| 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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| 16 | # if you use the prefix #D- for comments to be extracted. |
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| 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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| 21 | #D-LibIGCM_sys for Jean-Zay |
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| 22 | #D-#================================================== |
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| 23 | #D- |
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| 24 | #D- This ksh library if a layer under some usefull |
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| 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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| 45 | # | | Cp/Exe/param/files | | | | |
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| 46 | # | | Chmod Qsub | | | | |
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| 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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| 64 | # Host user names project maxCpuTime |
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| 65 | # $hostname ou hostname |
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| 66 | typeset HOST=${HOST:=$( hostname )} |
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| 67 | # $username ou whoami |
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| 68 | typeset LOGIN=${LOGIN:=$( whoami )} |
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| 69 | # $hostname of the MASTER job |
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| 70 | typeset MASTER=jeanzay |
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| 71 | # add default project set by ins_job |
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| 72 | typeset PROJECT=$( 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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| 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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| 81 | # Submit command |
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| 82 | typeset SUBMIT=${SUBMIT:=sbatch} |
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| 83 | # rsync with path |
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| 84 | typeset -r RSYNC=/usr/bin/rsync |
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| 85 | # RSYNC_opt args to rsync |
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| 86 | typeset -r RSYNC_opt="-va" |
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| 87 | # ie storage filesystem |
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| 88 | typeset -r STOREHOST=${MASTER} |
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| 89 | typeset -r REMOTE_RSYNC=/usr/bin/rsync |
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| 90 | |
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| 91 | #==================================================== |
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| 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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| 97 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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| 98 | #==================================================== |
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| 99 | if [ X${TaskType} = Xcomputing ] ; then |
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| 100 | IGCM_debug_Print 1 "Modules will be loaded later in IGCM_sys_activ_variables." |
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| 101 | else |
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| 102 | module purge > /dev/null 2>&1 |
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| 103 | . /gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_jeanzay > /dev/null 2>&1 |
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| 104 | |
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| 105 | . /gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_atlas_jeanzay > /dev/null 2>&1 |
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| 106 | |
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| 107 | # export PCMDI_MP=/ccc/work/cont003/igcmg/igcmg/PCMDI-MP |
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| 108 | export UVCDAT_ANONYMOUS_LOG=FALSE |
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| 109 | fi |
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| 110 | |
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| 111 | # FYI |
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| 112 | [ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:" |
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| 113 | [ ! X${TaskType} = Xchecking ] && module list |
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| 114 | |
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| 115 | # For AddNoise (not yet AddPertu3DOCE) |
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| 116 | export PATH=${PATH}:/gpfswork/rech/psl/commun/Tools/AddNoise/bin |
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| 117 | |
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| 118 | # For rebuild |
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| 119 | export PATH=${PATH}:/gpfswork/rech/psl/commun/Tools/rebuild/modipsl_IOIPSL_PLUS_v2_2_4/bin |
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| 120 | |
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| 121 | #==================================================== |
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| 122 | # Host specific DIRECTORIES |
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| 123 | #==================================================== |
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| 124 | |
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| 125 | #==================================================== |
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| 126 | #- MirrorlibIGCM for frontend |
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| 127 | typeset -r MirrorlibIGCM=${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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| 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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| 139 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${SLURM_SUBMIT_DIR}} |
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| 140 | |
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| 141 | #==================================================== |
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| 142 | #- IN |
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| 143 | typeset -r R_IN=${R_IN:=/gpfswork/rech/psl/commun/IGCM} |
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| 144 | |
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| 145 | #==================================================== |
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| 146 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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| 147 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${SCRATCH}/RUN_DIR/${SLURM_JOBID}_${$}} |
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| 148 | |
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| 149 | #==================================================== |
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| 150 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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| 151 | typeset -r OUTCOMMAND_PATH=/tmp |
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| 152 | |
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| 153 | #==================================================== |
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| 154 | #- HOST_MPIRUN_COMMAND |
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| 155 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time srun "} |
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| 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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| 161 | #==================================================== |
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| 162 | #- set PackDefault to true |
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| 163 | PackDefault=true |
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| 164 | |
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| 165 | #==================================================== |
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| 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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| 171 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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| 172 | |
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| 173 | #==================================================== |
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| 174 | #- Number of computing cores per node |
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| 175 | #- |
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| 176 | NB_CORE_PER_NODE=40 |
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| 177 | |
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| 178 | #D-#================================================== |
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| 179 | #D-function IGCM_sys_defineArchives |
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| 180 | #D-* Purpose: |
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| 181 | #D-* Load dfldatadir module : According to project used for submission (default) or set in config.card (optional) |
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| 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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| 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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| 188 | #D-* Examples: |
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| 189 | #D- |
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| 190 | function IGCM_sys_defineArchives { |
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| 191 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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| 192 | |
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| 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${config_UserChoices_DataProject} = DEFAULT ]; then |
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| 195 | # The variable DataProject is not set in in section UserChoices in config.card or it is set to DEFAULT |
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| 196 | # Default option: Set DataProject according to the project used for submission |
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| 197 | DataProject=${PROJECT} |
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| 198 | else |
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| 199 | # Use the project set by the variable DataProject in section UserChoices in config.card |
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| 200 | IGCM_debug_Print 1 "Use DataProject as set in config.card : ${config_UserChoices_DataProject}" |
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| 201 | DataProject=${config_UserChoices_DataProject} |
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| 202 | fi |
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| 203 | IGCM_debug_Print 1 "Data project for output to be used: ${DataProject}" |
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| 204 | |
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| 205 | #==================================================== |
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| 206 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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| 207 | #- DataProject = for is the dataproject for Training account at Idris |
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| 208 | #- they are not store in rech but in another partition |
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| 209 | if [ X${DataProject} = Xfor ]; then |
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| 210 | typeset -r RUN_DIR_PATH=$SCRATCH/RUN_DIR/${SLURM_JOBID}_${$} |
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| 211 | else |
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| 212 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/gpfsscratch/rech/${DataProject}/${LOGIN}/RUN_DIR/${SLURM_JOBID}_${$}} |
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| 213 | fi |
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| 214 | |
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| 215 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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| 216 | #==================================================== |
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| 217 | #- ARCHIVE (dedicated to large files) |
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| 218 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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| 219 | else |
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| 220 | if [ X${DataProject} = Xfor ]; then |
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| 221 | ARCHIVE=$STORE |
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| 222 | else |
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| 223 | #==================================================== |
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| 224 | #- ARCHIVE (dedicated to large files) |
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| 225 | ARCHIVE=/gpfsstore/rech/${DataProject}/${LOGIN} |
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| 226 | fi |
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| 227 | fi |
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| 228 | |
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| 229 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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| 230 | #==================================================== |
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| 231 | #- STORAGE (dedicated to small/medium files) |
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| 232 | STORAGE=${config_UserChoices_STORAGE} |
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| 233 | else |
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| 234 | #==================================================== |
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| 235 | #- STORAGE (dedicated to small/medium files) |
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| 236 | if [ X${DataProject} = Xfor ]; then |
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| 237 | STORAGE=$WORK |
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| 238 | else |
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| 239 | STORAGE=/gpfswork/rech/${DataProject}/${LOGIN} |
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| 240 | fi |
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| 241 | fi |
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| 242 | |
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| 243 | if [ X${config_UserChoices_SpaceName} = XTEST ]; then |
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| 244 | #==================================================== |
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| 245 | #- R_OUT |
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| 246 | if [ X${DataProject} = Xfor ]; then |
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| 247 | R_OUT=$SCRATCH/IGCM_OUT |
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| 248 | else |
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| 249 | R_OUT=/gpfsscratch/rech/${DataProject}/${LOGIN}/IGCM_OUT |
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| 250 | fi |
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| 251 | #==================================================== |
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| 252 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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| 253 | R_FIG=${R_OUT} |
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| 254 | |
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| 255 | IGCM_debug_Print 1 "SpaceName=TEST ==> OVERRULE destination path directories" |
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| 256 | |
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| 257 | else |
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| 258 | #==================================================== |
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| 259 | #- R_OUT |
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| 260 | R_OUT=${ARCHIVE}/IGCM_OUT |
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| 261 | |
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| 262 | #==================================================== |
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| 263 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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| 264 | R_FIG=${STORAGE}/IGCM_OUT |
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| 265 | fi |
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| 266 | |
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| 267 | #==================================================== |
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| 268 | #- CMIP6 (hosting CMIP6 files produced by XIOS2 and configured by dr2xml) |
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| 269 | CMIP6_BUF=${STORAGE}/IGCM_OUT |
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| 270 | |
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| 271 | #==================================================== |
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| 272 | #- R_BUF (ONLY FOR double copy an scratch) |
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| 273 | |
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| 274 | if [ X${DataProject} = Xfor ]; then |
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| 275 | R_BUF=$SCRATCH/IGCM_OUT |
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| 276 | else |
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| 277 | R_BUF=/gpfsscratch/rech/${DataProject}/${LOGIN}/IGCM_OUT |
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| 278 | fi |
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| 279 | |
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| 280 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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| 281 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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| 282 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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| 283 | |
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| 284 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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| 285 | } |
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| 286 | |
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| 287 | #D-#================================================== |
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| 288 | #D-function IGCM_sys_RshArchive |
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| 289 | #D-* Purpose: Archive rsh command |
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| 290 | #D-* Examples: |
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| 291 | #D- |
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| 292 | function IGCM_sys_RshArchive { |
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| 293 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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| 294 | /bin/ksh <<-EOF |
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| 295 | ${@} |
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| 296 | EOF |
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| 297 | status=$? |
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| 298 | if [ ${status} -gt 0 ] ; then |
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| 299 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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| 300 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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| 301 | fi |
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| 302 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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| 303 | } |
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| 304 | |
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| 305 | #D-#================================================== |
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| 306 | #D-function IGCM_sys_RshArchive_NoError |
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| 307 | #D-* Purpose: Archive rsh command, without error |
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| 308 | #D-* used only in monitoring.job |
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| 309 | #D-* Examples: |
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| 310 | #D- |
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| 311 | function IGCM_sys_RshArchive_NoError { |
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| 312 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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| 313 | /bin/ksh <<-EOF |
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| 314 | ${@} 2> /dev/null |
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| 315 | EOF |
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| 316 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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| 317 | } |
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| 318 | |
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| 319 | #D-#================================================== |
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| 320 | #D-function IGCM_sys_MkdirArchive |
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| 321 | #D-* Purpose: Mkdir on Archive |
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| 322 | #D-* Examples: |
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| 323 | #D- |
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| 324 | function IGCM_sys_MkdirArchive { |
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| 325 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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| 326 | if ( $DEBUG_sys ) ; then |
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| 327 | echo "IGCM_sys_MkdirArchive :" $@ |
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| 328 | fi |
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| 329 | #- creation de repertoire sur le serveur fichier |
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| 330 | if [ ! -d ${1} ]; then |
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| 331 | \mkdir -p $1 |
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| 332 | status=$? |
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| 333 | |
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| 334 | if [ ${status} -gt 0 ] ; then |
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| 335 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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| 336 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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| 337 | fi |
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| 338 | fi |
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| 339 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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| 340 | } |
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| 341 | |
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| 342 | #D-#================================================== |
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| 343 | #D-function IGCM_sys_TestDirArchive |
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| 344 | #D-* Purpose: Test Directory that must exists on Archive |
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| 345 | #D-* Examples: |
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| 346 | #D- |
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| 347 | function IGCM_sys_TestDirArchive { |
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| 348 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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| 349 | if ( $DEBUG_sys ) ; then |
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| 350 | echo "IGCM_sys_TestDirArchive :" $@ |
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| 351 | fi |
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| 352 | typeset ExistFlag |
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| 353 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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| 354 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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| 355 | return ${ExistFlag} |
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| 356 | } |
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| 357 | |
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| 358 | #D-#================================================== |
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| 359 | #D-function IGCM_sys_IsFileArchived |
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| 360 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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| 361 | #D-* Examples: |
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| 362 | #D- |
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| 363 | function IGCM_sys_IsFileArchived { |
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| 364 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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| 365 | if ( $DEBUG_sys ) ; then |
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| 366 | echo "IGCM_sys_IsFileArchived :" $@ |
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| 367 | fi |
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| 368 | typeset IsArchivedFlag |
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| 369 | # To be implemented on Jean Zay |
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| 370 | # IsArchivedFlag=$( [ X$( echo $@ | grep ^\/ccc\/store ) != X ] && echo 0 || echo 1 ) |
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| 371 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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| 372 | |
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| 373 | return ${IsArchivedFlag} |
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| 374 | } |
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| 375 | |
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| 376 | #D-#================================================== |
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| 377 | #D-function IGCM_sys_TestFileArchive |
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| 378 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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| 379 | #D-* Examples: |
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| 380 | #D- |
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| 381 | function IGCM_sys_TestFileArchive { |
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| 382 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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| 383 | typeset ExistFlag |
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| 384 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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| 385 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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| 386 | |
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| 387 | return ${ExistFlag} |
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| 388 | } |
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| 389 | |
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| 390 | #D-#================================================== |
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| 391 | #D-function IGCM_sys_CountFileArchive |
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| 392 | #D-* Purpose: Count files on Archive filesystem |
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| 393 | #D-* Examples: |
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| 394 | #D- |
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| 395 | function IGCM_sys_CountFileArchive { |
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| 396 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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| 397 | ls ${@} 2>/dev/null | wc -l |
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| 398 | if [ $? -gt 0 ] ; then |
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| 399 | echo "IGCM_sys_CountFileArchive : erreur." |
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| 400 | fi |
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| 401 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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| 402 | } |
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| 403 | |
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| 404 | #D-#================================================== |
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| 405 | #D-function IGCM_sys_Tree |
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| 406 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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| 407 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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| 408 | #D- |
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| 409 | function IGCM_sys_Tree { |
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| 410 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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| 411 | if ( $DEBUG_sys ) ; then |
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| 412 | echo "IGCM_sys_Tree :" $@ |
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| 413 | fi |
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| 414 | |
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| 415 | \ls -lR ${@} |
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| 416 | |
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| 417 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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| 418 | } |
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| 419 | |
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| 420 | #D-#================================================== |
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| 421 | #D-function IGCM_sys_Qsub |
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| 422 | #D-* Purpose: Qsub new job |
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| 423 | #D-* Examples: |
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| 424 | #D- |
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| 425 | function IGCM_sys_Qsub { |
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| 426 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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| 427 | if ( $DEBUG_sys ) ; then |
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| 428 | echo "IGCM_sys_Qsub :" $@ |
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| 429 | fi |
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| 430 | typeset options status |
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| 431 | options="-o ${SUBMIT_DIR}/${Script_Output} -e ${SUBMIT_DIR}/${Script_Output}" |
|---|
| 432 | |
|---|
| 433 | /usr/bin/time sbatch ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 434 | status=$? |
|---|
| 435 | |
|---|
| 436 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 437 | if [ ${status} -gt 0 ] ; then |
|---|
| 438 | IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}" |
|---|
| 439 | IGCM_debug_Exit "IGCM_sys_Qsub" |
|---|
| 440 | else |
|---|
| 441 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
|---|
| 442 | fi |
|---|
| 443 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
|---|
| 444 | } |
|---|
| 445 | |
|---|
| 446 | #D-#================================================== |
|---|
| 447 | #D-function IGCM_sys_QsubPost |
|---|
| 448 | #D-* Purpose: Qsub new job on scalaire |
|---|
| 449 | #D-* Examples: |
|---|
| 450 | #D- |
|---|
| 451 | function IGCM_sys_QsubPost { |
|---|
| 452 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
|---|
| 453 | if ( $DEBUG_sys ) ; then |
|---|
| 454 | echo "IGCM_sys_QsubPost :" $@ |
|---|
| 455 | fi |
|---|
| 456 | typeset options status |
|---|
| 457 | options="-o ${POST_DIR}/${Script_Post_Output}.out -e ${POST_DIR}/${Script_Post_Output}.out" |
|---|
| 458 | |
|---|
| 459 | sbatch ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 460 | status=$? |
|---|
| 461 | |
|---|
| 462 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 463 | if [ ${status} -gt 0 ] ; then |
|---|
| 464 | IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}" |
|---|
| 465 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
|---|
| 466 | else |
|---|
| 467 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
|---|
| 468 | fi |
|---|
| 469 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
|---|
| 470 | } |
|---|
| 471 | |
|---|
| 472 | #D-************************* |
|---|
| 473 | #D- File transfer functions |
|---|
| 474 | #D-************************* |
|---|
| 475 | #D- |
|---|
| 476 | |
|---|
| 477 | #D-#================================================== |
|---|
| 478 | #D-function IGCM_sys_RmRunDir |
|---|
| 479 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
|---|
| 480 | #D- scheduler will do the job) |
|---|
| 481 | #D-* Examples: |
|---|
| 482 | #D- |
|---|
| 483 | function IGCM_sys_RmRunDir { |
|---|
| 484 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
|---|
| 485 | if ( $DEBUG_sys ) ; then |
|---|
| 486 | echo "IGCM_sys_RmRunDir :" $@ |
|---|
| 487 | fi |
|---|
| 488 | |
|---|
| 489 | typeset status |
|---|
| 490 | |
|---|
| 491 | echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 492 | \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 493 | status=$? |
|---|
| 494 | |
|---|
| 495 | if [ ${status} -gt 0 ] ; then |
|---|
| 496 | IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}." |
|---|
| 497 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 498 | IGCM_debug_Exit "IGCM_sys_RmRunDir" |
|---|
| 499 | else |
|---|
| 500 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 501 | fi |
|---|
| 502 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
|---|
| 503 | } |
|---|
| 504 | |
|---|
| 505 | #D-#================================================== |
|---|
| 506 | #D-function IGCM_sys_Put_Dir |
|---|
| 507 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
|---|
| 508 | #D-* Examples: |
|---|
| 509 | #D- |
|---|
| 510 | function IGCM_sys_Put_Dir { |
|---|
| 511 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
|---|
| 512 | if ( $DEBUG_sys ) ; then |
|---|
| 513 | echo "IGCM_sys_Put_Dir :" $@ |
|---|
| 514 | fi |
|---|
| 515 | if [ $DRYRUN = 0 ]; then |
|---|
| 516 | if [ ! -d ${1} ] ; then |
|---|
| 517 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
|---|
| 518 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
|---|
| 519 | return |
|---|
| 520 | fi |
|---|
| 521 | |
|---|
| 522 | typeset status |
|---|
| 523 | |
|---|
| 524 | # Only if we use rsync |
|---|
| 525 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
|---|
| 526 | # |
|---|
| 527 | #USUAL WAY |
|---|
| 528 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 529 | status=$? |
|---|
| 530 | |
|---|
| 531 | if [ ${status} -gt 0 ] ; then |
|---|
| 532 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
|---|
| 533 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 534 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
|---|
| 535 | else |
|---|
| 536 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 537 | fi |
|---|
| 538 | fi |
|---|
| 539 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
|---|
| 540 | } |
|---|
| 541 | |
|---|
| 542 | #D-#================================================== |
|---|
| 543 | #D-function IGCM_sys_Get_Dir |
|---|
| 544 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
|---|
| 545 | #D-* Examples: |
|---|
| 546 | #D- |
|---|
| 547 | function IGCM_sys_Get_Dir { |
|---|
| 548 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
|---|
| 549 | if ( $DEBUG_sys ) ; then |
|---|
| 550 | echo "IGCM_sys_Get_Dir :" $@ |
|---|
| 551 | fi |
|---|
| 552 | if [ $DRYRUN = 0 ]; then |
|---|
| 553 | typeset NB_ESSAI DELAI status i |
|---|
| 554 | # number of tentative |
|---|
| 555 | NB_ESSAI=3 |
|---|
| 556 | # time delay between tentative |
|---|
| 557 | DELAI=2 |
|---|
| 558 | |
|---|
| 559 | # |
|---|
| 560 | # USUAL WAY |
|---|
| 561 | # add here command to demigrate all offline files to reduce time of this command |
|---|
| 562 | # actually on Jean Zay files are not archive on bands |
|---|
| 563 | |
|---|
| 564 | i=0 |
|---|
| 565 | while [ $i -lt $NB_ESSAI ] ; do |
|---|
| 566 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 567 | status=$? |
|---|
| 568 | if [ ${status} -gt 0 ] ; then |
|---|
| 569 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
|---|
| 570 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
|---|
| 571 | sleep $DELAI |
|---|
| 572 | else |
|---|
| 573 | break |
|---|
| 574 | fi |
|---|
| 575 | (( i = i + 1 )) |
|---|
| 576 | done |
|---|
| 577 | |
|---|
| 578 | if [ ${status} -gt 0 ] ; then |
|---|
| 579 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
|---|
| 580 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 581 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
|---|
| 582 | else |
|---|
| 583 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 584 | fi |
|---|
| 585 | fi |
|---|
| 586 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
|---|
| 587 | } |
|---|
| 588 | |
|---|
| 589 | #D-#================================================== |
|---|
| 590 | #D-function IGCM_sys_Put_Rest |
|---|
| 591 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
|---|
| 592 | #D- File and target directory must exist. |
|---|
| 593 | #D-* Examples: |
|---|
| 594 | #D- |
|---|
| 595 | function IGCM_sys_Put_Rest { |
|---|
| 596 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
|---|
| 597 | if ( $DEBUG_sys ) ; then |
|---|
| 598 | echo "IGCM_sys_Put_Rest :" $@ |
|---|
| 599 | fi |
|---|
| 600 | if [ $DRYRUN = 0 ]; then |
|---|
| 601 | if [ ! -f ${1} ] ; then |
|---|
| 602 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
|---|
| 603 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
|---|
| 604 | fi |
|---|
| 605 | |
|---|
| 606 | typeset status |
|---|
| 607 | # |
|---|
| 608 | # USUAL WAY |
|---|
| 609 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 610 | status=$? |
|---|
| 611 | |
|---|
| 612 | # #RSYNC WITH NETWORK SSH CALL |
|---|
| 613 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 614 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 615 | |
|---|
| 616 | # #RSYNC WITH NFS USE |
|---|
| 617 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 618 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 619 | |
|---|
| 620 | # status=$? |
|---|
| 621 | # IGCM_sys_Rsync_out $status |
|---|
| 622 | |
|---|
| 623 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 624 | # (( status=status+$? )) |
|---|
| 625 | |
|---|
| 626 | if [ ${status} -gt 0 ] ; then |
|---|
| 627 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
|---|
| 628 | [ -f ${1} ] && ls -l ${1} |
|---|
| 629 | [ -f ${2} ] && ls -l ${2} |
|---|
| 630 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
|---|
| 631 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 632 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
|---|
| 633 | else |
|---|
| 634 | |
|---|
| 635 | if [ X${JobType} = XRUN ] ; then |
|---|
| 636 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
|---|
| 637 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
|---|
| 638 | fi |
|---|
| 639 | |
|---|
| 640 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 641 | fi |
|---|
| 642 | fi |
|---|
| 643 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
|---|
| 644 | } |
|---|
| 645 | |
|---|
| 646 | #D-#================================================== |
|---|
| 647 | #D-function IGCM_sys_Put_Out |
|---|
| 648 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
|---|
| 649 | #D-* Examples: |
|---|
| 650 | #D- |
|---|
| 651 | function IGCM_sys_Put_Out { |
|---|
| 652 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
|---|
| 653 | if ( $DEBUG_sys ) ; then |
|---|
| 654 | echo "IGCM_sys_Put_Out :" $@ |
|---|
| 655 | fi |
|---|
| 656 | |
|---|
| 657 | typeset NB_ESSAI DELAI status i exist skip |
|---|
| 658 | typeset fileDeviceNumberInHex directoryDeviceNumberInHex |
|---|
| 659 | |
|---|
| 660 | # number of tentative |
|---|
| 661 | NB_ESSAI=3 |
|---|
| 662 | # time delay between tentative |
|---|
| 663 | DELAI=2 |
|---|
| 664 | |
|---|
| 665 | if [ $DRYRUN = 0 ]; then |
|---|
| 666 | if [ ! -f ${1} ] ; then |
|---|
| 667 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
|---|
| 668 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
|---|
| 669 | return 1 |
|---|
| 670 | fi |
|---|
| 671 | # |
|---|
| 672 | IGCM_sys_MkdirArchive $( dirname $2 ) |
|---|
| 673 | # |
|---|
| 674 | exist=false |
|---|
| 675 | skip=false |
|---|
| 676 | if [ -f $2 ] ; then |
|---|
| 677 | IGCM_debug_Print 1 "$2 already exist" |
|---|
| 678 | # add here command to demigrate all offline files to reduce time of this command |
|---|
| 679 | # actually on Jean Zay files are not archive on bands |
|---|
| 680 | |
|---|
| 681 | exist=true |
|---|
| 682 | if [ "X$( diff $1 $2 )" = X ] ; then |
|---|
| 683 | IGCM_debug_Print 2 "$1 and $2 are the same file, we skip the copy" |
|---|
| 684 | skip=true |
|---|
| 685 | else |
|---|
| 686 | IGCM_debug_Print 2 "$1 and $2 are not the same file, we force the copy" |
|---|
| 687 | skip=false |
|---|
| 688 | fi |
|---|
| 689 | fi |
|---|
| 690 | # |
|---|
| 691 | if ( [ X${exist} = Xtrue ] && [ X${skip} = Xfalse ] ) ; then |
|---|
| 692 | IGCM_sys_Chmod u+w $2 |
|---|
| 693 | fi |
|---|
| 694 | |
|---|
| 695 | if [ X${skip} = Xfalse ] ; then |
|---|
| 696 | i=0 |
|---|
| 697 | while [ $i -lt $NB_ESSAI ] ; do |
|---|
| 698 | # Identify file system |
|---|
| 699 | fileDeviceNumberInHex=$( stat -c %d $1 ) |
|---|
| 700 | status=$? |
|---|
| 701 | if [ ${status} -gt 0 ] ; then |
|---|
| 702 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
|---|
| 703 | fi |
|---|
| 704 | # Identify file system |
|---|
| 705 | directoryDeviceNumberInHex=$( stat -c %d $( dirname $2 ) ) |
|---|
| 706 | status=$? |
|---|
| 707 | if [ ${status} -gt 0 ] ; then |
|---|
| 708 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
|---|
| 709 | fi |
|---|
| 710 | |
|---|
| 711 | if ( [ ${fileDeviceNumberInHex} -ne ${directoryDeviceNumberInHex} ] || [ X$3 = XNOMOVE ] ) ; then |
|---|
| 712 | # They are not on the same device. USUAL WAY |
|---|
| 713 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 714 | status=$? |
|---|
| 715 | else |
|---|
| 716 | # They are on the same device. NOT SO USUAL WAY |
|---|
| 717 | \mv $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 718 | status=$? |
|---|
| 719 | fi |
|---|
| 720 | if [ ${status} -gt 0 ]; then |
|---|
| 721 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status} ${i}/${NB_ESSAI}" |
|---|
| 722 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : sleep ${DELAI} seconds and try again." |
|---|
| 723 | [ -f ${1} ] && ls -l ${1} |
|---|
| 724 | [ -f ${2} ] && ls -l ${2} |
|---|
| 725 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
|---|
| 726 | sleep $DELAI |
|---|
| 727 | else |
|---|
| 728 | break |
|---|
| 729 | fi |
|---|
| 730 | (( i = i + 1 )) |
|---|
| 731 | done |
|---|
| 732 | fi |
|---|
| 733 | |
|---|
| 734 | # #RSYNC WITH NETWORK SSH CALL |
|---|
| 735 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 736 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 737 | |
|---|
| 738 | # #RSYNC WITH NFS USE |
|---|
| 739 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 740 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 741 | |
|---|
| 742 | # status=$? |
|---|
| 743 | # IGCM_sys_Rsync_out $status |
|---|
| 744 | |
|---|
| 745 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 746 | # (( status=status+$? )) |
|---|
| 747 | |
|---|
| 748 | if [ ${status} -gt 0 ] ; then |
|---|
| 749 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status}" |
|---|
| 750 | [ -f ${1} ] && ls -l ${1} |
|---|
| 751 | [ -f ${2} ] && ls -l ${2} |
|---|
| 752 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
|---|
| 753 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 754 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
|---|
| 755 | else |
|---|
| 756 | |
|---|
| 757 | if [ X${JobType} = XRUN ] ; then |
|---|
| 758 | if [ X${3} = X ] ; then |
|---|
| 759 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
|---|
| 760 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
|---|
| 761 | fi |
|---|
| 762 | fi |
|---|
| 763 | |
|---|
| 764 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 765 | fi |
|---|
| 766 | fi |
|---|
| 767 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
|---|
| 768 | return 0 |
|---|
| 769 | } |
|---|
| 770 | |
|---|
| 771 | #D-#================================================== |
|---|
| 772 | #D-function IGCM_sys_Get |
|---|
| 773 | #D-* Purpose: Get a file from ${ARCHIVE} |
|---|
| 774 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
|---|
| 775 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
|---|
| 776 | function IGCM_sys_Get { |
|---|
| 777 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
|---|
| 778 | |
|---|
| 779 | typeset DEST dm_liste target file_work |
|---|
| 780 | typeset NB_ESSAI DELAI status i |
|---|
| 781 | |
|---|
| 782 | if ( $DEBUG_sys ) ; then |
|---|
| 783 | echo "IGCM_sys_Get :" $@ |
|---|
| 784 | fi |
|---|
| 785 | |
|---|
| 786 | # number of tentative |
|---|
| 787 | NB_ESSAI=3 |
|---|
| 788 | # time delay between tentative |
|---|
| 789 | DELAI=2 |
|---|
| 790 | |
|---|
| 791 | if [ $DRYRUN -le 2 ]; then |
|---|
| 792 | if [ X${1} = X'/l' ] ; then |
|---|
| 793 | eval set +A dm_liste \${${2}} |
|---|
| 794 | else |
|---|
| 795 | eval set +A dm_liste ${1} |
|---|
| 796 | fi |
|---|
| 797 | eval DEST=\${${#}} |
|---|
| 798 | # add here command to demigrate all offline files to reduce time of this command |
|---|
| 799 | # actually on Jean Zay files are not archive on bands |
|---|
| 800 | |
|---|
| 801 | status=$? |
|---|
| 802 | if [ ${status} -gt 0 ] ; then |
|---|
| 803 | echo "WARNING IGCM_sys_Get : error code ${status}" |
|---|
| 804 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 805 | echo "WARNING IGCM_sys_Get : will stop later if the cp fails." |
|---|
| 806 | fi |
|---|
| 807 | |
|---|
| 808 | #if [ ${status} -gt 0 ] ; then |
|---|
| 809 | # if [ ! "X$( grep "Lost dmusrcmd connection" ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )" = "X" ] ; then |
|---|
| 810 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 811 | # echo "WARNING IGCM_sys_Get : Lost dmusrcmd connection : " |
|---|
| 812 | # sleep 30 |
|---|
| 813 | # echo "We try another time" |
|---|
| 814 | ## dmget ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 815 | # ccc_hsm get ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 816 | # status=$? |
|---|
| 817 | # if [ ${status} -gt 0 ] ; then |
|---|
| 818 | # echo "ERROR IGCM_sys_Get : again demigration error :" |
|---|
| 819 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 820 | # IGCM_debug_Exit "IGCM_sys_Get" |
|---|
| 821 | # fi |
|---|
| 822 | # else |
|---|
| 823 | # echo "ERROR IGCM_sys_Get : demigration error :" |
|---|
| 824 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 825 | # IGCM_debug_Exit "IGCM_sys_Get" |
|---|
| 826 | # fi |
|---|
| 827 | #fi |
|---|
| 828 | |
|---|
| 829 | # #RSYNC WITH NETWORK SSH CALL |
|---|
| 830 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 831 | # ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 832 | |
|---|
| 833 | # #RSYNC WITH NFS USE |
|---|
| 834 | # echo ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 835 | # ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 836 | |
|---|
| 837 | # status=$? |
|---|
| 838 | # IGCM_sys_Rsync_out $status |
|---|
| 839 | |
|---|
| 840 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 841 | # (( status=status+$? )) |
|---|
| 842 | |
|---|
| 843 | #USUAL WAY |
|---|
| 844 | if [ X${1} = X'/l' ] ; then |
|---|
| 845 | for target in ${dm_liste[*]} ; do |
|---|
| 846 | local_file=$( basename ${target} ) |
|---|
| 847 | # test if the target file is present before the loop |
|---|
| 848 | IGCM_sys_TestFileArchive ${target} |
|---|
| 849 | status=$? |
|---|
| 850 | if [ ${status} -gt 0 ] ; then |
|---|
| 851 | echo "IGCM_sys_Get, ERROR : regular file ${target} DOES NOT EXIST ." |
|---|
| 852 | IGCM_debug_Exit "IGCM_sys_Get" |
|---|
| 853 | else |
|---|
| 854 | i=0 |
|---|
| 855 | while [ $i -lt $NB_ESSAI ] ; do |
|---|
| 856 | #if [ X${DoLink} = Xtrue ] ; then |
|---|
| 857 | # \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 858 | # status=$? |
|---|
| 859 | # else |
|---|
| 860 | # \cp ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 861 | # status=$? |
|---|
| 862 | #fi |
|---|
| 863 | \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 864 | status=$? |
|---|
| 865 | if [ ${status} -gt 0 ]; then |
|---|
| 866 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}" |
|---|
| 867 | IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again." |
|---|
| 868 | sleep $DELAI |
|---|
| 869 | else |
|---|
| 870 | break |
|---|
| 871 | fi |
|---|
| 872 | (( i = i + 1 )) |
|---|
| 873 | done |
|---|
| 874 | if [ ${status} -gt 0 ] ; then |
|---|
| 875 | echo "IGCM_sys_Get : error" |
|---|
| 876 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 877 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 878 | IGCM_debug_Exit "IGCM_sys_Get" |
|---|
| 879 | else |
|---|
| 880 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 881 | fi |
|---|
| 882 | fi |
|---|
| 883 | done |
|---|
| 884 | else |
|---|
| 885 | i=0 |
|---|
| 886 | while [ $i -lt $NB_ESSAI ] ; do |
|---|
| 887 | \cp ${dm_liste} ${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 888 | status=$? |
|---|
| 889 | if [ ${status} -gt 0 ]; then |
|---|
| 890 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}" |
|---|
| 891 | IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again." |
|---|
| 892 | sleep $DELAI |
|---|
| 893 | else |
|---|
| 894 | break |
|---|
| 895 | fi |
|---|
| 896 | (( i = i + 1 )) |
|---|
| 897 | done |
|---|
| 898 | if [ ${status} -gt 0 ] ; then |
|---|
| 899 | echo "IGCM_sys_Get : error" |
|---|
| 900 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 901 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 902 | IGCM_debug_Exit "IGCM_sys_Get" |
|---|
| 903 | else |
|---|
| 904 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 905 | fi |
|---|
| 906 | fi |
|---|
| 907 | fi |
|---|
| 908 | IGCM_debug_PopStack "IGCM_sys_Get" |
|---|
| 909 | } |
|---|
| 910 | |
|---|
| 911 | #D-#================================================== |
|---|
| 912 | #D-function IGCM_sys_GetDate_Monitoring |
|---|
| 913 | #D-* Purpose: get the last year for which the monitoring has been computed |
|---|
| 914 | #D-* Examples: |
|---|
| 915 | #D- |
|---|
| 916 | function IGCM_sys_GetDate_Monitoring { |
|---|
| 917 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
|---|
| 918 | if ( $DEBUG_sys ) ; then |
|---|
| 919 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
|---|
| 920 | fi |
|---|
| 921 | |
|---|
| 922 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
|---|
| 923 | |
|---|
| 924 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
|---|
| 925 | } |
|---|
| 926 | |
|---|
| 927 | #D-#================================================== |
|---|
| 928 | #D-function IGCM_sys_Dods_Rm |
|---|
| 929 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
|---|
| 930 | #D-* Examples: |
|---|
| 931 | #D- |
|---|
| 932 | function IGCM_sys_Dods_Rm { |
|---|
| 933 | if ( $DEBUG_sys ) ; then |
|---|
| 934 | echo "IGCM_sys_Dods_Rm :" $@ |
|---|
| 935 | fi |
|---|
| 936 | typeset status |
|---|
| 937 | if [ $DRYRUN = 0 ]; then |
|---|
| 938 | |
|---|
| 939 | # if [ ! -d /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} ] ; then |
|---|
| 940 | # echo "WARNING : IGCM_sys_Dods_Rm /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} DOES NOT EXIST ." |
|---|
| 941 | # echo "Nothing has been done." |
|---|
| 942 | # return |
|---|
| 943 | # fi |
|---|
| 944 | |
|---|
| 945 | if [ "$#" -eq 1 ]; then |
|---|
| 946 | # $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS}/${1} # > out_dods_rm 2>&1 |
|---|
| 947 | status=$? |
|---|
| 948 | else |
|---|
| 949 | # $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS} # > out_dods_rm 2>&1 |
|---|
| 950 | status=$? |
|---|
| 951 | fi |
|---|
| 952 | |
|---|
| 953 | # if [ ${status} -gt 0 ] ; then |
|---|
| 954 | # echo "IGCM_sys_Dods_Rm : error." |
|---|
| 955 | # cat out_dods_rm |
|---|
| 956 | # IGCM_debug_Exit "IGCM_sys_Dods_Rm" |
|---|
| 957 | # else |
|---|
| 958 | # rm out_dods_rm |
|---|
| 959 | # fi |
|---|
| 960 | |
|---|
| 961 | fi |
|---|
| 962 | return $status |
|---|
| 963 | } |
|---|
| 964 | |
|---|
| 965 | #D-#================================================== |
|---|
| 966 | #D-function IGCM_sys_Dods_Cp |
|---|
| 967 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
|---|
| 968 | #D-* Examples: |
|---|
| 969 | #D- |
|---|
| 970 | function IGCM_sys_Dods_Cp { |
|---|
| 971 | if ( $DEBUG_sys ) ; then |
|---|
| 972 | echo "IGCM_sys_Dods_Cp :" $@ |
|---|
| 973 | fi |
|---|
| 974 | typeset status |
|---|
| 975 | if [ $DRYRUN = 0 ]; then |
|---|
| 976 | |
|---|
| 977 | # if [ ! -d ${R_SAVE}/${1} ] ; then |
|---|
| 978 | # echo "WARNING : IGCM_sys_Dods_Cp ${R_SAVE}/${1} DOES NOT EXIST ." |
|---|
| 979 | # echo "Nothing has been done." |
|---|
| 980 | # return |
|---|
| 981 | # fi |
|---|
| 982 | |
|---|
| 983 | # $(ccc_home -u igcmg)/Tools/irene/thredds_cp ${1} public/${LOGIN}/${R_DODS} # > out_dods_cp 2>&1 |
|---|
| 984 | |
|---|
| 985 | status=$? |
|---|
| 986 | |
|---|
| 987 | # if [ ${status} -gt 0 ] ; then |
|---|
| 988 | # echo "IGCM_sys_Dods_Cp : error." |
|---|
| 989 | # cat out_dods_cp |
|---|
| 990 | # IGCM_debug_Exit "IGCM_sys_Dods_Cp" |
|---|
| 991 | # else |
|---|
| 992 | # rm out_dods_cp |
|---|
| 993 | # fi |
|---|
| 994 | |
|---|
| 995 | fi |
|---|
| 996 | return $status |
|---|
| 997 | } |
|---|
| 998 | |
|---|
| 999 | #D-#================================================== |
|---|
| 1000 | #D-function IGCM_sys_Put_Dods |
|---|
| 1001 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. |
|---|
| 1002 | #D-* Examples: |
|---|
| 1003 | #D- |
|---|
| 1004 | function IGCM_sys_Put_Dods { |
|---|
| 1005 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
|---|
| 1006 | if ( $DEBUG_sys ) ; then |
|---|
| 1007 | echo "IGCM_sys_Put_Dods :" $@ |
|---|
| 1008 | fi |
|---|
| 1009 | typeset status |
|---|
| 1010 | if [ $DRYRUN = 0 ]; then |
|---|
| 1011 | if ( [ ! -d ${R_SAVE}/${1} ] && [ ! -d ${R_FIGR}/${1} ] ) ; then |
|---|
| 1012 | echo "WARNING IGCM_sys_Put_Dods : None of the following directories exist. Exactly one should." |
|---|
| 1013 | echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} DOES NOT EXIST." |
|---|
| 1014 | echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} DOES NOT EXIST." |
|---|
| 1015 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
|---|
| 1016 | return |
|---|
| 1017 | fi |
|---|
| 1018 | |
|---|
| 1019 | if ( [ -d ${R_SAVE}/${1} ] && [ -d ${R_FIGR}/${1} ] ) ; then |
|---|
| 1020 | echo "WARNING IGCM_sys_Put_Dods : Both of the following directories exist. Exactly one should." |
|---|
| 1021 | echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} EXISTS." |
|---|
| 1022 | echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} EXISTS." |
|---|
| 1023 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
|---|
| 1024 | return |
|---|
| 1025 | fi |
|---|
| 1026 | # |
|---|
| 1027 | if [ -d ${R_SAVE}/${1} ] ; then |
|---|
| 1028 | cd ${R_SAVE} |
|---|
| 1029 | elif [ -d ${R_FIGR}/${1} ] ; then |
|---|
| 1030 | cd ${R_FIGR} |
|---|
| 1031 | fi |
|---|
| 1032 | |
|---|
| 1033 | IGCM_sys_Dods_Rm ${1} |
|---|
| 1034 | IGCM_sys_Dods_Cp ${1} |
|---|
| 1035 | status=0 |
|---|
| 1036 | |
|---|
| 1037 | if [ ${status} -gt 0 ] ; then |
|---|
| 1038 | echo "IGCM_sys_Put_Dods : error." |
|---|
| 1039 | IGCM_debug_Exit "IGCM_sys_Put_Dods" |
|---|
| 1040 | fi |
|---|
| 1041 | fi |
|---|
| 1042 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
|---|
| 1043 | } |
|---|
| 1044 | |
|---|
| 1045 | ############################################################## |
|---|
| 1046 | # REBUILD OPERATOR |
|---|
| 1047 | |
|---|
| 1048 | #D-#================================================== |
|---|
| 1049 | #D-function IGCM_sys_sync |
|---|
| 1050 | #D-* Purpose: flush buffer on disk |
|---|
| 1051 | #D-* Examples: |
|---|
| 1052 | #D- |
|---|
| 1053 | function IGCM_sys_sync { |
|---|
| 1054 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
|---|
| 1055 | if ( $DEBUG_sys ) ; then |
|---|
| 1056 | echo "IGCM_sys_sync :" $@ |
|---|
| 1057 | fi |
|---|
| 1058 | |
|---|
| 1059 | /bin/sync |
|---|
| 1060 | |
|---|
| 1061 | IGCM_debug_PopStack "IGCM_sys_sync" |
|---|
| 1062 | } |
|---|
| 1063 | |
|---|
| 1064 | ############################################################ |
|---|
| 1065 | # Activate Running Environnment Variables |
|---|
| 1066 | |
|---|
| 1067 | #D-#================================================== |
|---|
| 1068 | #D-function IGCM_sys_activ_variables |
|---|
| 1069 | #D-* Purpose: set environement variables prior to execution |
|---|
| 1070 | #D-* Examples: |
|---|
| 1071 | #D- |
|---|
| 1072 | function IGCM_sys_activ_variables { |
|---|
| 1073 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
|---|
| 1074 | if ( $DEBUG_sys ) ; then |
|---|
| 1075 | echo "IGCM_sys_activ_variables" |
|---|
| 1076 | fi |
|---|
| 1077 | |
|---|
| 1078 | # -------------------------------------------------------------------- |
|---|
| 1079 | #D- MODULE specifications |
|---|
| 1080 | # -------------------------------------------------------------------- |
|---|
| 1081 | # Source the file EnvFile containing all module load needed to run the model. |
|---|
| 1082 | # EnvFile can be specified in config.card. If this is the case and if the file exists, |
|---|
| 1083 | # it will be used. Otherwise a default file will be used. |
|---|
| 1084 | if [ ! X${config_UserChoices_EnvFile} = X ] && [ -f ${config_UserChoices_EnvFile} ] ; then |
|---|
| 1085 | # EnvFile is set in config.card and the file exists |
|---|
| 1086 | IGCM_debug_Print 1 "EnvFile set in config.card will be used" |
|---|
| 1087 | EnvFile=${config_UserChoices_EnvFile} |
|---|
| 1088 | else |
|---|
| 1089 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Default modules will be used" |
|---|
| 1090 | module purge > /dev/null 2>&1 |
|---|
| 1091 | EnvFile=/gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_jeanzay |
|---|
| 1092 | fi |
|---|
| 1093 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Following EnvFile will be used :" |
|---|
| 1094 | IGCM_debug_Print 1 ${EnvFile} |
|---|
| 1095 | . ${EnvFile} |
|---|
| 1096 | |
|---|
| 1097 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Now loaded modules for Jean-Zay. " |
|---|
| 1098 | module list |
|---|
| 1099 | |
|---|
| 1100 | # -------------------------------------------------------------------- |
|---|
| 1101 | #D- MPI specifications |
|---|
| 1102 | # -------------------------------------------------------------------- |
|---|
| 1103 | |
|---|
| 1104 | # -------------------------------------------------------------------- |
|---|
| 1105 | #D- Other specifications |
|---|
| 1106 | # -------------------------------------------------------------------- |
|---|
| 1107 | |
|---|
| 1108 | ulimit -s unlimited |
|---|
| 1109 | if [ ${executionType} -eq 2 ] ; then |
|---|
| 1110 | export SLURM_HOSTFILE=./hostlist |
|---|
| 1111 | fi |
|---|
| 1112 | |
|---|
| 1113 | |
|---|
| 1114 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
|---|
| 1115 | } |
|---|
| 1116 | |
|---|
| 1117 | ############################################################ |
|---|
| 1118 | # Desactivate Running Environnment Variables |
|---|
| 1119 | |
|---|
| 1120 | #D-#================================================== |
|---|
| 1121 | #D-function IGCM_sys_desactiv_variables |
|---|
| 1122 | #D-* Purpose: unset environement variables after execution |
|---|
| 1123 | #D-* Examples: |
|---|
| 1124 | #D- |
|---|
| 1125 | function IGCM_sys_desactiv_variables { |
|---|
| 1126 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
|---|
| 1127 | if ( $DEBUG_sys ) ; then |
|---|
| 1128 | echo "IGCM_sys_desactiv_variables" |
|---|
| 1129 | fi |
|---|
| 1130 | # -------------------------------------------------------------------- |
|---|
| 1131 | #D- MPI specifications |
|---|
| 1132 | # -------------------------------------------------------------------- |
|---|
| 1133 | if [ ${executionType} -eq 2 ] ; then |
|---|
| 1134 | unset SLURM_HOSTFILE |
|---|
| 1135 | fi |
|---|
| 1136 | # -------------------------------------------------------------------- |
|---|
| 1137 | #D- Other specifications |
|---|
| 1138 | # -------------------------------------------------------------------- |
|---|
| 1139 | |
|---|
| 1140 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
|---|
| 1141 | } |
|---|
| 1142 | |
|---|
| 1143 | ############################################################ |
|---|
| 1144 | # Update job headers to be used by the scheduler |
|---|
| 1145 | |
|---|
| 1146 | #D-#================================================== |
|---|
| 1147 | #D-function IGCM_sys_updateHeaders |
|---|
| 1148 | #D-* Purpose: Update job headers to be used by the scheduler |
|---|
| 1149 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
|---|
| 1150 | #D- |
|---|
| 1151 | function IGCM_sys_updateHeaders { |
|---|
| 1152 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
|---|
| 1153 | if ( $DEBUG_sys ) ; then |
|---|
| 1154 | echo "IGCM_sys_updateHeaders" |
|---|
| 1155 | fi |
|---|
| 1156 | typeset file |
|---|
| 1157 | file=$1 |
|---|
| 1158 | |
|---|
| 1159 | if [ ${executionType} -eq 1 ] ; then |
|---|
| 1160 | # MPMD + MPI |
|---|
| 1161 | sed -e "/::openMPthreads::/d" \ |
|---|
| 1162 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
|---|
| 1163 | ${file} > ${file}.tmp |
|---|
| 1164 | |
|---|
| 1165 | elif [ ${executionType} -eq 2 ] ; then |
|---|
| 1166 | # MPMD + MPI + OMP |
|---|
| 1167 | (( nodeNumber = coreNumber / NB_CORE_PER_NODE )) |
|---|
| 1168 | [ $(( ${coreNumber} % ${NB_CORE_PER_NODE} )) -ne 0 ] && (( nodeNumber = nodeNumber + 1 )) |
|---|
| 1169 | sed -e "/::openMPthreads::/d" \ |
|---|
| 1170 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
|---|
| 1171 | -e "/ntasks/i\#SBATCH --nodes=${nodeNumber}"\ |
|---|
| 1172 | -e "/ntasks/i\#SBATCH --exclusive" \ |
|---|
| 1173 | ${file} > ${file}.tmp |
|---|
| 1174 | elif [ ${executionType} -eq 3 ] ; then |
|---|
| 1175 | # SPMD + MPI/OMP |
|---|
| 1176 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
|---|
| 1177 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
|---|
| 1178 | ${file} > ${file}.tmp |
|---|
| 1179 | |
|---|
| 1180 | elif [ ${executionType} -eq 4 ] ; then |
|---|
| 1181 | # SPMD + MPI only |
|---|
| 1182 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
|---|
| 1183 | -e "/::openMPthreads::/d" \ |
|---|
| 1184 | ${file} > ${file}.tmp |
|---|
| 1185 | |
|---|
| 1186 | elif [ ${executionType} -eq 5 ] ; then |
|---|
| 1187 | # SPMD + OMP only |
|---|
| 1188 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
|---|
| 1189 | -e "/::JobNumProcTot::/d" \ |
|---|
| 1190 | ${file} > ${file}.tmp |
|---|
| 1191 | |
|---|
| 1192 | elif [ ${executionType} -eq 6 ] ; then |
|---|
| 1193 | # SEQUENTIAL THEN |
|---|
| 1194 | sed -e "s/::JobNumProcTot::/1/" \ |
|---|
| 1195 | -e "/::openMPthreads::/d" \ |
|---|
| 1196 | ${file} > ${file}.tmp |
|---|
| 1197 | |
|---|
| 1198 | fi |
|---|
| 1199 | |
|---|
| 1200 | IGCM_sys_Mv ${file}.tmp ${file} |
|---|
| 1201 | |
|---|
| 1202 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
|---|
| 1203 | } |
|---|
| 1204 | |
|---|
| 1205 | ############################################################ |
|---|
| 1206 | # Build MPI/OMP scripts run file (dummy function) |
|---|
| 1207 | |
|---|
| 1208 | #D-#================================================== |
|---|
| 1209 | #D-function IGCM_sys_build_run_file |
|---|
| 1210 | #D-* Purpose: build run file (deprecated) |
|---|
| 1211 | #D-* Examples: |
|---|
| 1212 | #D- |
|---|
| 1213 | function IGCM_sys_build_run_file { |
|---|
| 1214 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
|---|
| 1215 | } |
|---|
| 1216 | |
|---|
| 1217 | ############################################################ |
|---|
| 1218 | # Build MPI/OMP scripts |
|---|
| 1219 | |
|---|
| 1220 | #D-#================================================== |
|---|
| 1221 | #D-function IGCM_sys_build_execution_scripts |
|---|
| 1222 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
|---|
| 1223 | #D-* Examples: |
|---|
| 1224 | #D- |
|---|
| 1225 | function IGCM_sys_build_execution_scripts |
|---|
| 1226 | { |
|---|
| 1227 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
|---|
| 1228 | if ( $DEBUG_sys ) ; then |
|---|
| 1229 | echo "IGCM_sys_build_execution_scripts " $@ |
|---|
| 1230 | fi |
|---|
| 1231 | IGCM_debug_Print 1 "executionType= ${executionType}" |
|---|
| 1232 | EXECUTION=${HOST_MPIRUN_COMMAND} |
|---|
| 1233 | |
|---|
| 1234 | if ( ${OK_PARA_MPMD} ) ; then |
|---|
| 1235 | |
|---|
| 1236 | # MPMD mode |
|---|
| 1237 | # 1 MPI only : executionType=1 |
|---|
| 1238 | # 2 MPI/OpenMP : executionType=2 |
|---|
| 1239 | |
|---|
| 1240 | if [ -f run_file ] ; then |
|---|
| 1241 | IGCM_sys_Rm -f run_file |
|---|
| 1242 | fi |
|---|
| 1243 | touch run_file |
|---|
| 1244 | |
|---|
| 1245 | # case 1 : Only MPI (MPMD) |
|---|
| 1246 | if ( ! ${OK_PARA_OMP} ) ; then |
|---|
| 1247 | # Build run_file |
|---|
| 1248 | current_core=0 |
|---|
| 1249 | # First loop on the components for the coupler ie oasis (only if oasis3) |
|---|
| 1250 | # the coupler ie oasis3 must be the first one |
|---|
| 1251 | for comp in ${config_ListOfComponents[*]} ; do |
|---|
| 1252 | |
|---|
| 1253 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
|---|
| 1254 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
|---|
| 1255 | |
|---|
| 1256 | # Only if the component has an executable |
|---|
| 1257 | if ( [ "X${ExeNameOut}" != X\"\" ] ) ; then |
|---|
| 1258 | |
|---|
| 1259 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
|---|
| 1260 | (( end_core = ${current_core} + ${comp_proc_mpi_loc} - 1 )) |
|---|
| 1261 | echo "${current_core}-${end_core} ./${ExeNameOut}" >> run_file |
|---|
| 1262 | (( current_core = ${end_core} + 1 )) |
|---|
| 1263 | fi |
|---|
| 1264 | done |
|---|
| 1265 | |
|---|
| 1266 | EXECUTION="${HOST_MPIRUN_COMMAND} --multi-prog ./run_file" |
|---|
| 1267 | |
|---|
| 1268 | IGCM_sys_Chmod u+x run_file |
|---|
| 1269 | if ( $DEBUG_sys ) ; then |
|---|
| 1270 | echo "run_file contains : " |
|---|
| 1271 | cat run_file |
|---|
| 1272 | fi |
|---|
| 1273 | |
|---|
| 1274 | else |
|---|
| 1275 | |
|---|
| 1276 | # 2 MPI/OpenMP : executionType=2 |
|---|
| 1277 | |
|---|
| 1278 | # MPI-OpenMP (MPMD) |
|---|
| 1279 | # export SLURM_HOSTFILE=./hostlist |
|---|
| 1280 | # srun --cpu-bind=none --distribution=arbitrary --multi-prog ./run_file |
|---|
| 1281 | # example of hostlist file : |
|---|
| 1282 | # r3i3n33 |
|---|
| 1283 | # r3i3n33 |
|---|
| 1284 | # ... |
|---|
| 1285 | # example of run_file : |
|---|
| 1286 | # 0 taskset -c 0-4 ./script_lmdz.x.ksh |
|---|
| 1287 | # 1 taskset -c 5-9 ./script_lmdz.x.ksh |
|---|
| 1288 | #... |
|---|
| 1289 | # 32 taskset -c 0 ./script_opa.xx.ksh |
|---|
| 1290 | # 33 taskset -c 1 ./script_opa.xx.ksh |
|---|
| 1291 | #... |
|---|
| 1292 | # 62 taskset -c 30 ./script_xios.x.ksh |
|---|
| 1293 | |
|---|
| 1294 | # Hosts treatment |
|---|
| 1295 | IFS=$'\n'; set -f |
|---|
| 1296 | listnodes=($(< <( scontrol show hostnames $SLURM_JOB_NODELIST ))) |
|---|
| 1297 | unset IFS; set +f |
|---|
| 1298 | rm -f hostlist |
|---|
| 1299 | |
|---|
| 1300 | # Loop on the components to build run_file and script_exec files |
|---|
| 1301 | rank=0 |
|---|
| 1302 | current_core=0 |
|---|
| 1303 | |
|---|
| 1304 | for comp in ${config_ListOfComponents[*]} ; do |
|---|
| 1305 | |
|---|
| 1306 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
|---|
| 1307 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
|---|
| 1308 | |
|---|
| 1309 | # Not possible if oasis has an executable (i.e old version of oasis3) |
|---|
| 1310 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
|---|
| 1311 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
|---|
| 1312 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
|---|
| 1313 | IGCM_debug_Verif_Exit |
|---|
| 1314 | fi |
|---|
| 1315 | |
|---|
| 1316 | # Only if we really have an executable for the component : |
|---|
| 1317 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
|---|
| 1318 | |
|---|
| 1319 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
|---|
| 1320 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
|---|
| 1321 | eval comp_proc_nod_loc=\${${comp}_PROC_NOD} |
|---|
| 1322 | |
|---|
| 1323 | |
|---|
| 1324 | # Build script files |
|---|
| 1325 | |
|---|
| 1326 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
|---|
| 1327 | echo "" >> script_${ExeNameOut}.ksh |
|---|
| 1328 | if [ ${comp_proc_omp_loc} -gt 1 ] ; then |
|---|
| 1329 | # Check if the number of threads is correct |
|---|
| 1330 | case ${comp_proc_omp_loc} in |
|---|
| 1331 | 2|4|5|10|20) |
|---|
| 1332 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
|---|
| 1333 | ;; |
|---|
| 1334 | *) |
|---|
| 1335 | IGCM_debug_Exit "ERROR with OMP parameters !" |
|---|
| 1336 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
|---|
| 1337 | IGCM_debug_Print 2 "Only 2,4,5,10,20 as number of OMP threads are possible " |
|---|
| 1338 | IGCM_debug_Verif_Exit |
|---|
| 1339 | ;; |
|---|
| 1340 | esac |
|---|
| 1341 | echo "export OMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
|---|
| 1342 | echo "export OMP_PLACES=cores" >> script_${ExeNameOut}.ksh |
|---|
| 1343 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
|---|
| 1344 | |
|---|
| 1345 | fi |
|---|
| 1346 | |
|---|
| 1347 | # to have out/err per process on different files |
|---|
| 1348 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh |
|---|
| 1349 | |
|---|
| 1350 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
|---|
| 1351 | |
|---|
| 1352 | # Complete run_file |
|---|
| 1353 | if [ ${comp_proc_nod_loc} -gt 1 ] ; then |
|---|
| 1354 | (( offset_comp_proc_loc = NB_CORE_PER_NODE / (comp_proc_mpi_loc / comp_proc_nod_loc) )) |
|---|
| 1355 | else |
|---|
| 1356 | (( offset_comp_proc_loc = comp_proc_omp_loc )) |
|---|
| 1357 | fi |
|---|
| 1358 | |
|---|
| 1359 | for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do |
|---|
| 1360 | (( index_host = current_core / NB_CORE_PER_NODE )) |
|---|
| 1361 | host_value=${listnodes[${index_host}]} |
|---|
| 1362 | (( slot = current_core % NB_CORE_PER_NODE )) |
|---|
| 1363 | echo "$host_value" >> hostlist |
|---|
| 1364 | echo "$rank taskset -c $slot-$((slot+comp_proc_omp_loc-1)) ./script_${ExeNameOut}.ksh" >> run_file |
|---|
| 1365 | (( rank = rank + 1 )) |
|---|
| 1366 | (( current_core = current_core + offset_comp_proc_loc )) |
|---|
| 1367 | done |
|---|
| 1368 | fi |
|---|
| 1369 | done |
|---|
| 1370 | |
|---|
| 1371 | ## variable added to stop after 60s instead of 600s by default. |
|---|
| 1372 | ## This is used when no error comes from executables and when something stopped an executable without notice. |
|---|
| 1373 | export SLURM_WAIT=60 |
|---|
| 1374 | |
|---|
| 1375 | EXECUTION="${HOST_MPIRUN_COMMAND} --cpu-bind=none --distribution=arbitrary --multi-prog ./run_file" |
|---|
| 1376 | |
|---|
| 1377 | IGCM_sys_Chmod u+x run_file |
|---|
| 1378 | if ( $DEBUG_sys ) ; then |
|---|
| 1379 | echo "run_file contains : " |
|---|
| 1380 | cat run_file |
|---|
| 1381 | fi |
|---|
| 1382 | |
|---|
| 1383 | fi # if ${OK_PARA_MPMD} |
|---|
| 1384 | |
|---|
| 1385 | else |
|---|
| 1386 | # Only one executable (SPMD mode): executionType=3, 4, 5 and 6 |
|---|
| 1387 | |
|---|
| 1388 | for comp in ${config_ListOfComponents[*]} ; do |
|---|
| 1389 | |
|---|
| 1390 | # Only if we really have an executable for the component : |
|---|
| 1391 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
|---|
| 1392 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
|---|
| 1393 | |
|---|
| 1394 | # Build script files |
|---|
| 1395 | |
|---|
| 1396 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
|---|
| 1397 | echo "" >> script_${ExeNameOut}.ksh |
|---|
| 1398 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
|---|
| 1399 | |
|---|
| 1400 | if ( ${OK_PARA_OMP} ) ; then |
|---|
| 1401 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
|---|
| 1402 | # Check if the number of threads is correct |
|---|
| 1403 | case ${comp_proc_omp_loc} in |
|---|
| 1404 | 2|4|5|10|20) |
|---|
| 1405 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
|---|
| 1406 | ;; |
|---|
| 1407 | *) |
|---|
| 1408 | IGCM_debug_Exit "ERROR with OMP parameters !" |
|---|
| 1409 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
|---|
| 1410 | IGCM_debug_Print 2 "Only 2,4,5,10,20 as number of OMP threads are possible " |
|---|
| 1411 | IGCM_debug_Verif_Exit |
|---|
| 1412 | ;; |
|---|
| 1413 | esac |
|---|
| 1414 | echo "" >> script_${ExeNameOut}.ksh |
|---|
| 1415 | echo "export OMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
|---|
| 1416 | echo "export OMP_PLACES=cores" >> script_${ExeNameOut}.ksh |
|---|
| 1417 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
|---|
| 1418 | fi |
|---|
| 1419 | |
|---|
| 1420 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
|---|
| 1421 | |
|---|
| 1422 | # To have out/err per process on different files |
|---|
| 1423 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh |
|---|
| 1424 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
|---|
| 1425 | |
|---|
| 1426 | IGCM_debug_Print 1 "sys Irene : script_${ExeNameOut}.ksh contains" |
|---|
| 1427 | cat script_${ExeNameOut}.ksh |
|---|
| 1428 | |
|---|
| 1429 | fi |
|---|
| 1430 | |
|---|
| 1431 | done |
|---|
| 1432 | |
|---|
| 1433 | fi # ${OK_PARA_MPMD} |
|---|
| 1434 | |
|---|
| 1435 | IGCM_debug_Print 1 "sys Irene : execution command is " |
|---|
| 1436 | IGCM_debug_Print 1 "$EXECUTION" |
|---|
| 1437 | |
|---|
| 1438 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
|---|
| 1439 | } |
|---|
| 1440 | |
|---|
| 1441 | #D-#================================================== |
|---|
| 1442 | #D-function IGCM_sys_check_path |
|---|
| 1443 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
|---|
| 1444 | #D-* do not point to an important use directory. Stop immediately in that case. |
|---|
| 1445 | #D-* Examples: |
|---|
| 1446 | #D- |
|---|
| 1447 | function IGCM_sys_check_path { |
|---|
| 1448 | IGCM_debug_PushStack "IGCM_sys_check_path" |
|---|
| 1449 | if ( $DEBUG_sys ) ; then |
|---|
| 1450 | echo "IGCM_sys_check_path" |
|---|
| 1451 | fi |
|---|
| 1452 | |
|---|
| 1453 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${WORK} ] || [ X${RUN_DIR_PATH} = X${SCRATCH} ] || [ X${RUN_DIR_PATH} = X${STORE} ] ) ; then |
|---|
| 1454 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
|---|
| 1455 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
|---|
| 1456 | IGCM_debug_Exit "This will stop the job" |
|---|
| 1457 | elif ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X/gpfswork/rech/${DataProject}/${LOGIN} ] || [ X${RUN_DIR_PATH} = X/gpfsscratch/rech/${DataProject}/${LOGIN} ] || [ X${RUN_DIR_PATH} = X/gpfsstore/rech/${DataProject}/${LOGIN} ] ) ; then |
|---|
| 1458 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
|---|
| 1459 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
|---|
| 1460 | IGCM_debug_Exit "This will stop the job" |
|---|
| 1461 | fi |
|---|
| 1462 | IGCM_debug_PopStack "IGCM_sys_check_path" |
|---|
| 1463 | } |
|---|
| 1464 | |
|---|
| 1465 | #D-#================================================== |
|---|
| 1466 | #D-function IGCM_sys_check_quota |
|---|
| 1467 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
|---|
| 1468 | #D-* Examples: |
|---|
| 1469 | #D- |
|---|
| 1470 | function IGCM_sys_check_quota { |
|---|
| 1471 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
|---|
| 1472 | 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)" |
|---|
| 1473 | # if ( $DEBUG_sys ) ; then |
|---|
| 1474 | # echo "IGCM_sys_check_quota" |
|---|
| 1475 | # fi |
|---|
| 1476 | # # Limit of quota (in %) |
|---|
| 1477 | # limit_quota=90 |
|---|
| 1478 | # |
|---|
| 1479 | # # Check of the volume |
|---|
| 1480 | # volume_quota=$(ccc_quota | grep ' scratch' | gawk '{print $2}') |
|---|
| 1481 | # volume_avail=$(ccc_quota | grep ' scratch' | gawk '{print $3}') |
|---|
| 1482 | # |
|---|
| 1483 | # if ( [ ! X${volume_quota} = X ] && [ ! ${volume_quota} = "-" ] ) ; then |
|---|
| 1484 | # |
|---|
| 1485 | # unit_avail=${volume_avail: -1} |
|---|
| 1486 | # unit_quota=${volume_quota: -1} |
|---|
| 1487 | # |
|---|
| 1488 | # if [ "${unit_quota}" = "*" ] ; then |
|---|
| 1489 | # IGCM_debug_Print 1 "Please, check your quota of volume on scratch" |
|---|
| 1490 | # IGCM_debug_Print 1 "More than 100% of your quota is used" |
|---|
| 1491 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
|---|
| 1492 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
|---|
| 1493 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
|---|
| 1494 | # IGCM_debug_Verif_Exit |
|---|
| 1495 | # fi |
|---|
| 1496 | # |
|---|
| 1497 | # temp_avail=${volume_avail%%${volume_avail: -1}*} |
|---|
| 1498 | # temp_quota=${volume_quota%%${volume_quota: -1}*} |
|---|
| 1499 | # |
|---|
| 1500 | # if [ ! ${unit_avail} = ${unit_quota} ] ; then |
|---|
| 1501 | # |
|---|
| 1502 | # # Convertion |
|---|
| 1503 | # if [ ${volume_avail: -1} = "T" ] ; then |
|---|
| 1504 | # (( temp_avail = temp_avail * 1000000000000 )) |
|---|
| 1505 | # elif [ ${volume_avail: -1} = "G" ] ; then |
|---|
| 1506 | # (( temp_avail = temp_avail * 1000000000 )) |
|---|
| 1507 | # elif [ ${volume_avail: -1} = "M" ] ; then |
|---|
| 1508 | # (( temp_avail = temp_avail * 1000000 )) |
|---|
| 1509 | # elif [ ${volume_avail: -1} = "k" ] ; then |
|---|
| 1510 | # (( temp_avail = temp_avail * 1000 )) |
|---|
| 1511 | # else |
|---|
| 1512 | # (( temp_avail = volume_avail )) |
|---|
| 1513 | # fi |
|---|
| 1514 | # if [ ${volume_quota: -1} = "T" ] ; then |
|---|
| 1515 | # (( temp_quota = temp_quota * 1000000000000 )) |
|---|
| 1516 | # elif [ ${volume_quota: -1} = "G" ] ; then |
|---|
| 1517 | # (( temp_quota = temp_quota * 1000000000 )) |
|---|
| 1518 | # elif [ ${volume_quota: -1} = "M" ] ; then |
|---|
| 1519 | # (( temp_quota = temp_quota * 1000000 )) |
|---|
| 1520 | # elif [ ${volume_quota: -1} = "k" ] ; then |
|---|
| 1521 | # (( temp_quota = temp_quota * 1000 )) |
|---|
| 1522 | # else |
|---|
| 1523 | # (( temp_quota = volume_quota )) |
|---|
| 1524 | # fi |
|---|
| 1525 | # fi |
|---|
| 1526 | # |
|---|
| 1527 | # quota_volume=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc) |
|---|
| 1528 | ## echo "volume ratio is " $quota_volume |
|---|
| 1529 | # |
|---|
| 1530 | # if [ ${quota_volume} -ge ${limit_quota} ] ; then |
|---|
| 1531 | # IGCM_debug_Print 1 "Please, check your quota of volume on scratch" |
|---|
| 1532 | # IGCM_debug_Print 1 "${quota_volume}% of your quota is used" |
|---|
| 1533 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
|---|
| 1534 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
|---|
| 1535 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
|---|
| 1536 | # IGCM_debug_Verif_Exit |
|---|
| 1537 | # fi |
|---|
| 1538 | # |
|---|
| 1539 | # fi |
|---|
| 1540 | # |
|---|
| 1541 | ## Check of the number of inodes |
|---|
| 1542 | # |
|---|
| 1543 | # inode_quota=$(ccc_quota | grep ' scratch' | gawk '{print $6}') |
|---|
| 1544 | # inode_avail=$(ccc_quota | grep ' scratch' | gawk '{print $7}') |
|---|
| 1545 | # |
|---|
| 1546 | # if ( [ ! X${inode_quota} = X ] && [ ! ${inode_quota} = "-" ] ) ; then |
|---|
| 1547 | # |
|---|
| 1548 | # unit_avail=${inode_avail: -1} |
|---|
| 1549 | # unit_quota=${inode_quota: -1} |
|---|
| 1550 | # |
|---|
| 1551 | # if [ "${unit_quota}" = "*" ] ; then |
|---|
| 1552 | # IGCM_debug_Print 1 "Please, check your quota of inode on scratch" |
|---|
| 1553 | # IGCM_debug_Print 1 "More than 100% of your quota is used" |
|---|
| 1554 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
|---|
| 1555 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
|---|
| 1556 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
|---|
| 1557 | # IGCM_debug_Verif_Exit |
|---|
| 1558 | # fi |
|---|
| 1559 | # |
|---|
| 1560 | # temp_avail=${inode_avail%%${inode_avail: -1}*} |
|---|
| 1561 | # temp_quota=${inode_quota%%${inode_quota: -1}*} |
|---|
| 1562 | # |
|---|
| 1563 | # if [ ! ${unit_avail} = ${unit_quota} ] ; then |
|---|
| 1564 | # |
|---|
| 1565 | # # Convertion |
|---|
| 1566 | # if [ ${inode_avail: -1} = "T" ] ; then |
|---|
| 1567 | # (( temp_avail = temp_avail * 1000000000000 )) |
|---|
| 1568 | # elif [ ${inode_avail: -1} = "G" ] ; then |
|---|
| 1569 | # (( temp_avail = temp_avail * 1000000000 )) |
|---|
| 1570 | # elif [ ${inode_avail: -1} = "M" ] ; then |
|---|
| 1571 | # (( temp_avail = temp_avail * 1000000 )) |
|---|
| 1572 | # elif [ ${inode_avail: -1} = "k" ] ; then |
|---|
| 1573 | # (( temp_avail = temp_avail * 1000 )) |
|---|
| 1574 | # else |
|---|
| 1575 | # (( temp_avail = inode_avail )) |
|---|
| 1576 | # fi |
|---|
| 1577 | # |
|---|
| 1578 | # if [ ${inode_quota: -1} = "T" ] ; then |
|---|
| 1579 | # (( temp_quota = temp_quota * 1000000000000 )) |
|---|
| 1580 | # elif [ ${inode_quota: -1} = "G" ] ; then |
|---|
| 1581 | # (( temp_quota = temp_quota * 1000000000 )) |
|---|
| 1582 | # elif [ ${inode_quota: -1} = "M" ] ; then |
|---|
| 1583 | # (( temp_quota = temp_quota * 1000000 )) |
|---|
| 1584 | # elif [ ${inode_quota: -1} = "k" ] ; then |
|---|
| 1585 | # (( temp_quota = temp_quota * 1000 )) |
|---|
| 1586 | # else |
|---|
| 1587 | # (( temp_quota = inode_quota )) |
|---|
| 1588 | # fi |
|---|
| 1589 | # fi |
|---|
| 1590 | # quota_inode=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc) |
|---|
| 1591 | ## echo "inode ratio is " $quota_inode |
|---|
| 1592 | # |
|---|
| 1593 | # if [ ${quota_inode} -ge ${limit_quota} ] ; then |
|---|
| 1594 | # IGCM_debug_Print 1 "Please, check your quota of inode on scratch" |
|---|
| 1595 | # IGCM_debug_Print 1 "${quota_inode}% of your quota is used" |
|---|
| 1596 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
|---|
| 1597 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
|---|
| 1598 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
|---|
| 1599 | # IGCM_debug_Verif_Exit |
|---|
| 1600 | # fi |
|---|
| 1601 | # fi |
|---|
| 1602 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
|---|
| 1603 | } |
|---|
| 1604 | |
|---|
| 1605 | #D-#================================================== |
|---|
| 1606 | #D-function IGCM_sys_projectAccounting |
|---|
| 1607 | #D-* Purpose: store project accounting information in a file |
|---|
| 1608 | #D-* Examples: |
|---|
| 1609 | #D- |
|---|
| 1610 | function IGCM_sys_projectAccounting { |
|---|
| 1611 | IGCM_debug_PushStack "IGCM_sys_projectAccounting" |
|---|
| 1612 | if ( $DEBUG_sys ) ; then |
|---|
| 1613 | echo "IGCM_sys_check_quota" |
|---|
| 1614 | fi |
|---|
| 1615 | #need to implemented on Jean Zay |
|---|
| 1616 | touch $1 |
|---|
| 1617 | # ssh irene191 /usr/bin/ccc_myproject > $1 |
|---|
| 1618 | |
|---|
| 1619 | IGCM_debug_PopStack "IGCM_sys_projectAccounting" |
|---|
| 1620 | } |
|---|
| 1621 | |
|---|
| 1622 | #D-#================================================== |
|---|
| 1623 | #D-function IGCM_sys_getJobSchedulerID |
|---|
| 1624 | #D-* Purpose: Get the job ID during execution |
|---|
| 1625 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
|---|
| 1626 | #D- |
|---|
| 1627 | function IGCM_sys_getJobSchedulerID { |
|---|
| 1628 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
|---|
| 1629 | if ( $DEBUG_sys ) ; then |
|---|
| 1630 | echo "IGCM_sys_getJobSchedulerID" |
|---|
| 1631 | fi |
|---|
| 1632 | |
|---|
| 1633 | eval ${1}=${SLURM_JOBID} |
|---|
| 1634 | |
|---|
| 1635 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
|---|
| 1636 | } |
|---|
| 1637 | |
|---|
| 1638 | #D-#================================================== |
|---|
| 1639 | #D-function IGCM_sys_GetJobID |
|---|
| 1640 | #D-* Purpose: Get the job ID from the JobName |
|---|
| 1641 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
|---|
| 1642 | #D- |
|---|
| 1643 | function IGCM_sys_GetJobID { |
|---|
| 1644 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
|---|
| 1645 | if ( $DEBUG_sys ) ; then |
|---|
| 1646 | echo "IGCM_sys_GetJobID" |
|---|
| 1647 | fi |
|---|
| 1648 | |
|---|
| 1649 | ID=$( squeue -u $user | grep Job_${config_UserChoices_JobName} | gawk ' { print $1}' ) |
|---|
| 1650 | |
|---|
| 1651 | |
|---|
| 1652 | eval ${3}=${ID} |
|---|
| 1653 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
|---|
| 1654 | } |
|---|
| 1655 | |
|---|
| 1656 | #D-#================================================== |
|---|
| 1657 | #D-function IGCM_sys_CountJobInQueue |
|---|
| 1658 | #D-* Purpose: Count number of users job |
|---|
| 1659 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
|---|
| 1660 | #D- |
|---|
| 1661 | function IGCM_sys_CountJobInQueue { |
|---|
| 1662 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
|---|
| 1663 | if ( $DEBUG_sys ) ; then |
|---|
| 1664 | echo "IGCM_sys_CountJobInQueue" |
|---|
| 1665 | fi |
|---|
| 1666 | |
|---|
| 1667 | # With -f option, the full job name is given in the last column |
|---|
| 1668 | NbRun=$(squeue -u $user | \ |
|---|
| 1669 | grep -v JOBID | gawk 'BEGIN { x=0 } ( $NF ~ JobName ) { x=x+1 } END { print x }' ) |
|---|
| 1670 | |
|---|
| 1671 | eval ${2}=${NbRun} |
|---|
| 1672 | |
|---|
| 1673 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
|---|
| 1674 | } |
|---|
| 1675 | |
|---|
| 1676 | #D-#================================================== |
|---|
| 1677 | #D-function IGCM_sys_ListJobInQueue |
|---|
| 1678 | #D-* Purpose: Produce a list of users computing jobs (excluding post-processing) |
|---|
| 1679 | #D-* Examples: IGCM_sys_ListJobInQueue ${User} JobNameList |
|---|
| 1680 | #D- |
|---|
| 1681 | function IGCM_sys_ListJobInQueue { |
|---|
| 1682 | IGCM_debug_PushStack "IGCM_sys_ListJobInQueue" |
|---|
| 1683 | if ( $DEBUG_sys ) ; then |
|---|
| 1684 | echo "IGCM_sys_ListJobInQueue" |
|---|
| 1685 | fi |
|---|
| 1686 | |
|---|
| 1687 | # to be implemented on Jean Zay |
|---|
| 1688 | set -A JobList $( squeue -u $user | gawk '{print $3}' | grep -v NAME) |
|---|
| 1689 | # # With -f option, the full job name is given in the last column |
|---|
| 1690 | # set -A JobList $( ccc_mstat -f | gawk -v User=$1 \ |
|---|
| 1691 | # '( $2 == User && \ |
|---|
| 1692 | # $NF != /TS/ && \ |
|---|
| 1693 | # $NF !~ /PACK/ && \ |
|---|
| 1694 | # $NF !~ /REBUILD/ && \ |
|---|
| 1695 | # $NF !~ /pack/ ) \ |
|---|
| 1696 | # { print $NF }' | sed -e "s/\(.*\)\.[0-9]*/\1/" ) |
|---|
| 1697 | # |
|---|
| 1698 | eval set -A ${2} ${JobList[*]} |
|---|
| 1699 | |
|---|
| 1700 | IGCM_debug_PopStack "IGCM_sys_ListJobInQueue" |
|---|
| 1701 | } |
|---|
| 1702 | |
|---|
| 1703 | #D-#================================================== |
|---|
| 1704 | #D-function IGCM_sys_atlas |
|---|
| 1705 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
|---|
| 1706 | #D-* Examples: |
|---|
| 1707 | #D- |
|---|
| 1708 | function IGCM_sys_atlas { |
|---|
| 1709 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
|---|
| 1710 | if ( $DEBUG_sys ) ; then |
|---|
| 1711 | echo "IGCM_sys_atlas :" $@ |
|---|
| 1712 | fi |
|---|
| 1713 | |
|---|
| 1714 | typeset status |
|---|
| 1715 | # To be implemented on Jean Zay |
|---|
| 1716 | # |
|---|
| 1717 | # \ccc_mprun atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
|---|
| 1718 | # status=$? |
|---|
| 1719 | # if [ ${status} -gt 0 ] ; then |
|---|
| 1720 | # echo "IGCM_sys_atlas : error code ${status}" |
|---|
| 1721 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 1722 | # \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
|---|
| 1723 | # IGCM_debug_PopStack "IGCM_sys_atlas" |
|---|
| 1724 | # return 1 |
|---|
| 1725 | # else |
|---|
| 1726 | # IGCM_debug_PopStack "IGCM_sys_atlas" |
|---|
| 1727 | # return 0 |
|---|
| 1728 | # fi |
|---|
| 1729 | # |
|---|
| 1730 | IGCM_debug_PopStack "IGCM_sys_atlas" |
|---|
| 1731 | } |
|---|
| 1732 | |
|---|
| 1733 | #D-#================================================== |
|---|
| 1734 | #D-function IGCM_sys_rebuild_nemo |
|---|
| 1735 | #D-* Purpose: rebuild nemo parallel files with nemo specific rebuild on curie |
|---|
| 1736 | #D-* Examples: |
|---|
| 1737 | #D- |
|---|
| 1738 | |
|---|
| 1739 | function IGCM_sys_rebuild_nemo { |
|---|
| 1740 | IGCM_debug_PushStack "IGCM_sys_rebuild_nemo" $@ |
|---|
| 1741 | if ( $DEBUG_sys ) ; then |
|---|
| 1742 | echo "IGCM_sys_rebuild_nemo :" $@ |
|---|
| 1743 | fi |
|---|
| 1744 | |
|---|
| 1745 | /gpfswork/rech/psl/commun/Tools/rebuild_nemo/bin/rebuild_nemo ${1} ${2} |
|---|
| 1746 | |
|---|
| 1747 | IGCM_debug_PopStack "IGCM_sys_rebuild_nemo" |
|---|
| 1748 | } |
|---|
| 1749 | |
|---|
