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computing:batch:jobscriptexample

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computing:batch:jobscriptexample [2013/12/11 23:59] – ngadiubacomputing:batch:jobscriptexample [2017/05/29 15:41] – [Example 2] iwn
Line 1: Line 1:
 + ===== Example 1 =====
 +
 +<file text submitExample.sh>
 +
   #!/bin/bash   #!/bin/bash
   #################################   #################################
Line 128: Line 132:
   #  our shared home   #  our shared home
   scramv1 list > myout.txt 2>myerr.txt   scramv1 list > myout.txt 2>myerr.txt
 +  
   lcg-ls -b -D srmv2 -l srm://t3se01.psi.ch:8443/srm/managerv2?SFN=/pnfs/psi.ch/cms/ >> myout.txt 2>>myerr.txt   lcg-ls -b -D srmv2 -l srm://t3se01.psi.ch:8443/srm/managerv2?SFN=/pnfs/psi.ch/cms/ >> myout.txt 2>>myerr.txt
 +  
   # create a dummy file for copying back to the SE   # create a dummy file for copying back to the SE
   dd if=/dev/urandom of=mybigfile count=100 &>/dev/null   dd if=/dev/urandom of=mybigfile count=100 &>/dev/null
 +  
   CMSSW_DIR=/shome/feichtinger/cmssw_test/CMSSW_2_1_6   CMSSW_DIR=/shome/feichtinger/cmssw_test/CMSSW_2_1_6
   CMSSW_CONFIG_FILE=$CMSSW_DIR/demoanalyzer-classic.cfg   CMSSW_CONFIG_FILE=$CMSSW_DIR/demoanalyzer-classic.cfg
 +  
   cd $CMSSW_DIR/src   cd $CMSSW_DIR/src
   eval `scramv1 runtime -sh`   eval `scramv1 runtime -sh`
Line 143: Line 147:
      exit 1      exit 1
   fi   fi
 +  
   cd $WORKDIR   cd $WORKDIR
   cmsRun $CMSSW_CONFIG_FILE maxEvents=$1 firstEvent=$2 inputFiles=$3 seed=$4> myout.txt 2>myerr.txt   cmsRun $CMSSW_CONFIG_FILE maxEvents=$1 firstEvent=$2 inputFiles=$3 seed=$4> myout.txt 2>myerr.txt
 +  
   #### RETRIEVAL OF OUTPUT FILES AND CLEANING UP ############################   #### RETRIEVAL OF OUTPUT FILES AND CLEANING UP ############################
   cd $WORKDIR   cd $WORKDIR
Line 158: Line 162:
       echo "########################################################"       echo "########################################################"
   fi   fi
 +  
   if test x"$OUTFILES" != x; then   if test x"$OUTFILES" != x; then
      mkdir -p $RESULTDIR      mkdir -p $RESULTDIR
Line 203: Line 207:
   echo "Wallclock running time: $RUNTIME s"   echo "Wallclock running time: $RUNTIME s"
   exit 0   exit 0
 +  
 +</file>
 +
 +
 + ===== Example 2 =====
 +
 +Trimmed version.
 +
 +
 +<file text submitExample2.sh>
 +
 +#! /bin/bash
 +# https://wiki.chipp.ch/twiki/bin/view/CmsTier3/HowToSubmitJobs
 +# run with qsub -q all.q submitAnalysis.sh
 +
 +printf "###################################################\n"
 +printf "##   Run Analysis with input %-20s##\n" $1
 +printf "###################################################\n"
 +
 +DBG=2 # debugging level
 +INPUT=$1;
 +JOBLOGFILES="myout.txt myerr.txt"
 +OUTFILES="*.png"
 +TOPWORKDIR=/scratch/`whoami`
 +JOBDIR="analysis/$1"
 +BASEDIR="/shome/myusername/CMSSW_5_3_24/src/myAnalysisFolder"
 +CMSSW_DIR="/shome/myusername/CMSSW_5_3_24"
 +
 +WORKDIR=$TOPWORKDIR/$JOBDIR
 +OUTDIR=$BASEDIR/$JOBDIR     # for output files
 +RESULTDIR=$BASEDIR/$JOBDIR  # for log files
 +
 +# to save large output files on storage element
 +SEUSERSUBDIR="analysis/$1"
 +SEOUTFILES="*.root"
 +USER_SE_HOME="root://t3dcachedb.psi.ch:1094/pnfs/psi.ch/cms/trivcat/store/user/$USER"
 +SERESULTDIR=$USER_SE_HOME/$SEUSERSUBDIR
 +
 +
 +
 +##### MONITORING/DEBUG INFORMATION ########################################
 +
 +# write job report (stdout of this script)
 +mkdir -p /shome/myusername/CMSSW_5_3_24/src/myAnalysisFolder/analysis
 +#$ -o /shome/myusername/CMSSW_5_3_24/src/myAnalysisFolder/analysis
 +#$ -e /shome/myusername/CMSSW_5_3_24/src/myAnalysisFolder/analysis
 +
 +DATE_START=`date +%s`
 +echo "Job started at " `date`
 +cat <<EOF
 +
 +###########################################
 +##       QUEUEING SYSTEM SETTINGS:       ##
 +###########################################
 +  HOME=$HOME
 +  USER=$USER
 +  JOB_ID=$JOB_ID
 +  JOB_NAME=$JOB_NAME
 +  HOSTNAME=$HOSTNAME
 +  TASK_ID=$TASK_ID
 +  QUEUE=$QUEUE
 +EOF
 +
 +if test 0"$DBG" -gt 0; then
 +    echo " "
 +    echo "###########################################"
 +    echo "##         Environment Variables         ##"
 +    echo "###########################################"
 +    env
 +fi
 +
 +
 +
 +##### SET ENVIRONMENT #####################################################
 +
 +mkdir -p $WORKDIR
 +if test ! -d "$WORKDIR"; then
 +    echo "ERROR: Failed to create workdir ($WORKDIR)! Aborting..." >&2
 +    exit 1
 +fi
 +cd $WORKDIR
 +
 +cat <<EOF
 +
 +###########################################
 +##             JOB SETTINGS:             ##
 +###########################################
 +  BASEDIR=$BASEDIR
 +  WORKDIR=$WORKDIR
 +  RESULTDIR=$RESULTDIR
 +  SERESULTDIR=$SERESULTDIR
 +EOF
 +
 +
 +
 +echo " "
 +echo "###########################################"
 +echo "##         MY FUNCTIONALITY CODE         ##"
 +echo "###########################################"
 +
 +source $VO_CMS_SW_DIR/cmsset_default.sh 2>> myerr.txt
 +cd $CMSSW_DIR/src
 +eval `scramv1 runtime -sh` >> myout.txt 2>> myerr.txt
 +if test $? -ne 0; then
 +    echo "ERROR: Failed to source scram environment" >&2
 +    exit 1
 +fi
 +
 +cd $WORKDIR
 +echo "python $BASEDIR/myAnalysis.py $INPUT >> myout.txt 2>> myerr.txt"
 +python $BASEDIR/myAnalysis.py $INPUT >> myout.txt 2>> myerr.txt
 +ls >> myout.txt 2>> myerr.txt
 +
 +
 +
 +##### RETRIEVAL OF OUTPUT FILES AND CLEANING UP ###########################
 +
 +cd $WORKDIR
 +if test 0"$DBG" -gt 0; then
 +    echo " "
 +    echo "###########################################################"
 +    echo "##   MY OUTPUT WILL BE MOVED TO \$RESULTDIR and \$OUTDIR   ##"
 +    echo "###########################################################"
 +    echo "  \$RESULTDIR=$RESULTDIR"
 +    echo "  \$OUTDIR=$OUTDIR"
 +    echo "pwd: " `pwd`
 +    ls -Rl
 +fi
 +
 +# copy log files to $RESULTDIR
 +if test x"$JOBLOGFILES" != x; then
 +    mkdir -p $RESULTDIR
 +    if test ! -e "$RESULTDIR"; then
 +        echo "ERROR: Failed to create $RESULTDIR ...Aborting..." >&2
 +    fi
 +    for n in $JOBLOGFILES; do
 +        if test ! -e $WORKDIR/$n; then
 +            echo "WARNING: Cannot find output file $WORKDIR/$n. Ignoring it" >&2
 +        else
 +            echo ">>> copying $n from $WORKDIR to $RESULTDIR"
 +            cp -a $WORKDIR/$n $RESULTDIR/$n
 +            if test $? -ne 0; then
 +                echo "ERROR: Failed to copy $WORKDIR/$n to $RESULTDIR/$n" >&2
 +            fi
 +    fi
 +    done
 +fi
 +
 +# copy output files to $OUTDIR
 +if test x"$OUTFILES" != x; then
 +    mkdir -p $OUTDIR
 +    if test ! -e "$OUTDIR"; then
 +          echo "ERROR: Failed to create $OUTDIR ...Aborting..." >&2
 +    fi
 +    for n in $OUTFILES; do
 +        if test ! -e $WORKDIR/$n; then
 +            echo "WARNING: Cannot find output file $WORKDIR/$n. Ignoring it" >&2
 +        else
 +            echo ">>> copying $n from $WORKDIR to $OUTDIR"
 +         cp -a $WORKDIR/$n $OUTDIR/$n
 +            if test $? -ne 0; then
 +                echo "ERROR: Failed to copy $WORKDIR/$n to $OUTDIR/$n" >&2
 +            fi
 +        fi
 +    done
 +fi
 +
 +
 +# copy large files to $SERESULTDIR
 +if test x"$SEOUTFILES" != x; then
 +    if test ! -e "$SERESULTDIR"; then
 +          echo "ERROR: Failed to create $SERESULTDIR ...Aborting..." >&2
 +    fi
 +    if test 0"$DBG" -ge 2; then
 +        srmdebug="-v"
 +    fi
 +    for n in $SEOUTFILES; do
 +        if test ! -e $WORKDIR/$n; then
 +            echo "WARNING: Cannot find output file $WORKDIR/$n. Ignoring it" >&2
 +        else
 +            echo "xrdcp -f $WORKDIR/$n $SERESULTDIR/$n" >&2
 +            xrdcp $srmdebug -d $DBG -f $WORKDIR/$n $SERESULTDIR/$n
 +            if test $? -ne 0; then
 +                echo "ERROR: Failed to copy $WORKDIR/$n to $SERESULTDIR/$n" >&2
 +            fi
 +        fi
 +    done
 +fi
 +
 +# cleaning working directory
 +echo ">>> Cleaning up $WORKDIR"
 +rm -rf $WORKDIR
 +
 +
 +
 +###########################################################################
 +
 +DATE_END=`date +%s`
 +RUNTIME=$((DATE_END-DATE_START))
 +echo " "
 +echo "#####################################################"
 +echo "    Job finished at " `date`
 +echo "    Wallclock running time: $(( $RUNTIME / 3600 )):$(( $RUNTIME % 3600 /60 )):$(( $RUNTIME % 60 )) "
 +echo "#####################################################"
 +echo " "
 +exit 0
 +
 +</file>
computing/batch/jobscriptexample.txt · Last modified: 2017/06/07 20:59 by iwn

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