx24-x86

----------------------------------------------------------------------------

all.q@ws06.visac.uq.edu.au     BIP   0/2       1.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws07.visac.uq.edu.au     BIP   0/2       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws08.visac.uq.edu.au     BIP   0/2       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws09.visac.uq.edu.au     BIP   0/2       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws10.visac.uq.edu.au     BIP   0/2       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws11.visac.uq.edu.au     BIP   0/2       0.01     lx24-x86

----------------------------------------------------------------------------

all.q@ws12.visac.uq.edu.au     BIP   0/2       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws13.visac.uq.edu.au     BIP   0/1       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws14.visac.uq.edu.au     BIP   0/2       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws15.visac.uq.edu.au     BIP   0/2       -NA-     lx24-x86      au

----------------------------------------------------------------------------

all.q@ws17.visac.uq.edu.au     BIP   0/2       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws18.visac.uq.edu.au     BIP   0/2       1.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws19.visac.uq.edu.au     BIP   0/2       0.00     lx24-x86

----------------------------------------------------------------------------

all.q@ws20.visac.uq.edu.au     BIP   0/2       -NA-     lx24-x86      au

----------------------------------------------------------------------------

mathematica@ws01.visac.uq.edu. BIP   1/1       1.00     lx24-x86

    115 0.55500 Dermo_a    uqdgree5     r     06/13/2008 00:26:50     1

----------------------------------------------------------------------------

mathematica@ws02.visac.uq.edu. BIP   1/1       1.00     lx24-x86

    116 0.55500 Dermo_b    uqdgree5     r     06/13/2008 00:28:50     1

----------------------------------------------------------------------------

mathematica@ws03.visac.uq.edu. BIP   1/1       1.00     lx24-x86

    119 0.55500 Dermo_e    uqdgree5     r     06/13/2008 00:29:20     1

----------------------------------------------------------------------------

mathematica@ws04.visac.uq.edu. BIP   1/1       1.00     lx24-x86

    117 0.55500 Dermo_c    uqdgree5     r     06/13/2008 00:29:05     1

----------------------------------------------------------------------------

mathematica@ws05.visac.uq.edu. BIP   1/1       1.02     lx24-x86

    120 0.55500 Dermo_f    uqdgree5     r     06/13/2008 12:09:35     1

----------------------------------------------------------------------------

mathematica@ws06.visac.uq.edu. BIP   1/1       1.00     lx24-x86

    118 0.55500 Dermo_d    uqdgree5     r     06/13/2008 00:29:05     1


############################################################################

 - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS

############################################################################

    121 0.55500 Dermo_g    uqdgree5     qw    06/13/2008 00:29:11     1

    122 0.55500 Dermo_h    uqdgree5     qw    06/13/2008 00:29:14     1

6. Relax and wait for the results to arrive. 
There are options for emailing you when your job is started, aborted or finished such as

#$ -m abe
#$ -M someone@somewhere.else

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