TORQUE template script example: Difference between revisions
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#!/bin/bash | == The environment setup == | ||
### Inherit all current environment variables | 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: | ||
#PBS -V | |||
### Job name | export RELION_QSUB_EXTRA1="Max number of hours in queue" | ||
#PBS -N | export RELION_QSUB_EXTRA1_DEFAULT="72" | ||
export RELION_QSUB_TEMPLATE="/gpfs/fs1/home/bioinfo/scheres/relion-0.9/bin/qsub.bash" | |||
### Output and Error | |||
#PBS - | |||
The command used for job submission (to be given in the GUI) is <code>qsub</code>. | |||
== 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 | ### Queue name | ||
#PBS -q XXXqueueXXX | #PBS -q XXXqueueXXX | ||
| Line 17: | Line 30: | ||
### Switch to the working directory; | ### Switch to the working directory; | ||
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
### Run: | |||
mpirun --bynode -np XXXmpinodesXXX XXXcommandXXX | mpirun --bynode -np XXXmpinodesXXX XXXcommandXXX | ||
echo "done" | echo "done" | ||
Latest revision as of 13:25, 13 November 2017
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 command used for job submission (to be given in the GUI) is qsub.
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"