[1518] | 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:: 1512 $ Revision of last commit |
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| 7 | # $Author:: acosce $ Author of last commit |
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| 8 | # $Date:: 2020-01-14 18:52:20 +0100 (Tue, 14 Jan 2020) $ 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 Irene-amd |
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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=${DEBUG_sys:=true} |
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| 37 | |
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| 38 | #==================================================== |
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| 39 | # Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get) |
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[1576] | 40 | if ([ X${DRYRUN} != X ] && [ ${DRYRUN} = 4 ]) ; then |
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[1569] | 41 | typeset -r DRYRUN=0 |
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| 42 | typeset -r DRYRUN_DEBUG=4 |
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| 43 | else |
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| 44 | typeset -r DRYRUN=${DRYRUN:=0} |
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| 45 | typeset -r DRYRUN_DEBUG=0 |
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| 46 | fi |
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[1518] | 47 | |
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| 48 | # YOU MUST COMPILE YOUR EXE FILES FOR DRYRUN MODE ! |
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| 49 | # ------------------------------------------------------------------------------------- |
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| 50 | # | DRYRUN= | Date computations, | sys_Get | Exe | sys_Put_Out; sys_Put_Rest | |
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| 51 | # | | Cp/Exe/param/files | | | | |
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| 52 | # | | Chmod Qsub | | | | |
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| 53 | # ------------------------------------------------------------------------------------- |
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| 54 | # | 0 | yes | yes | yes | yes | |
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| 55 | # ------------------------------------------------------------------------------------- |
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| 56 | # | 1 | yes | yes | yes | no | |
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| 57 | # ------------------------------------------------------------------------------------- |
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| 58 | # | 2 | yes | yes | no | no | |
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| 59 | # ------------------------------------------------------------------------------------- |
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| 60 | # | 3 | yes | no | no | no | |
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| 61 | # ------------------------------------------------------------------------------------- |
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[1569] | 62 | # | 4 | yes | yes | creation of RUN_DIR and Job_debug | |
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| 63 | # ------------------------------------------------------------------------------------- |
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[1518] | 64 | |
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[1569] | 65 | |
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[1518] | 66 | #===================================================== |
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| 67 | # Global Variables : |
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| 68 | #===================================================== |
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| 69 | # Language : "fr" or "en" |
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| 70 | typeset -r MYLANG="fr" |
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| 71 | |
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| 72 | #===================================================== |
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| 73 | # Host user names project maxCpuTime |
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| 74 | # $hostname ou hostname |
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| 75 | typeset HOST=${HOST:=$( hostname )} |
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| 76 | # $username ou whoami |
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| 77 | typeset LOGIN=${LOGIN:=$( whoami )} |
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| 78 | # $hostname of the MASTER job |
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| 79 | typeset MASTER=irene-amd |
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| 80 | # add default project on irene-amd |
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| 81 | typeset PROJECT=$(echo ${BRIDGE_MSUB_PROJECT:=::default_project::} | cut -d@ -f1 ) |
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| 82 | # jobWarningDelay in seconds |
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| 83 | typeset jobWarningDelay=${BRIDGE_MSUB_MAXTIME} |
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| 84 | |
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| 85 | #D- |
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| 86 | #D-#================================================== |
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| 87 | #D-Program used in libIGCM |
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| 88 | #D-#================================================== |
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| 89 | |
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| 90 | # Submit command |
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| 91 | typeset SUBMIT=${SUBMIT:=ccc_msub} |
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| 92 | # rsync with path |
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| 93 | typeset -r RSYNC=/usr/bin/rsync |
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| 94 | # RSYNC_opt args to rsync |
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| 95 | typeset -r RSYNC_opt="-va" |
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| 96 | # ie storage filesystem |
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| 97 | typeset -r STOREHOST=${MASTER} |
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| 98 | typeset -r REMOTE_RSYNC=/usr/bin/rsync |
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| 99 | |
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| 100 | #==================================================== |
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| 101 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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| 102 | #==================================================== |
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[1581] | 103 | typeset CCCOS=${CCCOS:=$( ccc_os )} |
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| 104 | |
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[1518] | 105 | if [ X${TaskType} = Xcomputing ] ; then |
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| 106 | IGCM_debug_Print 1 "Modules will be loaded later in IGCM_sys_activ_variables." |
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| 107 | else |
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| 108 | module purge > /dev/null 2>&1 |
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[1581] | 109 | if [ X${CCCOS} = X"Rhel_8__x86_64" ] ; then |
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| 110 | . $( ccc_home -u igcmg)/MachineEnvironment/irene/env_atlas_irene > /dev/null 2>&1 |
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| 111 | else |
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| 112 | . $( ccc_home -u igcmg)/MachineEnvironment/irene-amd_prev/env_irene-amd > /dev/null 2>&1 |
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| 113 | . $( ccc_home -u igcmg)/MachineEnvironment/irene-amd_prev/env_atlas_irene-amd > /dev/null 2>&1 |
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| 114 | fi |
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[1518] | 115 | |
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| 116 | export PCMDI_MP=/ccc/work/cont003/igcmg/igcmg/PCMDI-MP |
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| 117 | export UVCDAT_ANONYMOUS_LOG=FALSE |
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| 118 | fi |
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| 119 | |
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| 120 | # FYI |
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| 121 | [ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:" |
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| 122 | [ ! X${TaskType} = Xchecking ] && module list |
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| 123 | |
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| 124 | # For AddNoise and AddPertu3DOCE |
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[1582] | 125 | export PATH=${PATH}:$(ccc_home -u igcmg)/Tools/irene/bin |
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[1518] | 126 | |
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| 127 | # For rebuild |
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[1582] | 128 | export PATH=${PATH}:$(ccc_home -u igcmg)/Tools/irene/rebuild/modipsl/bin |
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[1518] | 129 | |
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| 130 | #==================================================== |
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| 131 | # Host specific DIRECTORIES |
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| 132 | #==================================================== |
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| 133 | |
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| 134 | # ============ CESIUM START ============ # |
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| 135 | |
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| 136 | #==================================================== |
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| 137 | #- Mirror libIGCM from titane to cesium if needed |
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| 138 | #ROOTSYS=$( echo ${libIGCM} | gawk -F"/" '{print $3}' ) |
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| 139 | #if [ ! ${ROOTSYS} = "home" ] ; then |
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| 140 | # typeset -r MirrorlibIGCM=${MirrorlibIGCM:=true} |
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| 141 | #else |
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| 142 | # typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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| 143 | #fi |
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| 144 | |
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| 145 | #==================================================== |
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| 146 | #- libIGCM_POST |
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| 147 | #if ( ${MirrorlibIGCM} ) ; then |
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| 148 | # PATHlibIGCM=$( echo ${libIGCM} | gawk -F"${LOGIN}/" '{print $2}' | sed -e "s&/libIGCM&&" ) |
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| 149 | # typeset -r libIGCM_POST=${HOME}/MIRROR/${PATHlibIGCM}/libIGCM |
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| 150 | #else |
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| 151 | # typeset -r libIGCM_POST=${libIGCM} |
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| 152 | #fi |
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| 153 | |
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| 154 | # ============ CESIUM END ============ # |
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| 155 | |
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| 156 | #==================================================== |
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| 157 | #- MirrorlibIGCM for frontend |
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| 158 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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| 159 | |
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| 160 | #==================================================== |
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| 161 | #- libIGCM_POST for frontend |
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| 162 | typeset -r libIGCM_POST=${libIGCM} |
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| 163 | |
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| 164 | #==================================================== |
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| 165 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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| 166 | typeset -r R_EXE="${MODIPSL}/bin" |
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| 167 | |
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| 168 | #==================================================== |
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| 169 | #- SUBMIT_DIR : submission dir |
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| 170 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${BRIDGE_MSUB_PWD}} |
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| 171 | |
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| 172 | #==================================================== |
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| 173 | #- IN |
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| 174 | typeset -r R_IN=${R_IN:=/ccc/work/cont003/igcmg/igcmg/IGCM} |
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| 175 | |
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| 176 | #==================================================== |
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| 177 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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| 178 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${CCCSCRATCHDIR}/RUN_DIR/${BRIDGE_MSUB_JOBID}_${$}} |
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| 179 | |
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| 180 | #==================================================== |
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| 181 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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| 182 | typeset -r OUTCOMMAND_PATH=/tmp |
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| 183 | |
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| 184 | #==================================================== |
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| 185 | #- HOST_MPIRUN_COMMAND |
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| 186 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time ccc_mprun -E-K1 "} |
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| 187 | |
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| 188 | #==================================================== |
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| 189 | #- Max number of arguments passed to nco operator or demigration command |
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| 190 | UNIX_MAX_LIMIT=360 |
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| 191 | |
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| 192 | #==================================================== |
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| 193 | #- set PackDefault to true on irene-amd |
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| 194 | PackDefault=true |
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| 195 | |
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| 196 | #==================================================== |
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| 197 | #- Default number of MPI task for IPSL coupled model |
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| 198 | #- required for backward compatibility |
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| 199 | #- |
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| 200 | DEFAULT_NUM_PROC_OCE=5 |
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| 201 | DEFAULT_NUM_PROC_CPL=1 |
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| 202 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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| 203 | |
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| 204 | #==================================================== |
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| 205 | #- Number of computing cores per node |
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| 206 | #- |
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[1524] | 207 | NB_CORE_PER_NODE=128 |
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[1518] | 208 | |
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| 209 | #D-#================================================== |
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| 210 | #D-function IGCM_sys_defineArchives |
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| 211 | #D-* Purpose: |
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| 212 | #D-* Load dfldatadir module : According to project used for submission (default) or set in config.card (optional) |
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| 213 | #D-* Define ARCHIVE : Dedicated to large files |
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| 214 | #D-* Define STORAGE : Dedicated to small/medium files |
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| 215 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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| 216 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) |
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| 217 | #D-* Define R_BUF : Output tree located on CCCSCRATCHDIR hosting files waiting for rebuild or pack processes |
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| 218 | #D-* if SpaceName=TEST everything is stored on CCCSCRATCHDIR |
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| 219 | #D-* Examples: |
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| 220 | #D- |
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| 221 | function IGCM_sys_defineArchives { |
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| 222 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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| 223 | |
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| 224 | # Load dfldatadir depending on the project used for submission (default) or set in config.card (optional) |
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| 225 | if [ X${config_UserChoices_DataProject} = X ] || [ X${config_UserChoices_DataProject} = DEFAULT ]; then |
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| 226 | # Default option: Change the dfldatadir according to the project used for submission |
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| 227 | # The variable DataProject in section UserChoices in config.card is not set or is set to DEFAULT |
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| 228 | if [ X"$( echo ${PROJECT} | grep cmip6 )" != "X" ] ; then |
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| 229 | module switch dfldatadir dfldatadir/gencmip6 |
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| 230 | IGCM_debug_Print 1 "Load dfldatadir for forced gencmip6 project" |
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| 231 | else |
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| 232 | module switch dfldatadir dfldatadir/${PROJECT} |
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| 233 | IGCM_debug_Print 1 "Load dfldatadir for project ${PROJECT}" |
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| 234 | fi |
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| 235 | else |
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| 236 | # Use the project set by the variable DataProject in section UserChoices in config.card |
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| 237 | module switch dfldatadir dfldatadir/${config_UserChoices_DataProject} |
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| 238 | IGCM_debug_Print 1 "Load dfldatadir for DataProject red in config.card : ${config_UserChoices_DataProject}" |
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| 239 | fi |
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| 240 | |
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| 241 | #==================================================== |
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| 242 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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| 243 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${CCCSCRATCHDIR}/RUN_DIR/${BRIDGE_MSUB_JOBID}_${$}} |
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| 244 | |
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| 245 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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| 246 | #==================================================== |
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| 247 | #- ARCHIVE (dedicated to large files) |
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| 248 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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| 249 | else |
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| 250 | #==================================================== |
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| 251 | #- ARCHIVE (dedicated to large files) |
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| 252 | ARCHIVE=${CCCSTOREDIR} |
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| 253 | fi |
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| 254 | |
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| 255 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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| 256 | #==================================================== |
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| 257 | #- STORAGE (dedicated to small/medium files) |
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| 258 | STORAGE=${config_UserChoices_STORAGE} |
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| 259 | else |
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| 260 | #==================================================== |
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| 261 | #- STORAGE (dedicated to small/medium files) |
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| 262 | STORAGE=${CCCWORKDIR} |
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| 263 | fi |
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| 264 | |
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| 265 | if [ X${config_UserChoices_SpaceName} = XTEST ]; then |
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| 266 | #==================================================== |
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| 267 | #- R_OUT |
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| 268 | R_OUT=${CCCSCRATCHDIR}/IGCM_OUT |
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| 269 | |
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| 270 | #==================================================== |
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| 271 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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| 272 | R_FIG=${CCCSCRATCHDIR}/IGCM_OUT |
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| 273 | |
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| 274 | IGCM_debug_Print 1 "SpaceName=TEST ==> OVERRULE destination path directories" |
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| 275 | |
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| 276 | else |
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| 277 | #==================================================== |
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| 278 | #- R_OUT |
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| 279 | R_OUT=${ARCHIVE}/IGCM_OUT |
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| 280 | |
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| 281 | #==================================================== |
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| 282 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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| 283 | R_FIG=${STORAGE}/IGCM_OUT |
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| 284 | fi |
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| 285 | |
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| 286 | #==================================================== |
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| 287 | #- CMIP6 (hosting CMIP6 files produced by XIOS2 and configured by dr2xml) |
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| 288 | CMIP6_BUF=${STORAGE}/IGCM_OUT |
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| 289 | |
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| 290 | #==================================================== |
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| 291 | #- R_BUF (ONLY FOR double copy an scratch) |
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| 292 | R_BUF=${CCCSCRATCHDIR}/IGCM_OUT |
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| 293 | |
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| 294 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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| 295 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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| 296 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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| 297 | |
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| 298 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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| 299 | } |
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| 300 | |
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| 301 | #D-#================================================== |
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| 302 | #D-function IGCM_sys_RshArchive |
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| 303 | #D-* Purpose: Archive rsh command |
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| 304 | #D-* Examples: |
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| 305 | #D- |
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| 306 | function IGCM_sys_RshArchive { |
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| 307 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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| 308 | /bin/ksh <<-EOF |
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| 309 | ${@} |
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| 310 | EOF |
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| 311 | status=$? |
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| 312 | if [ ${status} -gt 0 ] ; then |
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| 313 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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| 314 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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| 315 | fi |
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| 316 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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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_RshArchive_NoError |
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| 321 | #D-* Purpose: Archive rsh command, without error |
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| 322 | #D-* used only in monitoring.job |
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| 323 | #D-* Examples: |
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| 324 | #D- |
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| 325 | function IGCM_sys_RshArchive_NoError { |
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| 326 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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| 327 | /bin/ksh <<-EOF |
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| 328 | ${@} 2> /dev/null |
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| 329 | EOF |
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| 330 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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| 331 | } |
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| 332 | |
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| 333 | #D-#================================================== |
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| 334 | #D-function IGCM_sys_MkdirArchive |
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| 335 | #D-* Purpose: Mkdir on Archive |
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| 336 | #D-* Examples: |
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| 337 | #D- |
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| 338 | function IGCM_sys_MkdirArchive { |
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| 339 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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| 340 | if ( $DEBUG_sys ) ; then |
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| 341 | echo "IGCM_sys_MkdirArchive :" $@ |
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| 342 | fi |
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| 343 | #- creation de repertoire sur le serveur fichier |
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| 344 | if [ ! -d ${1} ]; then |
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| 345 | \mkdir -p $1 |
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| 346 | status=$? |
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| 347 | |
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| 348 | if [ ${status} -gt 0 ] ; then |
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| 349 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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| 350 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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| 351 | fi |
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| 352 | fi |
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| 353 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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| 354 | } |
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| 355 | |
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| 356 | #D-#================================================== |
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| 357 | #D-function IGCM_sys_TestDirArchive |
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| 358 | #D-* Purpose: Test Directory that must exists on Archive |
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| 359 | #D-* Examples: |
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| 360 | #D- |
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| 361 | function IGCM_sys_TestDirArchive { |
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| 362 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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| 363 | if ( $DEBUG_sys ) ; then |
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| 364 | echo "IGCM_sys_TestDirArchive :" $@ |
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| 365 | fi |
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| 366 | typeset ExistFlag |
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| 367 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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| 368 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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| 369 | return ${ExistFlag} |
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| 370 | } |
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| 371 | |
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| 372 | #D-#================================================== |
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| 373 | #D-function IGCM_sys_IsFileArchived |
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| 374 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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| 375 | #D-* Examples: |
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| 376 | #D- |
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| 377 | function IGCM_sys_IsFileArchived { |
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| 378 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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| 379 | if ( $DEBUG_sys ) ; then |
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| 380 | echo "IGCM_sys_IsFileArchived :" $@ |
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| 381 | fi |
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| 382 | typeset IsArchivedFlag |
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| 383 | IsArchivedFlag=$( [ X$( echo $@ | grep ^\/ccc\/store ) != X ] && echo 0 || echo 1 ) |
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| 384 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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| 385 | |
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| 386 | return ${IsArchivedFlag} |
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| 387 | } |
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| 388 | |
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| 389 | #D-#================================================== |
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| 390 | #D-function IGCM_sys_TestFileArchive |
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| 391 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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| 392 | #D-* Examples: |
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| 393 | #D- |
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| 394 | function IGCM_sys_TestFileArchive { |
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| 395 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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| 396 | typeset ExistFlag |
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| 397 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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| 398 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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| 399 | |
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| 400 | return ${ExistFlag} |
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| 401 | } |
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| 402 | |
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| 403 | #D-#================================================== |
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| 404 | #D-function IGCM_sys_CountFileArchive |
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| 405 | #D-* Purpose: Count files on Archive filesystem |
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| 406 | #D-* Examples: |
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| 407 | #D- |
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| 408 | function IGCM_sys_CountFileArchive { |
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| 409 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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| 410 | ls ${@} 2>/dev/null | wc -l |
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| 411 | if [ $? -gt 0 ] ; then |
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| 412 | echo "IGCM_sys_CountFileArchive : erreur." |
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| 413 | fi |
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| 414 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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| 415 | } |
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| 416 | |
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| 417 | #D-#================================================== |
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| 418 | #D-function IGCM_sys_Tree |
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| 419 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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| 420 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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| 421 | #D- |
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| 422 | function IGCM_sys_Tree { |
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| 423 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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| 424 | if ( $DEBUG_sys ) ; then |
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| 425 | echo "IGCM_sys_Tree :" $@ |
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| 426 | fi |
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| 427 | |
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| 428 | \ls -lR ${@} |
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| 429 | |
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| 430 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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| 431 | } |
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| 432 | |
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| 433 | #D-#================================================== |
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| 434 | #D-function IGCM_sys_Qsub |
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| 435 | #D-* Purpose: Qsub new job |
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| 436 | #D-* Examples: |
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| 437 | #D- |
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| 438 | function IGCM_sys_Qsub { |
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| 439 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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| 440 | if ( $DEBUG_sys ) ; then |
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| 441 | echo "IGCM_sys_Qsub :" $@ |
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| 442 | fi |
---|
| 443 | typeset options status |
---|
| 444 | options="-o ${SUBMIT_DIR}/${Script_Output} -e ${SUBMIT_DIR}/${Script_Output}" |
---|
| 445 | |
---|
| 446 | /usr/bin/ccc_msub ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 447 | status=$? |
---|
| 448 | |
---|
| 449 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 450 | if [ ${status} -gt 0 ] ; then |
---|
| 451 | IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}" |
---|
| 452 | IGCM_debug_Exit "IGCM_sys_Qsub" |
---|
| 453 | else |
---|
| 454 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
---|
| 455 | fi |
---|
| 456 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
---|
| 457 | } |
---|
| 458 | |
---|
| 459 | #D-#================================================== |
---|
| 460 | #D-function IGCM_sys_QsubPost |
---|
| 461 | #D-* Purpose: Qsub new job on scalaire |
---|
| 462 | #D-* Examples: |
---|
| 463 | #D- |
---|
| 464 | function IGCM_sys_QsubPost { |
---|
| 465 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
---|
| 466 | if ( $DEBUG_sys ) ; then |
---|
| 467 | echo "IGCM_sys_QsubPost :" $@ |
---|
| 468 | fi |
---|
| 469 | typeset options status |
---|
| 470 | options="-Q normal -o ${POST_DIR}/${Script_Post_Output}.out -e ${POST_DIR}/${Script_Post_Output}.out" |
---|
| 471 | |
---|
| 472 | /usr/bin/ccc_msub ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 473 | status=$? |
---|
| 474 | |
---|
| 475 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 476 | if [ ${status} -gt 0 ] ; then |
---|
| 477 | IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}" |
---|
| 478 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
---|
| 479 | else |
---|
| 480 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
---|
| 481 | fi |
---|
| 482 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
---|
| 483 | } |
---|
| 484 | |
---|
| 485 | #D-************************* |
---|
| 486 | #D- File transfer functions |
---|
| 487 | #D-************************* |
---|
| 488 | #D- |
---|
| 489 | |
---|
| 490 | #D-#================================================== |
---|
| 491 | #D-function IGCM_sys_RmRunDir |
---|
| 492 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
---|
| 493 | #D- scheduler will do the job) |
---|
| 494 | #D-* Examples: |
---|
| 495 | #D- |
---|
| 496 | function IGCM_sys_RmRunDir { |
---|
| 497 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
---|
| 498 | if ( $DEBUG_sys ) ; then |
---|
| 499 | echo "IGCM_sys_RmRunDir :" $@ |
---|
| 500 | fi |
---|
| 501 | |
---|
| 502 | typeset status |
---|
| 503 | |
---|
| 504 | echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 505 | \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 506 | status=$? |
---|
| 507 | |
---|
| 508 | if [ ${status} -gt 0 ] ; then |
---|
| 509 | IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}." |
---|
| 510 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 511 | IGCM_debug_Exit "IGCM_sys_RmRunDir" |
---|
| 512 | else |
---|
| 513 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 514 | fi |
---|
| 515 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
---|
| 516 | } |
---|
| 517 | |
---|
| 518 | #D-#================================================== |
---|
| 519 | #D-function IGCM_sys_Put_Dir |
---|
| 520 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
---|
| 521 | #D-* Examples: |
---|
| 522 | #D- |
---|
| 523 | function IGCM_sys_Put_Dir { |
---|
| 524 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
---|
| 525 | if ( $DEBUG_sys ) ; then |
---|
| 526 | echo "IGCM_sys_Put_Dir :" $@ |
---|
| 527 | fi |
---|
| 528 | if [ $DRYRUN = 0 ]; then |
---|
| 529 | if [ ! -d ${1} ] ; then |
---|
| 530 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
---|
| 531 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
| 532 | return |
---|
| 533 | fi |
---|
| 534 | |
---|
| 535 | typeset status |
---|
| 536 | |
---|
| 537 | # Only if we use rsync |
---|
| 538 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
---|
| 539 | # |
---|
| 540 | #USUAL WAY |
---|
| 541 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 542 | status=$? |
---|
| 543 | |
---|
| 544 | if [ ${status} -gt 0 ] ; then |
---|
| 545 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
---|
| 546 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 547 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
---|
| 548 | else |
---|
| 549 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 550 | fi |
---|
| 551 | fi |
---|
| 552 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
| 553 | } |
---|
| 554 | |
---|
| 555 | #D-#================================================== |
---|
| 556 | #D-function IGCM_sys_Get_Dir |
---|
| 557 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
| 558 | #D-* Examples: |
---|
| 559 | #D- |
---|
| 560 | function IGCM_sys_Get_Dir { |
---|
| 561 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
| 562 | if ( $DEBUG_sys ) ; then |
---|
| 563 | echo "IGCM_sys_Get_Dir :" $@ |
---|
| 564 | fi |
---|
| 565 | if [ $DRYRUN = 0 ]; then |
---|
| 566 | typeset NB_ESSAI DELAI status i |
---|
| 567 | # number of tentative |
---|
| 568 | NB_ESSAI=3 |
---|
| 569 | # time delay between tentative |
---|
| 570 | DELAI=2 |
---|
| 571 | |
---|
| 572 | # |
---|
| 573 | # USUAL WAY |
---|
| 574 | # add 'ccc_hsm get' (to demigrate all offline files) to reduce time of this command : |
---|
| 575 | ccc_hsm get -r $1 |
---|
| 576 | |
---|
| 577 | i=0 |
---|
| 578 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 579 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 580 | status=$? |
---|
| 581 | if [ ${status} -gt 0 ] ; then |
---|
| 582 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 583 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
| 584 | sleep $DELAI |
---|
| 585 | else |
---|
| 586 | break |
---|
| 587 | fi |
---|
| 588 | (( i = i + 1 )) |
---|
| 589 | done |
---|
| 590 | |
---|
| 591 | if [ ${status} -gt 0 ] ; then |
---|
| 592 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
| 593 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 594 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
| 595 | else |
---|
| 596 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 597 | fi |
---|
| 598 | fi |
---|
| 599 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
| 600 | } |
---|
| 601 | |
---|
| 602 | #D-#================================================== |
---|
| 603 | #D-function IGCM_sys_Put_Rest |
---|
| 604 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
| 605 | #D- File and target directory must exist. |
---|
| 606 | #D-* Examples: |
---|
| 607 | #D- |
---|
| 608 | function IGCM_sys_Put_Rest { |
---|
| 609 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
| 610 | if ( $DEBUG_sys ) ; then |
---|
| 611 | echo "IGCM_sys_Put_Rest :" $@ |
---|
| 612 | fi |
---|
| 613 | if [ $DRYRUN = 0 ]; then |
---|
| 614 | if [ ! -f ${1} ] ; then |
---|
| 615 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
| 616 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
| 617 | fi |
---|
| 618 | |
---|
| 619 | typeset status |
---|
| 620 | # |
---|
| 621 | # USUAL WAY |
---|
| 622 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 623 | status=$? |
---|
| 624 | |
---|
| 625 | # #RSYNC WITH NETWORK SSH CALL |
---|
| 626 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 627 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 628 | |
---|
| 629 | # #RSYNC WITH NFS USE |
---|
| 630 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 631 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 632 | |
---|
| 633 | # status=$? |
---|
| 634 | # IGCM_sys_Rsync_out $status |
---|
| 635 | |
---|
| 636 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 637 | # (( status=status+$? )) |
---|
| 638 | |
---|
| 639 | if [ ${status} -gt 0 ] ; then |
---|
| 640 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
| 641 | [ -f ${1} ] && ls -l ${1} |
---|
| 642 | [ -f ${2} ] && ls -l ${2} |
---|
| 643 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
| 644 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 645 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
| 646 | else |
---|
| 647 | |
---|
| 648 | if [ X${JobType} = XRUN ] ; then |
---|
| 649 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 650 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 651 | fi |
---|
| 652 | |
---|
| 653 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 654 | fi |
---|
| 655 | fi |
---|
| 656 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
| 657 | } |
---|
| 658 | |
---|
| 659 | #D-#================================================== |
---|
| 660 | #D-function IGCM_sys_Put_Out |
---|
| 661 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
| 662 | #D-* Examples: |
---|
| 663 | #D- |
---|
| 664 | function IGCM_sys_Put_Out { |
---|
| 665 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
| 666 | if ( $DEBUG_sys ) ; then |
---|
| 667 | echo "IGCM_sys_Put_Out :" $@ |
---|
| 668 | fi |
---|
| 669 | |
---|
| 670 | typeset NB_ESSAI DELAI status i exist skip |
---|
| 671 | typeset fileDeviceNumberInHex directoryDeviceNumberInHex |
---|
| 672 | |
---|
| 673 | # number of tentative |
---|
| 674 | NB_ESSAI=3 |
---|
| 675 | # time delay between tentative |
---|
| 676 | DELAI=2 |
---|
| 677 | |
---|
| 678 | if [ $DRYRUN = 0 ]; then |
---|
| 679 | if [ ! -f ${1} ] ; then |
---|
| 680 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
| 681 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 682 | return 1 |
---|
| 683 | fi |
---|
| 684 | # |
---|
| 685 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
| 686 | # |
---|
| 687 | exist=false |
---|
| 688 | skip=false |
---|
| 689 | if [ -f $2 ] ; then |
---|
| 690 | IGCM_debug_Print 1 "$2 already exist" |
---|
| 691 | ccc_hsm get $2 |
---|
| 692 | exist=true |
---|
| 693 | if [ "X$( diff $1 $2 )" = X ] ; then |
---|
| 694 | IGCM_debug_Print 2 "$1 and $2 are the same file, we skip the copy" |
---|
| 695 | skip=true |
---|
| 696 | else |
---|
| 697 | IGCM_debug_Print 2 "$1 and $2 are not the same file, we force the copy" |
---|
| 698 | skip=false |
---|
| 699 | fi |
---|
| 700 | fi |
---|
| 701 | # |
---|
| 702 | if ( [ X${exist} = Xtrue ] && [ X${skip} = Xfalse ] ) ; then |
---|
| 703 | IGCM_sys_Chmod u+w $2 |
---|
| 704 | fi |
---|
| 705 | |
---|
| 706 | if [ X${skip} = Xfalse ] ; then |
---|
| 707 | i=0 |
---|
| 708 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 709 | # Identify file system |
---|
| 710 | fileDeviceNumberInHex=$( stat -c %d $1 ) |
---|
| 711 | status=$? |
---|
| 712 | if [ ${status} -gt 0 ] ; then |
---|
| 713 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
| 714 | fi |
---|
| 715 | # Identify file system |
---|
| 716 | directoryDeviceNumberInHex=$( stat -c %d $( dirname $2 ) ) |
---|
| 717 | status=$? |
---|
| 718 | if [ ${status} -gt 0 ] ; then |
---|
| 719 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
| 720 | fi |
---|
| 721 | |
---|
| 722 | if ( [ ${fileDeviceNumberInHex} -ne ${directoryDeviceNumberInHex} ] || [ X$3 = XNOMOVE ] ) ; then |
---|
| 723 | # They are not on the same device. USUAL WAY |
---|
| 724 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 725 | status=$? |
---|
| 726 | else |
---|
| 727 | # They are on the same device. NOT SO USUAL WAY |
---|
| 728 | \mv $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 729 | status=$? |
---|
| 730 | fi |
---|
| 731 | if [ ${status} -gt 0 ]; then |
---|
| 732 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 733 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : sleep ${DELAI} seconds and try again." |
---|
| 734 | [ -f ${1} ] && ls -l ${1} |
---|
| 735 | [ -f ${2} ] && ls -l ${2} |
---|
| 736 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
| 737 | sleep $DELAI |
---|
| 738 | else |
---|
| 739 | break |
---|
| 740 | fi |
---|
| 741 | (( i = i + 1 )) |
---|
| 742 | done |
---|
| 743 | fi |
---|
| 744 | |
---|
| 745 | # #RSYNC WITH NETWORK SSH CALL |
---|
| 746 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 747 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 748 | |
---|
| 749 | # #RSYNC WITH NFS USE |
---|
| 750 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 751 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 752 | |
---|
| 753 | # status=$? |
---|
| 754 | # IGCM_sys_Rsync_out $status |
---|
| 755 | |
---|
| 756 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 757 | # (( status=status+$? )) |
---|
| 758 | |
---|
| 759 | if [ ${status} -gt 0 ] ; then |
---|
| 760 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status}" |
---|
| 761 | [ -f ${1} ] && ls -l ${1} |
---|
| 762 | [ -f ${2} ] && ls -l ${2} |
---|
| 763 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
| 764 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 765 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
| 766 | else |
---|
| 767 | |
---|
| 768 | if [ X${JobType} = XRUN ] ; then |
---|
| 769 | if [ X${3} = X ] ; then |
---|
| 770 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 771 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 772 | fi |
---|
| 773 | fi |
---|
| 774 | |
---|
| 775 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 776 | fi |
---|
| 777 | fi |
---|
| 778 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 779 | return 0 |
---|
| 780 | } |
---|
| 781 | |
---|
| 782 | #D-#================================================== |
---|
| 783 | #D-function IGCM_sys_Get |
---|
| 784 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
| 785 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
| 786 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
| 787 | function IGCM_sys_Get { |
---|
| 788 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
| 789 | |
---|
| 790 | typeset DEST dm_liste target file_work |
---|
| 791 | typeset NB_ESSAI DELAI status i |
---|
| 792 | |
---|
| 793 | if ( $DEBUG_sys ) ; then |
---|
| 794 | echo "IGCM_sys_Get :" $@ |
---|
| 795 | fi |
---|
| 796 | |
---|
| 797 | # number of tentative |
---|
| 798 | NB_ESSAI=3 |
---|
| 799 | # time delay between tentative |
---|
| 800 | DELAI=2 |
---|
| 801 | |
---|
| 802 | if [ $DRYRUN -le 2 ]; then |
---|
| 803 | if [ X${1} = X'/l' ] ; then |
---|
| 804 | eval set +A dm_liste \${${2}} |
---|
| 805 | else |
---|
| 806 | eval set +A dm_liste ${1} |
---|
| 807 | fi |
---|
| 808 | eval DEST=\${${#}} |
---|
| 809 | ccc_hsm get ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 810 | status=$? |
---|
| 811 | if [ ${status} -gt 0 ] ; then |
---|
| 812 | echo "WARNING IGCM_sys_Get : error code ${status}" |
---|
| 813 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 814 | echo "WARNING IGCM_sys_Get : will stop later if the cp fails." |
---|
| 815 | fi |
---|
| 816 | |
---|
| 817 | #if [ ${status} -gt 0 ] ; then |
---|
| 818 | # if [ ! "X$( grep "Lost dmusrcmd connection" ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )" = "X" ] ; then |
---|
| 819 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 820 | # echo "WARNING IGCM_sys_Get : Lost dmusrcmd connection : " |
---|
| 821 | # sleep 30 |
---|
| 822 | # echo "We try another time" |
---|
| 823 | ## dmget ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 824 | # ccc_hsm get ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 825 | # status=$? |
---|
| 826 | # if [ ${status} -gt 0 ] ; then |
---|
| 827 | # echo "ERROR IGCM_sys_Get : again demigration error :" |
---|
| 828 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 829 | # IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 830 | # fi |
---|
| 831 | # else |
---|
| 832 | # echo "ERROR IGCM_sys_Get : demigration error :" |
---|
| 833 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 834 | # IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 835 | # fi |
---|
| 836 | #fi |
---|
| 837 | |
---|
| 838 | # #RSYNC WITH NETWORK SSH CALL |
---|
| 839 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 840 | # ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 841 | |
---|
| 842 | # #RSYNC WITH NFS USE |
---|
| 843 | # echo ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 844 | # ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 845 | |
---|
| 846 | # status=$? |
---|
| 847 | # IGCM_sys_Rsync_out $status |
---|
| 848 | |
---|
| 849 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 850 | # (( status=status+$? )) |
---|
| 851 | |
---|
| 852 | #USUAL WAY |
---|
| 853 | if [ X${1} = X'/l' ] ; then |
---|
| 854 | for target in ${dm_liste[*]} ; do |
---|
| 855 | local_file=$( basename ${target} ) |
---|
| 856 | # test if the target file is present before the loop |
---|
| 857 | IGCM_sys_TestFileArchive ${target} |
---|
| 858 | status=$? |
---|
| 859 | if [ ${status} -gt 0 ] ; then |
---|
| 860 | echo "IGCM_sys_Get, ERROR : regular file ${target} DOES NOT EXIST ." |
---|
| 861 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 862 | else |
---|
| 863 | i=0 |
---|
| 864 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 865 | #if [ X${DoLink} = Xtrue ] ; then |
---|
| 866 | # \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 867 | # status=$? |
---|
| 868 | # else |
---|
| 869 | # \cp ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 870 | # status=$? |
---|
| 871 | #fi |
---|
| 872 | \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 873 | status=$? |
---|
| 874 | if [ ${status} -gt 0 ]; then |
---|
| 875 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 876 | IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again." |
---|
| 877 | sleep $DELAI |
---|
| 878 | else |
---|
| 879 | break |
---|
| 880 | fi |
---|
| 881 | (( i = i + 1 )) |
---|
| 882 | done |
---|
| 883 | if [ ${status} -gt 0 ] ; then |
---|
| 884 | echo "IGCM_sys_Get : error" |
---|
| 885 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 886 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 887 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 888 | else |
---|
| 889 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 890 | fi |
---|
| 891 | fi |
---|
| 892 | done |
---|
| 893 | else |
---|
| 894 | i=0 |
---|
| 895 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 896 | \cp ${dm_liste} ${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 897 | status=$? |
---|
| 898 | if [ ${status} -gt 0 ]; then |
---|
| 899 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 900 | IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again." |
---|
| 901 | sleep $DELAI |
---|
| 902 | else |
---|
| 903 | break |
---|
| 904 | fi |
---|
| 905 | (( i = i + 1 )) |
---|
| 906 | done |
---|
| 907 | if [ ${status} -gt 0 ] ; then |
---|
| 908 | echo "IGCM_sys_Get : error" |
---|
| 909 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 910 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 911 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 912 | else |
---|
| 913 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 914 | fi |
---|
| 915 | fi |
---|
| 916 | fi |
---|
| 917 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
| 918 | } |
---|
| 919 | |
---|
| 920 | #D-#================================================== |
---|
| 921 | #D-function IGCM_sys_GetDate_Monitoring |
---|
| 922 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
| 923 | #D-* Examples: |
---|
| 924 | #D- |
---|
| 925 | function IGCM_sys_GetDate_Monitoring { |
---|
| 926 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
| 927 | if ( $DEBUG_sys ) ; then |
---|
| 928 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
| 929 | fi |
---|
| 930 | |
---|
| 931 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
| 932 | |
---|
| 933 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
| 934 | } |
---|
| 935 | |
---|
| 936 | #D-#================================================== |
---|
| 937 | #D-function IGCM_sys_Dods_Rm |
---|
| 938 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
| 939 | #D-* Examples: |
---|
| 940 | #D- |
---|
| 941 | function IGCM_sys_Dods_Rm { |
---|
| 942 | if ( $DEBUG_sys ) ; then |
---|
| 943 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
| 944 | fi |
---|
| 945 | typeset status |
---|
| 946 | if [ $DRYRUN = 0 ]; then |
---|
| 947 | |
---|
| 948 | # if [ ! -d /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} ] ; then |
---|
| 949 | # echo "WARNING : IGCM_sys_Dods_Rm /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} DOES NOT EXIST ." |
---|
| 950 | # echo "Nothing has been done." |
---|
| 951 | # return |
---|
| 952 | # fi |
---|
| 953 | |
---|
| 954 | if [ "$#" -eq 1 ]; then |
---|
[1582] | 955 | $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS}/${1} # > out_dods_rm 2>&1 |
---|
[1518] | 956 | status=$? |
---|
| 957 | else |
---|
[1582] | 958 | $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS} # > out_dods_rm 2>&1 |
---|
[1518] | 959 | status=$? |
---|
| 960 | fi |
---|
| 961 | |
---|
| 962 | # if [ ${status} -gt 0 ] ; then |
---|
| 963 | # echo "IGCM_sys_Dods_Rm : error." |
---|
| 964 | # cat out_dods_rm |
---|
| 965 | # IGCM_debug_Exit "IGCM_sys_Dods_Rm" |
---|
| 966 | # else |
---|
| 967 | # rm out_dods_rm |
---|
| 968 | # fi |
---|
| 969 | |
---|
| 970 | fi |
---|
| 971 | return $status |
---|
| 972 | } |
---|
| 973 | |
---|
| 974 | #D-#================================================== |
---|
| 975 | #D-function IGCM_sys_Dods_Cp |
---|
| 976 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
| 977 | #D-* Examples: |
---|
| 978 | #D- |
---|
| 979 | function IGCM_sys_Dods_Cp { |
---|
| 980 | if ( $DEBUG_sys ) ; then |
---|
| 981 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
| 982 | fi |
---|
| 983 | typeset status |
---|
| 984 | if [ $DRYRUN = 0 ]; then |
---|
| 985 | |
---|
| 986 | # if [ ! -d ${R_SAVE}/${1} ] ; then |
---|
| 987 | # echo "WARNING : IGCM_sys_Dods_Cp ${R_SAVE}/${1} DOES NOT EXIST ." |
---|
| 988 | # echo "Nothing has been done." |
---|
| 989 | # return |
---|
| 990 | # fi |
---|
| 991 | |
---|
[1582] | 992 | $(ccc_home -u igcmg)/Tools/irene/thredds_cp ${1} public/${LOGIN}/${R_DODS} # > out_dods_cp 2>&1 |
---|
[1518] | 993 | status=$? |
---|
| 994 | |
---|
| 995 | # if [ ${status} -gt 0 ] ; then |
---|
| 996 | # echo "IGCM_sys_Dods_Cp : error." |
---|
| 997 | # cat out_dods_cp |
---|
| 998 | # IGCM_debug_Exit "IGCM_sys_Dods_Cp" |
---|
| 999 | # else |
---|
| 1000 | # rm out_dods_cp |
---|
| 1001 | # fi |
---|
| 1002 | |
---|
| 1003 | fi |
---|
| 1004 | return $status |
---|
| 1005 | } |
---|
| 1006 | |
---|
| 1007 | #D-#================================================== |
---|
| 1008 | #D-function IGCM_sys_Put_Dods |
---|
| 1009 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. |
---|
| 1010 | #D-* Examples: |
---|
| 1011 | #D- |
---|
| 1012 | function IGCM_sys_Put_Dods { |
---|
| 1013 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
| 1014 | if ( $DEBUG_sys ) ; then |
---|
| 1015 | echo "IGCM_sys_Put_Dods :" $@ |
---|
| 1016 | fi |
---|
| 1017 | typeset status |
---|
| 1018 | if [ $DRYRUN = 0 ]; then |
---|
| 1019 | if ( [ ! -d ${R_SAVE}/${1} ] && [ ! -d ${R_FIGR}/${1} ] ) ; then |
---|
| 1020 | echo "WARNING IGCM_sys_Put_Dods : None of the following directories exist. Exactly one should." |
---|
| 1021 | echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} DOES NOT EXIST." |
---|
| 1022 | echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} DOES NOT EXIST." |
---|
| 1023 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
| 1024 | return |
---|
| 1025 | fi |
---|
| 1026 | |
---|
| 1027 | if ( [ -d ${R_SAVE}/${1} ] && [ -d ${R_FIGR}/${1} ] ) ; then |
---|
| 1028 | echo "WARNING IGCM_sys_Put_Dods : Both of the following directories exist. Exactly one should." |
---|
| 1029 | echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} EXISTS." |
---|
| 1030 | echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} EXISTS." |
---|
| 1031 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
| 1032 | return |
---|
| 1033 | fi |
---|
| 1034 | # |
---|
| 1035 | if [ -d ${R_SAVE}/${1} ] ; then |
---|
| 1036 | cd ${R_SAVE} |
---|
| 1037 | elif [ -d ${R_FIGR}/${1} ] ; then |
---|
| 1038 | cd ${R_FIGR} |
---|
| 1039 | fi |
---|
| 1040 | |
---|
| 1041 | IGCM_sys_Dods_Rm ${1} |
---|
| 1042 | IGCM_sys_Dods_Cp ${1} |
---|
| 1043 | status=0 |
---|
| 1044 | |
---|
| 1045 | if [ ${status} -gt 0 ] ; then |
---|
| 1046 | echo "IGCM_sys_Put_Dods : error." |
---|
| 1047 | IGCM_debug_Exit "IGCM_sys_Put_Dods" |
---|
| 1048 | fi |
---|
| 1049 | fi |
---|
| 1050 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
| 1051 | } |
---|
| 1052 | |
---|
| 1053 | ############################################################## |
---|
| 1054 | # REBUILD OPERATOR |
---|
| 1055 | |
---|
| 1056 | #D-#================================================== |
---|
| 1057 | #D-function IGCM_sys_sync |
---|
| 1058 | #D-* Purpose: flush buffer on disk |
---|
| 1059 | #D-* Examples: |
---|
| 1060 | #D- |
---|
| 1061 | function IGCM_sys_sync { |
---|
| 1062 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
| 1063 | if ( $DEBUG_sys ) ; then |
---|
| 1064 | echo "IGCM_sys_sync :" $@ |
---|
| 1065 | fi |
---|
| 1066 | |
---|
| 1067 | /bin/sync |
---|
| 1068 | |
---|
| 1069 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
| 1070 | } |
---|
| 1071 | |
---|
| 1072 | ############################################################ |
---|
| 1073 | # Activate Running Environnment Variables |
---|
| 1074 | |
---|
| 1075 | #D-#================================================== |
---|
| 1076 | #D-function IGCM_sys_activ_variables |
---|
| 1077 | #D-* Purpose: set environement variables prior to execution |
---|
| 1078 | #D-* Examples: |
---|
| 1079 | #D- |
---|
| 1080 | function IGCM_sys_activ_variables { |
---|
| 1081 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
| 1082 | if ( $DEBUG_sys ) ; then |
---|
| 1083 | echo "IGCM_sys_activ_variables" |
---|
| 1084 | fi |
---|
| 1085 | |
---|
| 1086 | # -------------------------------------------------------------------- |
---|
| 1087 | #D- MODULE specifications |
---|
| 1088 | # -------------------------------------------------------------------- |
---|
| 1089 | # Source the file EnvFile containing all module load needed to run the model. |
---|
| 1090 | # EnvFile can be specified in config.card. If this is the case and if the file exists, |
---|
| 1091 | # it will be used. Otherwise a default file will be used. |
---|
| 1092 | if [ ! X${config_UserChoices_EnvFile} = X ] && [ -f ${config_UserChoices_EnvFile} ] ; then |
---|
| 1093 | # EnvFile is set in config.card and the file exists |
---|
| 1094 | IGCM_debug_Print 1 "EnvFile set in config.card will be used" |
---|
| 1095 | EnvFile=${config_UserChoices_EnvFile} |
---|
| 1096 | else |
---|
| 1097 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Default modules will be used" |
---|
| 1098 | module purge > /dev/null 2>&1 |
---|
| 1099 | if [ X${compilerVersion} = XV19 ] ; then |
---|
| 1100 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Using compiler version V19" |
---|
| 1101 | EnvFile=$( ccc_home -u igcmg)/MachineEnvironment/irene-amd/env_irene-amd > /dev/null 2>&1 |
---|
| 1102 | else |
---|
| 1103 | IGCM_debug_Exit "This compiler version is not yet supported : ${compilerVersion}" |
---|
| 1104 | fi |
---|
| 1105 | fi |
---|
| 1106 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Following EnvFile will be used :" |
---|
| 1107 | IGCM_debug_Print 1 ${EnvFile} |
---|
| 1108 | . ${EnvFile} |
---|
| 1109 | |
---|
| 1110 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Now loaded modules for Irene-amd. " |
---|
| 1111 | module list |
---|
| 1112 | |
---|
| 1113 | # -------------------------------------------------------------------- |
---|
| 1114 | #D- MPI specifications |
---|
| 1115 | # -------------------------------------------------------------------- |
---|
| 1116 | |
---|
| 1117 | # -------------------------------------------------------------------- |
---|
| 1118 | #D- Other specifications |
---|
| 1119 | # -------------------------------------------------------------------- |
---|
| 1120 | |
---|
| 1121 | ulimit -s unlimited |
---|
| 1122 | |
---|
| 1123 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
| 1124 | } |
---|
| 1125 | |
---|
| 1126 | ############################################################ |
---|
| 1127 | # Desactivate Running Environnment Variables |
---|
| 1128 | |
---|
| 1129 | #D-#================================================== |
---|
| 1130 | #D-function IGCM_sys_desactiv_variables |
---|
| 1131 | #D-* Purpose: unset environement variables after execution |
---|
| 1132 | #D-* Examples: |
---|
| 1133 | #D- |
---|
| 1134 | function IGCM_sys_desactiv_variables { |
---|
| 1135 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
| 1136 | if ( $DEBUG_sys ) ; then |
---|
| 1137 | echo "IGCM_sys_desactiv_variables" |
---|
| 1138 | fi |
---|
| 1139 | # -------------------------------------------------------------------- |
---|
| 1140 | #D- MPI specifications |
---|
| 1141 | # -------------------------------------------------------------------- |
---|
| 1142 | |
---|
| 1143 | # -------------------------------------------------------------------- |
---|
| 1144 | #D- Other specifications |
---|
| 1145 | # -------------------------------------------------------------------- |
---|
| 1146 | |
---|
| 1147 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
| 1148 | } |
---|
| 1149 | |
---|
| 1150 | ############################################################ |
---|
| 1151 | # Update job headers to be used by the scheduler |
---|
| 1152 | |
---|
| 1153 | #D-#================================================== |
---|
| 1154 | #D-function IGCM_sys_updateHeaders |
---|
| 1155 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
| 1156 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
| 1157 | #D- |
---|
| 1158 | function IGCM_sys_updateHeaders { |
---|
| 1159 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
| 1160 | if ( $DEBUG_sys ) ; then |
---|
| 1161 | echo "IGCM_sys_updateHeaders" |
---|
| 1162 | fi |
---|
| 1163 | typeset file |
---|
| 1164 | file=$1 |
---|
| 1165 | |
---|
[1528] | 1166 | # In case of use of DEDICATED option XIOS servers, do not share xios nodes with xios clients |
---|
| 1167 | # Compute the number of core to add to force the use of a new node for xios servers |
---|
[1544] | 1168 | |
---|
| 1169 | if [ "X${IOS_OK_DEDICATED}" == "X" ] ; then |
---|
| 1170 | (( IOS_OK_DEDICATED = 0 )) |
---|
| 1171 | fi |
---|
| 1172 | |
---|
| 1173 | |
---|
[1528] | 1174 | if [ ${IOS_OK_DEDICATED} -eq 1 ] ; then |
---|
| 1175 | (( current_core_noxios = coreNumber - IOS_PROC_MPI * IOS_PROC_OMP * IOS_PROC_DEP )) |
---|
| 1176 | (( first_comp_proc_dep_loc = 1 + NB_CORE_PER_NODE - current_core_noxios % NB_CORE_PER_NODE )) |
---|
| 1177 | (( second_comp_proc_mpi_loc = IOS_PROC_MPI - 1 )) |
---|
[1593] | 1178 | (( coreNumber_final = current_core_noxios - 1 + first_comp_proc_dep_loc * 2 + second_comp_proc_mpi_loc * IOS_PROC_OMP * IOS_PROC_DEP )) |
---|
| 1179 | else |
---|
| 1180 | (( coreNumber_final = coreNumber )) |
---|
[1528] | 1181 | fi |
---|
| 1182 | |
---|
[1518] | 1183 | if [ ${executionType} -eq 1 ] ; then |
---|
| 1184 | # MPMD + MPI |
---|
| 1185 | sed -e "/::openMPthreads::/d" \ |
---|
[1593] | 1186 | -e "s/::JobNumProcTot::/${coreNumber_final}/" \ |
---|
[1518] | 1187 | ${file} > ${file}.tmp |
---|
| 1188 | |
---|
| 1189 | elif [ ${executionType} -eq 2 ] ; then |
---|
[1519] | 1190 | # MPMD + MPI + OMP :ccc_mprun |
---|
| 1191 | sed -e "/::openMPthreads::/d" \ |
---|
[1593] | 1192 | -e "s/::JobNumProcTot::/${coreNumber_final}/" \ |
---|
[1519] | 1193 | ${file} > ${file}.tmp |
---|
| 1194 | |
---|
[1518] | 1195 | elif [ ${executionType} -eq 3 ] ; then |
---|
| 1196 | # SPMD + MPI/OMP |
---|
| 1197 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 1198 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 1199 | -e "/#MSUB -x/d" \ |
---|
| 1200 | ${file} > ${file}.tmp |
---|
| 1201 | |
---|
| 1202 | elif [ ${executionType} -eq 4 ] ; then |
---|
| 1203 | # SPMD + MPI only |
---|
| 1204 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 1205 | -e "/::openMPthreads::/d" \ |
---|
| 1206 | -e "/#MSUB -x/d" \ |
---|
| 1207 | ${file} > ${file}.tmp |
---|
| 1208 | |
---|
| 1209 | elif [ ${executionType} -eq 5 ] ; then |
---|
| 1210 | # SPMD + OMP only |
---|
| 1211 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 1212 | -e "/::JobNumProcTot::/d" \ |
---|
| 1213 | -e "/#MSUB -x/d" \ |
---|
| 1214 | ${file} > ${file}.tmp |
---|
| 1215 | |
---|
| 1216 | elif [ ${executionType} -eq 6 ] ; then |
---|
| 1217 | # SEQUENTIAL THEN |
---|
| 1218 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
| 1219 | -e "/::openMPthreads::/d" \ |
---|
| 1220 | -e "/#MSUB -x/d" \ |
---|
| 1221 | ${file} > ${file}.tmp |
---|
| 1222 | |
---|
| 1223 | fi |
---|
| 1224 | |
---|
| 1225 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
| 1226 | |
---|
| 1227 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
| 1228 | } |
---|
| 1229 | |
---|
| 1230 | ############################################################ |
---|
| 1231 | # Build MPI/OMP scripts run file (dummy function) |
---|
| 1232 | |
---|
| 1233 | #D-#================================================== |
---|
| 1234 | #D-function IGCM_sys_build_run_file |
---|
| 1235 | #D-* Purpose: build run file (deprecated) |
---|
| 1236 | #D-* Examples: |
---|
| 1237 | #D- |
---|
| 1238 | function IGCM_sys_build_run_file { |
---|
| 1239 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
| 1240 | } |
---|
| 1241 | |
---|
| 1242 | ############################################################ |
---|
| 1243 | # Build MPI/OMP scripts |
---|
| 1244 | |
---|
| 1245 | #D-#================================================== |
---|
| 1246 | #D-function IGCM_sys_build_execution_scripts |
---|
| 1247 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
| 1248 | #D-* Examples: |
---|
| 1249 | #D- |
---|
| 1250 | function IGCM_sys_build_execution_scripts |
---|
| 1251 | { |
---|
| 1252 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
| 1253 | if ( $DEBUG_sys ) ; then |
---|
| 1254 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
| 1255 | fi |
---|
| 1256 | |
---|
| 1257 | EXECUTION=${HOST_MPIRUN_COMMAND} |
---|
| 1258 | |
---|
| 1259 | if ( ${OK_PARA_MPMD} ) ; then |
---|
| 1260 | |
---|
| 1261 | # MPMD mode |
---|
| 1262 | # 1 MPI only |
---|
| 1263 | # 2 MPI/OpenMP mpirun method |
---|
| 1264 | # 3 MPI/OpenMP ccc_mprun method |
---|
| 1265 | |
---|
| 1266 | if [ -f run_file ] ; then |
---|
| 1267 | IGCM_sys_Rm -f run_file |
---|
| 1268 | fi |
---|
| 1269 | touch run_file |
---|
| 1270 | |
---|
| 1271 | # case 1 : Only MPI (MPMD) |
---|
| 1272 | if ( ! ${OK_PARA_OMP} ) ; then |
---|
| 1273 | |
---|
| 1274 | # Build run_file |
---|
| 1275 | |
---|
| 1276 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
| 1277 | # the coupler ie oasis3 must be the first one |
---|
| 1278 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1279 | |
---|
| 1280 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 1281 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1282 | |
---|
| 1283 | # for CPL component only |
---|
| 1284 | if [ "X${comp}" = "XCPL" ] && [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
| 1285 | |
---|
| 1286 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1287 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 1288 | echo "${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file |
---|
| 1289 | fi |
---|
| 1290 | done |
---|
| 1291 | |
---|
| 1292 | # Then second loop on the components |
---|
| 1293 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1294 | |
---|
| 1295 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 1296 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1297 | |
---|
| 1298 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
| 1299 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
| 1300 | |
---|
| 1301 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1302 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
[1528] | 1303 | eval comp_proc_dep_loc=\${${comp}_PROC_DEP} |
---|
| 1304 | |
---|
| 1305 | # In case of use of DEDICATED option XIOS servers, do not share xios nodes with xios clients |
---|
| 1306 | # Compute the number of core to add to force the use of a new node for xios servers |
---|
| 1307 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XIOS" ] ) ; then |
---|
| 1308 | if [ ${IOS_OK_DEDICATED} -eq 1 ] ; then |
---|
| 1309 | (( current_core_noxios = coreNumber - comp_proc_mpi_loc * comp_proc_dep_loc )) |
---|
| 1310 | (( first_comp_proc_dep_loc = 1 + NB_CORE_PER_NODE - current_core_noxios % NB_CORE_PER_NODE )) |
---|
| 1311 | (( second_comp_proc_mpi_loc = comp_proc_mpi_loc - 1 )) |
---|
| 1312 | if [ ${comp_proc_dep_loc} -lt ${first_comp_proc_dep_loc} ] ; then |
---|
| 1313 | echo "1-${first_comp_proc_dep_loc} ./${ExeNameOut}" >>run_file |
---|
| 1314 | if [ ${comp_proc_mpi_loc} -gt 1 ] ; then |
---|
| 1315 | echo "${second_comp_proc_mpi_loc}-${comp_proc_dep_loc} ./${ExeNameOut}" >>run_file |
---|
| 1316 | fi |
---|
| 1317 | else |
---|
| 1318 | echo "${comp_proc_mpi_loc}-${comp_proc_dep_loc} ./${ExeNameOut}" >>run_file |
---|
| 1319 | fi |
---|
| 1320 | else |
---|
| 1321 | echo "${comp_proc_mpi_loc}-${comp_proc_dep_loc} ./${ExeNameOut}" >>run_file |
---|
| 1322 | fi |
---|
| 1323 | else |
---|
| 1324 | echo "${comp_proc_mpi_loc}-${comp_proc_dep_loc} ./${ExeNameOut}" >>run_file |
---|
| 1325 | fi |
---|
| 1326 | |
---|
| 1327 | |
---|
[1518] | 1328 | fi |
---|
| 1329 | done |
---|
| 1330 | |
---|
[1528] | 1331 | ## module advised by TGCC (instead of 2 variables) |
---|
| 1332 | module load feature/bridge/heterogenous_mpmd |
---|
| 1333 | |
---|
[1518] | 1334 | EXECUTION="${HOST_MPIRUN_COMMAND} -f ./run_file" |
---|
| 1335 | |
---|
| 1336 | IGCM_sys_Chmod u+x run_file |
---|
| 1337 | if ( $DEBUG_sys ) ; then |
---|
| 1338 | echo "run_file contains : " |
---|
| 1339 | cat run_file |
---|
| 1340 | fi |
---|
| 1341 | |
---|
| 1342 | elif ( [ "X${config_UserChoices_ExecutionModeOnCurie}" = "Xmpirun" ] ) ; then |
---|
| 1343 | |
---|
| 1344 | # 2 MPI/OpenMP mpirun method |
---|
| 1345 | |
---|
| 1346 | # Use of mpirun instead of ccc_mprun |
---|
| 1347 | EXECUTION="time mpirun" |
---|
| 1348 | |
---|
| 1349 | # Hosts treatment |
---|
| 1350 | ${EXECUTION} hostname | sort | uniq > hosts.tmp |
---|
| 1351 | |
---|
| 1352 | i=0 |
---|
| 1353 | rm -f hosts rankfile |
---|
| 1354 | IGCM_debug_Print 1 "sys Irene-amd, Hosts available :" |
---|
| 1355 | for nodes in `cat hosts.tmp` |
---|
| 1356 | do |
---|
| 1357 | host[$i]=$nodes |
---|
| 1358 | echo "${host[$i]}" >> hosts |
---|
| 1359 | IGCM_debug_Print 1 ${host[$i]} |
---|
| 1360 | i=$((i+1)) |
---|
| 1361 | done |
---|
| 1362 | rm -f hosts.tmp |
---|
| 1363 | |
---|
| 1364 | listnodes=${host[*]} |
---|
| 1365 | |
---|
| 1366 | EXECUTION="${EXECUTION} -hostfile hosts -rankfile rankfile" |
---|
| 1367 | |
---|
| 1368 | # Initialisation |
---|
| 1369 | rank=0 |
---|
| 1370 | current_core=0 |
---|
| 1371 | init_exec=n |
---|
| 1372 | |
---|
| 1373 | # Loop on the components |
---|
| 1374 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1375 | |
---|
| 1376 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 1377 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1378 | |
---|
| 1379 | # Not possible if oasis has an executable (i.e old version of oasis3) |
---|
| 1380 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
---|
| 1381 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
---|
| 1382 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
---|
| 1383 | IGCM_debug_Verif_Exit |
---|
| 1384 | fi |
---|
| 1385 | |
---|
| 1386 | # Only if we really have an executable for the component : |
---|
| 1387 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
| 1388 | |
---|
| 1389 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1390 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 1391 | eval comp_proc_nod_loc=\${${comp}_PROC_NOD} |
---|
| 1392 | |
---|
| 1393 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1394 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1395 | if [ ${comp_proc_omp_loc} -gt 1 ] ; then |
---|
| 1396 | |
---|
| 1397 | # Check if the number of threads is correct |
---|
| 1398 | case ${comp_proc_omp_loc} in |
---|
| 1399 | 2|4|8|16) |
---|
| 1400 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
---|
| 1401 | ;; |
---|
| 1402 | *) |
---|
| 1403 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
| 1404 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
| 1405 | IGCM_debug_Print 2 "Only 2,4,8,16 as number of OMP threads are possible " |
---|
| 1406 | IGCM_debug_Verif_Exit |
---|
| 1407 | ;; |
---|
| 1408 | esac |
---|
| 1409 | echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 1410 | echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 1411 | echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 1412 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1413 | fi |
---|
| 1414 | |
---|
| 1415 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1416 | echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK )) " >> script_${ExeNameOut}.ksh |
---|
| 1417 | echo "MYMPIRANK=\$(printf '%3.3d\n' \${MYMPIRANK})" >> script_${ExeNameOut}.ksh |
---|
| 1418 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh |
---|
| 1419 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1420 | |
---|
| 1421 | if [ ${init_exec} = y ] ; then |
---|
| 1422 | EXECUTION="${EXECUTION} : -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
| 1423 | else |
---|
| 1424 | EXECUTION="${EXECUTION} -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
| 1425 | init_exec=y |
---|
| 1426 | fi |
---|
| 1427 | |
---|
| 1428 | # Build rankfile : method used to assign cores and nodes for the MPI process |
---|
| 1429 | # Ex : |
---|
| 1430 | #rank 0=curie5296 slot=0,1,2,3 |
---|
| 1431 | #rank 1=curie5296 slot=4,5,6,7 |
---|
| 1432 | # Example of final command : |
---|
| 1433 | # mpirun -hostfile hosts -rankfile rankfile -np 27 ./script_lmdz.x.ksh : -np 5 ./script_opa.xx.ksh |
---|
| 1434 | # with script_lmdz.x.ksh : |
---|
| 1435 | # #!/bin/ksh |
---|
| 1436 | #export KMP_STACKSIZE=3g |
---|
| 1437 | #export KMP_LIBRARY=turnaround |
---|
| 1438 | #export MKL_SERIAL=YES |
---|
| 1439 | #OMP_NUM_THREADS=4 |
---|
| 1440 | #./lmdz.x |
---|
| 1441 | if [ ${comp_proc_nod_loc} -gt 1 ] ; then |
---|
| 1442 | (( offset_comp_proc_loc = NB_CORE_PER_NODE / (comp_proc_mpi_loc / comp_proc_nod_loc) )) |
---|
| 1443 | else |
---|
| 1444 | (( offset_comp_proc_loc = comp_proc_omp_loc )) |
---|
| 1445 | fi |
---|
| 1446 | for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do |
---|
| 1447 | (( index_host = current_core / NB_CORE_PER_NODE )) |
---|
| 1448 | host_value=${host[${index_host}]} |
---|
| 1449 | (( slot = current_core % NB_CORE_PER_NODE )) |
---|
| 1450 | virg="," |
---|
| 1451 | string_final="" |
---|
| 1452 | for index in `seq $slot $(($slot+$comp_proc_omp_loc-1))`; do |
---|
| 1453 | string=$index$virg |
---|
| 1454 | string_final=$string_final$string |
---|
| 1455 | done |
---|
| 1456 | string_final=$( echo $string_final | sed "s/.$//" ) |
---|
| 1457 | echo "rank $rank=$host_value slot=$string_final" >> rankfile |
---|
| 1458 | (( rank = rank + 1 )) |
---|
| 1459 | (( current_core = current_core + offset_comp_proc_loc )) |
---|
| 1460 | done |
---|
| 1461 | fi |
---|
| 1462 | done |
---|
| 1463 | |
---|
| 1464 | elif ( [ "X${config_UserChoices_ExecutionModeOnCurie}" = "X" ] || [ "X${config_UserChoices_ExecutionModeOnCurie}" = "Xccc_mprun" ] ) ; then |
---|
| 1465 | |
---|
| 1466 | # 3 MPI/OpenMP ccc_mprun method |
---|
| 1467 | |
---|
| 1468 | # MPI-OpenMP (MPMD) |
---|
| 1469 | # example of run_file |
---|
| 1470 | # 71-8 env OMP_NUM_THREADS=8 ./script_lmdz.x.ksh |
---|
| 1471 | # 480-1 env OMP_NUM_THREADS=1 ./script_opa.xx.ksh |
---|
| 1472 | # 1-1 env OMP_NUM_THREADS=1 ./script_xios.x.ksh |
---|
| 1473 | |
---|
| 1474 | # Loop on the components |
---|
| 1475 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1476 | |
---|
| 1477 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 1478 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1479 | |
---|
| 1480 | # Not possible if oasis has an executable (i.e old version of oasis3) |
---|
| 1481 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
---|
| 1482 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
---|
| 1483 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
---|
| 1484 | IGCM_debug_Verif_Exit |
---|
| 1485 | fi |
---|
| 1486 | |
---|
| 1487 | # Only if we really have an executable for the component : |
---|
| 1488 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
| 1489 | |
---|
| 1490 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1491 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
[1528] | 1492 | eval comp_proc_dep_loc=\${${comp}_PROC_DEP} |
---|
[1518] | 1493 | |
---|
[1528] | 1494 | # Compute number of cores per process |
---|
| 1495 | (( comp_proc_omp_dep_loc = comp_proc_omp_loc * comp_proc_dep_loc )) |
---|
| 1496 | |
---|
[1518] | 1497 | # Build script files |
---|
| 1498 | |
---|
| 1499 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1500 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1501 | if [ ${comp_proc_omp_loc} -gt 1 ] ; then |
---|
| 1502 | |
---|
| 1503 | # Check if the number of threads is correct |
---|
| 1504 | case ${comp_proc_omp_loc} in |
---|
[1524] | 1505 | 2|4|8|16) |
---|
[1518] | 1506 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
---|
| 1507 | ;; |
---|
| 1508 | *) |
---|
| 1509 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
| 1510 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
[1524] | 1511 | IGCM_debug_Print 2 "Only 2,4,8,16 as number of OMP threads are possible " |
---|
[1518] | 1512 | IGCM_debug_Verif_Exit |
---|
| 1513 | ;; |
---|
| 1514 | esac |
---|
| 1515 | ### only for LMDZ? |
---|
| 1516 | echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 1517 | echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 1518 | echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 1519 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1520 | |
---|
| 1521 | fi |
---|
| 1522 | |
---|
| 1523 | # to have out/err per process on different files |
---|
| 1524 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh |
---|
| 1525 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1526 | |
---|
| 1527 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1528 | |
---|
| 1529 | # Complete run_file |
---|
| 1530 | |
---|
[1528] | 1531 | # In case of use of DEDICATED option XIOS servers, do not share xios nodes with xios clients |
---|
| 1532 | # Compute the number of core to add to force the use of a new node for xios servers |
---|
| 1533 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XIOS" ] ) ; then |
---|
| 1534 | if [ ${IOS_OK_DEDICATED} -eq 1 ] ; then |
---|
| 1535 | (( current_core_noxios = coreNumber - comp_proc_mpi_loc * comp_proc_omp_dep_loc )) |
---|
| 1536 | (( first_comp_proc_dep_loc = 1 + NB_CORE_PER_NODE - current_core_noxios % NB_CORE_PER_NODE )) |
---|
| 1537 | (( second_comp_proc_mpi_loc = comp_proc_mpi_loc - 1 )) |
---|
| 1538 | if [ ${comp_proc_omp_dep_loc} -lt ${first_comp_proc_dep_loc} ] ; then |
---|
| 1539 | echo "1-${first_comp_proc_dep_loc} env OMP_NUM_THREADS=1 ./script_${ExeNameOut}.ksh " >>run_file |
---|
| 1540 | if [ ${comp_proc_mpi_loc} -gt 1 ] ; then |
---|
[1531] | 1541 | echo "${second_comp_proc_mpi_loc}-${comp_proc_omp_dep_loc} env OMP_NUM_THREADS=1 ./script_${ExeNameOut}.ksh " >>run_file |
---|
[1528] | 1542 | fi |
---|
| 1543 | else |
---|
| 1544 | echo "${comp_proc_mpi_loc}-${comp_proc_omp_dep_loc} env OMP_NUM_THREADS=1 ./script_${ExeNameOut}.ksh " >>run_file |
---|
| 1545 | fi |
---|
| 1546 | else |
---|
| 1547 | echo "${comp_proc_mpi_loc}-${comp_proc_omp_dep_loc} env OMP_NUM_THREADS=1 ./script_${ExeNameOut}.ksh " >>run_file |
---|
| 1548 | fi |
---|
| 1549 | else |
---|
| 1550 | echo "${comp_proc_mpi_loc}-${comp_proc_omp_dep_loc} env OMP_NUM_THREADS=${comp_proc_omp_loc} ./script_${ExeNameOut}.ksh " >>run_file |
---|
| 1551 | fi |
---|
[1518] | 1552 | |
---|
| 1553 | fi |
---|
| 1554 | done |
---|
| 1555 | |
---|
| 1556 | ## variable added to stop after 60s instead of 600s by default. |
---|
| 1557 | ## This is used when no error comes from executables and when something stopped an executable without notice. |
---|
| 1558 | export SLURM_WAIT=60 |
---|
| 1559 | |
---|
| 1560 | ## module advised by TGCC (instead of 2 variables) |
---|
| 1561 | module load feature/bridge/heterogenous_mpmd |
---|
| 1562 | |
---|
| 1563 | # set EXECUTION for ccc_mprun case (similar to #1 : MPI only MPMD method) |
---|
| 1564 | |
---|
| 1565 | EXECUTION="${HOST_MPIRUN_COMMAND} -f ./run_file" |
---|
| 1566 | |
---|
| 1567 | IGCM_sys_Chmod u+x run_file |
---|
| 1568 | if ( $DEBUG_sys ) ; then |
---|
| 1569 | echo "run_file contains : " |
---|
| 1570 | cat run_file |
---|
| 1571 | fi |
---|
| 1572 | |
---|
| 1573 | else |
---|
| 1574 | |
---|
| 1575 | IGCM_debug_Print 1 "sys Curie : choose mpirun or ccc_mprun in config.card for ExecutionModeOnCurie" |
---|
| 1576 | |
---|
| 1577 | fi # 1 2 or 3 if ${OK_PARA_MPMD} |
---|
| 1578 | |
---|
| 1579 | else |
---|
| 1580 | # Only one executable (SPMD mode). |
---|
| 1581 | |
---|
| 1582 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1583 | |
---|
| 1584 | # Only if we really have an executable for the component : |
---|
| 1585 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1586 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
| 1587 | |
---|
| 1588 | # Build script files |
---|
| 1589 | |
---|
| 1590 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1591 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1592 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1593 | |
---|
| 1594 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 1595 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 1596 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1597 | echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 1598 | echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 1599 | echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 1600 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1601 | fi |
---|
| 1602 | |
---|
| 1603 | if ( ${OK_PARA_MPI} ) ; then |
---|
| 1604 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1605 | # Default : ccc_mprun used if nb_proc gt 1 |
---|
| 1606 | # to have out/err per process on different files |
---|
| 1607 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh |
---|
| 1608 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1609 | EXECUTION="${HOST_MPIRUN_COMMAND} -n ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
| 1610 | else |
---|
| 1611 | # Default : ccc_mprun is NOT used if nb_proc eq 1 |
---|
| 1612 | # to have out/err per process on different files |
---|
| 1613 | echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
| 1614 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1615 | EXECUTION="/usr/bin/time ./script_${ExeNameOut}.ksh" |
---|
| 1616 | fi |
---|
| 1617 | |
---|
| 1618 | IGCM_debug_Print 1 "sys Irene-amd : script_${ExeNameOut}.ksh contains" |
---|
| 1619 | cat script_${ExeNameOut}.ksh |
---|
| 1620 | |
---|
| 1621 | fi |
---|
| 1622 | |
---|
| 1623 | done |
---|
| 1624 | |
---|
| 1625 | fi # ${OK_PARA_MPMD} |
---|
| 1626 | |
---|
| 1627 | IGCM_debug_Print 1 "sys Irene-amd : execution command is " |
---|
| 1628 | IGCM_debug_Print 1 "$EXECUTION" |
---|
| 1629 | |
---|
| 1630 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
| 1631 | } |
---|
| 1632 | |
---|
| 1633 | #D-#================================================== |
---|
| 1634 | #D-function IGCM_sys_check_path |
---|
| 1635 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
| 1636 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
| 1637 | #D-* Examples: |
---|
| 1638 | #D- |
---|
| 1639 | function IGCM_sys_check_path { |
---|
| 1640 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
| 1641 | if ( $DEBUG_sys ) ; then |
---|
| 1642 | echo "IGCM_sys_check_path" |
---|
| 1643 | fi |
---|
| 1644 | |
---|
| 1645 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${CCCWORKDIR} ] || [ X${RUN_DIR_PATH} = X${CCCSCRATCHDIR} ] || [ X${RUN_DIR_PATH} = X${CCCSTOREDIR} ] ) ; then |
---|
| 1646 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
| 1647 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
| 1648 | IGCM_debug_Exit "This will stop the job" |
---|
| 1649 | fi |
---|
| 1650 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
| 1651 | } |
---|
| 1652 | |
---|
| 1653 | #D-#================================================== |
---|
| 1654 | #D-function IGCM_sys_check_quota |
---|
| 1655 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
| 1656 | #D-* Examples: |
---|
| 1657 | #D- |
---|
| 1658 | function IGCM_sys_check_quota { |
---|
| 1659 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
| 1660 | if ( $DEBUG_sys ) ; then |
---|
| 1661 | echo "IGCM_sys_check_quota" |
---|
| 1662 | fi |
---|
| 1663 | # Limit of quota (in %) |
---|
| 1664 | limit_quota=90 |
---|
| 1665 | |
---|
| 1666 | # Check of the volume |
---|
| 1667 | volume_quota=$(ccc_quota | grep ' scratch' | gawk '{print $2}') |
---|
| 1668 | volume_avail=$(ccc_quota | grep ' scratch' | gawk '{print $3}') |
---|
| 1669 | |
---|
| 1670 | if ( [ ! X${volume_quota} = X ] && [ ! ${volume_quota} = "-" ] ) ; then |
---|
| 1671 | |
---|
| 1672 | unit_avail=${volume_avail: -1} |
---|
| 1673 | unit_quota=${volume_quota: -1} |
---|
| 1674 | |
---|
| 1675 | if [ "${unit_quota}" = "*" ] ; then |
---|
| 1676 | IGCM_debug_Print 1 "Please, check your quota of volume on scratch" |
---|
| 1677 | IGCM_debug_Print 1 "More than 100% of your quota is used" |
---|
| 1678 | IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
| 1679 | IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
| 1680 | IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
| 1681 | IGCM_debug_Verif_Exit |
---|
| 1682 | fi |
---|
| 1683 | |
---|
| 1684 | temp_avail=${volume_avail%%${volume_avail: -1}*} |
---|
| 1685 | temp_quota=${volume_quota%%${volume_quota: -1}*} |
---|
| 1686 | |
---|
| 1687 | if [ ! ${unit_avail} = ${unit_quota} ] ; then |
---|
| 1688 | |
---|
| 1689 | # Convertion |
---|
| 1690 | if [ ${volume_avail: -1} = "T" ] ; then |
---|
| 1691 | (( temp_avail = temp_avail * 1000000000000 )) |
---|
| 1692 | elif [ ${volume_avail: -1} = "G" ] ; then |
---|
| 1693 | (( temp_avail = temp_avail * 1000000000 )) |
---|
| 1694 | elif [ ${volume_avail: -1} = "M" ] ; then |
---|
| 1695 | (( temp_avail = temp_avail * 1000000 )) |
---|
| 1696 | elif [ ${volume_avail: -1} = "k" ] ; then |
---|
| 1697 | (( temp_avail = temp_avail * 1000 )) |
---|
| 1698 | else |
---|
| 1699 | (( temp_avail = volume_avail )) |
---|
| 1700 | fi |
---|
| 1701 | if [ ${volume_quota: -1} = "T" ] ; then |
---|
| 1702 | (( temp_quota = temp_quota * 1000000000000 )) |
---|
| 1703 | elif [ ${volume_quota: -1} = "G" ] ; then |
---|
| 1704 | (( temp_quota = temp_quota * 1000000000 )) |
---|
| 1705 | elif [ ${volume_quota: -1} = "M" ] ; then |
---|
| 1706 | (( temp_quota = temp_quota * 1000000 )) |
---|
| 1707 | elif [ ${volume_quota: -1} = "k" ] ; then |
---|
| 1708 | (( temp_quota = temp_quota * 1000 )) |
---|
| 1709 | else |
---|
| 1710 | (( temp_quota = volume_quota )) |
---|
| 1711 | fi |
---|
| 1712 | fi |
---|
| 1713 | |
---|
| 1714 | quota_volume=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc) |
---|
| 1715 | # echo "volume ratio is " $quota_volume |
---|
| 1716 | |
---|
| 1717 | if [ ${quota_volume} -ge ${limit_quota} ] ; then |
---|
| 1718 | IGCM_debug_Print 1 "Please, check your quota of volume on scratch" |
---|
| 1719 | IGCM_debug_Print 1 "${quota_volume}% of your quota is used" |
---|
| 1720 | IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
| 1721 | IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
| 1722 | IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
| 1723 | IGCM_debug_Verif_Exit |
---|
| 1724 | fi |
---|
| 1725 | |
---|
| 1726 | fi |
---|
| 1727 | |
---|
| 1728 | # Check of the number of inodes |
---|
| 1729 | |
---|
| 1730 | inode_quota=$(ccc_quota | grep ' scratch' | gawk '{print $6}') |
---|
| 1731 | inode_avail=$(ccc_quota | grep ' scratch' | gawk '{print $7}') |
---|
| 1732 | |
---|
| 1733 | if ( [ ! X${inode_quota} = X ] && [ ! ${inode_quota} = "-" ] ) ; then |
---|
| 1734 | |
---|
| 1735 | unit_avail=${inode_avail: -1} |
---|
| 1736 | unit_quota=${inode_quota: -1} |
---|
| 1737 | |
---|
| 1738 | if [ "${unit_quota}" = "*" ] ; then |
---|
| 1739 | IGCM_debug_Print 1 "Please, check your quota of inode on scratch" |
---|
| 1740 | IGCM_debug_Print 1 "More than 100% of your quota is used" |
---|
| 1741 | IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
| 1742 | IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
| 1743 | IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
| 1744 | IGCM_debug_Verif_Exit |
---|
| 1745 | fi |
---|
| 1746 | |
---|
| 1747 | temp_avail=${inode_avail%%${inode_avail: -1}*} |
---|
| 1748 | temp_quota=${inode_quota%%${inode_quota: -1}*} |
---|
| 1749 | |
---|
| 1750 | if [ ! ${unit_avail} = ${unit_quota} ] ; then |
---|
| 1751 | |
---|
| 1752 | # Convertion |
---|
| 1753 | if [ ${inode_avail: -1} = "T" ] ; then |
---|
| 1754 | (( temp_avail = temp_avail * 1000000000000 )) |
---|
| 1755 | elif [ ${inode_avail: -1} = "G" ] ; then |
---|
| 1756 | (( temp_avail = temp_avail * 1000000000 )) |
---|
| 1757 | elif [ ${inode_avail: -1} = "M" ] ; then |
---|
| 1758 | (( temp_avail = temp_avail * 1000000 )) |
---|
| 1759 | elif [ ${inode_avail: -1} = "k" ] ; then |
---|
| 1760 | (( temp_avail = temp_avail * 1000 )) |
---|
| 1761 | else |
---|
| 1762 | (( temp_avail = inode_avail )) |
---|
| 1763 | fi |
---|
| 1764 | |
---|
| 1765 | if [ ${inode_quota: -1} = "T" ] ; then |
---|
| 1766 | (( temp_quota = temp_quota * 1000000000000 )) |
---|
| 1767 | elif [ ${inode_quota: -1} = "G" ] ; then |
---|
| 1768 | (( temp_quota = temp_quota * 1000000000 )) |
---|
| 1769 | elif [ ${inode_quota: -1} = "M" ] ; then |
---|
| 1770 | (( temp_quota = temp_quota * 1000000 )) |
---|
| 1771 | elif [ ${inode_quota: -1} = "k" ] ; then |
---|
| 1772 | (( temp_quota = temp_quota * 1000 )) |
---|
| 1773 | else |
---|
| 1774 | (( temp_quota = inode_quota )) |
---|
| 1775 | fi |
---|
| 1776 | fi |
---|
| 1777 | quota_inode=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc) |
---|
| 1778 | # echo "inode ratio is " $quota_inode |
---|
| 1779 | |
---|
| 1780 | if [ ${quota_inode} -ge ${limit_quota} ] ; then |
---|
| 1781 | IGCM_debug_Print 1 "Please, check your quota of inode on scratch" |
---|
| 1782 | IGCM_debug_Print 1 "${quota_inode}% of your quota is used" |
---|
| 1783 | IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
| 1784 | IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
| 1785 | IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
| 1786 | IGCM_debug_Verif_Exit |
---|
| 1787 | fi |
---|
| 1788 | fi |
---|
| 1789 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
| 1790 | } |
---|
| 1791 | |
---|
| 1792 | #D-#================================================== |
---|
| 1793 | #D-function IGCM_sys_projectAccounting |
---|
| 1794 | #D-* Purpose: store project accounting information in a file |
---|
| 1795 | #D-* Examples: |
---|
| 1796 | #D- |
---|
| 1797 | function IGCM_sys_projectAccounting { |
---|
| 1798 | IGCM_debug_PushStack "IGCM_sys_projectAccounting" |
---|
| 1799 | if ( $DEBUG_sys ) ; then |
---|
| 1800 | echo "IGCM_sys_check_quota" |
---|
| 1801 | fi |
---|
| 1802 | |
---|
| 1803 | ssh irene194 /usr/bin/ccc_myproject > $1 |
---|
| 1804 | |
---|
| 1805 | IGCM_debug_PopStack "IGCM_sys_projectAccounting" |
---|
| 1806 | } |
---|
| 1807 | |
---|
| 1808 | #D-#================================================== |
---|
| 1809 | #D-function IGCM_sys_getJobSchedulerID |
---|
| 1810 | #D-* Purpose: Get the job ID during execution |
---|
| 1811 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
| 1812 | #D- |
---|
| 1813 | function IGCM_sys_getJobSchedulerID { |
---|
| 1814 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
| 1815 | if ( $DEBUG_sys ) ; then |
---|
| 1816 | echo "IGCM_sys_getJobSchedulerID" |
---|
| 1817 | fi |
---|
| 1818 | eval ${1}=${BRIDGE_MSUB_JOBID} |
---|
| 1819 | |
---|
| 1820 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
| 1821 | } |
---|
| 1822 | |
---|
| 1823 | #D-#================================================== |
---|
| 1824 | #D-function IGCM_sys_GetJobID |
---|
| 1825 | #D-* Purpose: Get the job ID from the JobName |
---|
| 1826 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
| 1827 | #D- |
---|
| 1828 | function IGCM_sys_GetJobID { |
---|
| 1829 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
| 1830 | if ( $DEBUG_sys ) ; then |
---|
| 1831 | echo "IGCM_sys_GetJobID" |
---|
| 1832 | fi |
---|
| 1833 | |
---|
| 1834 | # With -f option, the full job name is given in the last column |
---|
| 1835 | ID=$( ccc_mstat -f -u $2 | \ |
---|
| 1836 | gawk -v JobName=$1 '( $NF ~ JobName ) { print $1 }' ) |
---|
| 1837 | |
---|
| 1838 | eval ${3}=${ID} |
---|
| 1839 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
| 1840 | } |
---|
| 1841 | |
---|
| 1842 | #D-#================================================== |
---|
| 1843 | #D-function IGCM_sys_CountJobInQueue |
---|
| 1844 | #D-* Purpose: Count number of users job |
---|
| 1845 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
| 1846 | #D- |
---|
| 1847 | function IGCM_sys_CountJobInQueue { |
---|
| 1848 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
| 1849 | if ( $DEBUG_sys ) ; then |
---|
| 1850 | echo "IGCM_sys_CountJobInQueue" |
---|
| 1851 | fi |
---|
| 1852 | |
---|
| 1853 | # With -f option, the full job name is given in the last column |
---|
| 1854 | NbRun=$( ccc_mstat -f | gawk -v JobName=$1 'BEGIN { x=0 } ( $NF ~ JobName ) { x=x+1 } END { print x }' ) |
---|
| 1855 | |
---|
| 1856 | eval ${2}=${NbRun} |
---|
| 1857 | |
---|
| 1858 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
| 1859 | } |
---|
| 1860 | |
---|
| 1861 | #D-#================================================== |
---|
| 1862 | #D-function IGCM_sys_ListJobInQueue |
---|
| 1863 | #D-* Purpose: Produce a list of users computing jobs (excluding post-processing) |
---|
| 1864 | #D-* Examples: IGCM_sys_ListJobInQueue ${User} JobNameList |
---|
| 1865 | #D- |
---|
| 1866 | function IGCM_sys_ListJobInQueue { |
---|
| 1867 | IGCM_debug_PushStack "IGCM_sys_ListJobInQueue" |
---|
| 1868 | if ( $DEBUG_sys ) ; then |
---|
| 1869 | echo "IGCM_sys_ListJobInQueue" |
---|
| 1870 | fi |
---|
| 1871 | |
---|
| 1872 | # With -f option, the full job name is given in the last column |
---|
| 1873 | set -A JobList $( ccc_mstat -f | gawk -v User=$1 \ |
---|
| 1874 | '( $2 == User && \ |
---|
| 1875 | $NF != /TS/ && \ |
---|
| 1876 | $NF !~ /PACK/ && \ |
---|
| 1877 | $NF !~ /REBUILD/ && \ |
---|
| 1878 | $NF !~ /pack/ ) \ |
---|
| 1879 | { print $NF }' | sed -e "s/\(.*\)\.[0-9]*/\1/" ) |
---|
| 1880 | |
---|
| 1881 | eval set -A ${2} ${JobList[*]} |
---|
| 1882 | |
---|
| 1883 | IGCM_debug_PopStack "IGCM_sys_ListJobInQueue" |
---|
| 1884 | } |
---|
| 1885 | |
---|
| 1886 | #D-#================================================== |
---|
| 1887 | #D-function IGCM_sys_atlas |
---|
| 1888 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
---|
| 1889 | #D-* Examples: |
---|
| 1890 | #D- |
---|
| 1891 | function IGCM_sys_atlas { |
---|
| 1892 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
---|
| 1893 | if ( $DEBUG_sys ) ; then |
---|
| 1894 | echo "IGCM_sys_atlas :" $@ |
---|
| 1895 | fi |
---|
| 1896 | |
---|
| 1897 | typeset status |
---|
| 1898 | |
---|
| 1899 | \ccc_mprun atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 1900 | status=$? |
---|
| 1901 | if [ ${status} -gt 0 ] ; then |
---|
| 1902 | echo "IGCM_sys_atlas : error code ${status}" |
---|
| 1903 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1904 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1905 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1906 | return 1 |
---|
| 1907 | else |
---|
| 1908 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1909 | return 0 |
---|
| 1910 | fi |
---|
| 1911 | |
---|
| 1912 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1913 | } |
---|
| 1914 | |
---|
| 1915 | #D-#================================================== |
---|
| 1916 | #D-function IGCM_sys_rebuild_nemo |
---|
| 1917 | #D-* Purpose: rebuild nemo parallel files with nemo specific rebuild on curie |
---|
| 1918 | #D-* Examples: |
---|
| 1919 | #D- |
---|
| 1920 | |
---|
| 1921 | function IGCM_sys_rebuild_nemo { |
---|
| 1922 | IGCM_debug_PushStack "IGCM_sys_rebuild_nemo" $@ |
---|
| 1923 | if ( $DEBUG_sys ) ; then |
---|
| 1924 | echo "IGCM_sys_rebuild_nemo :" $@ |
---|
| 1925 | fi |
---|
| 1926 | |
---|
[1582] | 1927 | $( ccc_home -u igcmg)/Tools/irene/bin/rebuild_nemo ${1} ${2} |
---|
[1518] | 1928 | |
---|
| 1929 | IGCM_debug_PopStack "IGCM_sys_rebuild_nemo" |
---|
| 1930 | } |
---|
| 1931 | |
---|