SGE template script example: Difference between revisions
Jump to navigation
Jump to search
| Line 13: | Line 13: | ||
<code> | <code> | ||
#!/bin/tcsh | #!/bin/tcsh | ||
#$ -pe XXXqueueXXX XXXnodesXXX | #$ -pe XXXqueueXXX XXXnodesXXX | ||
#$ -l dedicated=XXXdedicatedXXX | #$ -l dedicated=XXXdedicatedXXX | ||
#$ -e XXXerrfileXXX | #$ -e XXXerrfileXXX | ||
#$ -o XXXoutfileXXX | #$ -o XXXoutfileXXX | ||
#$ -A Relion | #$ -A Relion | ||
#$ -cwd | #$ -cwd | ||
#$ -S /bin/tcsh | #$ -S /bin/tcsh | ||
# Environment | # Environment | ||
source ~/.cshrc | source ~/.cshrc | ||
mpiexec -n XXXmpinodesXXX XXXcommandXXX | 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