TORQUE template script example: Difference between revisions
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== The environment setup == | |||
Because the TORQUE queue at the CNB-CSIC requires a maximum wall-clock-time, one needs to define the XXXextra1XXX variable. In their environment (.bashrc) one includes: | |||
<code> | |||
export RELION_QSUB_EXTRA1="Max number of hours in queue" | |||
export RELION_QSUB_EXTRA1_DEFAULT="72" | |||
export RELION_QSUB_TEMPLATE="/gpfs/fs1/home/bioinfo/scheres/relion-0.9/bin/qsub.bash" | |||
</code> | |||
== The template script == | == The template script == | ||
The following script is saved as /gpfs/fs1/home/bioinfo/scheres/relion-0.9/bin/qsub.bash: | |||
<code> | <code> | ||
#!/bin/bash | #!/bin/bash | ||
Line 20: | Line 31: | ||
mpirun --bynode -np XXXmpinodesXXX XXXcommandXXX | mpirun --bynode -np XXXmpinodesXXX XXXcommandXXX | ||
echo "done" | echo "done" | ||
</code> | </code> |
Revision as of 16:58, 4 October 2011
The environment setup
Because the TORQUE queue at the CNB-CSIC requires a maximum wall-clock-time, one needs to define the XXXextra1XXX variable. In their environment (.bashrc) one includes:
export RELION_QSUB_EXTRA1="Max number of hours in queue"
export RELION_QSUB_EXTRA1_DEFAULT="72"
export RELION_QSUB_TEMPLATE="/gpfs/fs1/home/bioinfo/scheres/relion-0.9/bin/qsub.bash"
The template script
The following script is saved as /gpfs/fs1/home/bioinfo/scheres/relion-0.9/bin/qsub.bash:
#!/bin/bash
### Inherit all current environment variables
#PBS -V
### Job name
#PBS -N XXXnameXXX
### Keep Output and Error
#PBS -k eo
### Queue name
#PBS -q XXXqueueXXX
### Specify the number of nodes and thread (ppn) for your job.
#PBS -l nodes=XXXmpinodesXXX:ppn=XXXthreadsXXX
### Tell PBS the anticipated run-time for your job, where walltime=HH:MM:SS
###PBS -l walltime=XXXextra1XXX:00:00
#################################
### Switch to the working directory;
cd $PBS_O_WORKDIR
### Run:
mpirun --bynode -np XXXmpinodesXXX XXXcommandXXX
echo "done"