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#!/bin/bash
#MSUB -N {{{JOBNAME}}} # name of the job
#MSUB -l nodes={{{NODES}}}:ppn={{{CPU}}} # specify number of nodes and cpu to reserve
#MSUB -o {{{STDOUT}}} # output is sent to logfile, stdout + stderr by default
#MSUB -e {{{STDOUT}}} # output is sent to logfile, stdout + stderr by default
#MSUB -q {{{QUEUE}}} # Job queue
#MSUB -l walltime={{{WALLTIME}}} # Walltime in minutes
#MSUB -l mem={{{MEMORY}}} # Memory requirements in Kbytes
#MSUB -r y # make the jobs re-runnable.
#MSUB -V # -V export all env of user to compute nodes
#MSUB -j oe # merge output from stdout and stderr
#MSUB -S /bin/bash # use bash shell
#MSUB -d {{{CWD}}} # the workding dir for each job, this is <flow_path>/tmp
#MSUB -M {{{EMAIL}}} # email address of the person
#MSUB -m n # when to send a email
#MSUB {{{DEPENDENCY}}} # Don't remove dependency args come here
#MSUB {{{EXTRA_OPTS}}} # Any extra arguments passed onto queue(), don't change. Format handled by R
## ------- REMOVE one # to make QUEUE work
## ------------------------------ n o t e s -------------------------##
## All variables specified above are replaced on the fly.
## Most of them come from the flow_definition file.
## This is a core component of how flowr interacts with the cluster.
## Please refer to the platform manual, before editing this file
## ------------------------------------------------------------------##
## --- DO NOT EDIT from below here---- ##
# following will always overwrite previous output file, if any. See https://github.com/sahilseth/flowr/issues/13
set +o noclobber
touch {{{TRIGGER}}}
echo 'BGN at' $(date)
##--- add some custom module commands
{{{MODULE_CMDS}}}
## --- command to run comes here (flow_mat)
{{{CMD}}}
exitstat=$?
echo 'END at' $(date)
echo ${exitstat} > {{{TRIGGER}}}
exit ${exitstat}