| 1 | ##################################################### |
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| 2 | # Author : Simona Flavoni for NEMO |
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| 3 | # Contact : sflod@locean-ipsl.upmc.fr |
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| 4 | # |
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| 5 | # ---------------------------------------------------------------------- |
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| 6 | # NEMO/SETTE , NEMO Consortium (2010) |
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| 7 | # Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt) |
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| 8 | # ---------------------------------------------------------------------- |
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| 9 | # |
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| 10 | # Some scripts called by sette.sh |
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| 11 | # prepare_job.sh : creates the job script for running job |
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| 12 | ###################################################### |
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| 13 | #set -vx |
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| 14 | set -o posix |
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| 15 | #set -u |
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| 16 | #set -e |
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| 17 | #+ |
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| 18 | # |
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| 19 | # ================ |
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| 20 | # prepare_job.sh |
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| 21 | # ================ |
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| 22 | # |
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| 23 | # ------------------------------------------------- |
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| 24 | # script that creates the job script for NEMO tests |
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| 25 | # ------------------------------------------------- |
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| 26 | # |
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| 27 | # SYNOPSIS |
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| 28 | # ======== |
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| 29 | # |
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| 30 | # :: |
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| 31 | # |
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| 32 | # $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE |
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| 33 | # |
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| 34 | # |
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| 35 | # DESCRIPTION |
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| 36 | # =========== |
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| 37 | # |
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| 38 | # Part of the SETTE package to run tests for NEMO |
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| 39 | # |
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| 40 | # prepare the script $JOB_FILE to run the tests |
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| 41 | # |
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| 42 | # EXAMPLES |
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| 43 | # ======== |
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| 44 | # |
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| 45 | # :: |
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| 46 | # |
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| 47 | # $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG $JOB_FILE |
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| 48 | # |
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| 49 | # prepare the $JOB_FILE for execution |
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| 50 | # |
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| 51 | # |
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| 52 | # TODO |
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| 53 | # ==== |
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| 54 | # |
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| 55 | # option debug |
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| 56 | # |
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| 57 | # |
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| 58 | # EVOLUTIONS |
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| 59 | # ========== |
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| 60 | # |
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| 61 | # $Id: prepare_job.sh 3050 2011-11-07 14:11:34Z acc $ |
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| 62 | # |
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| 63 | # |
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| 64 | # |
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| 65 | # * creation |
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| 66 | # |
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| 67 | #- |
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| 68 | # |
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| 69 | |
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| 70 | usage=" Usage : ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE NUM_XIO_SERVERS" |
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| 71 | usage=" example : ./prepare_job.sh input_ORCA2_LIM_PISCES.cfg 8 SHORT no/yes $JOB_FILE 0 2" |
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| 72 | |
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| 73 | |
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| 74 | minargcount=6 |
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| 75 | if [ ${#} -lt ${minargcount} ] |
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| 76 | then |
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| 77 | echo "not enough arguments for prepare_job.sh script" |
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| 78 | echo "control number of argument of prepare_job.sh in sette.sh" |
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| 79 | echo "${usage}" |
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| 80 | exit 1 |
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| 81 | fi |
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| 82 | unset minargcount |
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| 83 | if [ ! -f ${SETTE_DIR}/output.sette ] ; then |
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| 84 | touch ${SETTE_DIR}/output.sette |
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| 85 | fi |
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| 86 | |
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| 87 | # |
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| 88 | # set and export TEST_NAME. It will be used within the post_test_tidyup function |
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| 89 | # |
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| 90 | INPUTARFILE=$1 |
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| 91 | NB_PROC=$2 |
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| 92 | TEST_NAME=$3 |
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| 93 | MPI_FLAG=$4 |
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| 94 | JOB_FILE=$5 |
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| 95 | NXIO_PROC=$6 |
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| 96 | |
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| 97 | # export EXE_DIR. This directory is used to execute model |
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| 98 | # |
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| 99 | # |
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| 100 | # |
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| 101 | echo "date: `date`" >> ${SETTE_DIR}/output.sette |
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| 102 | echo "" >> ${SETTE_DIR}/output.sette |
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| 103 | echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette |
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| 104 | echo "" >> ${SETTE_DIR}/output.sette |
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| 105 | echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette |
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| 106 | echo "`more ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette |
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| 107 | echo "" >> ${SETTE_DIR}/output.sette |
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| 108 | echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette |
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| 109 | echo "" >> ${SETTE_DIR}/output.sette |
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| 110 | echo "executing script : \"fcm_job $@\" " >> ${SETTE_DIR}/output.sette |
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| 111 | echo " " >> ${SETTE_DIR}/output.sette |
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| 112 | |
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| 113 | ################################################################ |
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| 114 | # SET INPUT |
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| 115 | # get the input tarfile if needed |
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| 116 | if [ "$(cat ${SETTE_DIR}/$INPUTARFILE | wc -w)" -ne 0 ] ; then |
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| 117 | echo "looking for input files in ${SETTE_DIR}/$INPUTARFILE " >> ${SETTE_DIR}/output.sette |
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| 118 | # number of tarfiles: NBTAR |
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| 119 | NBTAR=`cat ${SETTE_DIR}/$INPUTARFILE |wc -l` |
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| 120 | echo "NB of tarfiles ${NBTAR} " >> ${SETTE_DIR}/output.sette |
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| 121 | # loop on tarfiles |
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| 122 | # read file name and directory |
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| 123 | while read tar_file dir_conf_forc |
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| 124 | do |
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| 125 | 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 |
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| 126 | if [ -f ${FORCING_DIR}/${tar_file} ] && [ -d ${FORCING_DIR}/${dir_conf_forc} ] ; then |
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| 127 | # Tarfile and input dir ar there, only check the links |
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| 128 | echo "Tarfile and input dir ar there, only check the links" >> ${SETTE_DIR}/output.sette |
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| 129 | # extract tarfile |
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| 130 | else |
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| 131 | |
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| 132 | if [ ! -f ${FORCING_DIR}/${tar_file} ] ; then |
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| 133 | echo "tarfile ${FORCING_DIR}/${tar_file} cannot be found we stop " ; exit 2 ; fi |
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| 134 | |
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| 135 | echo "mkdir ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette |
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| 136 | mkdir ${FORCING_DIR}/${dir_conf_forc} |
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| 137 | cd ${FORCING_DIR}/${dir_conf_forc} |
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| 138 | echo " extract from tarfile ${FORCING_DIR}/${tar_file} in ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette |
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| 139 | tar xvof ${FORCING_DIR}/${tar_file} ; gunzip -f `find . -name "*.gz"` |
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| 140 | fi |
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| 141 | # Tarfile and input dir ar there, only check the links |
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| 142 | cd ${FORCING_DIR}/${dir_conf_forc} |
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| 143 | for fida in * |
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| 144 | do |
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| 145 | [ -f ${EXE_DIR}/${fida} ] || ln -s ${FORCING_DIR}/${dir_conf_forc}/${fida} ${EXE_DIR}/${fida} |
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| 146 | done |
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| 147 | done < ${SETTE_DIR}/$INPUTARFILE |
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| 148 | |
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| 149 | else |
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| 150 | echo "no input file to be searched " |
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| 151 | fi |
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| 152 | ################################################################ |
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| 153 | |
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| 154 | ################################################################ |
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| 155 | # RUN OPA |
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| 156 | cd ${EXE_DIR} |
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| 157 | if [ ! -r ${EXE_DIR}/opa ] |
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| 158 | then |
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| 159 | echo "executable opa does not exist" |
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| 160 | echo "executable opa does not exist, exit" >> ${SETTE_DIR}/output.sette |
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| 161 | exit 1 |
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| 162 | fi |
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| 163 | |
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| 164 | # example for NOCS ClusterVision system using SLURM batch submission (requires ${SETTE_DIR}/sette_batch_template file) |
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| 165 | # |
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| 166 | # if [ ${MPI_FLAG} == "no" ] ; then |
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| 167 | case ${COMPILER} in |
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| 168 | X64_MOBILIS) |
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| 169 | NB_REM=$( echo $NB_PROC $NXIO_PROC | awk '{print ( $1 + $2 ) % 16}') |
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| 170 | if [ ${NB_REM} == 0 ] ; then |
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| 171 | # number of processes required is an integer multiple of 16 |
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| 172 | # |
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| 173 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{print ($1 + $2 ) / 16}') |
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| 174 | else |
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| 175 | # |
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| 176 | # number of processes required is not an integer multiple of 16 |
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| 177 | # round up the number of nodes required. |
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| 178 | # |
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| 179 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{printf("%d",($1 + $2 ) / 16 + 1 )}') |
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| 180 | fi |
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| 181 | ;; |
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| 182 | XC_ARCHER_INTEL) |
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| 183 | # ocean cores are packed 24 to a node |
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| 184 | NB_REM=$( echo $NB_PROC | awk '{print ( $1 % 24 ) }') |
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| 185 | if [ ${NB_REM} == 0 ] ; then |
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| 186 | # number of processes required is an integer multiple of 24 |
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| 187 | # |
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| 188 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{print ($1) / 24}') |
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| 189 | else |
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| 190 | # |
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| 191 | # number of processes required is not an integer multiple of 24 |
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| 192 | # round up the number of nodes required. |
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| 193 | # |
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| 194 | NB_NODES=$( echo $NB_PROC | awk '{printf("%d",($1) / 24 + 1 )}') |
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| 195 | fi |
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| 196 | # xios cores are sparsely packed at 4 to a node |
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| 197 | # but can not share nodes with the ocean cores |
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| 198 | NB_REM=$( echo $NXIO_PROC | awk '{print ( $2 % 4 ) }') |
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| 199 | if [ ${NB_REM} == 0 ] ; then |
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| 200 | # number of processes required is an integer multiple of 4 |
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| 201 | # |
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| 202 | NB_NODES=$( echo $NB_NODES $NXIO_PROC | awk '{print ($1 + ( $2 / 4 ))}') |
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| 203 | else |
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| 204 | # |
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| 205 | # number of processes required is not an integer multiple of 4 |
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| 206 | # round up the number of nodes required. |
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| 207 | # |
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| 208 | NB_NODES=$( echo $NB_NODES $NXIO_PROC | awk '{print ($1 + ( $2 / 4 ) + 1)}') |
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| 209 | fi |
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| 210 | ;; |
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| 211 | XC40_METO*) #Setup for Met Office XC40 with any compiler |
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| 212 | # ocean cores are packed 32 to a node |
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| 213 | # If we need more than one node then have to use parallel queue and XIOS must have a node to itself |
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| 214 | NB_REM=$( echo $NB_PROC | awk '{print ( $1 % 32 ) }') |
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| 215 | if [ ${NB_REM} == 0 ] ; then |
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| 216 | # number of processes required is an integer multiple of 32 |
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| 217 | # |
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| 218 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{print ($1) / 32}') |
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| 219 | else |
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| 220 | # |
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| 221 | # number of processes required is not an integer multiple of 32 |
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| 222 | # round up the number of nodes required. |
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| 223 | # |
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| 224 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{printf("%d",($1) / 32 + 1 )}') |
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| 225 | fi |
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| 226 | # xios cores are sparsely packed at 4 to a node |
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| 227 | if [ $NXIO_PROC == 0 ] ; then |
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| 228 | NB_XNODES=0 |
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| 229 | else |
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| 230 | NB_REM=$( echo $NXIO_PROC | awk '{print ( $1 % 4 ) }') |
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| 231 | if [ ${NB_REM} == 0 ] ; then |
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| 232 | # number of processes required is an integer multiple of 4 |
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| 233 | # |
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| 234 | NB_XNODES=$( echo $NXIO_PROC | awk '{print (( $1 / 4 ) + 1)}') |
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| 235 | else |
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| 236 | # |
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| 237 | # number of processes required is not an integer multiple of 4 |
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| 238 | # round up the number of nodes required. |
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| 239 | # |
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| 240 | NB_XNODES=$( echo $NXIO_PROC | awk '{printf("%d",($1) / 4 + 1) }') |
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| 241 | fi |
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| 242 | fi |
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| 243 | if [ ${NB_XNODES} -ge 1 ] ; then |
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| 244 | NB_NODES=$((NB_NODES+NB_XNODES)) |
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| 245 | fi |
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| 246 | echo NB_XNODES=${NB_XNODES} |
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| 247 | echo Total NB_NODES=${NB_NODES} |
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| 248 | QUEUE=normal |
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| 249 | SELECT="select=$NB_NODES" |
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| 250 | module unload cray-snplauncher #Make sure snplauncher module is not loaded |
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| 251 | ;; |
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| 252 | openmpi_NAVITI_MERCATOR) |
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| 253 | echo NB_PROCS ${NB_PROC} |
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| 254 | echo NB_NODES ${NB_NODES} |
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| 255 | echo NB_PROC ${NB_PROC} |
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| 256 | if [ ${NB_PROC} -eq 1 ] ; then |
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| 257 | NB_NODES=1 |
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| 258 | QUEUE=monoproc |
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| 259 | NB_PROC_NODE=${NB_PROC} |
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| 260 | else |
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| 261 | if [ ${NB_PROC} -le 16 ] ; then |
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| 262 | NB_NODES=1 |
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| 263 | QUEUE=mono |
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| 264 | NB_PROC_NODE=${NB_PROC} |
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| 265 | else |
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| 266 | NB_NODES=$( echo $NB_PROC | awk '{print $1 - $1 % 16}' | awk '{print $1 / 16 }') |
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| 267 | QUEUE=multi |
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| 268 | NB_PROC_NODE=16 |
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| 269 | fi |
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| 270 | fi |
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| 271 | echo NB_PROCS ${NB_PROC} |
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| 272 | echo NB_NODES ${NB_NODES} |
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| 273 | echo NB_PROC_NODE ${NB_PROC_NODE} |
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| 274 | ;; |
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| 275 | *) |
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| 276 | NB_NODES=${NB_PROC} |
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| 277 | ;; |
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| 278 | |
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| 279 | esac |
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| 280 | # |
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| 281 | # Pass settings into job file by using sed to edit predefined strings |
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| 282 | # |
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| 283 | TOTAL_NPROCS=$(( $NB_PROC + $NXIO_PROC )) |
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| 284 | cat ${SETTE_DIR}/job_batch_template | sed -e"s/NODES/${NB_NODES}/" \ |
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| 285 | -e"s/TOTAL_NPROCS/${TOTAL_NPROCS}/" \ |
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| 286 | -e"s/NPROCS/${NB_PROC}/" \ |
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| 287 | -e"s/NXIOPROCS/${NXIO_PROC}/" \ |
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| 288 | -e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \ |
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| 289 | -e"s:DEF_EXE_DIR:${EXE_DIR}:" \ |
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| 290 | -e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \ |
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| 291 | -e"s:DEF_TOOLS_DIR:${TOOLS_DIR}:" \ |
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| 292 | -e"s:MPI_FLAG:${MPI_FLAG}:" \ |
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| 293 | -e"s:DEF_NEMO_VALIDATION:${NEMO_VALIDATION_DIR}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \ |
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| 294 | -e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job |
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| 295 | |
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| 296 | case ${COMPILER} in |
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| 297 | openmpi_NAVITI_MERCATOR) |
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| 298 | cat run_sette_test.job | sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \ |
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| 299 | -e"s:QUEUE:${QUEUE}:" > run_sette_test1.job |
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| 300 | mv run_sette_test1.job run_sette_test.job |
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| 301 | ;; |
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| 302 | XC40_METO*) |
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| 303 | cat run_sette_test.job | sed -e"s/SELECT/${SELECT}/" > run_sette_test1.job |
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| 304 | mv run_sette_test1.job run_sette_test.job |
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| 305 | ;; |
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| 306 | esac |
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| 307 | # |
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| 308 | # create the unique submission job script |
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| 309 | # |
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| 310 | if [ ! -f $JOB_FILE ] ; then |
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| 311 | mv run_sette_test.job $JOB_FILE |
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| 312 | else |
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| 313 | e=`grep -n "# END_BODY" ${JOB_FILE} | cut -d : -f 1` |
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| 314 | e=$(($e - 1)) |
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| 315 | head -$e $JOB_FILE > ${JOB_FILE}_new |
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| 316 | mv ${JOB_FILE}_new ${JOB_FILE} |
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| 317 | l=`wc -l run_sette_test.job | sed -e "s:run_sette_test.job::"` |
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| 318 | b=`grep -n "# BODY" run_sette_test.job | cut -d : -f 1` |
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| 319 | t=$(($l - $b)) |
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| 320 | tail -$t run_sette_test.job >> $JOB_FILE |
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| 321 | fi |
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| 322 | |
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| 323 | chmod a+x $JOB_FILE ; echo "$JOB_FILE is ready" |
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| 324 | |
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| 325 | #fi |
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