jobScript.sh

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#!/bin/bash

# This is the generic jobscript to run jobs on GridEngine
#
# The script supports up to 7 parameters.
#
# The user specific part of the script is indicated below.



par1="no"
par2="no"
par3="no"
par4="no"
par5="no"
par6="no"
par7="no"

if [ $# -lt 1 ]
then
        echo "Usage : jobScript.sh par1 [par2] [par2] [par3] [par4] [par5] [par6] [par7]"
        sleep 3
        exit
fi

case "$#" in

1)  par1=$1
    ;;
2)  par1=$1
    par2=$2
    ;;
3)  par1=$1
    par2=$2
    par3=$3
    ;;
4)  par1=$1
    par2=$2
    par3=$3
    par4=$4
    ;;
5)  par1=$1
    par2=$2
    par3=$3
    par4=$4
    par5=$5
    ;;
6)  par1=$1
    par2=$2
    par3=$3
    par4=$4
    par5=$5
    par6=$6
    ;;
7)  par1=$1
    par2=$2
    par3=$3
    par4=$4
    par5=$5
    par6=$6
    par7=$7
    ;;
*) echo "Unsupported number of arguments" 
   echo "Usage : jobScript.sh par1 [par2] [par2] [par3] [par4] [par5] [par6] [par7]"
   exit
   ;;
esac
    pathoutputlog=$par2 
    jobarrayFile=$par1

    # map back params for the job
    input=$(awk "NR==$SGE_TASK_ID" $jobarrayFile)   # get all params for this job
    
    
    par1=$(echo $input | cut -d " " -f1)
    par2=$(echo $input | cut -d " " -f2)
    par3=$(echo $input | cut -d " " -f3)
    par4=$(echo $input | cut -d " " -f4)
    par5=$(echo $input | cut -d " " -f5)
    par6=$(echo $input | cut -d " " -f6)
    par7=$(echo $input | cut -d " " -f7)

    echo "input: $input"
    echo "par1 = ${par1}"
    echo "par2 = ${par2}"
    echo "par3 = ${par3}"
    echo "par4 = ${par4}"
    echo "par5 = ${par5}"
    echo "par6 = ${par6}"
    echo "par7 = ${par7}"


    format='+%Y/%m/%d-%H:%M:%S'

    host=$(hostname)

    date $format
    echo ""               
    echo "--------------------------------"
    echo "RUNNING ON HOST : " $host
    echo "WORKING DIR     : " $(pwd)
    echo "USER is         : " $USER
    echo "JOBID           : $JOB_ID"
    echo "DISK USAGE /tmp :"
    df -h /tmp
    echo "--------------------------------"
    
    
    echo ""               
    echo "--------------------------------"
    echo "par1 = ${par1}"
    echo "par2 = ${par2}"
    echo "par3 = ${par3}"
    echo "par4 = ${par4}"
    echo "par5 = ${par5}"
    echo "par6 = ${par6}"
    echo "par7 = ${par7}"
    echo "--------------------------------"
    echo ""



    echo ""
    echo "--------------------------------"
    echo " DEBUG INFO"                     
    echo "==> Kernel version information :"
    uname -a                               
    echo "==> C compiler that built the kernel:"
    cat /proc/version                           
    echo "==> load on this node:"               
    mpstat -P ALL                               
    echo "==> actual compiler is"               
    gcc -v                                      
    echo "--------------------------------"     
    echo ""               








###################################################################
###################################################################
#   EDIT THIS PART TO EXECUTE YOUR JOB!



#----------------------
# evironment 
  echo "==> running enironment script ${par1}"
. ${par1}
#----------------------

  echo "==> ldd ${par2}"
  ldd $par2

  echo "==> execute program "

  outdir=$par4
  
  files=$(echo $par3 | sed 's/,/ /g')
  for file in $files
  do
     file=$(echo $file | sed 's/#/,/g')
     echo "==> $par2 $file $outdir $par5"
     time  $par2 $file $outdir $par5

     status=$?


     echo "------------------------------------"
     echo "MOVING OUTPUTFILES:"
     
     isList=$(echo $file | grep ",")
     
     if [ "${isList}" == "" ]
     then
        filename=$(basename ${file} | sed 's/.root$//')
        mv -v ${outdir}/${filename}_dst_apr12.root ${outdir}/root/
     else
     
        for f in $(echo $file | sed 's/,/ /g')
        do
          filename=$(basename ${f} | sed 's/.root$//')
          mv -v ${outdir}/${filename}_dst_apr12.root ${outdir}/root/
        done
     fi
  done
#---------------------------------------------------------------------



#   END EDIT YOUR EXECUT JOB!
###################################################################
###################################################################

    





    echo ""               
    echo "--------------------------------"
    echo "Job with params "
    echo "par1 = ${par1}"  
    echo "par2 = ${par2}"  
    echo "par3 = ${par3}"  
    echo "par4 = ${par4}"  
    echo "par5 = ${par5}"  
    echo "par6 = ${par6}"  
    echo "par7 = ${par7}"  
    echo "finsished!"      
    echo "--------------------------------"
    echo ""
    
    
    echo ""               
    echo "--------------------------------"
    echo "MONITOR ENVIRONMENT:"
    echo "JOB EXE   :---------------------"
    qstat -j $JOB_ID
    #echo "HOST LOAD :---------------------"
    #qhost -h $host
    #echo "OTHER JOBS ON HOST:-------------"
    #qhost -h $host -j
    echo "DISK USAGE /tmp :---------------"
    df -h /tmp 
    #echo "MEM/CPU USAGE :-----------------"
    #qstat -j $JOB_ID | grep usage
    echo "--------------------------------"
   
    
    
    
    date $format


    sleep 2
 
    # when running single file move log file name
    # to output filename
    if [ "$par3" == "$files" ]
    then  
       echo "MOVING LOG FILE"
       outfile=$(basename $par3)
       mv ${pathoutputlog}/${JOB_NAME}.o${JOB_ID}.${SGE_TASK_ID} ${pathoutputlog}/${outfile}.log
    fi