SGE template script example: Difference between revisions
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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: | 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" | setenv RELION_QSUB_TEMPLATE "/public/EM/RELION/relion/bin/qsub.csh" | ||
The command used for job submission (to be given in the GUI) is <code>qsub</code>. | The command used for job submission (to be given in the GUI) is <code>qsub</code>. | ||
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The following script is saved as /lmb/home/scheres/app/relion/bin/qsub.csh: | The following script is saved as /lmb/home/scheres/app/relion/bin/qsub.csh: | ||
#!/bin/tcsh | #!/bin/tcsh | ||
#$ -pe XXXqueueXXX | #$ -pe XXXqueueXXX XXXnodesXXX | ||
#$ -l dedicated=XXXdedicatedXXX | |||
#$ -e XXXerrfileXXX | #$ -e XXXerrfileXXX | ||
#$ -o XXXoutfileXXX | #$ -o XXXoutfileXXX | ||
#$ -A Relion | |||
#$ -cwd | #$ -cwd | ||
#$ -S /bin/tcsh | #$ -S /bin/tcsh | ||
# Environment | # Environment | ||
source / | source ~/.cshrc | ||
mpiexec | mpiexec -n XXXmpinodesXXX XXXcommandXXX | ||
Latest revision as of 13:41, 13 November 2017
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