[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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[3586] | 13 | #set -x |
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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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| 17 | # |
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[3586] | 18 | # |
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[3520] | 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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[3586] | 32 | # $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_INTERACT MPI_FLAG |
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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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[3586] | 38 | # Simple job for SET TESTS for NEMO (SETTE) |
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[3520] | 39 | # |
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[3586] | 40 | # get input files (if needed) : tar file |
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| 41 | # (note this job needs to have an input_CONFIG.cfg in which can be found input tar file name) |
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[3520] | 42 | # |
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[3586] | 43 | # runs job in interactive or batch mode : all jobs using 1 process are run interactive, and all MPP jobs are |
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| 44 | # |
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| 45 | # run in batch (MPI_INTERACT="no") or interactive (MPI_INTERACT="yes") see sette.sh and BATCH_TEMPLATE directory |
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| 46 | # |
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| 47 | # and call post_test_tidyup function (that moves in NEMO_VALIDATION_DIR solver.stat, tracer.stat (for LOBSTER & PISCES) & ocean.output) |
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| 48 | # |
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[3520] | 49 | # EXAMPLES |
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| 50 | # ======== |
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| 51 | # |
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| 52 | # :: |
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| 53 | # |
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[3586] | 54 | # $ ./fcm_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_INTERACT MPI_FLAG |
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[3520] | 55 | # |
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[3586] | 56 | # run a job of config GYRE with 1 processor SHORT test ( 5 days ) using an interactive run without mpirun |
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| 57 | # $ ./fcm_job.sh input_GYRE.cfg 1 SHORT yes no |
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[3520] | 58 | # |
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[3586] | 59 | # run a job of config ORCA2_LIM_PISCES with 8 processors test RESTARTABILITY submitting the job to the batch queue system and using mpirun |
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| 60 | # $ ./fcm_job.sh input_ORCA2_LIM_PISCES.cfg 8 LONG no yes |
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[3520] | 61 | # |
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[3586] | 62 | # |
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[3520] | 63 | # TODO |
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| 64 | # ==== |
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| 65 | # |
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| 66 | # option debug |
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| 67 | # |
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| 68 | # |
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| 69 | # EVOLUTIONS |
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| 70 | # ========== |
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| 71 | # |
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[3586] | 72 | # $Id: fcm_job.sh 3050 2011-11-07 14:11:34Z acc $ |
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[3520] | 73 | # |
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| 74 | # |
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| 75 | # |
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| 76 | # * creation |
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| 77 | # |
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| 78 | #- |
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| 79 | # |
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| 80 | |
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[3586] | 81 | usage=" Usage : ./fcm_job.sh input_CONFIG_NAME.cfg NUMBER_OF_PROCS TEST_NAME INTERACT MPI_FLAG" |
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| 82 | usage=" example : ./fcm_job.sh input_ORCA2_LIM_PISCES.cfg 8 SHORT no/yes no/yes" |
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[3520] | 83 | |
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| 84 | |
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| 85 | minargcount=5 |
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| 86 | if [ ${#} -lt ${minargcount} ] |
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| 87 | then |
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[3586] | 88 | echo "not enought arguments for fcm_job.sh script" |
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| 89 | echo "control number of argument of fcm_job.sh in sette.sh" |
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[3520] | 90 | echo "${usage}" |
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| 91 | exit 1 |
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| 92 | fi |
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| 93 | unset minargcount |
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| 94 | if [ ! -f ${SETTE_DIR}/output.sette ] ; then |
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| 95 | touch ${SETTE_DIR}/output.sette |
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| 96 | fi |
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| 97 | |
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| 98 | # |
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| 99 | # set and export TEST_NAME. It will be used within the post_test_tidyup function |
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| 100 | # |
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| 101 | INPUTARFILE=$1 |
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| 102 | NB_PROC=$2 |
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| 103 | TEST_NAME=$3 |
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| 104 | MPI_FLAG=$4 |
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| 105 | JOB_FILE=$5 |
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| 106 | |
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| 107 | # export EXE_DIR. This directory is used to execute model |
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| 108 | # |
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| 109 | export EXE_DIR |
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| 110 | # |
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| 111 | # |
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| 112 | echo "date: `date`" >> ${SETTE_DIR}/output.sette |
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| 113 | echo "" >> ${SETTE_DIR}/output.sette |
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| 114 | echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette |
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| 115 | echo "" >> ${SETTE_DIR}/output.sette |
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| 116 | echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette |
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| 117 | echo "`more ${SETTE_DIR}/../CONFIG/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette |
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| 118 | echo "" >> ${SETTE_DIR}/output.sette |
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| 119 | echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette |
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| 120 | echo "" >> ${SETTE_DIR}/output.sette |
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| 121 | echo "executing script : \"fcm_job $@\" " >> ${SETTE_DIR}/output.sette |
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| 122 | echo " " >> ${SETTE_DIR}/output.sette |
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| 123 | |
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| 124 | ################################################################ |
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| 125 | # SET INPUT |
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| 126 | # get the input tarfile if needed |
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| 127 | tar_file=$(sed -ne "1,1p" ${SETTE_DIR}/$INPUTARFILE) |
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| 128 | if [ "$(cat ${SETTE_DIR}/$INPUTARFILE | grep -c ".tar" )" -ne 0 ] ; then |
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| 129 | echo "looking for tar file" >> ${SETTE_DIR}/output.sette |
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| 130 | echo " " >> ${SETTE_DIR}/output.sette |
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| 131 | cp ${FORCING_DIR}/${tar_file} ${INPUT_DIR}/. |
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| 132 | echo "file in ${INPUT_DIR}" |
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| 133 | if [ ! -f ${INPUT_DIR}/${tar_file} ] ; then |
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| 134 | echo "PROBLEM during copy of tar file" >> ${SETTE_DIR}/output.sette |
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| 135 | echo "tar file IS NOT present in ${INPUT_DIR} directory " >> ${SETTE_DIR}/output.sette |
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| 136 | echo " " >> ${SETTE_DIR}/output.sette |
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| 137 | echo "PROBLEM during copy of tar file" |
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| 138 | exit 1 |
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| 139 | else |
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| 140 | cd ${EXE_DIR} ; tar xvof ${INPUT_DIR}/*.tar ; gunzip -f *gz |
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| 141 | fi |
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| 142 | fi |
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| 143 | |
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| 144 | if [ ! -f ${EXE_DIR}/namelist_ice ] ; then |
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| 145 | if [ -f ${EXE_DIR}/namelist_ice_lim2 ] ; then |
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| 146 | echo "choosing for namelist ice " >> ${SETTE_DIR}/output.sette |
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| 147 | echo " " >> ${SETTE_DIR}/output.sette |
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| 148 | cp ${EXE_DIR}/namelist_ice_lim2 ${EXE_DIR}/namelist_ice |
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| 149 | elif [ -f ${EXE_DIR}/namelist_ice_lim3 ] ; then |
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| 150 | cp ${EXE_DIR}/namelist_ice_lim3 ${EXE_DIR}/namelist_ice |
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| 151 | fi |
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| 152 | fi |
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| 153 | |
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| 154 | |
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| 155 | if [ "$(cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "agrif" )" -ne 0 ] ; then |
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| 156 | #- Namelist for ocean and ice (agrif fine grid) |
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| 157 | echo "choosing for namelist for AGRIF" >> ${SETTE_DIR}/output.sette |
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| 158 | echo " " >> ${SETTE_DIR}/output.sette |
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| 159 | cp ${EXE_DIR}/1_namelist_ice_lim2 ${EXE_DIR}/1_namelist_ice |
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| 160 | fi |
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| 161 | ################################################################ |
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| 162 | |
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| 163 | ################################################################ |
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| 164 | # RUN OPA |
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| 165 | cd ${EXE_DIR} |
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| 166 | if [ ! -r ${EXE_DIR}/opa ] |
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| 167 | then |
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| 168 | echo "executable opa does not exist" |
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| 169 | echo "executable opa does not exist, exit" >> ${SETTE_DIR}/output.sette |
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| 170 | exit 1 |
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| 171 | fi |
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[3586] | 172 | #if [ ${NB_PROC} == 1 ] ; then |
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| 173 | # echo "running opa" >> ${SETTE_DIR}/output.sette |
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| 174 | # echo " " >> ${SETTE_DIR}/output.sette |
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| 175 | # ./opa |
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| 176 | # |
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| 177 | # Tidy out output from this test and populate the NEMO_VALIDATION_DIR tree |
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| 178 | # |
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| 179 | # post_test_tidyup |
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| 180 | #else |
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| 181 | # echo "running opa in MPI" >> ${SETTE_DIR}/output.sette |
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| 182 | # echo " " >> ${SETTE_DIR}/output.sette |
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[3520] | 183 | |
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[3586] | 184 | # if [ ${MPI_INTERACT} == "yes" ] ; then |
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| 185 | # # |
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| 186 | # # example for brodie (NEC SX8) machine |
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| 187 | # # mpirun -np ${NB_PROC} opa |
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| 188 | # # example for dedale machine |
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| 189 | # # mpirun --mca btl self,tcp -np ${NB_PROC} opa |
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| 190 | # # example for vargas (IBM Power6) machine |
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| 191 | # mpiexec -n ${NB_PROC} opa |
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| 192 | # # |
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| 193 | # post_test_tidyup |
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| 194 | # fi |
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| 195 | # |
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[3520] | 196 | # example for NOCS Altix system using PBS batch submission (requires ${SETTE_DIR}/sette_batch_template file) |
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| 197 | # |
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[3586] | 198 | # if [ ${MPI_INTERACT} == "no" ] ; then |
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[3520] | 199 | case ${COMPILER} in |
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| 200 | ALTIX_NAUTILUS_MPT) |
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| 201 | NB_REM=$( echo $NB_PROC | awk '{print $1 % 4}') |
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| 202 | if [ ${NB_REM} == 0 ] ; then |
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| 203 | # number of processes required is an integer multiple of 4 |
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| 204 | # |
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[3583] | 205 | NB_NODES=$( echo $NB_PROC | awk '{print $1 $1 / 4}') |
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[3520] | 206 | else |
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| 207 | # |
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| 208 | # number of processes required is not an integer multiple of 4 |
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| 209 | # round up the number of nodes required. |
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| 210 | # |
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| 211 | NB_NODES=$( echo $NB_PROC | awk '{printf("%d",$1 / 4 + 1 )}') |
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| 212 | fi |
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| 213 | ;; |
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[3583] | 214 | ifort_MERCATOR_CLUSTER) |
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| 215 | echo NB_PROCS ${NB_PROC} |
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| 216 | echo NB_NODES ${NB_NODES} |
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| 217 | echo NB_PROC ${NB_PROC} |
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| 218 | if [ ${NB_PROC} -eq 1 ] ; then |
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| 219 | NB_NODES=1 |
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| 220 | QUEUE=monoproc |
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| 221 | NB_PROC_NODE=${NB_PROC} |
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| 222 | else |
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| 223 | if [ ${NB_PROC} -le 8 ] ; then |
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| 224 | NB_NODES=1 |
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| 225 | QUEUE=mono |
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| 226 | NB_PROC_NODE=${NB_PROC} |
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| 227 | else |
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| 228 | NB_NODES=$( echo $NB_PROC | awk '{print $1 - $1 % 8}' | awk '{print $1 / 8 }') |
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| 229 | QUEUE=multi |
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| 230 | NB_PROC_NODE=8 |
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| 231 | fi |
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| 232 | fi |
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| 233 | echo NB_PROCS ${NB_PROC} |
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| 234 | echo NB_NODES ${NB_NODES} |
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| 235 | echo NB_PROC_NODE ${NB_PROC_NODE} |
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| 236 | ;; |
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[3520] | 237 | *) |
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| 238 | NB_NODES=${NB_PROC} |
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| 239 | ;; |
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| 240 | |
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| 241 | esac |
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| 242 | # |
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| 243 | # Pass settings into job file by using sed to edit predefined strings |
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| 244 | # |
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[3583] | 245 | ((mem=5*NB_PROC)) |
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| 246 | echo NB_NODES NB_PROC QUEUE ${NB_NODES} ${NB_PROC} ${QUEUE} |
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| 247 | cat ${SETTE_DIR}/job_batch_template | sed -e"s/NODES/${NB_NODES}/" -e"s/NPROCSNODE/${NB_PROC_NODE}/" \ |
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| 248 | -e"s/NPROCS/${NB_PROC}/" \ |
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| 249 | -e"s/QUEUE/${QUEUE}/" -e"s/MEM/${mem}/" \ |
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[3586] | 250 | -e"s/QUEUE/${QUEUE}/" -e"s/MEM/${mem}/" \ |
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[3520] | 251 | -e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \ |
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| 252 | -e"s:DEF_EXE_DIR:${EXE_DIR}:" \ |
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| 253 | -e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \ |
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| 254 | -e"s:MPI_FLAG:${MPI_FLAG}:" \ |
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| 255 | -e"s:DEF_NEMO_VALIDATION:${NEMO_VALIDATION_DIR}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \ |
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| 256 | -e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job |
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| 257 | |
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| 258 | # |
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| 259 | # create the unique submission job script |
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| 260 | # |
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| 261 | if [ ! -f $JOB_FILE ] ; then |
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| 262 | mv run_sette_test.job $JOB_FILE |
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| 263 | else |
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| 264 | e=`grep -n "# END_BODY" ${JOB_FILE} | cut -d : -f 1` |
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| 265 | e=$(($e - 1)) |
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| 266 | head -$e $JOB_FILE > ${JOB_FILE}_new |
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| 267 | mv ${JOB_FILE}_new ${JOB_FILE} |
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| 268 | l=`wc -l run_sette_test.job | sed -e "s:run_sette_test.job::"` |
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| 269 | b=`grep -n "# BODY" run_sette_test.job | cut -d : -f 1` |
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| 270 | t=$(($l - $b)) |
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| 271 | tail -$t run_sette_test.job >> $JOB_FILE |
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| 272 | fi |
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| 273 | |
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[3586] | 274 | chmod a+x $JOB_FILE |
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[3520] | 275 | |
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| 276 | #fi |
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