SGE template script example: Difference between revisions
Jump to navigation
Jump to search
| Line 18: | Line 18: | ||
#$ -cwd | #$ -cwd | ||
#$ -S /bin/tcsh | #$ -S /bin/tcsh | ||
# | # The following sets PATH and LD_LIBRARY_PATH for RELION and MPI | ||
source /public/EM/RELION/relion.csh | source /public/EM/RELION/relion.csh | ||
# The actual command | # The actual command | ||
Revision as of 14:13, 6 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 "/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 XXXcoresXXX
#$ -e XXXerrfileXXX
#$ -o XXXoutfileXXX
#$ -cwd
#$ -S /bin/tcsh
# The following sets PATH and LD_LIBRARY_PATH for RELION and MPI
source /public/EM/RELION/relion.csh
# The actual command
mpiexec --bynode -n XXXmpinodesXXX XXXcommandXXX
echo "done"