Changes between Version 12 and Version 13 of Public/User_Guide/JUBE

Timestamp:

Aug 5, 2016, 5:19:24 PM (8 years ago)

Author:

Cristina Manzano

Comment:

—

Public/User_Guide/JUBE

@@ -216 +216 @@
 }}}
 
+3) Substitute set
+
+See for instance the following section in platform.xml
+
+{{{
+    <substituteset name="executesub">
+        <iofile in="${submit_script}.in" out="$submit_script" />
+        <sub source="#ENV#" dest="$env" />
+        <sub source="#NOTIFY_EMAIL#" dest="" />
+        <sub source="#BENCHNAME#" dest="$jube_benchmark_name" />
+        <sub source="#NODELIST#" dest="nodes=$nodes:$nodetype:ppn=$taskspernode" />
+        <sub source="#QUEUE#" dest="$queue" />
+        <sub source="#JOBPOLICY#" dest="NACCESSPOLICY:SINGLEJOB" />
+        <sub source="#TIME_LIMIT#" dest="$timelimit" />
+        <sub source="#PREPROCESS#" dest="" />
+        <sub source="#POSTPROCESS#" dest="" />
+        <sub source="#STARTER#" dest="$starter" />
+        <sub source="#ARGS_STARTER#" dest="$args_starter" />
+        <sub source="#MEASUREMENT#" dest="" />
+        <sub source="#STDOUTLOGFILE#" dest="$outlogfile" />
+        <sub source="#STDERRLOGFILE#" dest="$errlogfile" />
+        <sub source="#EXECUTABLE#" dest="" />
+        <sub source="#ARGS_EXECUTABLE#" dest="" />
+        <sub source="#FLAG#" dest="touch $done_file" />
+    </substituteset>
+}}}
+
+And in MAXW-DGTD-jube-master-SDV.modules.test.xml:
+
+{{{
+    <substituteset name="executesub" init_with="platform.xml">
+      <sub source="#NOTIFY_EMAIL#" dest="c.manzano@fz-juelich.de" />
+      <sub source="#PREPROCESS#" dest="date +'(start) %F %T (%s)'; module purge; module load $modules; export LD_LIBRARY_PATH=/usr/local/deep-er/sdv-benchmarks/libraries/scr/lib:/direct/Software/Extoll/SDV/lib:/usr/local/parastation/pscom/lib64:$LD_LIBRARY_PATH; export OMP_NUM_THREADS=1; export KMP_AFFINITY='verbose,compact'; source exe/scr.sh; mkdir -p $iopath; cd exe" />
+      <sub source="#POSTPROCESS#" dest="echo $LD_LIBRARY_PATH; echo $SCR_USER_NAME; echo $SCR_JOB_NAME; echo $SCR_JOB_ID; echo $SCR_CACHE_BASE; rm -rf $iopath; cd ..; date +'(finished) %F %T (%s)'" />
+      <sub source="#EXECUTABLE#" dest="gdL$k" />
+      <sub source="#ARGS_EXECUTABLE#" dest="" />
+    </substituteset>
+}}}
+
+This will tell JUBE to take the file ${submit_script}.in and create an output file named ${submit_script} with the occurrences #NOTIFY_EMAIL#, #QUEUE#, etc. substituted by the corresponding values.
+
+4) Step execute
+
+NOTE: For integrating an application the step prepare is not necessary and won't be covered in this guide. A slightly modificated version of the xml file is explained here.
+
+{{{
+    <step name="execute" shared="shared">
+      <use>MAXW-DGTD-exec</use>
+      <use from="MAXW-DGTD_specs.xml">MAXW-DGTDInputFile</use>
+      <use>executeset</use>
+      <use>executesub</use>
+      <use from="platform.xml">chainsub</use>
+      <use>systemParameter</use>
+      <use tag="!woman">MAXW-DGTDParameter-head</use>
+      <use tag="woman">MAXW-DGTDParameter-woman</use>
+      <use>MAXW-DGTDInputSub</use>
+      <use>MAXW-DGTDSCRSub</use>
+      <use from="platform.xml">jobfiles</use>
+      <use from="platform.xml">chainfiles</use>
+      <do>mkdir exe; chgrp deeper exe; chmod g+s exe; cp -pr exe_$testcase/* exe/</do>
+      <do>cp -p gdL$k exe/</do>
+      <do>rm -f exe/Data_Num*; cp -p Data_Num.out exe/Data_Num</do>
+      <do>rm -f exe/Data_IO*; cp -p Data_IO.out exe/Data_IO</do>
+      <do>rm -f exe/scr.sh*; cp -p scr.sh.out exe/scr.sh</do>
+      <do>rm -f exe/test.part*; cp -p test.part.gz exe/; gzip -d exe/test.part.gz</do>
+      <do>$chainjob_script $shared_job_info $submit_script</do>
+      <do done_file="$done_file"></do>
+      <do>chgrp deeper job.log job.err</do>
+    </step>
+}}}
+
+The interesting parts of this section are at the end. With 
+
+{{{
+<do>$chainjob_script $shared_job_info $submit_script</do>
+}}}
+
+you will submit a series of jobs (in this example 4, see section 2). The first job will run and the next one will wait until the first one is finished. The chainjob_script looks as follows:
+
+{{{
+cat /usr/local/jube2/platform/deep/deep-chainJobs.sh
+
+#!/usr/bin/env bash
+
+if [ $# -lt 2 ]
+then
+    echo "$0: ERROR (MISSING ARGUMENTS)"
+    exit 1
+fi
+
+LOCKFILE=$1
+shift
+SUBMITSCRIPT=$*
+
+
+if  [ -f $LOCKFILE ]
+then
+    DEPEND_JOBID=`head -1 $LOCKFILE`
+    JOBID=`qsub -W depend=afterany:${DEPEND_JOBID} $SUBMITSCRIPT`
+else
+    JOBID=`qsub $SUBMITSCRIPT`
+fi
+
+echo ${JOBID} > $LOCKFILE
+
+exit 0
+}}}
+
+In shared_jobinfo the jobid of the preceding job is stored. Notice that
+
+{{{
+${shared_jobinfo}=${shared_folder}/jobid=./shared/jobid
+}}}
+
+and all jobs see the folder ./shared in the sandbox.