43 lines
2.2 KiB
Plaintext
43 lines
2.2 KiB
Plaintext
##################################################################################################################################
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########################## ########################################
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########################## Trinity PBS job submission with multi part dependencies ########################################
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########################## ########################################
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##################################################################################################################################
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### Author: Josh Bowden, Alexie Papanicolaou, CSIRO
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### Version 1.0
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### QuantifyGraph p4b Script
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##################################################################################################################################
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JOBSTRING4b=""$HASHBANG"
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"$NODESCPUS"
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if [[ ! \$JOB_INDEX_PADDED ]];then
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echo \"Error: not a proper submission\"
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exit 255
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fi
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echo \"Processing quantifyGraph_commands index \$JOB_INDEX_PADDED \"
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cd "$OUTPUTDIR"
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export OMP_NUM_THREADS=1
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COREFILENAME=""$OUTPUTDIR"/chrysalis/quantifyGraph_commands.pbs"
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MYJOBQ=\$COREFILENAME.\$JOB_INDEX_PADDED
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JOB_FILESIZE=\$(stat -c%s \"$MYJOBQ\")
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if [ -s \"\$MYJOBQ.completed\" ] ; then
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JOB_COMPLETED_FILESIZE=\$(stat -c%s \"\$MYJOBQ.completed\")
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if [ \"\$JOB_FILESIZE\" != \"\$JOB_COMPLETED_FILESIZE\" ] ; then
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trap \" echo \\\"Please check \$MYJOBQ Chrysalis QuantifyGraph processes had enough walltime.\\\"; exit 255 \" INT TERM
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"$TRINITYPATH"/trinity-plugins/parafly/bin/ParaFly -CPU "$NCPU_P4" -v -failed_cmds \$MYJOBQ.failed -c \$MYJOBQ
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trap - INT TERM EXIT
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fi
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else
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trap \" echo \\\"Please check \$MYJOBQ Chrysalis QuantifyGraph processes had enough walltime.\\\"; exit 255 \" INT TERM
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"$TRINITYPATH"/trinity-plugins/parafly/bin/ParaFly -CPU "$NCPU_P4" -v -failed_cmds \$MYJOBQ.failed -c \$MYJOBQ
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trap - INT TERM EXIT
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fi
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sleep 30 # IO friendship for following butterfly job - sometimes butterfly fails to find output if io is overwhelmed
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exit
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"
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# Write the above script to a file for later execution
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echo "${JOBSTRING4b}" | cat -> "$JOBPREFIX"_p4b.sh
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