SGE template script example

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
# Environment
source /public/EM/RELION/relion.csh
# The actual command
mpiexec --bynode -n XXXmpinodesXXX XXXcommandXXX
echo "done"