[664] | 1 | #!/bin/ksh |
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[2] | 2 | |
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| 3 | #************************************************************** |
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| 4 | # Author: Sebastien Denvil, Martial Mancip |
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[373] | 5 | # Contact: Martial.Mancip__at__ipsl.jussieu.fr |
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| 6 | # $Revision:: $ Revision of last commit |
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| 7 | # $Author:: $ Author of last commit |
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| 8 | # $Date:: $ Date of last commit |
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[2] | 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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[664] | 16 | # if you use the prefix #D- for comments to be extracted. |
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[2] | 17 | # Extract with command: cat lib* | grep "^#D-" | cut -c "4-" |
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| 18 | #========================================================= |
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[664] | 19 | |
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[2] | 20 | #D-#================================================== |
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| 21 | #D-LibIGCM_sys Default host |
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| 22 | #D-#================================================== |
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| 23 | #D- |
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[664] | 24 | #D- This ksh library if a layer under some usefull |
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[800] | 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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[2] | 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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[117] | 34 | #==================================================== |
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[800] | 35 | # set DEBUG_sys to true to output calls of function |
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[2] | 36 | typeset -r DEBUG_sys=${DEBUG_sys:=true} |
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| 37 | |
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[117] | 38 | #==================================================== |
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[2] | 39 | # Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get) |
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| 40 | typeset -r DRYRUN=${DRYRUN:=0} |
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| 41 | |
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| 42 | # YOU MUST COMPILE YOUR EXE FILES FOR DRYRUN MODE ! |
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| 43 | # ------------------------------------------------------------------------------------- |
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| 44 | # | DRYRUN= | Date computations, | sys_Get | Exe | sys_Put_Out; sys_Put_Rest | |
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[809] | 45 | # | | Cp/Exe/param/files | | | | |
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| 46 | # | | Chmod Qsub | | | | |
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[2] | 47 | # ------------------------------------------------------------------------------------- |
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| 48 | # | 0 | yes | yes | yes | yes | |
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| 49 | # ------------------------------------------------------------------------------------- |
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| 50 | # | 1 | yes | yes | yes | no | |
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| 51 | # ------------------------------------------------------------------------------------- |
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| 52 | # | 2 | yes | yes | no | no | |
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| 53 | # ------------------------------------------------------------------------------------- |
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| 54 | # | 3 | yes | no | no | no | |
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| 55 | # ------------------------------------------------------------------------------------- |
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| 56 | |
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| 57 | #===================================================== |
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[800] | 58 | # Global Variables : |
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[2] | 59 | #===================================================== |
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| 60 | # Language : "fr" or "en" |
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| 61 | typeset -r MYLANG="fr" |
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| 62 | |
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| 63 | #===================================================== |
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[1300] | 64 | # Host user names project maxCpuTime |
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[217] | 65 | # $hostname ou hostname |
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[1180] | 66 | typeset HOST=${HOST:=$( hostname )} |
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[2] | 67 | # $username ou whoami |
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[1180] | 68 | typeset LOGIN=${LOGIN:=$( whoami )} |
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[71] | 69 | # $hostname of the MASTER job |
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[1180] | 70 | typeset MASTER=${MASTER:=$( hostname )} |
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[1201] | 71 | # project name |
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| 72 | typeset PROJECT=NONE |
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| 73 | # jobWarningDelay in seconds |
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| 74 | typeset jobWarningDelay=NONE |
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[2] | 75 | |
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| 76 | #D- |
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| 77 | #D-#================================================== |
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| 78 | #D-Program used in libIGCM |
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| 79 | #D-#================================================== |
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| 80 | |
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[742] | 81 | # Submit command |
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| 82 | typeset SUBMIT=${SUBMIT:=qsub} |
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[2] | 83 | # rsync with path |
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[664] | 84 | typeset -r RSYNC=/usr/bin/rsync |
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[800] | 85 | # RSYNC_opt args to rsync |
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[117] | 86 | typeset -r RSYNC_opt="-va" |
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[664] | 87 | # ie storage filesystem |
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| 88 | typeset -r STOREHOST=${MASTER} |
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[305] | 89 | |
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[2] | 90 | #==================================================== |
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[1180] | 91 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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[305] | 92 | #==================================================== |
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| 93 | #. /home/${LOGIN}/.atlas_env_${HOST}_ksh |
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[1180] | 94 | #export PATH=${PATH}:/home/${LOGIN}/rebuild/bin/ |
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[1485] | 95 | IGCM_debug_Print 1 "Modules will be loaded later in IGCM_sys_activ_variables." |
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[2] | 96 | |
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[117] | 97 | #==================================================== |
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[2] | 98 | # Host specific DIRECTORIES |
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| 99 | #==================================================== |
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| 100 | |
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| 101 | #==================================================== |
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[664] | 102 | #- MirrorlibIGCM for frontend |
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| 103 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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[2] | 104 | |
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| 105 | #==================================================== |
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[800] | 106 | #- libIGCM_POST for frontend |
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[343] | 107 | typeset -r libIGCM_POST=${libIGCM} |
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| 108 | |
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| 109 | #==================================================== |
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[664] | 110 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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| 111 | typeset -r R_EXE="${MODIPSL}/bin" |
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| 112 | |
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| 113 | #==================================================== |
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[2] | 114 | #- SUBMIT_DIR : submission dir |
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[1124] | 115 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PWD}} |
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[2] | 116 | |
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| 117 | #==================================================== |
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[725] | 118 | #- IN |
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[1484] | 119 | typeset -r R_IN=${R_IN:=/home_local/${LOGIN}/IGCM} |
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[725] | 120 | |
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| 121 | #==================================================== |
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[2] | 122 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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[1484] | 123 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/home_local/${LOGIN}/RUN_DIR/tmp$$} |
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[2] | 124 | |
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| 125 | #==================================================== |
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[1179] | 126 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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[1186] | 127 | typeset -r OUTCOMMAND_PATH=/tmp |
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[1179] | 128 | |
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| 129 | #==================================================== |
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[2] | 130 | #- HOST_MPIRUN_COMMAND |
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| 131 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="time mpirun"} |
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| 132 | |
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[61] | 133 | #==================================================== |
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| 134 | #- Max number of arguments passed to nco operator or demigration command |
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| 135 | UNIX_MAX_LIMIT=360 |
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| 136 | |
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[664] | 137 | #==================================================== |
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[1300] | 138 | #- set PackDefault to false on the default machine |
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[1180] | 139 | PackDefault=false |
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| 140 | |
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| 141 | #==================================================== |
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[664] | 142 | #- Default number of MPI task for IPSL coupled model |
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| 143 | #- required for backward compatibility |
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| 144 | #- |
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[1300] | 145 | DEFAULT_NUM_PROC_OCE=5 |
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[664] | 146 | DEFAULT_NUM_PROC_CPL=1 |
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| 147 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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| 148 | |
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[2] | 149 | #D-#================================================== |
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[1057] | 150 | #D-function IGCM_sys_defineArchives |
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| 151 | #D-* Purpose: |
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| 152 | #D-* Define ARCHIVE : Dedicated to large files |
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| 153 | #D-* Define STORAGE : Dedicated to small/medium files |
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| 154 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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| 155 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) |
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| 156 | #D-* Define R_BUF : Output tree located on STORAGE hosting files waiting for rebuild or pack processes |
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| 157 | #D-* if SpaceName=TEST nothing special will hapen |
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[725] | 158 | #D-* Examples: |
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| 159 | #D- |
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[1057] | 160 | function IGCM_sys_defineArchives { |
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| 161 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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| 162 | |
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[1060] | 163 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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[1057] | 164 | #==================================================== |
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| 165 | #- ARCHIVE (dedicated to large files) |
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[1063] | 166 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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[1057] | 167 | else |
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| 168 | #==================================================== |
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| 169 | #- ARCHIVE (dedicated to large files) |
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[1484] | 170 | ARCHIVE=${ARCHIVE:=/home_local/${LOGIN}} |
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[1057] | 171 | fi |
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| 172 | |
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[1060] | 173 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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[1057] | 174 | #==================================================== |
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| 175 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 176 | STORAGE=${config_UserChoices_STORAGE} |
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[1057] | 177 | else |
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| 178 | #==================================================== |
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| 179 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 180 | STORAGE=${ARCHIVE} |
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[1057] | 181 | fi |
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| 182 | |
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[1178] | 183 | # ON DEFAULT MACHINE NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST |
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[1057] | 184 | |
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| 185 | #==================================================== |
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| 186 | #- R_OUT |
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[1063] | 187 | R_OUT=${ARCHIVE}/IGCM_OUT |
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[1057] | 188 | |
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| 189 | #==================================================== |
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| 190 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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[1063] | 191 | R_FIG=${STORAGE}/IGCM_OUT |
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[1057] | 192 | |
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| 193 | #==================================================== |
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[1431] | 194 | #- CMIP6 (hosting CMIP6 files produced by XIOS2 and configured by dr2xml) |
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| 195 | CMIP6_BUF=${STORAGE}/IGCM_OUT |
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| 196 | |
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| 197 | #==================================================== |
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[1057] | 198 | #- R_BUF (ONLY FOR double copy an scratch) |
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[1063] | 199 | R_BUF=${STORAGE}/IGCM_OUT |
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[1057] | 200 | |
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| 201 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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| 202 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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| 203 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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| 204 | |
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| 205 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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[725] | 206 | } |
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| 207 | |
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| 208 | #D-#================================================== |
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[37] | 209 | #D-function IGCM_sys_RshArchive |
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| 210 | #D-* Purpose: Archive rsh command |
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| 211 | #D-* Examples: |
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| 212 | #D- |
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| 213 | function IGCM_sys_RshArchive { |
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[664] | 214 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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[800] | 215 | /bin/ksh <<-EOF |
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[40] | 216 | ${@} |
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| 217 | EOF |
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[811] | 218 | status=$? |
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| 219 | if [ ${status} -gt 0 ] ; then |
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| 220 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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[664] | 221 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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| 222 | fi |
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| 223 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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[37] | 224 | } |
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| 225 | |
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| 226 | #D-#================================================== |
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[1178] | 227 | #D-function IGCM_sys_RshArchive_NoError |
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| 228 | #D-* Purpose: Archive rsh command, without error |
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| 229 | #D-* used only in monitoring.job |
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| 230 | #D-* Examples: |
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| 231 | #D- |
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| 232 | function IGCM_sys_RshArchive_NoError { |
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| 233 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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| 234 | /bin/ksh <<-EOF |
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[1181] | 235 | ${@} 2> /dev/null |
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[1178] | 236 | EOF |
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| 237 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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| 238 | } |
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| 239 | |
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| 240 | #D-#================================================== |
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[2] | 241 | #D-function IGCM_sys_MkdirArchive |
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| 242 | #D-* Purpose: Mkdir on Archive |
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| 243 | #D-* Examples: |
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| 244 | #D- |
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| 245 | function IGCM_sys_MkdirArchive { |
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[664] | 246 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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| 247 | if ( $DEBUG_sys ) ; then |
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| 248 | echo "IGCM_sys_MkdirArchive :" $@ |
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| 249 | fi |
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[800] | 250 | #- creation de repertoire sur le serveur fichier |
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[1178] | 251 | if [ ! -d ${1} ]; then |
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| 252 | \mkdir -p $1 |
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| 253 | status=$? |
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[811] | 254 | |
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[1178] | 255 | if [ ${status} -gt 0 ] ; then |
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| 256 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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| 257 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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| 258 | fi |
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[664] | 259 | fi |
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| 260 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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[2] | 261 | } |
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| 262 | |
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| 263 | #D-#================================================== |
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| 264 | #D-function IGCM_sys_TestDirArchive |
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| 265 | #D-* Purpose: Test Directory that must exists on Archive |
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| 266 | #D-* Examples: |
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| 267 | #D- |
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| 268 | function IGCM_sys_TestDirArchive { |
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[664] | 269 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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| 270 | if ( $DEBUG_sys ) ; then |
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| 271 | echo "IGCM_sys_TestDirArchive :" $@ |
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| 272 | fi |
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| 273 | typeset ExistFlag |
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| 274 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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| 275 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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| 276 | return ${ExistFlag} |
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[2] | 277 | } |
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| 278 | |
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| 279 | #D-#================================================== |
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[800] | 280 | #D-function IGCM_sys_IsFileArchived |
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[1180] | 281 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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[800] | 282 | #D-* Examples: |
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| 283 | #D- |
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| 284 | function IGCM_sys_IsFileArchived { |
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| 285 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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| 286 | if ( $DEBUG_sys ) ; then |
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| 287 | echo "IGCM_sys_IsFileArchived :" $@ |
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| 288 | fi |
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| 289 | typeset IsArchivedFlag |
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| 290 | # Never archived for this system |
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| 291 | IsArchivedFlag=1 |
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| 292 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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| 293 | |
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| 294 | return ${IsArchivedFlag} |
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| 295 | } |
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| 296 | |
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| 297 | #D-#================================================== |
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[2] | 298 | #D-function IGCM_sys_TestFileArchive |
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| 299 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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| 300 | #D-* Examples: |
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| 301 | #D- |
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| 302 | function IGCM_sys_TestFileArchive { |
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[664] | 303 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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| 304 | typeset ExistFlag |
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| 305 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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| 306 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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[67] | 307 | |
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[664] | 308 | return ${ExistFlag} |
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[67] | 309 | } |
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| 310 | |
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| 311 | #D-#================================================== |
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| 312 | #D-function IGCM_sys_CountFileArchive |
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| 313 | #D-* Purpose: Count files on Archive filesystem |
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| 314 | #D-* Examples: |
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| 315 | #D- |
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| 316 | function IGCM_sys_CountFileArchive { |
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[664] | 317 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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| 318 | ls ${@} 2>/dev/null | wc -l |
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| 319 | if [ $? -gt 0 ] ; then |
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| 320 | echo "IGCM_sys_CountFileArchive : erreur." |
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| 321 | fi |
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| 322 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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[2] | 323 | } |
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| 324 | |
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| 325 | #D-#================================================== |
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| 326 | #D-function IGCM_sys_Tree |
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| 327 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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| 328 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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| 329 | #D- |
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| 330 | function IGCM_sys_Tree { |
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[664] | 331 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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| 332 | if ( $DEBUG_sys ) ; then |
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| 333 | echo "IGCM_sys_Tree :" $@ |
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| 334 | fi |
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[2] | 335 | |
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[1300] | 336 | \ls -lR ${@} |
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[2] | 337 | |
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[664] | 338 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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[2] | 339 | } |
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| 340 | |
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| 341 | #D-#================================================== |
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| 342 | #D-function IGCM_sys_Qsub |
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| 343 | #D-* Purpose: Qsub new job |
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| 344 | #D-* Examples: |
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| 345 | #D- |
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| 346 | function IGCM_sys_Qsub { |
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[664] | 347 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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| 348 | if ( $DEBUG_sys ) ; then |
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| 349 | echo "IGCM_sys_Qsub :" $@ |
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| 350 | fi |
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[800] | 351 | echo "${@} > ${SUBMIT_DIR}/${Script_Output} 2>&1 &" |
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| 352 | ${@} > ${SUBMIT_DIR}/${Script_Output} 2>&1 & |
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[664] | 353 | if [ $? -gt 0 ] ; then |
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[800] | 354 | echo "IGCM_sys_Qsub : erreur ${options} $1" |
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[664] | 355 | IGCM_debug_Exit "IGCM_sys_Qsub" |
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| 356 | fi |
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| 357 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
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[2] | 358 | } |
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| 359 | |
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| 360 | #D-#================================================== |
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| 361 | #D-function IGCM_sys_QsubPost |
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| 362 | #D-* Purpose: Qsub new job on scalaire |
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| 363 | #D-* Examples: |
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| 364 | #D- |
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| 365 | function IGCM_sys_QsubPost { |
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[664] | 366 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
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| 367 | if ( $DEBUG_sys ) ; then |
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| 368 | echo "IGCM_sys_QsubPost :" $@ |
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| 369 | fi |
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| 370 | echo "${libIGCM_POST}/$1.job > ${POST_DIR}/$1.${PeriodDateEnd}.out 2>&1 &" |
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| 371 | ${libIGCM_POST}/$1.job > ${POST_DIR}/${Script_Post_Output}.out 2>&1 & |
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| 372 | if [ $? -gt 0 ] ; then |
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| 373 | echo "IGCM_sys_QsubPost : erreur " $@ |
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| 374 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
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| 375 | fi |
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| 376 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
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[2] | 377 | } |
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| 378 | |
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| 379 | #D-************************* |
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[664] | 380 | #D- File transfer functions |
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[2] | 381 | #D-************************* |
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| 382 | #D- |
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| 383 | |
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| 384 | #D-#================================================== |
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[203] | 385 | #D-function IGCM_sys_RmRunDir |
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| 386 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
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| 387 | #D- scheduler will do the job) |
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| 388 | #D-* Examples: |
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| 389 | #D- |
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| 390 | function IGCM_sys_RmRunDir { |
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[1057] | 391 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
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[664] | 392 | if ( $DEBUG_sys ) ; then |
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| 393 | echo "IGCM_sys_RmRunDir :" $@ |
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[1183] | 394 | IGCM_debug_Print 1 "Dummy call, let the user do that." |
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[664] | 395 | fi |
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| 396 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
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[203] | 397 | } |
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| 398 | |
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| 399 | #D-#================================================== |
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[2] | 400 | #D-function IGCM_sys_Put_Dir |
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| 401 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
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| 402 | #D-* Examples: |
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| 403 | #D- |
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| 404 | function IGCM_sys_Put_Dir { |
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[664] | 405 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
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| 406 | if ( $DEBUG_sys ) ; then |
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| 407 | echo "IGCM_sys_Put_Dir :" $@ |
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| 408 | fi |
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| 409 | if [ $DRYRUN = 0 ]; then |
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| 410 | if [ ! -d ${1} ] ; then |
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| 411 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
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| 412 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
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| 413 | return |
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[2] | 414 | fi |
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| 415 | |
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[717] | 416 | typeset status |
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[2] | 417 | |
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[717] | 418 | # Only if we use rsync |
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| 419 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
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| 420 | # |
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| 421 | #USUAL WAY |
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[1179] | 422 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[717] | 423 | status=$? |
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[2] | 424 | |
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[717] | 425 | if [ ${status} -gt 0 ] ; then |
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[811] | 426 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
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[1179] | 427 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[664] | 428 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
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[2] | 429 | else |
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[1179] | 430 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[2] | 431 | fi |
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[664] | 432 | fi |
---|
| 433 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
[2] | 434 | } |
---|
| 435 | |
---|
| 436 | #D-#================================================== |
---|
| 437 | #D-function IGCM_sys_Get_Dir |
---|
[717] | 438 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
[2] | 439 | #D-* Examples: |
---|
| 440 | #D- |
---|
| 441 | function IGCM_sys_Get_Dir { |
---|
[664] | 442 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
| 443 | if ( $DEBUG_sys ) ; then |
---|
| 444 | echo "IGCM_sys_Get_Dir :" $@ |
---|
| 445 | fi |
---|
| 446 | if [ $DRYRUN = 0 ]; then |
---|
[1180] | 447 | typeset NB_ESSAI DELAI status i |
---|
| 448 | # number of tentative |
---|
| 449 | NB_ESSAI=3 |
---|
| 450 | # time delay between tentative |
---|
| 451 | DELAI=2 |
---|
[2] | 452 | |
---|
[1180] | 453 | # |
---|
| 454 | # USUAL WAY |
---|
| 455 | i=0 |
---|
| 456 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 457 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 458 | status=$? |
---|
| 459 | if [ ${status} -gt 0 ] ; then |
---|
| 460 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 461 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
| 462 | sleep $DELAI |
---|
| 463 | else |
---|
| 464 | break |
---|
| 465 | fi |
---|
| 466 | (( i = i + 1 )) |
---|
| 467 | done |
---|
[2] | 468 | |
---|
[811] | 469 | if [ ${status} -gt 0 ] ; then |
---|
| 470 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
[1179] | 471 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 472 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
[2] | 473 | else |
---|
[1179] | 474 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[2] | 475 | fi |
---|
[664] | 476 | fi |
---|
| 477 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
[2] | 478 | } |
---|
| 479 | |
---|
| 480 | #D-#================================================== |
---|
| 481 | #D-function IGCM_sys_Put_Rest |
---|
[717] | 482 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
[117] | 483 | #D- File and target directory must exist. |
---|
[2] | 484 | #D-* Examples: |
---|
| 485 | #D- |
---|
| 486 | function IGCM_sys_Put_Rest { |
---|
[664] | 487 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
| 488 | if ( $DEBUG_sys ) ; then |
---|
| 489 | echo "IGCM_sys_Put_Rest :" $@ |
---|
| 490 | fi |
---|
| 491 | if [ $DRYRUN = 0 ]; then |
---|
| 492 | if [ ! -f ${1} ] ; then |
---|
| 493 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
| 494 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
[2] | 495 | fi |
---|
[717] | 496 | |
---|
| 497 | typeset status |
---|
| 498 | # |
---|
[1178] | 499 | # USUAL WAY |
---|
[1179] | 500 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[717] | 501 | status=$? |
---|
[2] | 502 | |
---|
[717] | 503 | # #RSYNC WITH NETWORK SSH CALL |
---|
[1179] | 504 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 505 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[2] | 506 | |
---|
[717] | 507 | # #RSYNC WITH NFS USE |
---|
[1179] | 508 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 509 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[2] | 510 | |
---|
[717] | 511 | # status=$? |
---|
| 512 | # IGCM_sys_Rsync_out $status |
---|
| 513 | |
---|
[1179] | 514 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[717] | 515 | # (( status=status+$? )) |
---|
| 516 | |
---|
| 517 | if [ ${status} -gt 0 ] ; then |
---|
[1180] | 518 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
[1178] | 519 | [ -f ${1} ] && ls -l ${1} |
---|
| 520 | [ -f ${2} ] && ls -l ${2} |
---|
| 521 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
[1179] | 522 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 523 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
| 524 | else |
---|
[1178] | 525 | |
---|
| 526 | if [ X${JobType} = XRUN ] ; then |
---|
| 527 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 528 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 529 | fi |
---|
| 530 | |
---|
[1179] | 531 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 532 | fi |
---|
| 533 | fi |
---|
| 534 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
| 535 | } |
---|
[2] | 536 | |
---|
[664] | 537 | #D-#================================================== |
---|
[2] | 538 | #D-function IGCM_sys_Put_Out |
---|
[717] | 539 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
[2] | 540 | #D-* Examples: |
---|
| 541 | #D- |
---|
| 542 | function IGCM_sys_Put_Out { |
---|
[664] | 543 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
| 544 | if ( $DEBUG_sys ) ; then |
---|
| 545 | echo "IGCM_sys_Put_Out :" $@ |
---|
| 546 | fi |
---|
[811] | 547 | |
---|
| 548 | typeset status |
---|
| 549 | |
---|
[664] | 550 | if [ $DRYRUN = 0 ]; then |
---|
[811] | 551 | if [ ! -f ${1} ] ; then |
---|
[664] | 552 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
| 553 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 554 | return 1 |
---|
[2] | 555 | fi |
---|
[800] | 556 | # |
---|
[811] | 557 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
| 558 | # |
---|
[664] | 559 | if [ X${JobType} = XRUN ] ; then |
---|
| 560 | if [ X${3} = X ] ; then |
---|
| 561 | IGCM_sys_Chmod 444 ${1} |
---|
| 562 | fi |
---|
| 563 | fi |
---|
[800] | 564 | # |
---|
[2] | 565 | |
---|
[1179] | 566 | echo ${RSYNC} ${RSYNC_opt} $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 567 | ${RSYNC} ${RSYNC_opt} $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[811] | 568 | status=$? |
---|
| 569 | IGCM_sys_Rsync_out $status |
---|
[2] | 570 | |
---|
[1179] | 571 | ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[811] | 572 | (( status=status+$? )) |
---|
[2] | 573 | |
---|
[811] | 574 | if [ ${status} -gt 0 ] ; then |
---|
| 575 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : rsync failed error code ${status}" |
---|
[1179] | 576 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 577 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
[2] | 578 | else |
---|
[1179] | 579 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[2] | 580 | fi |
---|
[664] | 581 | fi |
---|
| 582 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 583 | return 0 |
---|
[2] | 584 | } |
---|
| 585 | |
---|
| 586 | #D-#================================================== |
---|
| 587 | #D-function IGCM_sys_Get |
---|
| 588 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
| 589 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
| 590 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
| 591 | function IGCM_sys_Get { |
---|
[664] | 592 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
[2] | 593 | |
---|
[811] | 594 | typeset DEST status dm_liste |
---|
[2] | 595 | |
---|
[664] | 596 | if ( $DEBUG_sys ) ; then |
---|
| 597 | echo "IGCM_sys_Get :" $@ |
---|
| 598 | fi |
---|
| 599 | if [ $DRYRUN -le 2 ]; then |
---|
| 600 | if [ X${1} = X'/l' ] ; then |
---|
| 601 | eval set +A dm_liste \${${2}} |
---|
| 602 | else |
---|
| 603 | dm_liste=${1} |
---|
[2] | 604 | fi |
---|
[664] | 605 | eval DEST=\${${#}} |
---|
[2] | 606 | |
---|
[800] | 607 | # test if the (first) file is present in the old computation : |
---|
[664] | 608 | IGCM_sys_TestFileArchive ${dm_liste[0]} |
---|
[811] | 609 | status=$? |
---|
| 610 | if [ ${status} -gt 0 ] ; then |
---|
[664] | 611 | echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." |
---|
| 612 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
[811] | 613 | return |
---|
[664] | 614 | fi |
---|
[2] | 615 | |
---|
[811] | 616 | #USUAL WAY |
---|
[1179] | 617 | \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[811] | 618 | status=$? |
---|
[2] | 619 | |
---|
[811] | 620 | if [ ${status} -gt 0 ] ; then |
---|
| 621 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}" |
---|
[1179] | 622 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 623 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
[2] | 624 | else |
---|
[1179] | 625 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[2] | 626 | fi |
---|
[664] | 627 | fi |
---|
| 628 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
[2] | 629 | } |
---|
| 630 | |
---|
| 631 | #D-#================================================== |
---|
[1178] | 632 | #D-function IGCM_sys_GetDate_Monitoring |
---|
| 633 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
| 634 | #D-* Examples: |
---|
| 635 | #D- |
---|
| 636 | function IGCM_sys_GetDate_Monitoring { |
---|
| 637 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
| 638 | if ( $DEBUG_sys ) ; then |
---|
| 639 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
| 640 | fi |
---|
| 641 | |
---|
| 642 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
| 643 | |
---|
| 644 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
| 645 | } |
---|
| 646 | |
---|
| 647 | #D-#================================================== |
---|
[343] | 648 | #D-function IGCM_sys_Dods_Rm |
---|
[717] | 649 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
[343] | 650 | #D-* Examples: |
---|
| 651 | #D- |
---|
| 652 | function IGCM_sys_Dods_Rm { |
---|
[664] | 653 | if ( $DEBUG_sys ) ; then |
---|
| 654 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
| 655 | fi |
---|
| 656 | return 0 |
---|
[343] | 657 | } |
---|
| 658 | |
---|
| 659 | #D-#================================================== |
---|
| 660 | #D-function IGCM_sys_Dods_Cp |
---|
[811] | 661 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
[343] | 662 | #D-* Examples: |
---|
| 663 | #D- |
---|
| 664 | function IGCM_sys_Dods_Cp { |
---|
[664] | 665 | if ( $DEBUG_sys ) ; then |
---|
| 666 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
| 667 | fi |
---|
| 668 | return 0 |
---|
[343] | 669 | } |
---|
| 670 | |
---|
| 671 | #D-#================================================== |
---|
[2] | 672 | #D-function IGCM_sys_Put_Dods |
---|
[811] | 673 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here |
---|
[2] | 674 | #D-* Examples: |
---|
| 675 | #D- |
---|
| 676 | function IGCM_sys_Put_Dods { |
---|
[664] | 677 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
| 678 | if ( $DEBUG_sys ) ; then |
---|
| 679 | echo "IGCM_sys_Put_Dods :" $@ |
---|
| 680 | fi |
---|
| 681 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
[2] | 682 | } |
---|
| 683 | |
---|
[664] | 684 | ############################################################## |
---|
| 685 | # REBUILD OPERATOR |
---|
[2] | 686 | |
---|
[811] | 687 | #D-#================================================== |
---|
[1163] | 688 | #D-function IGCM_sys_sync |
---|
[1300] | 689 | #D-* Purpose: flush buffer on disk (dummy function on Default machine) |
---|
[1163] | 690 | #D-* Examples: |
---|
| 691 | #D- |
---|
| 692 | function IGCM_sys_sync { |
---|
| 693 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
| 694 | if ( $DEBUG_sys ) ; then |
---|
| 695 | echo "IGCM_sys_sync :" $@ |
---|
| 696 | echo "Dummy call, let the system do that." |
---|
| 697 | fi |
---|
| 698 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
| 699 | } |
---|
| 700 | |
---|
[664] | 701 | ############################################################ |
---|
| 702 | # Activate Running Environnment Variables |
---|
| 703 | |
---|
[811] | 704 | #D-#================================================== |
---|
[1239] | 705 | #D-function IGCM_sys_activ_variables |
---|
[811] | 706 | #D-* Purpose: set environement variables prior to execution |
---|
| 707 | #D-* Examples: |
---|
| 708 | #D- |
---|
[664] | 709 | function IGCM_sys_activ_variables { |
---|
| 710 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
| 711 | if ( $DEBUG_sys ) ; then |
---|
| 712 | echo "IGCM_sys_activ_variables" |
---|
| 713 | fi |
---|
[811] | 714 | |
---|
| 715 | # -------------------------------------------------------------------- |
---|
[1485] | 716 | #D- MODULE specifications |
---|
| 717 | # -------------------------------------------------------------------- |
---|
| 718 | # Source the file EnvFile containing all module load needed to run the model. |
---|
| 719 | # EnvFile can be specified in config.card. If this is the case and if the file exists, |
---|
| 720 | # it will be used. Otherwise at default host, no file will be used. |
---|
| 721 | if [ ! X${config_UserChoices_EnvFile} = X ] && [ -f ${config_UserChoices_EnvFile} ] ; then |
---|
| 722 | # EnvFile is set in config.card and the file exists |
---|
| 723 | IGCM_debug_Print 1 "EnvFile set in config.card will be used" |
---|
| 724 | EnvFile=${config_UserChoices_EnvFile} |
---|
| 725 | |
---|
| 726 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Following EnvFile will be used :" |
---|
| 727 | IGCM_debug_Print 1 ${EnvFile} |
---|
| 728 | . ${EnvFile} |
---|
| 729 | else |
---|
| 730 | IGCM_debug_Print 1 "IGCM_sys_active_variables : No modules will be loaded in default set up." |
---|
| 731 | fi |
---|
| 732 | |
---|
| 733 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Now loaded modules for default system. " |
---|
| 734 | module list |
---|
| 735 | |
---|
| 736 | # -------------------------------------------------------------------- |
---|
[811] | 737 | #D- MPI specifications |
---|
| 738 | # -------------------------------------------------------------------- |
---|
| 739 | |
---|
| 740 | # -------------------------------------------------------------------- |
---|
| 741 | #D- Other specifications |
---|
| 742 | # -------------------------------------------------------------------- |
---|
| 743 | |
---|
[1300] | 744 | ulimit -s unlimited |
---|
| 745 | |
---|
[664] | 746 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
[2] | 747 | } |
---|
| 748 | |
---|
[664] | 749 | ############################################################ |
---|
| 750 | # Desactivate Running Environnment Variables |
---|
[2] | 751 | |
---|
[811] | 752 | #D-#================================================== |
---|
| 753 | #D-function IGCM_sys_desactiv_variables |
---|
| 754 | #D-* Purpose: unset environement variables after execution |
---|
| 755 | #D-* Examples: |
---|
| 756 | #D- |
---|
[664] | 757 | function IGCM_sys_desactiv_variables { |
---|
| 758 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
| 759 | if ( $DEBUG_sys ) ; then |
---|
| 760 | echo "IGCM_sys_desactiv_variables" |
---|
| 761 | fi |
---|
[811] | 762 | # -------------------------------------------------------------------- |
---|
| 763 | #D- MPI specifications |
---|
| 764 | # -------------------------------------------------------------------- |
---|
| 765 | |
---|
| 766 | # -------------------------------------------------------------------- |
---|
| 767 | #D- Other specifications |
---|
| 768 | # -------------------------------------------------------------------- |
---|
| 769 | |
---|
[664] | 770 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
| 771 | } |
---|
| 772 | |
---|
| 773 | ############################################################ |
---|
[1239] | 774 | # Update job headers to be used by the scheduler |
---|
| 775 | |
---|
| 776 | #D-#================================================== |
---|
| 777 | #D-function IGCM_sys_updateHeaders |
---|
| 778 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
| 779 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
| 780 | #D- |
---|
| 781 | function IGCM_sys_updateHeaders { |
---|
| 782 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
| 783 | if ( $DEBUG_sys ) ; then |
---|
| 784 | echo "IGCM_sys_updateHeaders" |
---|
| 785 | fi |
---|
| 786 | typeset file |
---|
| 787 | file=$1 |
---|
| 788 | |
---|
| 789 | if [ ${executionType} -eq 1 ] ; then |
---|
| 790 | # MPMD + MPI |
---|
| 791 | sed -e "/::openMPthreads::/d" \ |
---|
| 792 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 793 | ${file} > ${file}.tmp |
---|
| 794 | |
---|
| 795 | elif [ ${executionType} -eq 2 ] ; then |
---|
| 796 | # MPMD + MPI + OMP |
---|
| 797 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 798 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 799 | ${file} > ${file}.tmp |
---|
| 800 | |
---|
| 801 | elif [ ${executionType} -eq 3 ] ; then |
---|
| 802 | # SPMD + MPI/OMP |
---|
| 803 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 804 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 805 | ${file} > ${file}.tmp |
---|
| 806 | |
---|
| 807 | elif [ ${executionType} -eq 4 ] ; then |
---|
| 808 | # SPMD + MPI only |
---|
| 809 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 810 | -e "/::openMPthreads::/d" \ |
---|
| 811 | ${file} > ${file}.tmp |
---|
| 812 | |
---|
| 813 | elif [ ${executionType} -eq 5 ] ; then |
---|
| 814 | # SPMD + OMP only |
---|
| 815 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 816 | -e "/::JobNumProcTot::/d" \ |
---|
| 817 | ${file} > ${file}.tmp |
---|
| 818 | |
---|
| 819 | elif [ ${executionType} -eq 6 ] ; then |
---|
| 820 | # SEQUENTIAL THEN |
---|
| 821 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
| 822 | -e "/::openMPthreads::/d" \ |
---|
| 823 | ${file} > ${file}.tmp |
---|
| 824 | |
---|
| 825 | fi |
---|
| 826 | |
---|
| 827 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
| 828 | |
---|
| 829 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
| 830 | } |
---|
| 831 | |
---|
| 832 | ############################################################ |
---|
[800] | 833 | # Build MPI/OMP scripts run file (dummy function) |
---|
[664] | 834 | |
---|
[811] | 835 | #D-#================================================== |
---|
| 836 | #D-function IGCM_sys_build_run_file |
---|
| 837 | #D-* Purpose: build run file (deprecated) |
---|
| 838 | #D-* Examples: |
---|
| 839 | #D- |
---|
[664] | 840 | function IGCM_sys_build_run_file { |
---|
| 841 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
| 842 | } |
---|
| 843 | |
---|
| 844 | ############################################################ |
---|
| 845 | # Build MPI/OMP scripts |
---|
[811] | 846 | |
---|
| 847 | #D-#================================================== |
---|
| 848 | #D-function IGCM_sys_build_execution_scripts |
---|
| 849 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
| 850 | #D-* Examples: |
---|
| 851 | #D- |
---|
[664] | 852 | function IGCM_sys_build_execution_scripts |
---|
| 853 | { |
---|
| 854 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
| 855 | if ( $DEBUG_sys ) ; then |
---|
| 856 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
| 857 | fi |
---|
[1180] | 858 | |
---|
[1300] | 859 | EXECUTION=${HOST_MPIRUN_COMMAND} |
---|
[664] | 860 | |
---|
[1300] | 861 | # MPMD mode |
---|
[664] | 862 | if ( ${OK_PARA_MPMD} ) ; then |
---|
| 863 | |
---|
[1300] | 864 | # Only MPI (MPMD) |
---|
| 865 | if ( ! ${OK_PARA_OMP} ) ; then |
---|
[664] | 866 | |
---|
[1300] | 867 | if [ -f run_file ] ; then |
---|
| 868 | IGCM_sys_Rm -f run_file |
---|
| 869 | fi |
---|
| 870 | touch run_file |
---|
[664] | 871 | |
---|
[1300] | 872 | # Build run_file |
---|
| 873 | |
---|
| 874 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
| 875 | # the coupler ie oasis3 must be the first one |
---|
| 876 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 877 | |
---|
| 878 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 879 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 880 | |
---|
| 881 | # for CPL component only |
---|
| 882 | if [ "X${comp}" = "XCPL" ] && [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
| 883 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 884 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 885 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut} " >> run_file |
---|
| 886 | fi |
---|
| 887 | done |
---|
| 888 | |
---|
| 889 | # Then second loop on the components |
---|
| 890 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 891 | |
---|
| 892 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 893 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 894 | |
---|
| 895 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
| 896 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
| 897 | |
---|
| 898 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 899 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 900 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file |
---|
| 901 | fi |
---|
| 902 | done |
---|
| 903 | |
---|
| 904 | EXECUTION="${HOST_MPIRUN_COMMAND} --app ./run_file" |
---|
| 905 | |
---|
| 906 | IGCM_sys_Chmod u+x run_file |
---|
| 907 | if ( $DEBUG_sys ) ; then |
---|
| 908 | echo "run_file contains : " |
---|
| 909 | cat run_file |
---|
| 910 | fi |
---|
| 911 | |
---|
| 912 | # MPI-OpenMP (MPMD) |
---|
| 913 | else |
---|
| 914 | |
---|
[664] | 915 | # Hosts treatment |
---|
| 916 | ${HOST_MPIRUN_COMMAND} hostname | sort | uniq > hosts.tmp |
---|
| 917 | |
---|
| 918 | i=0 |
---|
| 919 | rm -f hosts |
---|
[1300] | 920 | IGCM_debug_Print 1 "sys $( hostname ), Hosts available :" |
---|
[664] | 921 | for nodes in `cat hosts.tmp` ; do |
---|
| 922 | host[$i]=$nodes |
---|
| 923 | echo "${host[$i]} slots=1 max_slots=1" >> hosts |
---|
| 924 | IGCM_debug_Print 1 ${host[$i]} |
---|
| 925 | i=$((i+1)) |
---|
| 926 | done |
---|
| 927 | rm -f hosts.tmp |
---|
| 928 | |
---|
| 929 | listnodes=${host[*]} |
---|
| 930 | |
---|
| 931 | EXECUTION="${HOST_MPIRUN_COMMAND} -hostfile hosts" |
---|
| 932 | |
---|
| 933 | # Initialisation |
---|
[1300] | 934 | rank=0 |
---|
| 935 | current_core=0 |
---|
| 936 | core_per_node=4 |
---|
[664] | 937 | init_exec=n |
---|
| 938 | |
---|
[1300] | 939 | # Loop on the components |
---|
[664] | 940 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 941 | |
---|
[1300] | 942 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 943 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[664] | 944 | |
---|
[1300] | 945 | # Not possible if oasis has an executable (i.e old version of oasis3) |
---|
| 946 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
---|
| 947 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
---|
| 948 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
---|
| 949 | IGCM_debug_Verif_Exit |
---|
[664] | 950 | fi |
---|
| 951 | |
---|
| 952 | # Only if we really have an executable for the component : |
---|
[1300] | 953 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
[664] | 954 | |
---|
| 955 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 956 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 957 | |
---|
| 958 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 959 | echo "" >> script_${ExeNameOut}.ksh |
---|
[1300] | 960 | if [ ${comp_proc_omp_loc} -gt 1 ] ; then |
---|
| 961 | |
---|
| 962 | # Check if the number of threads is correct |
---|
| 963 | case ${comp_proc_omp_loc} in |
---|
| 964 | 2|4) |
---|
| 965 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
---|
| 966 | ;; |
---|
| 967 | *) |
---|
| 968 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
| 969 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
| 970 | IGCM_debug_Print 2 "Only 2,4 as number of OMP threads are possible " |
---|
| 971 | IGCM_debug_Verif_Exit |
---|
| 972 | ;; |
---|
| 973 | esac |
---|
| 974 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 975 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 976 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 977 | echo "export OMP_STACKSIZE=200M" >> script_${ExeNameOut}.ksh |
---|
| 978 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 979 | fi |
---|
[1318] | 980 | |
---|
[1317] | 981 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
[1318] | 982 | echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK )) " >> script_${ExeNameOut}.ksh |
---|
| 983 | echo "MYMPIRANK=\$(printf '%3.3d\n' \${MYMPIRANK})" >> script_${ExeNameOut}.ksh |
---|
| 984 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh |
---|
[664] | 985 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 986 | |
---|
[1300] | 987 | if [ ${init_exec} = y ] ; then |
---|
| 988 | EXECUTION="${EXECUTION} : -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
| 989 | else |
---|
| 990 | EXECUTION="${EXECUTION} -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
| 991 | init_exec=y |
---|
| 992 | fi |
---|
[664] | 993 | |
---|
[1300] | 994 | # Build rankfile : method used to assign cores and nodes for the MPI process |
---|
| 995 | # Ex : |
---|
| 996 | #rank 0=curie5296 slot=0,1,2,3 |
---|
| 997 | #rank 1=curie5296 slot=4,5,6,7 |
---|
| 998 | # Example of final command : |
---|
| 999 | # mpirun -hostfile hosts -rankfile rankfile -np 27 ./script_lmdz.x.ksh : -np 5 ./script_opa.xx.ksh |
---|
| 1000 | # with script_lmdz.x.ksh : |
---|
| 1001 | # #!/bin/ksh |
---|
| 1002 | #export OMP_STACKSIZE=200M |
---|
| 1003 | #export OMP_NUM_THREADS=4 |
---|
| 1004 | #./lmdz.x |
---|
[664] | 1005 | |
---|
[1300] | 1006 | for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do |
---|
| 1007 | (( index_host = current_core / core_per_node )) |
---|
| 1008 | host_value=${host[${index_host}]} |
---|
| 1009 | (( slot = current_core % core_per_node )) |
---|
| 1010 | virg="," |
---|
| 1011 | string_final="" |
---|
| 1012 | for index in `seq $slot $(($slot+$comp_proc_omp_loc-1))`; do |
---|
| 1013 | string=$index$virg |
---|
| 1014 | string_final=$string_final$string |
---|
| 1015 | done |
---|
| 1016 | string_final=$( echo $string_final | sed "s/.$//" ) |
---|
| 1017 | echo "rank $rank=$host_value slot=$string_final" >> rankfile |
---|
| 1018 | (( rank = rank + 1 )) |
---|
| 1019 | (( current_core = current_core + comp_proc_omp_loc )) |
---|
[664] | 1020 | done |
---|
| 1021 | fi |
---|
| 1022 | done |
---|
[2] | 1023 | fi |
---|
| 1024 | |
---|
[1300] | 1025 | # Only one executable (SPMD mode). |
---|
| 1026 | else |
---|
[664] | 1027 | |
---|
| 1028 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1029 | |
---|
| 1030 | # Only if we really have an executable for the component : |
---|
| 1031 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1032 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
| 1033 | |
---|
| 1034 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1035 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1036 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 1037 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
[1300] | 1038 | echo "export OMP_STACKSIZE=200M" >> script_${ExeNameOut}.ksh |
---|
| 1039 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
[664] | 1040 | fi |
---|
[1484] | 1041 | |
---|
| 1042 | if [ ${mpiTasks} -eq 1 ] && [ ${openMPthreads} -eq 1 ] ; then |
---|
| 1043 | # Case with only one proc |
---|
| 1044 | # mpirun should not be used at obelix for only one proc |
---|
| 1045 | # Output text per process |
---|
| 1046 | echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
| 1047 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1048 | EXECUTION="time ./script_${ExeNameOut}.ksh" |
---|
| 1049 | elif ( ${OK_PARA_MPI} ) ; then |
---|
[664] | 1050 | # Default : mpirun used if nb_proc gt 1 |
---|
[1484] | 1051 | # Output text per process |
---|
[1317] | 1052 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${OMPI_COMM_WORLD_RANK} 2>out_${ExeNameOut}.err.\${OMPI_COMM_WORLD_RANK}" >> script_${ExeNameOut}.ksh |
---|
[664] | 1053 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1054 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
---|
[1484] | 1055 | elif [ ${executionType} -eq 6 ] ; then |
---|
| 1056 | # Sequentiel case: this is the same as the first case. |
---|
[1317] | 1057 | echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
[664] | 1058 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1059 | EXECUTION="time ./script_${ExeNameOut}.ksh" |
---|
[1484] | 1060 | else |
---|
| 1061 | # Strange case. |
---|
| 1062 | IGCM_debug_Exit "ERROR with OK_PARA_MPI" |
---|
| 1063 | IGCM_debug_Print 2 "sys Obelix : OK_PARA_MPI=False and mpiTask/openMPthreds different from 1" |
---|
| 1064 | IGCM_debug_Verif_Exit |
---|
[664] | 1065 | fi |
---|
[1178] | 1066 | |
---|
[1484] | 1067 | |
---|
[1178] | 1068 | IGCM_debug_Print 1 "sys $( hostname ) : script_${ExeNameOut}.ksh contains" |
---|
| 1069 | cat script_${ExeNameOut}.ksh |
---|
| 1070 | |
---|
[664] | 1071 | fi |
---|
[1180] | 1072 | |
---|
[664] | 1073 | done |
---|
| 1074 | |
---|
| 1075 | fi |
---|
| 1076 | |
---|
[811] | 1077 | IGCM_debug_Print 1 "sys $( hostname ) : execution command is" |
---|
| 1078 | IGCM_debug_Print 1 "$EXECUTION" |
---|
[664] | 1079 | |
---|
| 1080 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
[2] | 1081 | } |
---|
| 1082 | |
---|
[933] | 1083 | #D-#================================================== |
---|
| 1084 | #D-function IGCM_sys_check_path |
---|
| 1085 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
| 1086 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
| 1087 | #D-* Examples: |
---|
| 1088 | #D- |
---|
| 1089 | function IGCM_sys_check_path { |
---|
| 1090 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
| 1091 | if ( $DEBUG_sys ) ; then |
---|
| 1092 | echo "IGCM_sys_check_path" |
---|
| 1093 | fi |
---|
[811] | 1094 | |
---|
[933] | 1095 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then |
---|
| 1096 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
| 1097 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
[936] | 1098 | IGCM_debug_Exit "This will stop the job" |
---|
[933] | 1099 | fi |
---|
| 1100 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
| 1101 | } |
---|
| 1102 | |
---|
[811] | 1103 | #D-#================================================== |
---|
| 1104 | #D-function IGCM_sys_check_quota. Dummy call here |
---|
| 1105 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
| 1106 | #D-* Examples: |
---|
| 1107 | #D- |
---|
[664] | 1108 | function IGCM_sys_check_quota { |
---|
| 1109 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
| 1110 | if ( $DEBUG_sys ) ; then |
---|
| 1111 | echo "IGCM_sys_check_quota" |
---|
| 1112 | fi |
---|
[1300] | 1113 | |
---|
| 1114 | # TO BE IMPLEMENTED |
---|
| 1115 | |
---|
[664] | 1116 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
| 1117 | } |
---|
| 1118 | |
---|
[811] | 1119 | #D-#================================================== |
---|
[1286] | 1120 | #D-function IGCM_sys_projectAccounting |
---|
| 1121 | #D-* Purpose: store project accounting information in a file |
---|
| 1122 | #D-* Examples: |
---|
| 1123 | #D- |
---|
| 1124 | function IGCM_sys_projectAccounting { |
---|
| 1125 | IGCM_debug_PushStack "IGCM_sys_projectAccounting" |
---|
| 1126 | if ( $DEBUG_sys ) ; then |
---|
| 1127 | echo "IGCM_sys_check_quota" |
---|
| 1128 | fi |
---|
| 1129 | |
---|
| 1130 | touch $1 |
---|
| 1131 | |
---|
| 1132 | IGCM_debug_PopStack "IGCM_sys_projectAccounting" |
---|
| 1133 | } |
---|
| 1134 | |
---|
| 1135 | #D-#================================================== |
---|
[1244] | 1136 | #D-function IGCM_sys_getJobSchedulerID |
---|
| 1137 | #D-* Purpose: Get the job ID during execution |
---|
| 1138 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
| 1139 | #D- |
---|
| 1140 | function IGCM_sys_getJobSchedulerID { |
---|
| 1141 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
| 1142 | if ( $DEBUG_sys ) ; then |
---|
| 1143 | echo "IGCM_sys_getJobSchedulerID" |
---|
| 1144 | fi |
---|
| 1145 | |
---|
[1300] | 1146 | # N/A content |
---|
[1244] | 1147 | eval ${1}="N/A" |
---|
| 1148 | |
---|
| 1149 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
| 1150 | } |
---|
| 1151 | |
---|
| 1152 | #D-#================================================== |
---|
[1300] | 1153 | #D-function IGCM_sys_GetJobID |
---|
| 1154 | #D-* Purpose: Get the job ID from the JobName |
---|
| 1155 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
| 1156 | #D- |
---|
| 1157 | function IGCM_sys_GetJobID { |
---|
| 1158 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
| 1159 | if ( $DEBUG_sys ) ; then |
---|
| 1160 | echo "IGCM_sys_GetJobID" |
---|
| 1161 | fi |
---|
| 1162 | |
---|
| 1163 | # N/A content |
---|
| 1164 | eval ${3}="N/A" |
---|
| 1165 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
| 1166 | } |
---|
| 1167 | |
---|
| 1168 | #D-#================================================== |
---|
[811] | 1169 | #D-function IGCM_sys_CountJobInQueue |
---|
[1244] | 1170 | #D-* Purpose: Count number of users job |
---|
[811] | 1171 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
| 1172 | #D- |
---|
| 1173 | function IGCM_sys_CountJobInQueue { |
---|
| 1174 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
| 1175 | if ( $DEBUG_sys ) ; then |
---|
| 1176 | echo "IGCM_sys_CountJobInQueue" |
---|
| 1177 | fi |
---|
| 1178 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
| 1179 | } |
---|
[1272] | 1180 | |
---|
| 1181 | #D-#================================================== |
---|
| 1182 | #D-function IGCM_sys_atlas |
---|
| 1183 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
---|
| 1184 | #D-* Examples: |
---|
| 1185 | #D- |
---|
| 1186 | function IGCM_sys_atlas { |
---|
| 1187 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
---|
| 1188 | if ( $DEBUG_sys ) ; then |
---|
| 1189 | echo "IGCM_sys_atlas :" $@ |
---|
| 1190 | fi |
---|
| 1191 | |
---|
| 1192 | typeset status |
---|
| 1193 | |
---|
| 1194 | \atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 1195 | status=$? |
---|
| 1196 | if [ ${status} -gt 0 ] ; then |
---|
| 1197 | echo "IGCM_sys_atlas : error code ${status}" |
---|
| 1198 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1199 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1200 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1201 | return 1 |
---|
| 1202 | else |
---|
| 1203 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1204 | return 0 |
---|
| 1205 | fi |
---|
| 1206 | |
---|
| 1207 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1208 | } |
---|
| 1209 | |
---|
[1380] | 1210 | #D-#================================================== |
---|
| 1211 | #D-function IGCM_sys_rebuild_nemo |
---|
| 1212 | #D-* Purpose: rebuild nemo parallel files with general rebuild |
---|
| 1213 | #D-* Examples: |
---|
| 1214 | #D- |
---|
| 1215 | |
---|
| 1216 | function IGCM_sys_rebuild_nemo { |
---|
| 1217 | IGCM_debug_PushStack "IGCM_sys_rebuild_nemo" $@ |
---|
| 1218 | if ( $DEBUG_sys ) ; then |
---|
| 1219 | echo "IGCM_sys_rebuild_nemo :" $@ |
---|
| 1220 | fi |
---|
| 1221 | |
---|
| 1222 | nemo_generic_restart_file_name_out=${1} |
---|
| 1223 | nemo_extension_out=${3} |
---|
| 1224 | shift ; shift ; shift |
---|
| 1225 | |
---|
| 1226 | IGCM_sys_rebuild -o ${nemo_generic_restart_file_name_out}.${nemo_extension_out} $@ |
---|
| 1227 | |
---|
| 1228 | IGCM_debug_PopStack "IGCM_sys_rebuild_nemo" |
---|
| 1229 | } |
---|
| 1230 | |
---|