source: branches/2013/dev_MERGE_2013/NEMOGCM/SETTE/prepare_job.sh @ 4373

#####################################################
# Author : Simona Flavoni for NEMO
# Contact : sflod@locean-ipsl.upmc.fr
#
# ----------------------------------------------------------------------
# NEMO/SETTE , NEMO Consortium (2010)
# Software governed by the CeCILL licence     (NEMOGCM/NEMO_CeCILL.txt)
# ----------------------------------------------------------------------
#
# Some scripts called by sette.sh
# prepare_job.sh   : creates the job script for running job 
######################################################
#set -vx
set -o posix
#set -u
#set -e
#+
#
# ================
# prepare_job.sh
# ================
#
# -------------------------------------------------
# script that creates the job script for NEMO tests 
# -------------------------------------------------
#
# SYNOPSIS
# ========
#
# ::
#
#  $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE
#
#
# DESCRIPTION
# ===========
#
# Part of the SETTE package to run tests for NEMO
# 
# prepare the script $JOB_FILE to run the tests 
#
# EXAMPLES
# ========
#
# ::
#
#  $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG $JOB_FILE
#
# prepare the $JOB_FILE for execution 
#
#
# TODO
# ====
#
# option debug
#
#
# EVOLUTIONS
# ==========
#
# $Id: prepare_job.sh 3050 2011-11-07 14:11:34Z acc $
#
#
#
#   * creation
#
#-
#

usage=" Usage : ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE NUM_XIO_SERVERS"
usage=" example : ./prepare_job.sh input_ORCA2_LIM_PISCES.cfg 8 SHORT no/yes $JOB_FILE 0"


minargcount=6
        if [ ${#} -lt ${minargcount} ]
        then
                echo "not enough arguments for prepare_job.sh script"
                echo "control number of argument of prepare_job.sh in sette.sh"
                echo "${usage}"
        exit 1
        fi
        unset minargcount
   if [ ! -f ${SETTE_DIR}/output.sette ] ; then
           touch ${SETTE_DIR}/output.sette
   fi
       
#
# set and export TEST_NAME. It will be used within the post_test_tidyup function
#
INPUTARFILE=$1
NB_PROC=$2
TEST_NAME=$3
MPI_FLAG=$4
JOB_FILE=$5
NXIO_PROC=$6

# export EXE_DIR. This directory is used to execute model 
#
#
#
echo "date: `date`" >> ${SETTE_DIR}/output.sette
echo "" >> ${SETTE_DIR}/output.sette
echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette
echo "" >> ${SETTE_DIR}/output.sette
echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette
echo "`more ${SETTE_DIR}/../CONFIG/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette
echo "" >> ${SETTE_DIR}/output.sette
echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette
echo "" >> ${SETTE_DIR}/output.sette
echo "executing script : \"fcm_job $@\" " >> ${SETTE_DIR}/output.sette
echo "            " >> ${SETTE_DIR}/output.sette

################################################################
# SET INPUT 
# get the input tarfile if needed
if [ "$(cat ${SETTE_DIR}/$INPUTARFILE | wc -w)" -ne 0 ] ; then
   echo "looking for input files in ${SETTE_DIR}/$INPUTARFILE " >> ${SETTE_DIR}/output.sette
# number of tarfiles: NBTAR
   NBTAR=`cat ${SETTE_DIR}/$INPUTARFILE |wc -l` 
   echo "NB of tarfiles ${NBTAR} " >> ${SETTE_DIR}/output.sette
# loop on tarfiles
# read file name and directory
while read tar_file dir_conf_forc 
do
      echo looking for tarfile ${tar_file} and directory ${FORCING_DIR}/${dir_conf_forc} ; echo looking for tarfile ${tar_file} and directory ${FORCING_DIR}/${dir_conf_forc} >> ${SETTE_DIR}/output.sette
      if [ -f ${FORCING_DIR}/${tar_file} ] && [ -d ${FORCING_DIR}/${dir_conf_forc} ] ; then
# Tarfile and input dir ar there, only check the links
         echo "Tarfile and input dir ar there, only check the links" >> ${SETTE_DIR}/output.sette
# extract tarfile
      else 

if [ ! -f ${FORCING_DIR}/${tar_file} ] ; then  
     echo "tarfile  ${FORCING_DIR}/${tar_file} cannot be found we stop " ; exit 2 ; fi 

echo "mkdir ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette
         mkdir ${FORCING_DIR}/${dir_conf_forc}  
         cd    ${FORCING_DIR}/${dir_conf_forc}
echo " extract from tarfile ${FORCING_DIR}/${tar_file} in  ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette
         tar xvof ${FORCING_DIR}/${tar_file} ; gunzip -f `find . -name "*.gz"` 
      fi
# Tarfile and input dir ar there, only check the links
      cd ${FORCING_DIR}/${dir_conf_forc}
      for fida in *
         do
           [ -f ${EXE_DIR}/${fida} ] || ln -s ${FORCING_DIR}/${dir_conf_forc}/${fida} ${EXE_DIR}/${fida}
         done
    done < ${SETTE_DIR}/$INPUTARFILE

else
  echo "no input file to be searched "
fi
################################################################

##########################################################################
# COPY RESTART FILES (if needed; i.e. only for SHORT job in RESTART TESTS)
# get the input tarfile if needed
# SF : not ok for the moment because at this point is needed cn_exp variable,
# SF : here it it not known.
#\cd ${EXE_DIR}
#if [ "$(echo ${TEST_NAME} | grep -c "SHORT" )" -ne 0 ] ; then
#    for (( i=1; i<=${NB_PROC}; ${NB_PROC}++)) ; do
#        L_NPROC=`printf "%04d\n" $i`
#        ln -sf ../LONG/${NEW_CONF}_00000060_restart_${L_NPROC-1}.nc .
#    done
#fi
## SF : other way
##      for file in ../LONG/${NEW_CONF}_*restart_0*.nc ; do
##              ncpu=`echo $file | awk -F '_' '{print $NF}' | cut -f 1 -d '.'`
##              ln -sf ${file}  .
##      done
##fi
##########################################################################

################################################################
# RUN OPA
cd ${EXE_DIR}
if [ ! -r ${EXE_DIR}/opa ]
    then
    echo "executable opa does not exist"
    echo "executable opa does not exist, exit"  >> ${SETTE_DIR}/output.sette
    exit 1
fi

# example for NOCS Altix system using PBS batch submission (requires ${SETTE_DIR}/sette_batch_template file)
#
  #  if [ ${MPI_FLAG} == "no" ] ; then
      case ${COMPILER} in 
         ALTIX_NAUTILUS_MPT)
                                NB_REM=$( echo $NB_PROC $NXIO_PROC | awk '{print ( $1 + $2 ) % 4}')
               if [ ${NB_REM} == 0 ] ; then
               # number of processes required is an integer multiple of 4
               #
               NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{print ($1 + $2 ) / 4}')
            else
               #
               # number of processes required is not an integer multiple of 4
               # round up the number of nodes required.
               #
               NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{printf("%d",($1 + $2 ) / 4 + 1 )}')
                  fi
            ;;
                        ifort_MERCATOR_CLUSTER)
                                echo NB_PROCS ${NB_PROC}
                                echo NB_NODES ${NB_NODES}
                                echo  NB_PROC ${NB_PROC}
                                if [ ${NB_PROC} -eq 1 ] ; then
                                   NB_NODES=1
                                   QUEUE=monoproc
                                   NB_PROC_NODE=${NB_PROC}
                                else
                                   if [ ${NB_PROC} -le 8 ] ; then
                                      NB_NODES=1
                                      QUEUE=mono
                                      NB_PROC_NODE=${NB_PROC}
                                   else
                                      NB_NODES=$( echo $NB_PROC | awk '{print $1 - $1 % 8}'  | awk '{print $1 / 8 }')
                                      QUEUE=multi
                                      NB_PROC_NODE=8
                                  fi
                                fi
                                echo NB_PROCS     ${NB_PROC}
                                echo NB_NODES     ${NB_NODES}
                                echo NB_PROC_NODE ${NB_PROC_NODE}
                                ;;
         *)
            NB_NODES=${NB_PROC}
            ;;

      esac
#
# Pass settings into job file by using sed to edit predefined strings
#
        TOTAL_NPROCS=$(( $NB_PROC + $NXIO_PROC ))
        cat ${SETTE_DIR}/job_batch_template | sed -e"s/NODES/${NB_NODES}/" \
             -e"s/TOTAL_NPROCS/${TOTAL_NPROCS}/" \
             -e"s/NPROCS/${NB_PROC}/" \
             -e"s/NXIOPROCS/${NXIO_PROC}/" \
             -e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \
             -e"s:DEF_EXE_DIR:${EXE_DIR}:" \
             -e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \
             -e"s:MPI_FLAG:${MPI_FLAG}:" \
             -e"s:DEF_NEMO_VALIDATION:${NEMO_VALIDATION_DIR}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \
             -e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job

        case ${COMPILER} in
              ifort_MERCATOR_CLUSTER)
                    #cat run_sette_test.job | sed -e"s:QUEUE:${QUEUE}:" > run_sette_test1.job 
                    #cat run_sette_test.job | sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" > run_sette_test1.job 
                                                 #-e"s/NPROC_NODE/${NB_PROC_NODE}/" > run_sette_test1.job
                    cat run_sette_test.job | sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \
                                                 -e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
                    mv run_sette_test1.job run_sette_test.job
                    ;;
   esac
#
# create the unique submission job script
#
   if [ ! -f $JOB_FILE ] ; then
      mv run_sette_test.job $JOB_FILE
   else
       e=`grep -n "# END_BODY" ${JOB_FILE} | cut -d : -f 1`
            e=$(($e - 1))
       head -$e $JOB_FILE > ${JOB_FILE}_new 
       mv ${JOB_FILE}_new ${JOB_FILE}
       l=`wc -l run_sette_test.job | sed -e "s:run_sette_test.job::"`
       b=`grep -n "# BODY" run_sette_test.job | cut -d : -f 1`
       t=$(($l - $b))
       tail -$t run_sette_test.job >> $JOB_FILE
   fi
   
   chmod a+x $JOB_FILE ; echo "$JOB_FILE is ready"

#fi