Hi,
I’m starting to use HCP Pipelines in the WashU CHPC cluster, and got a bit
confused on the way jobs are submitted to it, so I’d like to confirm a few
details about this.
As far as I could tell, since the cluster takes PBS jobs, and because fsl_sub
works only in Sun Grid Engines(?), the way to run a Pipelines script
would be creating a PBS script that executes the Pipelines script with the
‘—runlocal’ command line option.
For example, to run the PreFreeSurferPipelineBatch.sh script, the PBS script
command would be '.PreFreeSurferPipelineBatch.sh —runlocal'
>From the code(*) I assume that given this command, the fsl_sub queuing is
>bypassed, and when the job is submitted to the cluster it will use the options
>specified in the PBS script.
Is that correct?
Thanks,
Carolina.
______________________
(*) For example, these lines in PreFreeSurferPipelineBatch.sh:
"if [ -n "${command_line_specified_run_local}" ] ; then
echo "About to run
${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh"
queuing_command=""
else
echo "About to use fsl_sub to queue or run
${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh"
queuing_command="${FSLDIR}/bin/fsl_sub ${QUEUE}"
fi"
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