SGE template script example: Difference between revisions

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

SGE template script example: Difference between revisions

Latest revision as of 13:41, 13 November 2017

The environment setup

The template script

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@@ Line 1: / Line 1: @@
-<code>
+== The environment setup ==
-\#!/bin/tcsh
-\#$ -pe XXXqueueXXX XXXcoresXXX
+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:
-\#$ -e XXXerrfileXXX
-\#$ -o XXXoutfileXXX
+ setenv RELION_QSUB_TEMPLATE "/public/EM/RELION/relion/bin/qsub.csh"
-\#$ -cwd
-\#$ -S /bin/tcsh
-\# Environment
+The command used for job submission (to be given in the GUI) is <code>qsub</code>.
-source ~/.cshrc
-mpiexec --bynode -n XXXmpinodesXXX XXXcommandXXX
+== The template script ==
-echo "done"
-</code>
+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