SGE template script example

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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