6.2 Running CO5BOLD on a Machine with Batch System

For longer simulations it is inconvenient to restart the individual jobs by hand. This task is done by a script originally from Hans-Günter Ludwig. Its basic function is sketched in Fig. 6.

Figure 6: Program scheme , Postscript version

Here comes an example of the script (rhd1.job) for a system without dedicated batch system. The submission of a job is done via nohup rhd1.job &:

%

{\color{DEFcolor}{\footnotesize\color{SHcolor}\begin{verbatim}

#!/bin/sh

#--- PBS -N rhd1

#--- PBS -l walltime=72:00:00 

#--- PBS -l nodes=1:ppn=4

#

# --- Job file for the execution of RHD on gunnar (Itanium 2, Uppsala) ---

# --- Source: rhd1.job, original from HGL                              ---

# --- Last modification: 2002-12-13                                    ---

#

#set -xv

#


BASEDIR=/users/bf/dat/job/j1


STADIR=${BASEDIR}/sta      # Start directory: contains *.par, rhd1.cmd, rhd1.job


WRKDIR=${BASEDIR}/wrk      # Work directory


BAKDIR=${BASEDIR}/bak      # Backup and output directory


RHDEXE=$STADIR/rhd.exe     # RHD program to be executed

#

#export NCPUS=4

#echo $NCPUS


export OMP_NUM_THREADS=1

#

# --- Jump into work directory ---


cd $WRKDIR

#

# --- Loop: execute RHD code (possibly) several times in one job --------------


for IRUN in 1


do


echo


echo 'CO5BOLD Run #' $IRUN


date

  #

  # --- Clear up work directory ---

  #set +e


rm *

  #set -e

  #

  ##############################################################################

  #

  #   --- Get old command file, select actual command line ---

  #   --- and read variables from command line             ---

  #


cp -p $STADIR/rhd1.cmd rhd1.cmd

  #


awk \

  '      /#/   { print; next}

        /\*/   { print; next}

        /\+/   { print; next}


DONE!="T"   { print >"cmdline"; printf "%-77s*\n", $0; DONE="T"; next}

               { print} ' rhd1.cmd | cat > dummy_nrhd.cmd

  #


read INFILE OUTFILE PARFILE ACT < cmdline


mv dummy_nrhd.cmd ${OUTFILE}_nrhd.cmd


echo ${INFILE}


echo ${OUTFILE}


echo ${PARFILE}


echo ${ACT}

  #

  ##############################################################################

  #


if [ "${ACT}" != dum ]


then

    ############################################################################

    #

    #   --- RHD execution ---

    #

    # --- Copy parameter file ---


cp -p ${STADIR}/${PARFILE} rhd.par

    #

    # --- Copy start file ---


if test -s ${BAKDIR}/${INFILE}


then


cp -p ${BAKDIR}/${INFILE} rhd.sta


else


cp -p ${STADIR}/${INFILE} rhd.sta


cp -p rhd.sta ${BAKDIR}/${INFILE}


fi

    # --- Copy executable ---


cp -p ${RHDEXE} rhd.exe

    #

    # --- Execute RHD ---

    ./rhd.exe > rhd.out


RHD_EXIT=$?

    #


if [ "$RHD_EXIT" != 0 ] || [ ! -s rhd.done ]


then

      # --- Exit status not zero, ---

      # --- error may have occurred during execution of rhd.exe ---


if [ "$RHD_EXIT" != 0 ]


then


echo 'Non-zero exit status ' $RHD_EXIT ' occurred during execution of RHD!'


else


echo 'No rhd.done file found: assume error during execution of RHD!'


fi


echo 'Execution of job chain terminated!'

      # --- Modify nrhd.cmd, set termination character "+" ---


awk \

      '      /#/   { print; next}

            /\*/   { print; next}

            /\+/   { print; next}


DONE!="T"   { printf "%-77s+\n", $0; DONE="T"; next}

                   { print} ' rhd1.cmd | cat > nrhd.cmd

      # --- Terminate chain by simulating ${ACT} = eoc ... ---


ACT=eoc


else

      # --- Modify command file: add '*' in appropriate column to indicate ---

      # --- proper execution                                               ---    


awk \

      '      /#/   { print; next}

            /\*/   { print; next}

            /\+/   { print; next}


DONE!="T"   { print >"cmdline"; printf "%-77s*\n", $0; DONE="T"; next}

                   { print} ' rhd1.cmd | cat > nrhd.cmd


fi

    #


ls -l

    #

    # --- Move data into backup directory ---


cp -p rhd.par  ${BAKDIR}/${PARFILE}


mv rhd.out  ${BAKDIR}/${OUTFILE}.out


mv rhd.par  ${BAKDIR}/${OUTFILE}.par

    #mv rhd.sta  ${BAKDIR}/${OUTFILE}.sta


mv rhd.end  ${BAKDIR}/${OUTFILE}.end


mv rhd.full ${BAKDIR}/${OUTFILE}.full


mv rhd.mean ${BAKDIR}/${OUTFILE}.mean


mv rhd.chu1 ${BAKDIR}/${OUTFILE}.chu1


chmod go+r ${BAKDIR}/${PARFILE} ${BAKDIR}/${OUTFILE}.*


chmod go-w ${BAKDIR}/${PARFILE} ${BAKDIR}/${OUTFILE}.*

    #

    ############################################################################


fi

  #

  #

  ##############################################################################

  #

  # --- Dispose modified command file for next job ---


cp -p nrhd.cmd $STADIR/rhd1.cmd

  #

  # --- Exit loop if end of chain reached ---


if test ${ACT} = eoc


then


break


fi

  #

  # --- End of loop ------------------------------------------------------------


done

#

# --- Submit next job if not end of chain reached---


if test ${ACT} != eoc


then


cd $STADIR


echo "Resubmit job"

#  /usr/local/bin/qsub rhd1.job

#  qsub rhd1.job

#  nice nohup rhd1.job &


nohup rhd1.job &


else


echo "End of job chain"


fi

#

################################################################################

%

A more detailed description of the script will come sometime in the future (e.g. from Sven's manual...).