SGE template script example: Difference between revisions
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| Line 13: | Line 13: | ||
<code> | <code> | ||
#!/bin/tcsh | #!/bin/tcsh | ||
#$ -pe XXXqueueXXX XXXnodesXXX | |||
#$ -l dedicated=XXXdedicatedXXX | |||
#$ -e XXXerrfileXXX | |||
#$ -o XXXoutfileXXX | |||
#$ -A Relion | |||
#$ -cwd | |||
#$ -S /bin/tcsh | |||
# Environment | |||
source ~/.cshrc | |||
mpiexec -n XXXmpinodesXXX XXXcommandXXX | |||
</code> | </code> | ||
Revision as of 12:54, 27 August 2015
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 "/public/EM/RELION/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 XXXnodesXXX
- $ -l dedicated=XXXdedicatedXXX
- $ -e XXXerrfileXXX
- $ -o XXXoutfileXXX
- $ -A Relion
- $ -cwd
- $ -S /bin/tcsh
- Environment
source ~/.cshrc
mpiexec -n XXXmpinodesXXX XXXcommandXXX