[622] | 1 | #!/bin/ksh |
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| 2 | |
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| 3 | #************************************************************** |
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| 4 | # Author: Sebastien Denvil, Martial Mancip, Arnaud Caubel |
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| 5 | # Contact: Arnaud.Caubel__at__lsce.ipsl.fr |
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| 6 | # $Revision:: $ Revision of last commit |
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| 7 | # $Author:: $ Author of last commit |
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| 8 | # $Date:: $ Date of last commit |
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| 9 | # IPSL (2006) |
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| 10 | # This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC |
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| 11 | # |
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| 12 | #************************************************************** |
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| 13 | |
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| 14 | #========================================================= |
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| 15 | # The documentation of this file can be automatically generated |
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[623] | 16 | # if you use the prefix #D- for comments to be extracted. |
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[622] | 17 | # Extract with command: cat lib* | grep "^#D-" | cut -c "4-" |
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| 18 | #========================================================= |
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| 19 | |
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| 20 | #D-#================================================== |
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[1490] | 21 | #D-LibIGCM_sys for Jean-Zay |
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[622] | 22 | #D-#================================================== |
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| 23 | #D- |
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[623] | 24 | #D- This ksh library if a layer under some usefull |
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[622] | 25 | #D-environment variables and shell commands. |
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| 26 | #D-All those definitions depend on host particularities. |
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| 27 | #D-It manages a stack mechanism and test validity of operations. |
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| 28 | #D-All function described bellow must be prefixed by IGCM_sys. |
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| 29 | |
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| 30 | #==================================================== |
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| 31 | # libIGCM_sys PARAMETERS |
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| 32 | #==================================================== |
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| 33 | |
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| 34 | #==================================================== |
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| 35 | # set DEBUG_sys to true to output calls of function |
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| 36 | typeset -r DEBUG_sys=${DEBUG_sys:=true} |
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| 37 | |
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| 38 | #==================================================== |
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| 39 | # Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get) |
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| 40 | typeset -r DRYRUN=${DRYRUN:=0} |
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| 41 | |
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| 42 | # YOU MUST COMPILE YOUR EXE FILES FOR DRYRUN MODE ! |
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| 43 | # ------------------------------------------------------------------------------------- |
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| 44 | # | DRYRUN= | Date computations, | sys_Get | Exe | sys_Put_Out; sys_Put_Rest | |
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[809] | 45 | # | | Cp/Exe/param/files | | | | |
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| 46 | # | | Chmod Qsub | | | | |
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[622] | 47 | # ------------------------------------------------------------------------------------- |
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| 48 | # | 0 | yes | yes | yes | yes | |
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| 49 | # ------------------------------------------------------------------------------------- |
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| 50 | # | 1 | yes | yes | yes | no | |
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| 51 | # ------------------------------------------------------------------------------------- |
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| 52 | # | 2 | yes | yes | no | no | |
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| 53 | # ------------------------------------------------------------------------------------- |
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| 54 | # | 3 | yes | no | no | no | |
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| 55 | # ------------------------------------------------------------------------------------- |
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| 56 | |
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| 57 | #===================================================== |
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| 58 | # Global Variables : |
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| 59 | #===================================================== |
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| 60 | # Language : "fr" or "en" |
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| 61 | typeset -r MYLANG="fr" |
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| 62 | |
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| 63 | #===================================================== |
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[1201] | 64 | # Host user names project maxCpuTime |
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[622] | 65 | # $hostname ou hostname |
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[1158] | 66 | typeset HOST=${HOST:=$( hostname )} |
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[622] | 67 | # $username ou whoami |
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[1158] | 68 | typeset LOGIN=${LOGIN:=$( whoami )} |
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[622] | 69 | # $hostname of the MASTER job |
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[1490] | 70 | typeset MASTER=jeanzay |
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| 71 | # add default project set by ins_job |
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| 72 | typeset PROJECT=$( echo ${SLURM_JOB_ACCOUNT:=::default_project::} | cut -c "1-3" ) |
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| 73 | ### jobWarningDelay in seconds |
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| 74 | ##typeset jobWarningDelay=${BRIDGE_MSUB_MAXTIME} |
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| 75 | |
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[622] | 76 | #D- |
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| 77 | #D-#================================================== |
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| 78 | #D-Program used in libIGCM |
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| 79 | #D-#================================================== |
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| 80 | |
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[742] | 81 | # Submit command |
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[1490] | 82 | typeset SUBMIT=${SUBMIT:=sbatch} |
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[622] | 83 | # rsync with path |
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| 84 | typeset -r RSYNC=/usr/bin/rsync |
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| 85 | # RSYNC_opt args to rsync |
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| 86 | typeset -r RSYNC_opt="-va" |
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| 87 | # ie storage filesystem |
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[623] | 88 | typeset -r STOREHOST=${MASTER} |
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[1180] | 89 | typeset -r REMOTE_RSYNC=/usr/bin/rsync |
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[622] | 90 | |
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| 91 | #==================================================== |
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[1490] | 92 | # Access to module command |
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| 93 | #==================================================== |
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| 94 | . /usr/share/Modules/init/ksh |
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| 95 | |
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| 96 | #==================================================== |
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[1180] | 97 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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[622] | 98 | #==================================================== |
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[996] | 99 | if [ X${TaskType} = Xcomputing ] ; then |
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[1485] | 100 | IGCM_debug_Print 1 "Modules will be loaded later in IGCM_sys_activ_variables." |
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[996] | 101 | else |
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[1413] | 102 | module purge > /dev/null 2>&1 |
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[1490] | 103 | . /gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_jeanzay > /dev/null 2>&1 |
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[1433] | 104 | |
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[1502] | 105 | . /gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_atlas_jeanzay > /dev/null 2>&1 |
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| 106 | |
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[1490] | 107 | # export PCMDI_MP=/ccc/work/cont003/igcmg/igcmg/PCMDI-MP |
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[1364] | 108 | export UVCDAT_ANONYMOUS_LOG=FALSE |
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[996] | 109 | fi |
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[1315] | 110 | |
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| 111 | # FYI |
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[1210] | 112 | [ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:" |
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| 113 | [ ! X${TaskType} = Xchecking ] && module list |
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[1208] | 114 | |
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[1495] | 115 | # For AddNoise (not yet AddPertu3DOCE) |
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| 116 | export PATH=${PATH}:/gpfswork/rech/psl/commun/Tools/AddNoise/bin |
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[622] | 117 | |
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[1457] | 118 | # For rebuild |
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[1495] | 119 | export PATH=${PATH}:/gpfswork/rech/psl/commun/Tools/rebuild/modipsl_IOIPSL_PLUS_v2_2_4/bin |
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[622] | 120 | |
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| 121 | #==================================================== |
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| 122 | # Host specific DIRECTORIES |
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| 123 | #==================================================== |
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| 124 | |
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| 125 | #==================================================== |
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[623] | 126 | #- MirrorlibIGCM for frontend |
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| 127 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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| 128 | |
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| 129 | #==================================================== |
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| 130 | #- libIGCM_POST for frontend |
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| 131 | typeset -r libIGCM_POST=${libIGCM} |
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| 132 | |
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| 133 | #==================================================== |
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[622] | 134 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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| 135 | typeset -r R_EXE="${MODIPSL}/bin" |
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| 136 | |
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| 137 | #==================================================== |
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| 138 | #- SUBMIT_DIR : submission dir |
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[1490] | 139 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${SLURM_SUBMIT_DIR}} |
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[622] | 140 | |
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| 141 | #==================================================== |
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| 142 | #- IN |
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[1490] | 143 | typeset -r R_IN=${R_IN:=/gpfswork/rech/psl/commun/IGCM} |
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[622] | 144 | |
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| 145 | #==================================================== |
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| 146 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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[1490] | 147 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${SCRATCH}/RUN_DIR/${SLURM_JOBID}_${$}} |
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[622] | 148 | |
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| 149 | #==================================================== |
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[1179] | 150 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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[1186] | 151 | typeset -r OUTCOMMAND_PATH=/tmp |
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[1179] | 152 | |
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| 153 | #==================================================== |
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[622] | 154 | #- HOST_MPIRUN_COMMAND |
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[1492] | 155 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time srun "} |
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[622] | 156 | |
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| 157 | #==================================================== |
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| 158 | #- Max number of arguments passed to nco operator or demigration command |
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| 159 | UNIX_MAX_LIMIT=360 |
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| 160 | |
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[623] | 161 | #==================================================== |
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[1490] | 162 | #- set PackDefault to true |
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[623] | 163 | PackDefault=true |
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| 164 | |
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[664] | 165 | #==================================================== |
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[623] | 166 | #- Default number of MPI task for IPSL coupled model |
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| 167 | #- required for backward compatibility |
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| 168 | #- |
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| 169 | DEFAULT_NUM_PROC_OCE=5 |
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| 170 | DEFAULT_NUM_PROC_CPL=1 |
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[637] | 171 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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[623] | 172 | |
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[1426] | 173 | #==================================================== |
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| 174 | #- Number of computing cores per node |
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| 175 | #- |
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[1492] | 176 | NB_CORE_PER_NODE=40 |
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[1426] | 177 | |
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[725] | 178 | #D-#================================================== |
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[1057] | 179 | #D-function IGCM_sys_defineArchives |
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| 180 | #D-* Purpose: |
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[1461] | 181 | #D-* Load dfldatadir module : According to project used for submission (default) or set in config.card (optional) |
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[1057] | 182 | #D-* Define ARCHIVE : Dedicated to large files |
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| 183 | #D-* Define STORAGE : Dedicated to small/medium files |
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| 184 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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[1490] | 185 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monsitoring and atlas, and/or small files) |
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| 186 | #D-* Define R_BUF : Output tree located on SCRATCH hosting files waiting for rebuild or pack processes |
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| 187 | #D-* if SpaceName=TEST everything is stored on SCRATCH |
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[725] | 188 | #D-* Examples: |
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| 189 | #D- |
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[1057] | 190 | function IGCM_sys_defineArchives { |
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| 191 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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[676] | 192 | |
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[1461] | 193 | # Load dfldatadir depending on the project used for submission (default) or set in config.card (optional) |
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| 194 | if [ X${config_UserChoices_DataProject} = X ] || [ X${config_UserChoices_DataProject} = DEFAULT ]; then |
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[1490] | 195 | # The variable DataProject is not set in in section UserChoices in config.card or it is set to DEFAULT |
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| 196 | # Default option: Change IDRPROJ according to the project used for submission |
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| 197 | |
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| 198 | # jg following line does not work in a submitted job: |
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| 199 | eval $(idrenv -d ${PROJECT}) |
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[1461] | 200 | else |
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| 201 | # Use the project set by the variable DataProject in section UserChoices in config.card |
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[1490] | 202 | eval $(idrenv -d ${config_UserChoices_DataProject}) |
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| 203 | IGCM_debug_Print 1 "Change DataProject red in config.card : ${config_UserChoices_DataProject}" |
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[1461] | 204 | fi |
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[1490] | 205 | IGCM_debug_Print 1 "Data project for output to be used: ${IDRPROJ}" |
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[1461] | 206 | |
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[1490] | 207 | #==================================================== |
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| 208 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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| 209 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${SCRATCH}/RUN_DIR/${SLURM_JOBID}_${$}} |
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[1474] | 210 | |
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[1060] | 211 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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[1057] | 212 | #==================================================== |
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| 213 | #- ARCHIVE (dedicated to large files) |
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[1063] | 214 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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[1057] | 215 | else |
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| 216 | #==================================================== |
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| 217 | #- ARCHIVE (dedicated to large files) |
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[1490] | 218 | ARCHIVE=${STORE} |
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[1057] | 219 | fi |
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[725] | 220 | |
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[1060] | 221 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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[1057] | 222 | #==================================================== |
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| 223 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 224 | STORAGE=${config_UserChoices_STORAGE} |
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[1057] | 225 | else |
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| 226 | #==================================================== |
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| 227 | #- STORAGE (dedicated to small/medium files) |
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[1490] | 228 | STORAGE=${WORK} |
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[1057] | 229 | fi |
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[725] | 230 | |
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[1057] | 231 | if [ X${config_UserChoices_SpaceName} = XTEST ]; then |
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| 232 | #==================================================== |
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| 233 | #- R_OUT |
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[1490] | 234 | R_OUT=${SCRATCH}/IGCM_OUT |
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[1057] | 235 | |
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| 236 | #==================================================== |
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| 237 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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[1490] | 238 | R_FIG=${SCRATCH}/IGCM_OUT |
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[1057] | 239 | |
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| 240 | IGCM_debug_Print 1 "SpaceName=TEST ==> OVERRULE destination path directories" |
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| 241 | |
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| 242 | else |
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| 243 | #==================================================== |
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| 244 | #- R_OUT |
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[1063] | 245 | R_OUT=${ARCHIVE}/IGCM_OUT |
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[1057] | 246 | |
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| 247 | #==================================================== |
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| 248 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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[1063] | 249 | R_FIG=${STORAGE}/IGCM_OUT |
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[1057] | 250 | fi |
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| 251 | |
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| 252 | #==================================================== |
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[1431] | 253 | #- CMIP6 (hosting CMIP6 files produced by XIOS2 and configured by dr2xml) |
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| 254 | CMIP6_BUF=${STORAGE}/IGCM_OUT |
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| 255 | |
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| 256 | #==================================================== |
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[1057] | 257 | #- R_BUF (ONLY FOR double copy an scratch) |
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[1490] | 258 | R_BUF=${SCRATCH}/IGCM_OUT |
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[1057] | 259 | |
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| 260 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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| 261 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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| 262 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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| 263 | |
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| 264 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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[725] | 265 | } |
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| 266 | |
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[622] | 267 | #D-#================================================== |
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| 268 | #D-function IGCM_sys_RshArchive |
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| 269 | #D-* Purpose: Archive rsh command |
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| 270 | #D-* Examples: |
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| 271 | #D- |
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| 272 | function IGCM_sys_RshArchive { |
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[623] | 273 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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| 274 | /bin/ksh <<-EOF |
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[622] | 275 | ${@} |
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| 276 | EOF |
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[811] | 277 | status=$? |
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| 278 | if [ ${status} -gt 0 ] ; then |
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| 279 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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[623] | 280 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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| 281 | fi |
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| 282 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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[622] | 283 | } |
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| 284 | |
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| 285 | #D-#================================================== |
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[845] | 286 | #D-function IGCM_sys_RshArchive_NoError |
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| 287 | #D-* Purpose: Archive rsh command, without error |
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| 288 | #D-* used only in monitoring.job |
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| 289 | #D-* Examples: |
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| 290 | #D- |
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| 291 | function IGCM_sys_RshArchive_NoError { |
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| 292 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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| 293 | /bin/ksh <<-EOF |
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[1181] | 294 | ${@} 2> /dev/null |
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[845] | 295 | EOF |
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| 296 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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| 297 | } |
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| 298 | |
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| 299 | #D-#================================================== |
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[622] | 300 | #D-function IGCM_sys_MkdirArchive |
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| 301 | #D-* Purpose: Mkdir on Archive |
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| 302 | #D-* Examples: |
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| 303 | #D- |
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| 304 | function IGCM_sys_MkdirArchive { |
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[623] | 305 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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| 306 | if ( $DEBUG_sys ) ; then |
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| 307 | echo "IGCM_sys_MkdirArchive :" $@ |
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| 308 | fi |
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| 309 | #- creation de repertoire sur le serveur fichier |
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| 310 | if [ ! -d ${1} ]; then |
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| 311 | \mkdir -p $1 |
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[811] | 312 | status=$? |
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| 313 | |
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| 314 | if [ ${status} -gt 0 ] ; then |
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| 315 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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[623] | 316 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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[622] | 317 | fi |
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[623] | 318 | fi |
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| 319 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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[622] | 320 | } |
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| 321 | |
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| 322 | #D-#================================================== |
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| 323 | #D-function IGCM_sys_TestDirArchive |
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| 324 | #D-* Purpose: Test Directory that must exists on Archive |
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| 325 | #D-* Examples: |
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| 326 | #D- |
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| 327 | function IGCM_sys_TestDirArchive { |
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[623] | 328 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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| 329 | if ( $DEBUG_sys ) ; then |
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| 330 | echo "IGCM_sys_TestDirArchive :" $@ |
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| 331 | fi |
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| 332 | typeset ExistFlag |
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| 333 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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| 334 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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| 335 | return ${ExistFlag} |
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[622] | 336 | } |
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| 337 | |
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| 338 | #D-#================================================== |
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[623] | 339 | #D-function IGCM_sys_IsFileArchived |
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[1179] | 340 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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[623] | 341 | #D-* Examples: |
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| 342 | #D- |
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| 343 | function IGCM_sys_IsFileArchived { |
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| 344 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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| 345 | if ( $DEBUG_sys ) ; then |
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| 346 | echo "IGCM_sys_IsFileArchived :" $@ |
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| 347 | fi |
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| 348 | typeset IsArchivedFlag |
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[1502] | 349 | # To be implemented on Jean Zay |
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| 350 | # IsArchivedFlag=$( [ X$( echo $@ | grep ^\/ccc\/store ) != X ] && echo 0 || echo 1 ) |
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[623] | 351 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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| 352 | |
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| 353 | return ${IsArchivedFlag} |
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| 354 | } |
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| 355 | |
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| 356 | #D-#================================================== |
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[622] | 357 | #D-function IGCM_sys_TestFileArchive |
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| 358 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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| 359 | #D-* Examples: |
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| 360 | #D- |
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| 361 | function IGCM_sys_TestFileArchive { |
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[623] | 362 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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| 363 | typeset ExistFlag |
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| 364 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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| 365 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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[622] | 366 | |
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[623] | 367 | return ${ExistFlag} |
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[622] | 368 | } |
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| 369 | |
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| 370 | #D-#================================================== |
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| 371 | #D-function IGCM_sys_CountFileArchive |
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| 372 | #D-* Purpose: Count files on Archive filesystem |
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| 373 | #D-* Examples: |
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| 374 | #D- |
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| 375 | function IGCM_sys_CountFileArchive { |
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[623] | 376 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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| 377 | ls ${@} 2>/dev/null | wc -l |
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| 378 | if [ $? -gt 0 ] ; then |
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| 379 | echo "IGCM_sys_CountFileArchive : erreur." |
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| 380 | fi |
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| 381 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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[622] | 382 | } |
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| 383 | |
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| 384 | #D-#================================================== |
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| 385 | #D-function IGCM_sys_Tree |
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| 386 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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| 387 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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| 388 | #D- |
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| 389 | function IGCM_sys_Tree { |
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[623] | 390 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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| 391 | if ( $DEBUG_sys ) ; then |
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| 392 | echo "IGCM_sys_Tree :" $@ |
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| 393 | fi |
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[622] | 394 | |
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[623] | 395 | \ls -lR ${@} |
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[622] | 396 | |
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[623] | 397 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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[622] | 398 | } |
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| 399 | |
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| 400 | #D-#================================================== |
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| 401 | #D-function IGCM_sys_Qsub |
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| 402 | #D-* Purpose: Qsub new job |
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| 403 | #D-* Examples: |
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| 404 | #D- |
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| 405 | function IGCM_sys_Qsub { |
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[623] | 406 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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| 407 | if ( $DEBUG_sys ) ; then |
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| 408 | echo "IGCM_sys_Qsub :" $@ |
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| 409 | fi |
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[811] | 410 | typeset options status |
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[923] | 411 | options="-o ${SUBMIT_DIR}/${Script_Output} -e ${SUBMIT_DIR}/${Script_Output}" |
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[622] | 412 | |
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[1490] | 413 | /usr/bin/time sbatch ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[811] | 414 | status=$? |
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[948] | 415 | |
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[1179] | 416 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[811] | 417 | if [ ${status} -gt 0 ] ; then |
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| 418 | IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}" |
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[623] | 419 | IGCM_debug_Exit "IGCM_sys_Qsub" |
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[948] | 420 | else |
---|
[1179] | 421 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
---|
[623] | 422 | fi |
---|
| 423 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
---|
[622] | 424 | } |
---|
| 425 | |
---|
| 426 | #D-#================================================== |
---|
| 427 | #D-function IGCM_sys_QsubPost |
---|
| 428 | #D-* Purpose: Qsub new job on scalaire |
---|
| 429 | #D-* Examples: |
---|
| 430 | #D- |
---|
| 431 | function IGCM_sys_QsubPost { |
---|
[623] | 432 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
---|
| 433 | if ( $DEBUG_sys ) ; then |
---|
| 434 | echo "IGCM_sys_QsubPost :" $@ |
---|
| 435 | fi |
---|
[923] | 436 | typeset options status |
---|
[1490] | 437 | options="-o ${POST_DIR}/${Script_Post_Output}.out -e ${POST_DIR}/${Script_Post_Output}.out" |
---|
[923] | 438 | |
---|
[1490] | 439 | sbatch ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[811] | 440 | status=$? |
---|
[948] | 441 | |
---|
[1179] | 442 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[811] | 443 | if [ ${status} -gt 0 ] ; then |
---|
[923] | 444 | IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}" |
---|
[623] | 445 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
---|
[948] | 446 | else |
---|
[1179] | 447 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
---|
[623] | 448 | fi |
---|
| 449 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
---|
[622] | 450 | } |
---|
| 451 | |
---|
| 452 | #D-************************* |
---|
[623] | 453 | #D- File transfer functions |
---|
[622] | 454 | #D-************************* |
---|
| 455 | #D- |
---|
| 456 | |
---|
| 457 | #D-#================================================== |
---|
| 458 | #D-function IGCM_sys_RmRunDir |
---|
| 459 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
---|
| 460 | #D- scheduler will do the job) |
---|
| 461 | #D-* Examples: |
---|
| 462 | #D- |
---|
| 463 | function IGCM_sys_RmRunDir { |
---|
[1057] | 464 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
---|
[623] | 465 | if ( $DEBUG_sys ) ; then |
---|
| 466 | echo "IGCM_sys_RmRunDir :" $@ |
---|
| 467 | fi |
---|
[622] | 468 | |
---|
[715] | 469 | typeset status |
---|
[622] | 470 | |
---|
[1179] | 471 | echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 472 | \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[715] | 473 | status=$? |
---|
[622] | 474 | |
---|
[715] | 475 | if [ ${status} -gt 0 ] ; then |
---|
[1183] | 476 | IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}." |
---|
[1179] | 477 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[623] | 478 | IGCM_debug_Exit "IGCM_sys_RmRunDir" |
---|
| 479 | else |
---|
[1179] | 480 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[623] | 481 | fi |
---|
| 482 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
---|
[622] | 483 | } |
---|
| 484 | |
---|
| 485 | #D-#================================================== |
---|
| 486 | #D-function IGCM_sys_Put_Dir |
---|
| 487 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
---|
| 488 | #D-* Examples: |
---|
| 489 | #D- |
---|
| 490 | function IGCM_sys_Put_Dir { |
---|
[623] | 491 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
---|
| 492 | if ( $DEBUG_sys ) ; then |
---|
| 493 | echo "IGCM_sys_Put_Dir :" $@ |
---|
| 494 | fi |
---|
| 495 | if [ $DRYRUN = 0 ]; then |
---|
| 496 | if [ ! -d ${1} ] ; then |
---|
| 497 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
---|
| 498 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
| 499 | return |
---|
[622] | 500 | fi |
---|
| 501 | |
---|
[715] | 502 | typeset status |
---|
[622] | 503 | |
---|
[623] | 504 | # Only if we use rsync |
---|
| 505 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
---|
| 506 | # |
---|
| 507 | #USUAL WAY |
---|
[1179] | 508 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[715] | 509 | status=$? |
---|
[622] | 510 | |
---|
[715] | 511 | if [ ${status} -gt 0 ] ; then |
---|
[811] | 512 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
---|
[1179] | 513 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[623] | 514 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
---|
[622] | 515 | else |
---|
[1179] | 516 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[622] | 517 | fi |
---|
[623] | 518 | fi |
---|
| 519 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
[622] | 520 | } |
---|
| 521 | |
---|
| 522 | #D-#================================================== |
---|
| 523 | #D-function IGCM_sys_Get_Dir |
---|
[623] | 524 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
[622] | 525 | #D-* Examples: |
---|
| 526 | #D- |
---|
| 527 | function IGCM_sys_Get_Dir { |
---|
[623] | 528 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
| 529 | if ( $DEBUG_sys ) ; then |
---|
| 530 | echo "IGCM_sys_Get_Dir :" $@ |
---|
| 531 | fi |
---|
| 532 | if [ $DRYRUN = 0 ]; then |
---|
[708] | 533 | typeset NB_ESSAI DELAI status i |
---|
| 534 | # number of tentative |
---|
| 535 | NB_ESSAI=3 |
---|
| 536 | # time delay between tentative |
---|
| 537 | DELAI=2 |
---|
[622] | 538 | |
---|
[676] | 539 | # |
---|
[708] | 540 | # USUAL WAY |
---|
[1502] | 541 | # add here command to demigrate all offline files to reduce time of this command |
---|
| 542 | # actually on Jean Zay files are not archive on bands |
---|
[622] | 543 | |
---|
[709] | 544 | i=0 |
---|
[708] | 545 | while [ $i -lt $NB_ESSAI ] ; do |
---|
[1179] | 546 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[708] | 547 | status=$? |
---|
[811] | 548 | if [ ${status} -gt 0 ] ; then |
---|
[713] | 549 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
[708] | 550 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
| 551 | sleep $DELAI |
---|
| 552 | else |
---|
| 553 | break |
---|
| 554 | fi |
---|
| 555 | (( i = i + 1 )) |
---|
| 556 | done |
---|
| 557 | |
---|
| 558 | if [ ${status} -gt 0 ] ; then |
---|
[1178] | 559 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
[1179] | 560 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[623] | 561 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
[622] | 562 | else |
---|
[1179] | 563 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[622] | 564 | fi |
---|
[623] | 565 | fi |
---|
| 566 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
[622] | 567 | } |
---|
| 568 | |
---|
| 569 | #D-#================================================== |
---|
| 570 | #D-function IGCM_sys_Put_Rest |
---|
[623] | 571 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
[622] | 572 | #D- File and target directory must exist. |
---|
| 573 | #D-* Examples: |
---|
| 574 | #D- |
---|
| 575 | function IGCM_sys_Put_Rest { |
---|
[623] | 576 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
| 577 | if ( $DEBUG_sys ) ; then |
---|
| 578 | echo "IGCM_sys_Put_Rest :" $@ |
---|
| 579 | fi |
---|
| 580 | if [ $DRYRUN = 0 ]; then |
---|
| 581 | if [ ! -f ${1} ] ; then |
---|
| 582 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
| 583 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
[622] | 584 | fi |
---|
| 585 | |
---|
[715] | 586 | typeset status |
---|
[623] | 587 | # |
---|
| 588 | # USUAL WAY |
---|
[1179] | 589 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[715] | 590 | status=$? |
---|
[622] | 591 | |
---|
[623] | 592 | # #RSYNC WITH NETWORK SSH CALL |
---|
[1179] | 593 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 594 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[622] | 595 | |
---|
[623] | 596 | # #RSYNC WITH NFS USE |
---|
[1179] | 597 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 598 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[622] | 599 | |
---|
[715] | 600 | # status=$? |
---|
| 601 | # IGCM_sys_Rsync_out $status |
---|
[622] | 602 | |
---|
[1179] | 603 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[715] | 604 | # (( status=status+$? )) |
---|
[623] | 605 | |
---|
[715] | 606 | if [ ${status} -gt 0 ] ; then |
---|
[1179] | 607 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
[765] | 608 | [ -f ${1} ] && ls -l ${1} |
---|
[759] | 609 | [ -f ${2} ] && ls -l ${2} |
---|
| 610 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
[1179] | 611 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[623] | 612 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
[622] | 613 | else |
---|
[759] | 614 | |
---|
| 615 | if [ X${JobType} = XRUN ] ; then |
---|
| 616 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 617 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 618 | fi |
---|
| 619 | |
---|
[1179] | 620 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[622] | 621 | fi |
---|
[623] | 622 | fi |
---|
| 623 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
[622] | 624 | } |
---|
| 625 | |
---|
| 626 | #D-#================================================== |
---|
| 627 | #D-function IGCM_sys_Put_Out |
---|
[623] | 628 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
[622] | 629 | #D-* Examples: |
---|
| 630 | #D- |
---|
| 631 | function IGCM_sys_Put_Out { |
---|
[623] | 632 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
| 633 | if ( $DEBUG_sys ) ; then |
---|
| 634 | echo "IGCM_sys_Put_Out :" $@ |
---|
| 635 | fi |
---|
[667] | 636 | |
---|
[711] | 637 | typeset NB_ESSAI DELAI status i exist skip |
---|
[1234] | 638 | typeset fileDeviceNumberInHex directoryDeviceNumberInHex |
---|
[667] | 639 | |
---|
| 640 | # number of tentative |
---|
[668] | 641 | NB_ESSAI=3 |
---|
[667] | 642 | # time delay between tentative |
---|
[668] | 643 | DELAI=2 |
---|
[667] | 644 | |
---|
[623] | 645 | if [ $DRYRUN = 0 ]; then |
---|
| 646 | if [ ! -f ${1} ] ; then |
---|
| 647 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
| 648 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 649 | return 1 |
---|
[622] | 650 | fi |
---|
[623] | 651 | # |
---|
| 652 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
| 653 | # |
---|
[711] | 654 | exist=false |
---|
| 655 | skip=false |
---|
| 656 | if [ -f $2 ] ; then |
---|
| 657 | IGCM_debug_Print 1 "$2 already exist" |
---|
[1502] | 658 | # add here command to demigrate all offline files to reduce time of this command |
---|
| 659 | # actually on Jean Zay files are not archive on bands |
---|
| 660 | |
---|
[711] | 661 | exist=true |
---|
| 662 | if [ "X$( diff $1 $2 )" = X ] ; then |
---|
| 663 | IGCM_debug_Print 2 "$1 and $2 are the same file, we skip the copy" |
---|
| 664 | skip=true |
---|
[667] | 665 | else |
---|
[711] | 666 | IGCM_debug_Print 2 "$1 and $2 are not the same file, we force the copy" |
---|
| 667 | skip=false |
---|
[667] | 668 | fi |
---|
[711] | 669 | fi |
---|
| 670 | # |
---|
| 671 | if ( [ X${exist} = Xtrue ] && [ X${skip} = Xfalse ] ) ; then |
---|
| 672 | IGCM_sys_Chmod u+w $2 |
---|
| 673 | fi |
---|
[622] | 674 | |
---|
[711] | 675 | if [ X${skip} = Xfalse ] ; then |
---|
[719] | 676 | i=0 |
---|
[711] | 677 | while [ $i -lt $NB_ESSAI ] ; do |
---|
[1234] | 678 | # Identify file system |
---|
| 679 | fileDeviceNumberInHex=$( stat -c %d $1 ) |
---|
| 680 | status=$? |
---|
| 681 | if [ ${status} -gt 0 ] ; then |
---|
| 682 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
| 683 | fi |
---|
| 684 | # Identify file system |
---|
| 685 | directoryDeviceNumberInHex=$( stat -c %d $( dirname $2 ) ) |
---|
| 686 | status=$? |
---|
| 687 | if [ ${status} -gt 0 ] ; then |
---|
| 688 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
| 689 | fi |
---|
| 690 | |
---|
[1412] | 691 | if ( [ ${fileDeviceNumberInHex} -ne ${directoryDeviceNumberInHex} ] || [ X$3 = XNOMOVE ] ) ; then |
---|
[1234] | 692 | # They are not on the same device. USUAL WAY |
---|
[1179] | 693 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[1037] | 694 | status=$? |
---|
| 695 | else |
---|
[1234] | 696 | # They are on the same device. NOT SO USUAL WAY |
---|
[1179] | 697 | \mv $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[1037] | 698 | status=$? |
---|
| 699 | fi |
---|
[711] | 700 | if [ ${status} -gt 0 ]; then |
---|
[713] | 701 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
[711] | 702 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : sleep ${DELAI} seconds and try again." |
---|
[765] | 703 | [ -f ${1} ] && ls -l ${1} |
---|
[759] | 704 | [ -f ${2} ] && ls -l ${2} |
---|
| 705 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
[711] | 706 | sleep $DELAI |
---|
| 707 | else |
---|
| 708 | break |
---|
| 709 | fi |
---|
| 710 | (( i = i + 1 )) |
---|
| 711 | done |
---|
| 712 | fi |
---|
| 713 | |
---|
[623] | 714 | # #RSYNC WITH NETWORK SSH CALL |
---|
[1179] | 715 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 716 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[622] | 717 | |
---|
[623] | 718 | # #RSYNC WITH NFS USE |
---|
[1179] | 719 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 720 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[622] | 721 | |
---|
[711] | 722 | # status=$? |
---|
| 723 | # IGCM_sys_Rsync_out $status |
---|
[622] | 724 | |
---|
[1179] | 725 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[711] | 726 | # (( status=status+$? )) |
---|
[622] | 727 | |
---|
[711] | 728 | if [ ${status} -gt 0 ] ; then |
---|
[1179] | 729 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status}" |
---|
[765] | 730 | [ -f ${1} ] && ls -l ${1} |
---|
[759] | 731 | [ -f ${2} ] && ls -l ${2} |
---|
| 732 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
[1179] | 733 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[623] | 734 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
[622] | 735 | else |
---|
[759] | 736 | |
---|
| 737 | if [ X${JobType} = XRUN ] ; then |
---|
| 738 | if [ X${3} = X ] ; then |
---|
| 739 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 740 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 741 | fi |
---|
| 742 | fi |
---|
| 743 | |
---|
[1179] | 744 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[622] | 745 | fi |
---|
[623] | 746 | fi |
---|
| 747 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 748 | return 0 |
---|
[622] | 749 | } |
---|
| 750 | |
---|
| 751 | #D-#================================================== |
---|
| 752 | #D-function IGCM_sys_Get |
---|
| 753 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
| 754 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
| 755 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
| 756 | function IGCM_sys_Get { |
---|
[623] | 757 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
[622] | 758 | |
---|
[773] | 759 | typeset DEST dm_liste target file_work |
---|
[667] | 760 | typeset NB_ESSAI DELAI status i |
---|
[622] | 761 | |
---|
[623] | 762 | if ( $DEBUG_sys ) ; then |
---|
| 763 | echo "IGCM_sys_Get :" $@ |
---|
| 764 | fi |
---|
[667] | 765 | |
---|
| 766 | # number of tentative |
---|
[668] | 767 | NB_ESSAI=3 |
---|
[667] | 768 | # time delay between tentative |
---|
[668] | 769 | DELAI=2 |
---|
[667] | 770 | |
---|
[623] | 771 | if [ $DRYRUN -le 2 ]; then |
---|
| 772 | if [ X${1} = X'/l' ] ; then |
---|
| 773 | eval set +A dm_liste \${${2}} |
---|
| 774 | else |
---|
| 775 | eval set +A dm_liste ${1} |
---|
[622] | 776 | fi |
---|
[623] | 777 | eval DEST=\${${#}} |
---|
[1502] | 778 | # add here command to demigrate all offline files to reduce time of this command |
---|
| 779 | # actually on Jean Zay files are not archive on bands |
---|
| 780 | |
---|
[715] | 781 | status=$? |
---|
| 782 | if [ ${status} -gt 0 ] ; then |
---|
| 783 | echo "WARNING IGCM_sys_Get : error code ${status}" |
---|
[1179] | 784 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[623] | 785 | echo "WARNING IGCM_sys_Get : will stop later if the cp fails." |
---|
| 786 | fi |
---|
[622] | 787 | |
---|
[715] | 788 | #if [ ${status} -gt 0 ] ; then |
---|
[1179] | 789 | # if [ ! "X$( grep "Lost dmusrcmd connection" ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )" = "X" ] ; then |
---|
| 790 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[785] | 791 | # echo "WARNING IGCM_sys_Get : Lost dmusrcmd connection : " |
---|
| 792 | # sleep 30 |
---|
| 793 | # echo "We try another time" |
---|
[1179] | 794 | ## dmget ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 795 | # ccc_hsm get ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[785] | 796 | # status=$? |
---|
| 797 | # if [ ${status} -gt 0 ] ; then |
---|
| 798 | # echo "ERROR IGCM_sys_Get : again demigration error :" |
---|
[1179] | 799 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[785] | 800 | # IGCM_debug_Exit "IGCM_sys_Get" |
---|
[623] | 801 | # fi |
---|
[785] | 802 | # else |
---|
| 803 | # echo "ERROR IGCM_sys_Get : demigration error :" |
---|
[1179] | 804 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[785] | 805 | # IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 806 | # fi |
---|
[623] | 807 | #fi |
---|
[622] | 808 | |
---|
[719] | 809 | # #RSYNC WITH NETWORK SSH CALL |
---|
[1179] | 810 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 811 | # ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[719] | 812 | |
---|
| 813 | # #RSYNC WITH NFS USE |
---|
[1179] | 814 | # echo ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 815 | # ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[719] | 816 | |
---|
| 817 | # status=$? |
---|
| 818 | # IGCM_sys_Rsync_out $status |
---|
| 819 | |
---|
[1179] | 820 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[719] | 821 | # (( status=status+$? )) |
---|
| 822 | |
---|
[623] | 823 | #USUAL WAY |
---|
| 824 | if [ X${1} = X'/l' ] ; then |
---|
| 825 | for target in ${dm_liste[*]} ; do |
---|
| 826 | local_file=$( basename ${target} ) |
---|
[668] | 827 | # test if the target file is present before the loop |
---|
| 828 | IGCM_sys_TestFileArchive ${target} |
---|
[715] | 829 | status=$? |
---|
| 830 | if [ ${status} -gt 0 ] ; then |
---|
[701] | 831 | echo "IGCM_sys_Get, ERROR : regular file ${target} DOES NOT EXIST ." |
---|
[668] | 832 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 833 | else |
---|
[719] | 834 | i=0 |
---|
[668] | 835 | while [ $i -lt $NB_ESSAI ] ; do |
---|
[1037] | 836 | #if [ X${DoLink} = Xtrue ] ; then |
---|
[1179] | 837 | # \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[1037] | 838 | # status=$? |
---|
| 839 | # else |
---|
[1179] | 840 | # \cp ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[1037] | 841 | # status=$? |
---|
| 842 | #fi |
---|
[1179] | 843 | \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[668] | 844 | status=$? |
---|
| 845 | if [ ${status} -gt 0 ]; then |
---|
[713] | 846 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
[676] | 847 | IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again." |
---|
| 848 | sleep $DELAI |
---|
[668] | 849 | else |
---|
[676] | 850 | break |
---|
[668] | 851 | fi |
---|
| 852 | (( i = i + 1 )) |
---|
| 853 | done |
---|
[719] | 854 | if [ ${status} -gt 0 ] ; then |
---|
| 855 | echo "IGCM_sys_Get : error" |
---|
[1179] | 856 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 857 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[719] | 858 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 859 | else |
---|
[1179] | 860 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[719] | 861 | fi |
---|
[668] | 862 | fi |
---|
[623] | 863 | done |
---|
| 864 | else |
---|
[719] | 865 | i=0 |
---|
| 866 | while [ $i -lt $NB_ESSAI ] ; do |
---|
[1179] | 867 | \cp ${dm_liste} ${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[719] | 868 | status=$? |
---|
| 869 | if [ ${status} -gt 0 ]; then |
---|
| 870 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 871 | IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again." |
---|
| 872 | sleep $DELAI |
---|
| 873 | else |
---|
| 874 | break |
---|
| 875 | fi |
---|
| 876 | (( i = i + 1 )) |
---|
| 877 | done |
---|
| 878 | if [ ${status} -gt 0 ] ; then |
---|
| 879 | echo "IGCM_sys_Get : error" |
---|
[1179] | 880 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 881 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[719] | 882 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 883 | else |
---|
[1179] | 884 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[719] | 885 | fi |
---|
[623] | 886 | fi |
---|
| 887 | fi |
---|
| 888 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
| 889 | } |
---|
[622] | 890 | |
---|
[623] | 891 | #D-#================================================== |
---|
[835] | 892 | #D-function IGCM_sys_GetDate_Monitoring |
---|
| 893 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
| 894 | #D-* Examples: |
---|
| 895 | #D- |
---|
| 896 | function IGCM_sys_GetDate_Monitoring { |
---|
| 897 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
| 898 | if ( $DEBUG_sys ) ; then |
---|
| 899 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
| 900 | fi |
---|
| 901 | |
---|
| 902 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
| 903 | |
---|
| 904 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
| 905 | } |
---|
| 906 | |
---|
| 907 | #D-#================================================== |
---|
[623] | 908 | #D-function IGCM_sys_Dods_Rm |
---|
| 909 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
| 910 | #D-* Examples: |
---|
| 911 | #D- |
---|
| 912 | function IGCM_sys_Dods_Rm { |
---|
| 913 | if ( $DEBUG_sys ) ; then |
---|
| 914 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
| 915 | fi |
---|
[715] | 916 | typeset status |
---|
[623] | 917 | if [ $DRYRUN = 0 ]; then |
---|
| 918 | |
---|
| 919 | # if [ ! -d /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} ] ; then |
---|
| 920 | # echo "WARNING : IGCM_sys_Dods_Rm /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} DOES NOT EXIST ." |
---|
| 921 | # echo "Nothing has been done." |
---|
| 922 | # return |
---|
| 923 | # fi |
---|
| 924 | |
---|
[1392] | 925 | if [ "$#" -eq 1 ]; then |
---|
[1502] | 926 | # $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS}/${1} # > out_dods_rm 2>&1 |
---|
[1392] | 927 | status=$? |
---|
| 928 | else |
---|
[1502] | 929 | # $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS} # > out_dods_rm 2>&1 |
---|
[1392] | 930 | status=$? |
---|
| 931 | fi |
---|
[623] | 932 | |
---|
[785] | 933 | # if [ ${status} -gt 0 ] ; then |
---|
| 934 | # echo "IGCM_sys_Dods_Rm : error." |
---|
| 935 | # cat out_dods_rm |
---|
| 936 | # IGCM_debug_Exit "IGCM_sys_Dods_Rm" |
---|
| 937 | # else |
---|
| 938 | # rm out_dods_rm |
---|
| 939 | # fi |
---|
[623] | 940 | |
---|
| 941 | fi |
---|
[715] | 942 | return $status |
---|
[623] | 943 | } |
---|
| 944 | |
---|
| 945 | #D-#================================================== |
---|
| 946 | #D-function IGCM_sys_Dods_Cp |
---|
| 947 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
| 948 | #D-* Examples: |
---|
| 949 | #D- |
---|
| 950 | function IGCM_sys_Dods_Cp { |
---|
| 951 | if ( $DEBUG_sys ) ; then |
---|
| 952 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
| 953 | fi |
---|
[715] | 954 | typeset status |
---|
[623] | 955 | if [ $DRYRUN = 0 ]; then |
---|
| 956 | |
---|
| 957 | # if [ ! -d ${R_SAVE}/${1} ] ; then |
---|
| 958 | # echo "WARNING : IGCM_sys_Dods_Cp ${R_SAVE}/${1} DOES NOT EXIST ." |
---|
| 959 | # echo "Nothing has been done." |
---|
| 960 | # return |
---|
| 961 | # fi |
---|
| 962 | |
---|
[1502] | 963 | # $(ccc_home -u igcmg)/Tools/irene/thredds_cp ${1} public/${LOGIN}/${R_DODS} # > out_dods_cp 2>&1 |
---|
| 964 | |
---|
[715] | 965 | status=$? |
---|
[623] | 966 | |
---|
[715] | 967 | # if [ ${status} -gt 0 ] ; then |
---|
[623] | 968 | # echo "IGCM_sys_Dods_Cp : error." |
---|
| 969 | # cat out_dods_cp |
---|
| 970 | # IGCM_debug_Exit "IGCM_sys_Dods_Cp" |
---|
| 971 | # else |
---|
| 972 | # rm out_dods_cp |
---|
| 973 | # fi |
---|
| 974 | |
---|
| 975 | fi |
---|
[715] | 976 | return $status |
---|
[623] | 977 | } |
---|
| 978 | |
---|
| 979 | #D-#================================================== |
---|
| 980 | #D-function IGCM_sys_Put_Dods |
---|
[1178] | 981 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. |
---|
[623] | 982 | #D-* Examples: |
---|
| 983 | #D- |
---|
| 984 | function IGCM_sys_Put_Dods { |
---|
| 985 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
| 986 | if ( $DEBUG_sys ) ; then |
---|
| 987 | echo "IGCM_sys_Put_Dods :" $@ |
---|
| 988 | fi |
---|
[715] | 989 | typeset status |
---|
[623] | 990 | if [ $DRYRUN = 0 ]; then |
---|
| 991 | if ( [ ! -d ${R_SAVE}/${1} ] && [ ! -d ${R_FIGR}/${1} ] ) ; then |
---|
| 992 | echo "WARNING IGCM_sys_Put_Dods : None of the following directories exist. Exactly one should." |
---|
| 993 | echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} DOES NOT EXIST." |
---|
| 994 | echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} DOES NOT EXIST." |
---|
| 995 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
| 996 | return |
---|
[622] | 997 | fi |
---|
[623] | 998 | |
---|
| 999 | if ( [ -d ${R_SAVE}/${1} ] && [ -d ${R_FIGR}/${1} ] ) ; then |
---|
| 1000 | echo "WARNING IGCM_sys_Put_Dods : Both of the following directories exist. Exactly one should." |
---|
| 1001 | echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} EXISTS." |
---|
| 1002 | echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} EXISTS." |
---|
| 1003 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
| 1004 | return |
---|
| 1005 | fi |
---|
| 1006 | # |
---|
| 1007 | if [ -d ${R_SAVE}/${1} ] ; then |
---|
| 1008 | cd ${R_SAVE} |
---|
| 1009 | elif [ -d ${R_FIGR}/${1} ] ; then |
---|
| 1010 | cd ${R_FIGR} |
---|
| 1011 | fi |
---|
| 1012 | |
---|
| 1013 | IGCM_sys_Dods_Rm ${1} |
---|
| 1014 | IGCM_sys_Dods_Cp ${1} |
---|
[715] | 1015 | status=0 |
---|
[623] | 1016 | |
---|
[715] | 1017 | if [ ${status} -gt 0 ] ; then |
---|
[623] | 1018 | echo "IGCM_sys_Put_Dods : error." |
---|
| 1019 | IGCM_debug_Exit "IGCM_sys_Put_Dods" |
---|
| 1020 | fi |
---|
| 1021 | fi |
---|
| 1022 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
[622] | 1023 | } |
---|
| 1024 | |
---|
| 1025 | ############################################################## |
---|
| 1026 | # REBUILD OPERATOR |
---|
| 1027 | |
---|
[811] | 1028 | #D-#================================================== |
---|
[1163] | 1029 | #D-function IGCM_sys_sync |
---|
| 1030 | #D-* Purpose: flush buffer on disk |
---|
| 1031 | #D-* Examples: |
---|
| 1032 | #D- |
---|
| 1033 | function IGCM_sys_sync { |
---|
| 1034 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
| 1035 | if ( $DEBUG_sys ) ; then |
---|
| 1036 | echo "IGCM_sys_sync :" $@ |
---|
| 1037 | fi |
---|
| 1038 | |
---|
| 1039 | /bin/sync |
---|
| 1040 | |
---|
| 1041 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
| 1042 | } |
---|
| 1043 | |
---|
[622] | 1044 | ############################################################ |
---|
| 1045 | # Activate Running Environnment Variables |
---|
| 1046 | |
---|
[811] | 1047 | #D-#================================================== |
---|
[1239] | 1048 | #D-function IGCM_sys_activ_variables |
---|
[811] | 1049 | #D-* Purpose: set environement variables prior to execution |
---|
| 1050 | #D-* Examples: |
---|
| 1051 | #D- |
---|
[622] | 1052 | function IGCM_sys_activ_variables { |
---|
[623] | 1053 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
| 1054 | if ( $DEBUG_sys ) ; then |
---|
| 1055 | echo "IGCM_sys_activ_variables" |
---|
| 1056 | fi |
---|
[622] | 1057 | |
---|
[811] | 1058 | # -------------------------------------------------------------------- |
---|
[1409] | 1059 | #D- MODULE specifications |
---|
| 1060 | # -------------------------------------------------------------------- |
---|
[1479] | 1061 | # Source the file EnvFile containing all module load needed to run the model. |
---|
[1485] | 1062 | # EnvFile can be specified in config.card. If this is the case and if the file exists, |
---|
| 1063 | # it will be used. Otherwise a default file will be used. |
---|
[1482] | 1064 | if [ ! X${config_UserChoices_EnvFile} = X ] && [ -f ${config_UserChoices_EnvFile} ] ; then |
---|
| 1065 | # EnvFile is set in config.card and the file exists |
---|
| 1066 | IGCM_debug_Print 1 "EnvFile set in config.card will be used" |
---|
| 1067 | EnvFile=${config_UserChoices_EnvFile} |
---|
| 1068 | else |
---|
[1479] | 1069 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Default modules will be used" |
---|
| 1070 | module purge > /dev/null 2>&1 |
---|
[1490] | 1071 | EnvFile=/gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_jeanzay |
---|
[1409] | 1072 | fi |
---|
[1479] | 1073 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Following EnvFile will be used :" |
---|
| 1074 | IGCM_debug_Print 1 ${EnvFile} |
---|
| 1075 | . ${EnvFile} |
---|
| 1076 | |
---|
[1490] | 1077 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Now loaded modules for Jean-Zay. " |
---|
[1433] | 1078 | module list |
---|
[1409] | 1079 | |
---|
| 1080 | # -------------------------------------------------------------------- |
---|
[811] | 1081 | #D- MPI specifications |
---|
| 1082 | # -------------------------------------------------------------------- |
---|
[1191] | 1083 | |
---|
[811] | 1084 | # -------------------------------------------------------------------- |
---|
| 1085 | #D- Other specifications |
---|
| 1086 | # -------------------------------------------------------------------- |
---|
| 1087 | |
---|
[623] | 1088 | ulimit -s unlimited |
---|
[622] | 1089 | |
---|
[623] | 1090 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
[622] | 1091 | } |
---|
| 1092 | |
---|
| 1093 | ############################################################ |
---|
| 1094 | # Desactivate Running Environnment Variables |
---|
| 1095 | |
---|
[811] | 1096 | #D-#================================================== |
---|
| 1097 | #D-function IGCM_sys_desactiv_variables |
---|
| 1098 | #D-* Purpose: unset environement variables after execution |
---|
| 1099 | #D-* Examples: |
---|
| 1100 | #D- |
---|
[622] | 1101 | function IGCM_sys_desactiv_variables { |
---|
[623] | 1102 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
| 1103 | if ( $DEBUG_sys ) ; then |
---|
| 1104 | echo "IGCM_sys_desactiv_variables" |
---|
| 1105 | fi |
---|
[811] | 1106 | # -------------------------------------------------------------------- |
---|
| 1107 | #D- MPI specifications |
---|
| 1108 | # -------------------------------------------------------------------- |
---|
| 1109 | |
---|
| 1110 | # -------------------------------------------------------------------- |
---|
| 1111 | #D- Other specifications |
---|
| 1112 | # -------------------------------------------------------------------- |
---|
| 1113 | |
---|
[623] | 1114 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
[622] | 1115 | } |
---|
| 1116 | |
---|
[623] | 1117 | ############################################################ |
---|
[1238] | 1118 | # Update job headers to be used by the scheduler |
---|
| 1119 | |
---|
| 1120 | #D-#================================================== |
---|
| 1121 | #D-function IGCM_sys_updateHeaders |
---|
| 1122 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
| 1123 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
| 1124 | #D- |
---|
| 1125 | function IGCM_sys_updateHeaders { |
---|
| 1126 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
| 1127 | if ( $DEBUG_sys ) ; then |
---|
| 1128 | echo "IGCM_sys_updateHeaders" |
---|
| 1129 | fi |
---|
| 1130 | typeset file |
---|
| 1131 | file=$1 |
---|
| 1132 | |
---|
| 1133 | if [ ${executionType} -eq 1 ] ; then |
---|
| 1134 | # MPMD + MPI |
---|
| 1135 | sed -e "/::openMPthreads::/d" \ |
---|
| 1136 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 1137 | ${file} > ${file}.tmp |
---|
| 1138 | |
---|
| 1139 | elif [ ${executionType} -eq 2 ] ; then |
---|
[1493] | 1140 | # MPMD + MPI + OMP |
---|
[1500] | 1141 | (( nodeNumber = coreNumber / NB_CORE_PER_NODE )) |
---|
| 1142 | [ $(( ${coreNumber} % ${NB_CORE_PER_NODE} )) -ne 0 ] && (( nodeNumber = nodeNumber + 1 )) |
---|
| 1143 | sed -e "/::openMPthreads::/d" \ |
---|
| 1144 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 1145 | -e "/ntasks/i\#SBATCH --nodes=${nodeNumber}"\ |
---|
| 1146 | -e "/ntasks/i\#SBATCH --exclusive" \ |
---|
| 1147 | ${file} > ${file}.tmp |
---|
[1238] | 1148 | elif [ ${executionType} -eq 3 ] ; then |
---|
| 1149 | # SPMD + MPI/OMP |
---|
| 1150 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 1151 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 1152 | ${file} > ${file}.tmp |
---|
| 1153 | |
---|
| 1154 | elif [ ${executionType} -eq 4 ] ; then |
---|
| 1155 | # SPMD + MPI only |
---|
| 1156 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 1157 | -e "/::openMPthreads::/d" \ |
---|
| 1158 | ${file} > ${file}.tmp |
---|
| 1159 | |
---|
| 1160 | elif [ ${executionType} -eq 5 ] ; then |
---|
| 1161 | # SPMD + OMP only |
---|
| 1162 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 1163 | -e "/::JobNumProcTot::/d" \ |
---|
| 1164 | ${file} > ${file}.tmp |
---|
| 1165 | |
---|
| 1166 | elif [ ${executionType} -eq 6 ] ; then |
---|
| 1167 | # SEQUENTIAL THEN |
---|
| 1168 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
| 1169 | -e "/::openMPthreads::/d" \ |
---|
| 1170 | ${file} > ${file}.tmp |
---|
| 1171 | |
---|
| 1172 | fi |
---|
| 1173 | |
---|
| 1174 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
| 1175 | |
---|
| 1176 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
| 1177 | } |
---|
| 1178 | |
---|
| 1179 | ############################################################ |
---|
[623] | 1180 | # Build MPI/OMP scripts run file (dummy function) |
---|
[622] | 1181 | |
---|
[811] | 1182 | #D-#================================================== |
---|
| 1183 | #D-function IGCM_sys_build_run_file |
---|
| 1184 | #D-* Purpose: build run file (deprecated) |
---|
| 1185 | #D-* Examples: |
---|
| 1186 | #D- |
---|
[622] | 1187 | function IGCM_sys_build_run_file { |
---|
[811] | 1188 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
[622] | 1189 | } |
---|
| 1190 | |
---|
| 1191 | ############################################################ |
---|
| 1192 | # Build MPI/OMP scripts |
---|
[811] | 1193 | |
---|
| 1194 | #D-#================================================== |
---|
| 1195 | #D-function IGCM_sys_build_execution_scripts |
---|
| 1196 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
| 1197 | #D-* Examples: |
---|
| 1198 | #D- |
---|
[623] | 1199 | function IGCM_sys_build_execution_scripts |
---|
[622] | 1200 | { |
---|
[623] | 1201 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
| 1202 | if ( $DEBUG_sys ) ; then |
---|
| 1203 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
| 1204 | fi |
---|
[1493] | 1205 | IGCM_debug_Print 1 "executionType= ${executionType}" |
---|
[623] | 1206 | EXECUTION=${HOST_MPIRUN_COMMAND} |
---|
[622] | 1207 | |
---|
[623] | 1208 | if ( ${OK_PARA_MPMD} ) ; then |
---|
[622] | 1209 | |
---|
[1390] | 1210 | # MPMD mode |
---|
[1493] | 1211 | # 1 MPI only : executionType=1 |
---|
| 1212 | # 2 MPI/OpenMP : executionType=2 |
---|
[1390] | 1213 | |
---|
[1381] | 1214 | if [ -f run_file ] ; then |
---|
| 1215 | IGCM_sys_Rm -f run_file |
---|
| 1216 | fi |
---|
| 1217 | touch run_file |
---|
| 1218 | |
---|
[1390] | 1219 | # case 1 : Only MPI (MPMD) |
---|
[1078] | 1220 | if ( ! ${OK_PARA_OMP} ) ; then |
---|
| 1221 | # Build run_file |
---|
[1492] | 1222 | current_core=0 |
---|
[1078] | 1223 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
| 1224 | # the coupler ie oasis3 must be the first one |
---|
| 1225 | for comp in ${config_ListOfComponents[*]} ; do |
---|
[622] | 1226 | |
---|
[1078] | 1227 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 1228 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[622] | 1229 | |
---|
[1492] | 1230 | # Only if the component has an executable |
---|
| 1231 | if ( [ "X${ExeNameOut}" != X\"\" ] ) ; then |
---|
[1000] | 1232 | |
---|
[1078] | 1233 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
[1492] | 1234 | (( end_core = ${current_core} + ${comp_proc_mpi_loc} - 1 )) |
---|
| 1235 | echo "${current_core}-${end_core} ./${ExeNameOut}" >> run_file |
---|
| 1236 | (( current_core = ${end_core} + 1 )) |
---|
[1078] | 1237 | fi |
---|
| 1238 | done |
---|
[622] | 1239 | |
---|
[1492] | 1240 | EXECUTION="${HOST_MPIRUN_COMMAND} --multi-prog ./run_file" |
---|
[622] | 1241 | |
---|
[1390] | 1242 | IGCM_sys_Chmod u+x run_file |
---|
| 1243 | if ( $DEBUG_sys ) ; then |
---|
| 1244 | echo "run_file contains : " |
---|
| 1245 | cat run_file |
---|
| 1246 | fi |
---|
| 1247 | |
---|
[1493] | 1248 | else |
---|
[1390] | 1249 | |
---|
[1493] | 1250 | # 2 MPI/OpenMP : executionType=2 |
---|
[1390] | 1251 | |
---|
[1381] | 1252 | # MPI-OpenMP (MPMD) |
---|
[1500] | 1253 | # export SLURM_HOSTFILE=./hostlist |
---|
| 1254 | # srun --cpu-bind=none --distribution=arbitrary --multi-prog ./run_file |
---|
| 1255 | # example of hostlist file : |
---|
| 1256 | # r3i3n33 |
---|
| 1257 | # r3i3n33 |
---|
| 1258 | # ... |
---|
| 1259 | # example of run_file : |
---|
| 1260 | # 0 taskset -c 0-4 ./script_lmdz.x.ksh |
---|
| 1261 | # 1 taskset -c 5-9 ./script_lmdz.x.ksh |
---|
| 1262 | #... |
---|
| 1263 | # 32 taskset -c 0 ./script_opa.xx.ksh |
---|
| 1264 | # 33 taskset -c 1 ./script_opa.xx.ksh |
---|
| 1265 | #... |
---|
| 1266 | # 62 taskset -c 30 ./script_xios.x.ksh |
---|
[622] | 1267 | |
---|
[1500] | 1268 | # Hosts treatment |
---|
| 1269 | IFS=$'\n'; set -f |
---|
| 1270 | listnodes=($(< <( scontrol show hostnames $SLURM_JOB_NODELIST ))) |
---|
| 1271 | unset IFS; set +f |
---|
| 1272 | rm -f hostlist |
---|
| 1273 | |
---|
| 1274 | # Loop on the components to build run_file and script_exec files |
---|
| 1275 | rank=0 |
---|
| 1276 | current_core=0 |
---|
| 1277 | |
---|
[1078] | 1278 | for comp in ${config_ListOfComponents[*]} ; do |
---|
[1000] | 1279 | |
---|
[1078] | 1280 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 1281 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[1000] | 1282 | |
---|
[1078] | 1283 | # Not possible if oasis has an executable (i.e old version of oasis3) |
---|
| 1284 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
---|
| 1285 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
---|
| 1286 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
---|
| 1287 | IGCM_debug_Verif_Exit |
---|
| 1288 | fi |
---|
[1000] | 1289 | |
---|
[1078] | 1290 | # Only if we really have an executable for the component : |
---|
| 1291 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
[1000] | 1292 | |
---|
[1078] | 1293 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1294 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
[1500] | 1295 | eval comp_proc_nod_loc=\${${comp}_PROC_NOD} |
---|
| 1296 | |
---|
[1000] | 1297 | |
---|
[1381] | 1298 | # Build script files |
---|
| 1299 | |
---|
[1078] | 1300 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1301 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1302 | if [ ${comp_proc_omp_loc} -gt 1 ] ; then |
---|
[1500] | 1303 | # Check if the number of threads is correct |
---|
| 1304 | case ${comp_proc_omp_loc} in |
---|
| 1305 | 2|4|5|10|20) |
---|
| 1306 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
---|
| 1307 | ;; |
---|
| 1308 | *) |
---|
| 1309 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
| 1310 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
| 1311 | IGCM_debug_Print 2 "Only 2,4,5,10,20 as number of OMP threads are possible " |
---|
| 1312 | IGCM_debug_Verif_Exit |
---|
| 1313 | ;; |
---|
| 1314 | esac |
---|
[1493] | 1315 | echo "export OMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 1316 | echo "export OMP_PLACES=cores" >> script_${ExeNameOut}.ksh |
---|
[1500] | 1317 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1318 | |
---|
[1078] | 1319 | fi |
---|
[1318] | 1320 | |
---|
[1381] | 1321 | # to have out/err per process on different files |
---|
| 1322 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh |
---|
[1078] | 1323 | |
---|
[1381] | 1324 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
[1078] | 1325 | |
---|
[1381] | 1326 | # Complete run_file |
---|
[1500] | 1327 | if [ ${comp_proc_nod_loc} -gt 1 ] ; then |
---|
| 1328 | (( offset_comp_proc_loc = NB_CORE_PER_NODE / (comp_proc_mpi_loc / comp_proc_nod_loc) )) |
---|
| 1329 | else |
---|
| 1330 | (( offset_comp_proc_loc = comp_proc_omp_loc )) |
---|
| 1331 | fi |
---|
[1000] | 1332 | |
---|
[1500] | 1333 | for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do |
---|
| 1334 | (( index_host = current_core / NB_CORE_PER_NODE )) |
---|
| 1335 | host_value=${listnodes[${index_host}]} |
---|
| 1336 | (( slot = current_core % NB_CORE_PER_NODE )) |
---|
| 1337 | echo "$host_value" >> hostlist |
---|
| 1338 | echo "$rank taskset -c $slot-$((slot+comp_proc_omp_loc-1)) ./script_${ExeNameOut}.ksh" >> run_file |
---|
| 1339 | (( rank = rank + 1 )) |
---|
| 1340 | (( current_core = current_core + offset_comp_proc_loc )) |
---|
| 1341 | done |
---|
[1078] | 1342 | fi |
---|
| 1343 | done |
---|
[1381] | 1344 | |
---|
[1385] | 1345 | ## variable added to stop after 60s instead of 600s by default. |
---|
| 1346 | ## This is used when no error comes from executables and when something stopped an executable without notice. |
---|
| 1347 | export SLURM_WAIT=60 |
---|
[1500] | 1348 | export SLURM_HOSTFILE=./hostlist |
---|
[1381] | 1349 | |
---|
[1500] | 1350 | EXECUTION="${HOST_MPIRUN_COMMAND} --cpu-bind=none --distribution=arbitrary --multi-prog ./run_file" |
---|
[1381] | 1351 | |
---|
[1390] | 1352 | IGCM_sys_Chmod u+x run_file |
---|
| 1353 | if ( $DEBUG_sys ) ; then |
---|
| 1354 | echo "run_file contains : " |
---|
| 1355 | cat run_file |
---|
| 1356 | fi |
---|
[1381] | 1357 | |
---|
[1493] | 1358 | fi # if ${OK_PARA_MPMD} |
---|
[1381] | 1359 | |
---|
[1390] | 1360 | else |
---|
[1493] | 1361 | # Only one executable (SPMD mode): executionType=3, 4, 5 and 6 |
---|
[1000] | 1362 | |
---|
[622] | 1363 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1364 | |
---|
[685] | 1365 | # Only if we really have an executable for the component : |
---|
[623] | 1366 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[685] | 1367 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
[622] | 1368 | |
---|
[1381] | 1369 | # Build script files |
---|
| 1370 | |
---|
[685] | 1371 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1372 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1373 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1374 | |
---|
| 1375 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 1376 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 1377 | echo "" >> script_${ExeNameOut}.ksh |
---|
[1493] | 1378 | echo "export OMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 1379 | echo "export OMP_PLACES=cores" >> script_${ExeNameOut}.ksh |
---|
[685] | 1380 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1381 | fi |
---|
| 1382 | |
---|
[1493] | 1383 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1384 | |
---|
| 1385 | # To have out/err per process on different files |
---|
| 1386 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh |
---|
| 1387 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
---|
[685] | 1388 | |
---|
[1462] | 1389 | IGCM_debug_Print 1 "sys Irene : script_${ExeNameOut}.ksh contains" |
---|
[685] | 1390 | cat script_${ExeNameOut}.ksh |
---|
| 1391 | |
---|
[623] | 1392 | fi |
---|
[622] | 1393 | |
---|
| 1394 | done |
---|
| 1395 | |
---|
[1390] | 1396 | fi # ${OK_PARA_MPMD} |
---|
[622] | 1397 | |
---|
[1462] | 1398 | IGCM_debug_Print 1 "sys Irene : execution command is " |
---|
[623] | 1399 | IGCM_debug_Print 1 "$EXECUTION" |
---|
[622] | 1400 | |
---|
[623] | 1401 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
[622] | 1402 | } |
---|
| 1403 | |
---|
[933] | 1404 | #D-#================================================== |
---|
| 1405 | #D-function IGCM_sys_check_path |
---|
| 1406 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
| 1407 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
| 1408 | #D-* Examples: |
---|
| 1409 | #D- |
---|
| 1410 | function IGCM_sys_check_path { |
---|
| 1411 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
| 1412 | if ( $DEBUG_sys ) ; then |
---|
| 1413 | echo "IGCM_sys_check_path" |
---|
| 1414 | fi |
---|
[811] | 1415 | |
---|
[1490] | 1416 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${WORK} ] || [ X${RUN_DIR_PATH} = X${SCRATCH} ] || [ X${RUN_DIR_PATH} = X${STORE} ] ) ; then |
---|
[933] | 1417 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
| 1418 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
[936] | 1419 | IGCM_debug_Exit "This will stop the job" |
---|
[933] | 1420 | fi |
---|
| 1421 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
| 1422 | } |
---|
| 1423 | |
---|
[811] | 1424 | #D-#================================================== |
---|
| 1425 | #D-function IGCM_sys_check_quota |
---|
| 1426 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
| 1427 | #D-* Examples: |
---|
| 1428 | #D- |
---|
[714] | 1429 | function IGCM_sys_check_quota { |
---|
[776] | 1430 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
[1502] | 1431 | echo "IGCM_sys_check_quota is desactivated on JeanZay because there is actually no way to check scratch quota on this computing center (2019.11.19)" |
---|
| 1432 | # if ( $DEBUG_sys ) ; then |
---|
| 1433 | # echo "IGCM_sys_check_quota" |
---|
| 1434 | # fi |
---|
| 1435 | # # Limit of quota (in %) |
---|
| 1436 | # limit_quota=90 |
---|
| 1437 | # |
---|
| 1438 | # # Check of the volume |
---|
| 1439 | # volume_quota=$(ccc_quota | grep ' scratch' | gawk '{print $2}') |
---|
| 1440 | # volume_avail=$(ccc_quota | grep ' scratch' | gawk '{print $3}') |
---|
| 1441 | # |
---|
| 1442 | # if ( [ ! X${volume_quota} = X ] && [ ! ${volume_quota} = "-" ] ) ; then |
---|
| 1443 | # |
---|
| 1444 | # unit_avail=${volume_avail: -1} |
---|
| 1445 | # unit_quota=${volume_quota: -1} |
---|
| 1446 | # |
---|
| 1447 | # if [ "${unit_quota}" = "*" ] ; then |
---|
| 1448 | # IGCM_debug_Print 1 "Please, check your quota of volume on scratch" |
---|
| 1449 | # IGCM_debug_Print 1 "More than 100% of your quota is used" |
---|
| 1450 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
| 1451 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
| 1452 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
| 1453 | # IGCM_debug_Verif_Exit |
---|
| 1454 | # fi |
---|
| 1455 | # |
---|
| 1456 | # temp_avail=${volume_avail%%${volume_avail: -1}*} |
---|
| 1457 | # temp_quota=${volume_quota%%${volume_quota: -1}*} |
---|
| 1458 | # |
---|
| 1459 | # if [ ! ${unit_avail} = ${unit_quota} ] ; then |
---|
| 1460 | # |
---|
| 1461 | # # Convertion |
---|
| 1462 | # if [ ${volume_avail: -1} = "T" ] ; then |
---|
| 1463 | # (( temp_avail = temp_avail * 1000000000000 )) |
---|
| 1464 | # elif [ ${volume_avail: -1} = "G" ] ; then |
---|
| 1465 | # (( temp_avail = temp_avail * 1000000000 )) |
---|
| 1466 | # elif [ ${volume_avail: -1} = "M" ] ; then |
---|
| 1467 | # (( temp_avail = temp_avail * 1000000 )) |
---|
| 1468 | # elif [ ${volume_avail: -1} = "k" ] ; then |
---|
| 1469 | # (( temp_avail = temp_avail * 1000 )) |
---|
| 1470 | # else |
---|
| 1471 | # (( temp_avail = volume_avail )) |
---|
| 1472 | # fi |
---|
| 1473 | # if [ ${volume_quota: -1} = "T" ] ; then |
---|
| 1474 | # (( temp_quota = temp_quota * 1000000000000 )) |
---|
| 1475 | # elif [ ${volume_quota: -1} = "G" ] ; then |
---|
| 1476 | # (( temp_quota = temp_quota * 1000000000 )) |
---|
| 1477 | # elif [ ${volume_quota: -1} = "M" ] ; then |
---|
| 1478 | # (( temp_quota = temp_quota * 1000000 )) |
---|
| 1479 | # elif [ ${volume_quota: -1} = "k" ] ; then |
---|
| 1480 | # (( temp_quota = temp_quota * 1000 )) |
---|
| 1481 | # else |
---|
| 1482 | # (( temp_quota = volume_quota )) |
---|
| 1483 | # fi |
---|
| 1484 | # fi |
---|
| 1485 | # |
---|
| 1486 | # quota_volume=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc) |
---|
| 1487 | ## echo "volume ratio is " $quota_volume |
---|
| 1488 | # |
---|
| 1489 | # if [ ${quota_volume} -ge ${limit_quota} ] ; then |
---|
| 1490 | # IGCM_debug_Print 1 "Please, check your quota of volume on scratch" |
---|
| 1491 | # IGCM_debug_Print 1 "${quota_volume}% of your quota is used" |
---|
| 1492 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
| 1493 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
| 1494 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
| 1495 | # IGCM_debug_Verif_Exit |
---|
| 1496 | # fi |
---|
| 1497 | # |
---|
| 1498 | # fi |
---|
| 1499 | # |
---|
| 1500 | ## Check of the number of inodes |
---|
| 1501 | # |
---|
| 1502 | # inode_quota=$(ccc_quota | grep ' scratch' | gawk '{print $6}') |
---|
| 1503 | # inode_avail=$(ccc_quota | grep ' scratch' | gawk '{print $7}') |
---|
| 1504 | # |
---|
| 1505 | # if ( [ ! X${inode_quota} = X ] && [ ! ${inode_quota} = "-" ] ) ; then |
---|
| 1506 | # |
---|
| 1507 | # unit_avail=${inode_avail: -1} |
---|
| 1508 | # unit_quota=${inode_quota: -1} |
---|
| 1509 | # |
---|
| 1510 | # if [ "${unit_quota}" = "*" ] ; then |
---|
| 1511 | # IGCM_debug_Print 1 "Please, check your quota of inode on scratch" |
---|
| 1512 | # IGCM_debug_Print 1 "More than 100% of your quota is used" |
---|
| 1513 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
| 1514 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
| 1515 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
| 1516 | # IGCM_debug_Verif_Exit |
---|
| 1517 | # fi |
---|
| 1518 | # |
---|
| 1519 | # temp_avail=${inode_avail%%${inode_avail: -1}*} |
---|
| 1520 | # temp_quota=${inode_quota%%${inode_quota: -1}*} |
---|
| 1521 | # |
---|
| 1522 | # if [ ! ${unit_avail} = ${unit_quota} ] ; then |
---|
| 1523 | # |
---|
| 1524 | # # Convertion |
---|
| 1525 | # if [ ${inode_avail: -1} = "T" ] ; then |
---|
| 1526 | # (( temp_avail = temp_avail * 1000000000000 )) |
---|
| 1527 | # elif [ ${inode_avail: -1} = "G" ] ; then |
---|
| 1528 | # (( temp_avail = temp_avail * 1000000000 )) |
---|
| 1529 | # elif [ ${inode_avail: -1} = "M" ] ; then |
---|
| 1530 | # (( temp_avail = temp_avail * 1000000 )) |
---|
| 1531 | # elif [ ${inode_avail: -1} = "k" ] ; then |
---|
| 1532 | # (( temp_avail = temp_avail * 1000 )) |
---|
| 1533 | # else |
---|
| 1534 | # (( temp_avail = inode_avail )) |
---|
| 1535 | # fi |
---|
| 1536 | # |
---|
| 1537 | # if [ ${inode_quota: -1} = "T" ] ; then |
---|
| 1538 | # (( temp_quota = temp_quota * 1000000000000 )) |
---|
| 1539 | # elif [ ${inode_quota: -1} = "G" ] ; then |
---|
| 1540 | # (( temp_quota = temp_quota * 1000000000 )) |
---|
| 1541 | # elif [ ${inode_quota: -1} = "M" ] ; then |
---|
| 1542 | # (( temp_quota = temp_quota * 1000000 )) |
---|
| 1543 | # elif [ ${inode_quota: -1} = "k" ] ; then |
---|
| 1544 | # (( temp_quota = temp_quota * 1000 )) |
---|
| 1545 | # else |
---|
| 1546 | # (( temp_quota = inode_quota )) |
---|
| 1547 | # fi |
---|
| 1548 | # fi |
---|
| 1549 | # quota_inode=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc) |
---|
| 1550 | ## echo "inode ratio is " $quota_inode |
---|
| 1551 | # |
---|
| 1552 | # if [ ${quota_inode} -ge ${limit_quota} ] ; then |
---|
| 1553 | # IGCM_debug_Print 1 "Please, check your quota of inode on scratch" |
---|
| 1554 | # IGCM_debug_Print 1 "${quota_inode}% of your quota is used" |
---|
| 1555 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
| 1556 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
| 1557 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
| 1558 | # IGCM_debug_Verif_Exit |
---|
| 1559 | # fi |
---|
| 1560 | # fi |
---|
[776] | 1561 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
[714] | 1562 | } |
---|
| 1563 | |
---|
[773] | 1564 | #D-#================================================== |
---|
[1286] | 1565 | #D-function IGCM_sys_projectAccounting |
---|
| 1566 | #D-* Purpose: store project accounting information in a file |
---|
| 1567 | #D-* Examples: |
---|
| 1568 | #D- |
---|
| 1569 | function IGCM_sys_projectAccounting { |
---|
| 1570 | IGCM_debug_PushStack "IGCM_sys_projectAccounting" |
---|
| 1571 | if ( $DEBUG_sys ) ; then |
---|
| 1572 | echo "IGCM_sys_check_quota" |
---|
| 1573 | fi |
---|
[1502] | 1574 | #need to implemented on Jean Zay |
---|
| 1575 | touch $1 |
---|
| 1576 | # ssh irene191 /usr/bin/ccc_myproject > $1 |
---|
[1286] | 1577 | |
---|
| 1578 | IGCM_debug_PopStack "IGCM_sys_projectAccounting" |
---|
| 1579 | } |
---|
| 1580 | |
---|
| 1581 | #D-#================================================== |
---|
[1244] | 1582 | #D-function IGCM_sys_getJobSchedulerID |
---|
| 1583 | #D-* Purpose: Get the job ID during execution |
---|
| 1584 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
| 1585 | #D- |
---|
| 1586 | function IGCM_sys_getJobSchedulerID { |
---|
| 1587 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
| 1588 | if ( $DEBUG_sys ) ; then |
---|
| 1589 | echo "IGCM_sys_getJobSchedulerID" |
---|
| 1590 | fi |
---|
| 1591 | |
---|
[1503] | 1592 | eval ${1}=${SLURM_JOBID} |
---|
[1244] | 1593 | |
---|
| 1594 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
| 1595 | } |
---|
| 1596 | |
---|
| 1597 | #D-#================================================== |
---|
[958] | 1598 | #D-function IGCM_sys_GetJobID |
---|
[1244] | 1599 | #D-* Purpose: Get the job ID from the JobName |
---|
[958] | 1600 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
| 1601 | #D- |
---|
| 1602 | function IGCM_sys_GetJobID { |
---|
| 1603 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
| 1604 | if ( $DEBUG_sys ) ; then |
---|
| 1605 | echo "IGCM_sys_GetJobID" |
---|
| 1606 | fi |
---|
| 1607 | |
---|
[1502] | 1608 | ID=$( squeue -u $user | grep Job_${config_UserChoices_JobName} | gawk ' { print $1}' ) |
---|
[958] | 1609 | |
---|
[1502] | 1610 | |
---|
[958] | 1611 | eval ${3}=${ID} |
---|
| 1612 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
| 1613 | } |
---|
| 1614 | |
---|
| 1615 | #D-#================================================== |
---|
[773] | 1616 | #D-function IGCM_sys_CountJobInQueue |
---|
[1244] | 1617 | #D-* Purpose: Count number of users job |
---|
[773] | 1618 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
| 1619 | #D- |
---|
| 1620 | function IGCM_sys_CountJobInQueue { |
---|
| 1621 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
| 1622 | if ( $DEBUG_sys ) ; then |
---|
| 1623 | echo "IGCM_sys_CountJobInQueue" |
---|
| 1624 | fi |
---|
| 1625 | |
---|
| 1626 | # With -f option, the full job name is given in the last column |
---|
[1502] | 1627 | NbRun=$(squeue -u $user | \ |
---|
| 1628 | grep -v JOBID | gawk 'BEGIN { x=0 } ( $NF ~ JobName ) { x=x+1 } END { print x }' ) |
---|
[773] | 1629 | |
---|
| 1630 | eval ${2}=${NbRun} |
---|
| 1631 | |
---|
| 1632 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
| 1633 | } |
---|
| 1634 | |
---|
[955] | 1635 | #D-#================================================== |
---|
| 1636 | #D-function IGCM_sys_ListJobInQueue |
---|
[1244] | 1637 | #D-* Purpose: Produce a list of users computing jobs (excluding post-processing) |
---|
[955] | 1638 | #D-* Examples: IGCM_sys_ListJobInQueue ${User} JobNameList |
---|
| 1639 | #D- |
---|
| 1640 | function IGCM_sys_ListJobInQueue { |
---|
| 1641 | IGCM_debug_PushStack "IGCM_sys_ListJobInQueue" |
---|
| 1642 | if ( $DEBUG_sys ) ; then |
---|
| 1643 | echo "IGCM_sys_ListJobInQueue" |
---|
| 1644 | fi |
---|
| 1645 | |
---|
[1502] | 1646 | # to be implemented on Jean Zay |
---|
| 1647 | set -A JobList $( squeue -u $user | gawk '{print $3}' | grep -v NAME) |
---|
| 1648 | # # With -f option, the full job name is given in the last column |
---|
| 1649 | # set -A JobList $( ccc_mstat -f | gawk -v User=$1 \ |
---|
| 1650 | # '( $2 == User && \ |
---|
| 1651 | # $NF != /TS/ && \ |
---|
| 1652 | # $NF !~ /PACK/ && \ |
---|
| 1653 | # $NF !~ /REBUILD/ && \ |
---|
| 1654 | # $NF !~ /pack/ ) \ |
---|
| 1655 | # { print $NF }' | sed -e "s/\(.*\)\.[0-9]*/\1/" ) |
---|
| 1656 | # |
---|
[955] | 1657 | eval set -A ${2} ${JobList[*]} |
---|
| 1658 | |
---|
| 1659 | IGCM_debug_PopStack "IGCM_sys_ListJobInQueue" |
---|
| 1660 | } |
---|
[1272] | 1661 | |
---|
| 1662 | #D-#================================================== |
---|
| 1663 | #D-function IGCM_sys_atlas |
---|
| 1664 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
---|
| 1665 | #D-* Examples: |
---|
| 1666 | #D- |
---|
| 1667 | function IGCM_sys_atlas { |
---|
| 1668 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
---|
| 1669 | if ( $DEBUG_sys ) ; then |
---|
| 1670 | echo "IGCM_sys_atlas :" $@ |
---|
| 1671 | fi |
---|
| 1672 | |
---|
| 1673 | typeset status |
---|
[1502] | 1674 | # To be implemented on Jean Zay |
---|
| 1675 | # |
---|
| 1676 | # \ccc_mprun atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 1677 | # status=$? |
---|
| 1678 | # if [ ${status} -gt 0 ] ; then |
---|
| 1679 | # echo "IGCM_sys_atlas : error code ${status}" |
---|
| 1680 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1681 | # \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1682 | # IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1683 | # return 1 |
---|
| 1684 | # else |
---|
| 1685 | # IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1686 | # return 0 |
---|
| 1687 | # fi |
---|
| 1688 | # |
---|
[1272] | 1689 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1690 | } |
---|
| 1691 | |
---|
[1380] | 1692 | #D-#================================================== |
---|
| 1693 | #D-function IGCM_sys_rebuild_nemo |
---|
| 1694 | #D-* Purpose: rebuild nemo parallel files with nemo specific rebuild on curie |
---|
| 1695 | #D-* Examples: |
---|
| 1696 | #D- |
---|
| 1697 | |
---|
| 1698 | function IGCM_sys_rebuild_nemo { |
---|
| 1699 | IGCM_debug_PushStack "IGCM_sys_rebuild_nemo" $@ |
---|
| 1700 | if ( $DEBUG_sys ) ; then |
---|
| 1701 | echo "IGCM_sys_rebuild_nemo :" $@ |
---|
| 1702 | fi |
---|
| 1703 | |
---|
[1496] | 1704 | /gpfswork/rech/psl/commun/Tools/rebuild_nemo/bin/rebuild_nemo ${1} ${2} |
---|
[1380] | 1705 | |
---|
| 1706 | IGCM_debug_PopStack "IGCM_sys_rebuild_nemo" |
---|
| 1707 | } |
---|
| 1708 | |
---|