SGE template script example: Difference between revisions
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== The environment setup == | |||
Because the SGE queue at the MRC-LMB requires no additional variables, none of the XXXextra1XXX or XXXextra2XXX variables is needed. In their environment (.cshrc) one includes: | |||
<code> | |||
setenv RELION_QSUB_TEMPLATE="/lmb/home/scheres/app/relion/bin/qsub.csh" | |||
</code> | |||
The command used for job submission (to be given in the GUI) is <code>qsub</code>. | |||
== The template script == | |||
The following script is saved as /lmb/home/scheres/app/relion/bin/qsub.csh: | |||
<code> | <code> | ||
#!/bin/tcsh | #!/bin/tcsh | ||
Revision as of 17:01, 4 October 2011
The environment setup
Because the SGE queue at the MRC-LMB requires no additional variables, none of the XXXextra1XXX or XXXextra2XXX variables is needed. In their environment (.cshrc) one includes:
setenv RELION_QSUB_TEMPLATE="/lmb/home/scheres/app/relion/bin/qsub.csh"
The command used for job submission (to be given in the GUI) is qsub.
The template script
The following script is saved as /lmb/home/scheres/app/relion/bin/qsub.csh:
#!/bin/tcsh
#$ -pe XXXqueueXXX XXXcoresXXX
#$ -e XXXerrfileXXX
#$ -o XXXoutfileXXX
#$ -cwd
#$ -S /bin/tcsh
# Environment
source ~/.cshrc
mpiexec --bynode -n XXXmpinodesXXX XXXcommandXXX
echo "done"