MBG wiki: SGE script to start a parallel job on the cluster

Difference (from prior major revision)

Changed: 1,3c1,5

<
< Cut-and-paste the script that follows in a reasonably named file like <i>myjob.sh</i>, edit the file and change the obvious things (like program name, arguments to program, name of log file, number of processors) and then submit the job with <b>qsub myjob.sh</b>. Check that it starts without problems using <b>qstat</b>.
< <code>

to

> To run a parallel MPI program on the cluster :
> * Create a dedicated directory somewhere in /work
> * Place all files needed by your job (and possibly also the executable) in this directory.
> * Create a file with a suitable name (like <i>myjob.sh</i>) containing the script that follows.
> <source>

Changed: 7c9

< # The name of the log file (MPI_log) ...

to

> # The name of the job (MPI_job) ...

Changed: 9c11

< #$ -N MPI_log

to

> #$ -N MPI_job

Added: 14a17,20

> # For the 'mpi_fast' environment you may want to define a master queue :
> #
> #$ -masterq server.q
> #

Changed: 32c38,41

< </code>

to

> </source>
> * Edit this file and change the obvious things (like program name, arguments to program, job name, number of processors).
> * Submit the job with <b>qsub myjob.sh</b>.
> * Check that it started without problems using <b>qstat</b>.

To run a parallel MPI program on the cluster :

Create a dedicated directory somewhere in /work
Place all files needed by your job (and possibly also the executable) in this directory.
Create a file with a suitable name (like myjob.sh) containing the script that follows.

Edit this file and change the obvious things (like program name, arguments to program, job name, number of processors).
Submit the job with qsub myjob.sh.
Check that it started without problems using qstat.