[3520] | 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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[3661] | 13 | #set -vx |
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[3520] | 14 | set -o posix |
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| 15 | #set -u |
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| 16 | #set -e |
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[3661] | 17 | #+ |
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[3520] | 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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[3661] | 32 | # $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE |
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[3520] | 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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[3661] | 38 | # Part of the SETTE package to run tests for NEMO |
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[3520] | 39 | # |
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[3661] | 40 | # prepare the script $JOB_FILE to run the tests |
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[3520] | 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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[3661] | 47 | # $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG $JOB_FILE |
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[3520] | 48 | # |
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[3661] | 49 | # prepare the $JOB_FILE for execution |
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[3520] | 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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[3661] | 61 | # $Id: prepare_job.sh 3050 2011-11-07 14:11:34Z acc $ |
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[3520] | 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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[7753] | 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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[9663] | 71 | usage=" example : ./prepare_job.sh input_ORCA2_ICE_PISCES.cfg 8 SHORT no/yes $JOB_FILE 0 2" |
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[3520] | 72 | |
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| 73 | |
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[4245] | 74 | minargcount=6 |
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[3520] | 75 | if [ ${#} -lt ${minargcount} ] |
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| 76 | then |
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[3661] | 77 | echo "not enough arguments for prepare_job.sh script" |
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| 78 | echo "control number of argument of prepare_job.sh in sette.sh" |
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[3520] | 79 | echo "${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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[4245] | 95 | NXIO_PROC=$6 |
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[11161] | 96 | NEMO_VALID=$7 |
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[3520] | 97 | |
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| 98 | # export EXE_DIR. This directory is used to execute model |
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| 99 | # |
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| 100 | # |
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| 101 | # |
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| 102 | echo "date: `date`" >> ${SETTE_DIR}/output.sette |
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| 103 | echo "" >> ${SETTE_DIR}/output.sette |
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| 104 | echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette |
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| 105 | echo "" >> ${SETTE_DIR}/output.sette |
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| 106 | echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette |
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[7715] | 107 | echo "`more ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette |
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[3520] | 108 | echo "" >> ${SETTE_DIR}/output.sette |
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| 109 | echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette |
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| 110 | echo "" >> ${SETTE_DIR}/output.sette |
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| 111 | echo "executing script : \"fcm_job $@\" " >> ${SETTE_DIR}/output.sette |
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| 112 | echo " " >> ${SETTE_DIR}/output.sette |
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| 113 | |
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| 114 | ################################################################ |
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[4147] | 115 | # SET INPUT |
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[3520] | 116 | # get the input tarfile if needed |
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[4147] | 117 | if [ "$(cat ${SETTE_DIR}/$INPUTARFILE | wc -w)" -ne 0 ] ; then |
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| 118 | echo "looking for input files in ${SETTE_DIR}/$INPUTARFILE " >> ${SETTE_DIR}/output.sette |
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| 119 | # number of tarfiles: NBTAR |
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| 120 | NBTAR=`cat ${SETTE_DIR}/$INPUTARFILE |wc -l` |
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| 121 | echo "NB of tarfiles ${NBTAR} " >> ${SETTE_DIR}/output.sette |
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| 122 | # loop on tarfiles |
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| 123 | # read file name and directory |
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[13292] | 124 | while read tar_file dir_conf_forc |
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| 125 | do |
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| 126 | echo looking for tarfile ${tar_file} and directory ${FORCING_DIR}/${dir_conf_forc} |
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| 127 | echo looking for tarfile ${tar_file} and directory ${FORCING_DIR}/${dir_conf_forc} >> ${SETTE_DIR}/output.sette |
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| 128 | if [ -d ${FORCING_DIR}/${dir_conf_forc} ] ; then |
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| 129 | # input dir ar there, only check the links |
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| 130 | echo "input dir ar there, only check the links" >> ${SETTE_DIR}/output.sette |
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| 131 | # extract tarfile |
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| 132 | else |
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| 133 | if [ ! -f ${FORCING_DIR}/${tar_file} ] ; then |
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| 134 | echo "tarfile ${FORCING_DIR}/${tar_file} cannot be found we stop " ; exit 2 ; fi |
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[3520] | 135 | |
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[13292] | 136 | echo " extract from tarfile ${FORCING_DIR}/${tar_file} in ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette |
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[3520] | 137 | |
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[13292] | 138 | istgz=$( echo ${FORCING_DIR}/${tar_file} | grep -c "gz$" ) |
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| 139 | if [ $istgz -eq 1 ] |
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| 140 | then |
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| 141 | withdir=$( tar tfz ${FORCING_DIR}/${tar_file} | head -n 1 | grep -c "${dir_conf_forc}/$" ) |
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| 142 | else |
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| 143 | withdir=$( tar tf ${FORCING_DIR}/${tar_file} | head -n 1 | grep -c "${dir_conf_forc}/$" ) |
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| 144 | fi |
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| 145 | if [ $withdir -eq 0 ] |
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| 146 | then |
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| 147 | mkdir ${FORCING_DIR}/${dir_conf_forc} |
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| 148 | cd ${FORCING_DIR}/${dir_conf_forc} |
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| 149 | else |
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| 150 | cd ${FORCING_DIR} |
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| 151 | fi |
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| 152 | if [ $istgz -eq 1 ] |
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| 153 | then |
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| 154 | tar xvfz ${FORCING_DIR}/${tar_file} |
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| 155 | else |
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| 156 | tar xvf ${FORCING_DIR}/${tar_file} |
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| 157 | [ $( ls -1 *gz 2>/dev/null | wc -l ) -gt 0 ] && gunzip -f *gz |
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| 158 | fi |
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| 159 | fi |
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| 160 | # Tarfile and input dir ar there, only check the links |
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| 161 | cd ${FORCING_DIR}/${dir_conf_forc} |
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| 162 | for fida in * |
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| 163 | do |
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[4147] | 164 | [ -f ${EXE_DIR}/${fida} ] || ln -s ${FORCING_DIR}/${dir_conf_forc}/${fida} ${EXE_DIR}/${fida} |
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[13292] | 165 | done |
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| 166 | done < ${SETTE_DIR}/$INPUTARFILE |
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| 167 | |
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[4147] | 168 | else |
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[13292] | 169 | echo "no input file to be searched " |
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[3520] | 170 | fi |
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| 171 | ################################################################ |
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| 172 | |
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| 173 | ################################################################ |
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| 174 | # RUN OPA |
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| 175 | cd ${EXE_DIR} |
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[9576] | 176 | if [ ! -r ${EXE_DIR}/nemo ] |
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[3520] | 177 | then |
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[9576] | 178 | echo "executable nemo does not exist" |
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| 179 | echo "executable nemo does not exist, exit" >> ${SETTE_DIR}/output.sette |
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[3520] | 180 | exit 1 |
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| 181 | fi |
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| 182 | |
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[4687] | 183 | # example for NOCS ClusterVision system using SLURM batch submission (requires ${SETTE_DIR}/sette_batch_template file) |
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[3520] | 184 | # |
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[3661] | 185 | # if [ ${MPI_FLAG} == "no" ] ; then |
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[3520] | 186 | case ${COMPILER} in |
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[13568] | 187 | X64_MOBILIS*) |
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[4687] | 188 | NB_REM=$( echo $NB_PROC $NXIO_PROC | awk '{print ( $1 + $2 ) % 16}') |
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[3520] | 189 | if [ ${NB_REM} == 0 ] ; then |
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[4687] | 190 | # number of processes required is an integer multiple of 16 |
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[3520] | 191 | # |
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[4687] | 192 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{print ($1 + $2 ) / 16}') |
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[3520] | 193 | else |
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| 194 | # |
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[4687] | 195 | # number of processes required is not an integer multiple of 16 |
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[3520] | 196 | # round up the number of nodes required. |
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| 197 | # |
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[4687] | 198 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{printf("%d",($1 + $2 ) / 16 + 1 )}') |
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[3520] | 199 | fi |
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| 200 | ;; |
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[13790] | 201 | X86_ARCHER2*) |
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[14825] | 202 | MK_TEMPLATE=$( /work/n01/shared/acc/mkslurm_settejob -S $NXIO_PROC -s 8 -m 4 -C $NB_PROC -g 2 -a n01-CLASS -j sette_job -t 20:00 > ${SETTE_DIR}/job_batch_template ) |
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[13790] | 203 | ;; |
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[5480] | 204 | XC40_METO*) #Setup for Met Office XC40 with any compiler |
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| 205 | # ocean cores are packed 32 to a node |
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| 206 | # If we need more than one node then have to use parallel queue and XIOS must have a node to itself |
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| 207 | NB_REM=$( echo $NB_PROC | awk '{print ( $1 % 32 ) }') |
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| 208 | if [ ${NB_REM} == 0 ] ; then |
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| 209 | # number of processes required is an integer multiple of 32 |
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| 210 | # |
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| 211 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{print ($1) / 32}') |
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| 212 | else |
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| 213 | # |
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| 214 | # number of processes required is not an integer multiple of 32 |
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| 215 | # round up the number of nodes required. |
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| 216 | # |
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| 217 | NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{printf("%d",($1) / 32 + 1 )}') |
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| 218 | fi |
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| 219 | # xios cores are sparsely packed at 4 to a node |
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| 220 | if [ $NXIO_PROC == 0 ] ; then |
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| 221 | NB_XNODES=0 |
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| 222 | else |
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| 223 | NB_REM=$( echo $NXIO_PROC | awk '{print ( $1 % 4 ) }') |
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| 224 | if [ ${NB_REM} == 0 ] ; then |
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| 225 | # number of processes required is an integer multiple of 4 |
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| 226 | # |
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| 227 | NB_XNODES=$( echo $NXIO_PROC | awk '{print (( $1 / 4 ) + 1)}') |
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| 228 | else |
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| 229 | # |
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| 230 | # number of processes required is not an integer multiple of 4 |
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| 231 | # round up the number of nodes required. |
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| 232 | # |
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| 233 | NB_XNODES=$( echo $NXIO_PROC | awk '{printf("%d",($1) / 4 + 1) }') |
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| 234 | fi |
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| 235 | fi |
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| 236 | if [ ${NB_XNODES} -ge 1 ] ; then |
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| 237 | NB_NODES=$((NB_NODES+NB_XNODES)) |
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| 238 | fi |
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| 239 | echo NB_XNODES=${NB_XNODES} |
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| 240 | echo Total NB_NODES=${NB_NODES} |
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[6140] | 241 | QUEUE=normal |
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| 242 | SELECT="select=$NB_NODES" |
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| 243 | module unload cray-snplauncher #Make sure snplauncher module is not loaded |
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[5480] | 244 | ;; |
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[11645] | 245 | X64_JEANZAY*) #Setup for Jean-Zay |
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[13329] | 246 | export GROUP_IDRIS=`echo ${IDRPROJ}` |
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[11645] | 247 | ;; |
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[12798] | 248 | openmpi_KARA_MERCATOR*) |
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[11805] | 249 | NB_PROC_NODE=32 |
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[12798] | 250 | NB_NODES=$( echo $NB_PROC | awk '{print $1 - $1 % $NB_PROC_NODE }' | awk '{print $1 / $NB_PROC_NODE }' ) |
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[9480] | 251 | if [ ${NB_PROC} -le 128 ] ; then |
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| 252 | QUEUE=multi |
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| 253 | fi |
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| 254 | ;; |
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[3520] | 255 | *) |
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| 256 | NB_NODES=${NB_PROC} |
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| 257 | ;; |
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| 258 | esac |
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| 259 | # |
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| 260 | # Pass settings into job file by using sed to edit predefined strings |
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| 261 | # |
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[4373] | 262 | TOTAL_NPROCS=$(( $NB_PROC + $NXIO_PROC )) |
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[12798] | 263 | cat ${SETTE_DIR}/job_batch_template | sed -e"s/\(=\| \)NODES/\1${NB_NODES}/" \ |
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[4373] | 264 | -e"s/TOTAL_NPROCS/${TOTAL_NPROCS}/" \ |
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[4245] | 265 | -e"s/NPROCS/${NB_PROC}/" \ |
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| 266 | -e"s/NXIOPROCS/${NXIO_PROC}/" \ |
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[3520] | 267 | -e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \ |
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| 268 | -e"s:DEF_EXE_DIR:${EXE_DIR}:" \ |
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| 269 | -e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \ |
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[8468] | 270 | -e"s:DEF_TOOLS_DIR:${TOOLS_DIR}:" \ |
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[3520] | 271 | -e"s:MPI_FLAG:${MPI_FLAG}:" \ |
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[11161] | 272 | -e"s:DEF_NEMO_VALIDATION:${NEMO_VALID}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \ |
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[3520] | 273 | -e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job |
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[3661] | 274 | |
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[3665] | 275 | case ${COMPILER} in |
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[9480] | 276 | openmpi_KARA_MERCATOR_XIOS ) |
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| 277 | cat run_sette_test.job | sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \ |
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| 278 | -e"s:QUEUE:${QUEUE}:" > run_sette_test1.job |
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| 279 | mv run_sette_test1.job run_sette_test.job |
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| 280 | ;; |
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[5480] | 281 | XC40_METO*) |
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[6140] | 282 | cat run_sette_test.job | sed -e"s/SELECT/${SELECT}/" > run_sette_test1.job |
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[5480] | 283 | mv run_sette_test1.job run_sette_test.job |
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| 284 | ;; |
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[11645] | 285 | X64_JEANZAY*) |
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| 286 | cat run_sette_test.job | sed -e"s/GROUP_IDRIS/${GROUP_IDRIS}/" > run_sette_test1.job |
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| 287 | mv run_sette_test1.job run_sette_test.job |
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| 288 | ;; |
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[3665] | 289 | esac |
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[3520] | 290 | # |
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| 291 | # create the unique submission job script |
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| 292 | # |
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| 293 | if [ ! -f $JOB_FILE ] ; then |
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| 294 | mv run_sette_test.job $JOB_FILE |
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| 295 | else |
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| 296 | e=`grep -n "# END_BODY" ${JOB_FILE} | cut -d : -f 1` |
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| 297 | e=$(($e - 1)) |
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| 298 | head -$e $JOB_FILE > ${JOB_FILE}_new |
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| 299 | mv ${JOB_FILE}_new ${JOB_FILE} |
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| 300 | l=`wc -l run_sette_test.job | sed -e "s:run_sette_test.job::"` |
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| 301 | b=`grep -n "# BODY" run_sette_test.job | cut -d : -f 1` |
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| 302 | t=$(($l - $b)) |
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| 303 | tail -$t run_sette_test.job >> $JOB_FILE |
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| 304 | fi |
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| 305 | |
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[3661] | 306 | chmod a+x $JOB_FILE ; echo "$JOB_FILE is ready" |
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[3520] | 307 | |
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| 308 | #fi |
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