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#!/bin/bash | |
#BSUB -J {{{JOBNAME}}} # name of the job | |
#BSUB -cwd {{{CWD}}} # the workding dir for each job, this is <flow_run_path>/uniqueid/tmp | |
#BSUB -o {{{STDOUT}}} # output is sent to logfile, stdout + stderr by default | |
#BSUB -e {{{STDERR}}} # output is sent to logfile, stdout + stderr by default | |
#BSUB -q {{{QUEUE}}} # Job queue | |
#BSUB -W {{{WALLTIME}}} # Walltime in hours (usually for LSF). Please consult your sysadmin. | |
#BSUB -M {{{MEMORY}}} # Memory requirements in Kbytes | |
#BSUB -n {{{CPU}}} # CPU reserved | |
#BSUB -R span[ptile={{{CPU}}}] # CPU reserved, all reserved on same node | |
#BSUB -R rusage[mem={{{MEMORY}}}] # memory reserved | |
#BSUB -r # make the jobs re-runnable | |
#BSUB {{{DEPENDENCY}}} # Don't remove dependency args come here | |
#BSUB {{{EXTRA_OPTS}}} # Any extra arguments passed onto queue() | |
## ------------------------------ 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} |