SGE template script example
Jump to navigation
Jump to search
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