##################################################### # 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" usage=" example : ./prepare_job.sh input_ORCA2_LIM_PISCES.cfg 8 SHORT no/yes $JOB_FILE" minargcount=5 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 # export EXE_DIR. This directory is used to execute model # export EXE_DIR # # 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 " " >> ${SETTE_DIR}/output.sette ################################################################ # SET INPUT # get the input tarfile if needed tar_file=$(sed -ne "1,1p" ${SETTE_DIR}/$INPUTARFILE) if [ "$(cat ${SETTE_DIR}/$INPUTARFILE | grep -c ".tar" )" -ne 0 ] ; then echo "looking for tar file" >> ${SETTE_DIR}/output.sette echo " " >> ${SETTE_DIR}/output.sette cp ${FORCING_DIR}/${tar_file} ${INPUT_DIR}/. echo "file in ${INPUT_DIR}" if [ ! -f ${INPUT_DIR}/${tar_file} ] ; then echo "PROBLEM during copy of tar file" >> ${SETTE_DIR}/output.sette echo "tar file IS NOT present in ${INPUT_DIR} directory " >> ${SETTE_DIR}/output.sette echo " " >> ${SETTE_DIR}/output.sette echo "PROBLEM during copy of tar file" exit 1 else cd ${EXE_DIR} ; tar xvof ${INPUT_DIR}/*.tar ; gunzip -f *gz fi fi if [ ! -f ${EXE_DIR}/namelist_ice ] ; then if [ -f ${EXE_DIR}/namelist_ice_lim2 ] ; then echo "choosing for namelist ice " >> ${SETTE_DIR}/output.sette echo " " >> ${SETTE_DIR}/output.sette cp ${EXE_DIR}/namelist_ice_lim2 ${EXE_DIR}/namelist_ice elif [ -f ${EXE_DIR}/namelist_ice_lim3 ] ; then cp ${EXE_DIR}/namelist_ice_lim3 ${EXE_DIR}/namelist_ice fi fi if [ "$(cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "agrif" )" -ne 0 ] ; then #- Namelist for ocean and ice (agrif fine grid) echo "choosing for namelist for AGRIF" >> ${SETTE_DIR}/output.sette echo " " >> ${SETTE_DIR}/output.sette cp ${EXE_DIR}/1_namelist_ice_lim2 ${EXE_DIR}/1_namelist_ice 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 | awk '{print $1 % 4}') if [ ${NB_REM} == 0 ] ; then # number of processes required is an integer multiple of 4 # NB_NODES=$( echo $NB_PROC | awk '{print $1 / 4}') else # # number of processes required is not an integer multiple of 4 # round up the number of nodes required. # NB_NODES=$( echo $NB_PROC | awk '{printf("%d",$1 / 4 + 1 )}') fi ;; *) NB_NODES=${NB_PROC} ;; esac # # Pass settings into job file by using sed to edit predefined strings # cat ${SETTE_DIR}/job_batch_template | sed -e"s/NODES/${NB_NODES}/" -e"s/NPROCS/${NB_PROC}/" \ -e"s:DEF_SETTE_DIR:${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 # # 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