dcmtk_journal_cpu

#!/bin/bash
# This script is used to update a Journal wiki page with the CPU used for a job.
# it requires 2 files for input :
#              1: a text copy of the wiki page ( option -w )
#              2: a text extraction of the cpu used on HPC ( option -c )
# class = @Run management tools@

usage() {
        echo
        echo "USAGE : $(basename $0 ) -w Journal_wiki.txt -c cpu_used.txt [-h] [-o output file] [-m machine ]"
        echo 
        echo "  PURPOSE:"
        echo "     Use accounting information hold in cpu_used.txt in order to finish the run's journal"
        echo "     created by dcmtk_journal_make."
        echo
        echo "  ARGUMENTS: (mandatory)"
        echo "     -w Journal_wiki.txt  :  the name of the text file created from the wiki page"
        echo "     -c cpu_used.txt      :  the name of the acounting file on HPC computer (see dcmtk_getcpu) "
        echo  
        echo "  OPTIONS:"
        echo "     -h                   :  this help message "
        echo "                          :  It can be obtained at https://reser.cines.fr/ with detailed option"
        echo "     -o output file       :  specify the output file name ( optional, default is Journal_cpu.txt )"
        echo "                          :  This file is then to be paste into the wiki, in place of the original table"
        echo "     -m machine           :  Specify the machine you are working on [occigen]. ada is also suported"
        echo "                             On ada, cpu_used_ada.txt file can be obtained with idrjar -d 01/01-nn/mm"
        echo
        exit
        }

chkfile()  {
           if [ ! -f $1 ] ; then 
            echo "ERROR : file $1 is missing "
            exit
           fi
           }

if [ $# = 0 ] ; then usage ; fi
raw_journal=''
cpu_list=''
cpu_journal=Journal_cpu.txt
ierr=0
machine=occigen

while getopts :hw:m:c:o: opt ; do
  case $opt in 
  (h) usage ;;
  (w) raw_journal=$OPTARG ;;
  (m) machine=$OPTARG ;;
  (c) cpu_list=$OPTARG ;;
  (o) cpu_journal=$OPTARG ;;
  (\?) echo $( basename $0 ): option -$OPTARG not valid. ; usage ;;
  esac
done

if [ ! $raw_journal ] ; then 
   ierr=1
   echo "ERROR : you must specify a Journal_wiki.txt file "
fi
if [ ! $cpu_list ] ; then 
   ierr=1
   echo "ERROR : you must specify a cpu_used.txt file "
fi

if [ $machine != ada -a  $machine != occigen  -a $machine != irene ] ; then
   ierr=1
   echo " ERROR : valid machines are  occigen irene and  ada "
fi

if [ $ierr = 1 ] ; then  echo "" ; usage ; fi 

chkfile $raw_journal
chkfile $cpu_list

case $machine in
  ( occigen | irene) 
  cat $cpu_list | awk 'NR != 1 { jobid=$2 ; cpu=$6 ;  i=index(cpu,"-"); t=substr(cpu,i+1) ; split(t,a,":") ; cpuh=substr(cpu,1,i-1)*24+ a[1]+a[2]/60.+a[3]/3600 ; print cpuh}' > ztmplist2
  cat $cpu_list | awk 'NR != 1 { jobid=$2 ; print jobid }' > zjobid ;;
  ( ada    )
  cat $cpu_list | awk  '{printf "%6.1f\n", $5*$7/3600.}' > ztmplist2
  cat $cpu_list | awk -F. '{print $2}' > zjobid ;;
esac

  paste zjobid ztmplist2 > ztmplist
# \rm ztmplist2 zjobid
  cmd=$(cat ztmplist | awk 'BEGIN{cmd= "sed "} { tpl= $1 "_CPU"; cmd= cmd " -e s/" tpl "/" $2"/" } END{ print cmd }' )
  echo $cmd
  cat $raw_journal | $cmd > $cpu_journal