[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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[664] | 64 | # Host and user names |
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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/${LOGIN}/rebuild/bin/ |
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[2] | 95 | |
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[117] | 96 | #==================================================== |
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[2] | 97 | # Host specific DIRECTORIES |
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| 98 | #==================================================== |
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| 99 | |
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| 100 | #==================================================== |
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[664] | 101 | #- MirrorlibIGCM for frontend |
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| 102 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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[2] | 103 | |
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| 104 | #==================================================== |
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[800] | 105 | #- libIGCM_POST for frontend |
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[343] | 106 | typeset -r libIGCM_POST=${libIGCM} |
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| 107 | |
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| 108 | #==================================================== |
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[664] | 109 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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| 110 | typeset -r R_EXE="${MODIPSL}/bin" |
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| 111 | |
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| 112 | #==================================================== |
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[2] | 113 | #- SUBMIT_DIR : submission dir |
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[1124] | 114 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PWD}} |
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[2] | 115 | |
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| 116 | #==================================================== |
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[725] | 117 | #- IN |
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| 118 | typeset -r R_IN=${R_IN:=/home/${LOGIN}/IGCM} |
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[800] | 119 | typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/home/${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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[1064] | 123 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/home/${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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[1180] | 138 | #- set PackDefault to false on obelix |
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| 139 | PackDefault=false |
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| 140 | |
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| 141 | #==================================================== |
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[664] | 142 | #- Number of core per node (max number of OpenMP task) |
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| 143 | NUM_COREPERNODE=1 |
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| 144 | |
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| 145 | #==================================================== |
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| 146 | #- Default number of MPI task for IPSL coupled model |
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| 147 | #- required for backward compatibility |
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| 148 | #- |
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| 149 | DEFAULT_NUM_PROC_OCE=1 |
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| 150 | DEFAULT_NUM_PROC_CPL=1 |
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| 151 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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| 152 | |
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[2] | 153 | #D-#================================================== |
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[1057] | 154 | #D-function IGCM_sys_defineArchives |
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| 155 | #D-* Purpose: |
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| 156 | #D-* Define ARCHIVE : Dedicated to large files |
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| 157 | #D-* Define STORAGE : Dedicated to small/medium files |
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| 158 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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| 159 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) |
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| 160 | #D-* Define R_BUF : Output tree located on STORAGE hosting files waiting for rebuild or pack processes |
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| 161 | #D-* if SpaceName=TEST nothing special will hapen |
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[725] | 162 | #D-* Examples: |
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| 163 | #D- |
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[1057] | 164 | function IGCM_sys_defineArchives { |
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| 165 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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| 166 | |
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[1060] | 167 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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[1057] | 168 | #==================================================== |
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| 169 | #- ARCHIVE (dedicated to large files) |
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[1063] | 170 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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[1057] | 171 | else |
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| 172 | #==================================================== |
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| 173 | #- ARCHIVE (dedicated to large files) |
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[1063] | 174 | ARCHIVE=${ARCHIVE:=/home/${LOGIN}} |
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[1057] | 175 | fi |
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| 176 | |
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[1060] | 177 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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[1057] | 178 | #==================================================== |
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| 179 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 180 | STORAGE=${config_UserChoices_STORAGE} |
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[1057] | 181 | else |
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| 182 | #==================================================== |
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| 183 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 184 | STORAGE=${ARCHIVE} |
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[1057] | 185 | fi |
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| 186 | |
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[1178] | 187 | # ON DEFAULT MACHINE NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST |
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[1057] | 188 | |
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| 189 | #==================================================== |
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| 190 | #- R_OUT |
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[1063] | 191 | R_OUT=${ARCHIVE}/IGCM_OUT |
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[1057] | 192 | |
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| 193 | #==================================================== |
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| 194 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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[1063] | 195 | R_FIG=${STORAGE}/IGCM_OUT |
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[1057] | 196 | |
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| 197 | #==================================================== |
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| 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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[1180] | 336 | \tree -f $@ |
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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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[785] | 395 | # IGCM_sys_Rm -rf ${RUN_DIR} |
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[664] | 396 | fi |
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| 397 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
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[203] | 398 | } |
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| 399 | |
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| 400 | #D-#================================================== |
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[2] | 401 | #D-function IGCM_sys_Put_Dir |
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| 402 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
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| 403 | #D-* Examples: |
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| 404 | #D- |
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| 405 | function IGCM_sys_Put_Dir { |
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[664] | 406 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
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| 407 | if ( $DEBUG_sys ) ; then |
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| 408 | echo "IGCM_sys_Put_Dir :" $@ |
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| 409 | fi |
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| 410 | if [ $DRYRUN = 0 ]; then |
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| 411 | if [ ! -d ${1} ] ; then |
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| 412 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
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| 413 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
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| 414 | return |
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[2] | 415 | fi |
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| 416 | |
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[717] | 417 | typeset status |
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[2] | 418 | |
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[717] | 419 | # Only if we use rsync |
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| 420 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
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| 421 | # |
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| 422 | #USUAL WAY |
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[1179] | 423 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[717] | 424 | status=$? |
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[2] | 425 | |
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[717] | 426 | if [ ${status} -gt 0 ] ; then |
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[811] | 427 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
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[1179] | 428 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[664] | 429 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
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[2] | 430 | else |
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[1179] | 431 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[2] | 432 | fi |
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[664] | 433 | fi |
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| 434 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
[2] | 435 | } |
---|
| 436 | |
---|
| 437 | #D-#================================================== |
---|
| 438 | #D-function IGCM_sys_Get_Dir |
---|
[717] | 439 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
[2] | 440 | #D-* Examples: |
---|
| 441 | #D- |
---|
| 442 | function IGCM_sys_Get_Dir { |
---|
[664] | 443 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
| 444 | if ( $DEBUG_sys ) ; then |
---|
| 445 | echo "IGCM_sys_Get_Dir :" $@ |
---|
| 446 | fi |
---|
| 447 | if [ $DRYRUN = 0 ]; then |
---|
[1180] | 448 | typeset NB_ESSAI DELAI status i |
---|
| 449 | # number of tentative |
---|
| 450 | NB_ESSAI=3 |
---|
| 451 | # time delay between tentative |
---|
| 452 | DELAI=2 |
---|
[2] | 453 | |
---|
[1180] | 454 | # |
---|
| 455 | # USUAL WAY |
---|
| 456 | i=0 |
---|
| 457 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 458 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 459 | status=$? |
---|
| 460 | if [ ${status} -gt 0 ] ; then |
---|
| 461 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 462 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
| 463 | sleep $DELAI |
---|
| 464 | else |
---|
| 465 | break |
---|
| 466 | fi |
---|
| 467 | (( i = i + 1 )) |
---|
| 468 | done |
---|
[2] | 469 | |
---|
[811] | 470 | if [ ${status} -gt 0 ] ; then |
---|
| 471 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
[1179] | 472 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 473 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
[2] | 474 | else |
---|
[1179] | 475 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[2] | 476 | fi |
---|
[664] | 477 | fi |
---|
| 478 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
[2] | 479 | } |
---|
| 480 | |
---|
| 481 | #D-#================================================== |
---|
| 482 | #D-function IGCM_sys_Put_Rest |
---|
[717] | 483 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
[117] | 484 | #D- File and target directory must exist. |
---|
[2] | 485 | #D-* Examples: |
---|
| 486 | #D- |
---|
| 487 | function IGCM_sys_Put_Rest { |
---|
[664] | 488 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
| 489 | if ( $DEBUG_sys ) ; then |
---|
| 490 | echo "IGCM_sys_Put_Rest :" $@ |
---|
| 491 | fi |
---|
| 492 | if [ $DRYRUN = 0 ]; then |
---|
| 493 | if [ ! -f ${1} ] ; then |
---|
| 494 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
| 495 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
[2] | 496 | fi |
---|
[717] | 497 | |
---|
| 498 | typeset status |
---|
| 499 | # |
---|
[1178] | 500 | # USUAL WAY |
---|
[1179] | 501 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[717] | 502 | status=$? |
---|
[2] | 503 | |
---|
[717] | 504 | # #RSYNC WITH NETWORK SSH CALL |
---|
[1179] | 505 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 506 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[2] | 507 | |
---|
[717] | 508 | # #RSYNC WITH NFS USE |
---|
[1179] | 509 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 510 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[2] | 511 | |
---|
[717] | 512 | # status=$? |
---|
| 513 | # IGCM_sys_Rsync_out $status |
---|
| 514 | |
---|
[1179] | 515 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[717] | 516 | # (( status=status+$? )) |
---|
| 517 | |
---|
| 518 | if [ ${status} -gt 0 ] ; then |
---|
[1180] | 519 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
[1178] | 520 | [ -f ${1} ] && ls -l ${1} |
---|
| 521 | [ -f ${2} ] && ls -l ${2} |
---|
| 522 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
[1179] | 523 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 524 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
| 525 | else |
---|
[1178] | 526 | |
---|
| 527 | if [ X${JobType} = XRUN ] ; then |
---|
| 528 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 529 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 530 | fi |
---|
| 531 | |
---|
[1179] | 532 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 533 | fi |
---|
| 534 | fi |
---|
| 535 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
| 536 | } |
---|
[2] | 537 | |
---|
[664] | 538 | #D-#================================================== |
---|
[2] | 539 | #D-function IGCM_sys_Put_Out |
---|
[717] | 540 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
[2] | 541 | #D-* Examples: |
---|
| 542 | #D- |
---|
| 543 | function IGCM_sys_Put_Out { |
---|
[664] | 544 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
| 545 | if ( $DEBUG_sys ) ; then |
---|
| 546 | echo "IGCM_sys_Put_Out :" $@ |
---|
| 547 | fi |
---|
[811] | 548 | |
---|
| 549 | typeset status |
---|
| 550 | |
---|
[664] | 551 | if [ $DRYRUN = 0 ]; then |
---|
[811] | 552 | if [ ! -f ${1} ] ; then |
---|
[664] | 553 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
| 554 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 555 | return 1 |
---|
[2] | 556 | fi |
---|
[800] | 557 | # |
---|
[811] | 558 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
| 559 | # |
---|
[664] | 560 | if [ X${JobType} = XRUN ] ; then |
---|
| 561 | if [ X${3} = X ] ; then |
---|
| 562 | IGCM_sys_Chmod 444 ${1} |
---|
| 563 | fi |
---|
| 564 | fi |
---|
[800] | 565 | # |
---|
[2] | 566 | |
---|
[1179] | 567 | echo ${RSYNC} ${RSYNC_opt} $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 568 | ${RSYNC} ${RSYNC_opt} $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[811] | 569 | status=$? |
---|
| 570 | IGCM_sys_Rsync_out $status |
---|
[2] | 571 | |
---|
[1179] | 572 | ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[811] | 573 | (( status=status+$? )) |
---|
[2] | 574 | |
---|
[811] | 575 | if [ ${status} -gt 0 ] ; then |
---|
| 576 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : rsync failed error code ${status}" |
---|
[1179] | 577 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 578 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
[2] | 579 | else |
---|
[1179] | 580 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[2] | 581 | fi |
---|
[664] | 582 | fi |
---|
| 583 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 584 | return 0 |
---|
[2] | 585 | } |
---|
| 586 | |
---|
| 587 | #D-#================================================== |
---|
| 588 | #D-function IGCM_sys_Get |
---|
| 589 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
| 590 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
| 591 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
| 592 | function IGCM_sys_Get { |
---|
[664] | 593 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
[2] | 594 | |
---|
[811] | 595 | typeset DEST status dm_liste |
---|
[2] | 596 | |
---|
[664] | 597 | if ( $DEBUG_sys ) ; then |
---|
| 598 | echo "IGCM_sys_Get :" $@ |
---|
| 599 | fi |
---|
| 600 | if [ $DRYRUN -le 2 ]; then |
---|
| 601 | if [ X${1} = X'/l' ] ; then |
---|
| 602 | eval set +A dm_liste \${${2}} |
---|
| 603 | else |
---|
| 604 | dm_liste=${1} |
---|
[2] | 605 | fi |
---|
[664] | 606 | eval DEST=\${${#}} |
---|
[2] | 607 | |
---|
[800] | 608 | # test if the (first) file is present in the old computation : |
---|
[664] | 609 | IGCM_sys_TestFileArchive ${dm_liste[0]} |
---|
[811] | 610 | status=$? |
---|
| 611 | if [ ${status} -gt 0 ] ; then |
---|
[664] | 612 | echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." |
---|
| 613 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
[811] | 614 | return |
---|
[664] | 615 | fi |
---|
[2] | 616 | |
---|
[811] | 617 | #USUAL WAY |
---|
[1179] | 618 | \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[811] | 619 | status=$? |
---|
[2] | 620 | |
---|
[811] | 621 | if [ ${status} -gt 0 ] ; then |
---|
| 622 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}" |
---|
[1179] | 623 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[664] | 624 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
[2] | 625 | else |
---|
[1179] | 626 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[2] | 627 | fi |
---|
[664] | 628 | fi |
---|
| 629 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
[2] | 630 | } |
---|
| 631 | |
---|
| 632 | #D-#================================================== |
---|
[1178] | 633 | #D-function IGCM_sys_GetDate_Monitoring |
---|
| 634 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
| 635 | #D-* Examples: |
---|
| 636 | #D- |
---|
| 637 | function IGCM_sys_GetDate_Monitoring { |
---|
| 638 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
| 639 | if ( $DEBUG_sys ) ; then |
---|
| 640 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
| 641 | fi |
---|
| 642 | |
---|
| 643 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
| 644 | |
---|
| 645 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
| 646 | } |
---|
| 647 | |
---|
| 648 | #D-#================================================== |
---|
[343] | 649 | #D-function IGCM_sys_Dods_Rm |
---|
[717] | 650 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
[343] | 651 | #D-* Examples: |
---|
| 652 | #D- |
---|
| 653 | function IGCM_sys_Dods_Rm { |
---|
[664] | 654 | if ( $DEBUG_sys ) ; then |
---|
| 655 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
| 656 | fi |
---|
| 657 | return 0 |
---|
[343] | 658 | } |
---|
| 659 | |
---|
| 660 | #D-#================================================== |
---|
| 661 | #D-function IGCM_sys_Dods_Cp |
---|
[811] | 662 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
[343] | 663 | #D-* Examples: |
---|
| 664 | #D- |
---|
| 665 | function IGCM_sys_Dods_Cp { |
---|
[664] | 666 | if ( $DEBUG_sys ) ; then |
---|
| 667 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
| 668 | fi |
---|
| 669 | return 0 |
---|
[343] | 670 | } |
---|
| 671 | |
---|
| 672 | #D-#================================================== |
---|
[2] | 673 | #D-function IGCM_sys_Put_Dods |
---|
[811] | 674 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here |
---|
[2] | 675 | #D-* Examples: |
---|
| 676 | #D- |
---|
| 677 | function IGCM_sys_Put_Dods { |
---|
[664] | 678 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
| 679 | if ( $DEBUG_sys ) ; then |
---|
| 680 | echo "IGCM_sys_Put_Dods :" $@ |
---|
| 681 | fi |
---|
| 682 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
[2] | 683 | } |
---|
| 684 | |
---|
[664] | 685 | ############################################################## |
---|
| 686 | # REBUILD OPERATOR |
---|
[2] | 687 | |
---|
[811] | 688 | #D-#================================================== |
---|
[1163] | 689 | #D-function IGCM_sys_sync |
---|
| 690 | #D-* Purpose: flush buffer on disk (dummy function on Ada) |
---|
| 691 | #D-* Examples: |
---|
| 692 | #D- |
---|
| 693 | function IGCM_sys_sync { |
---|
| 694 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
| 695 | if ( $DEBUG_sys ) ; then |
---|
| 696 | echo "IGCM_sys_sync :" $@ |
---|
| 697 | echo "Dummy call, let the system do that." |
---|
| 698 | fi |
---|
| 699 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
| 700 | } |
---|
| 701 | |
---|
[664] | 702 | ############################################################ |
---|
| 703 | # Activate Running Environnment Variables |
---|
| 704 | |
---|
[811] | 705 | #D-#================================================== |
---|
[1239] | 706 | #D-function IGCM_sys_activ_variables |
---|
[811] | 707 | #D-* Purpose: set environement variables prior to execution |
---|
| 708 | #D-* Examples: |
---|
| 709 | #D- |
---|
[664] | 710 | function IGCM_sys_activ_variables { |
---|
| 711 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
| 712 | if ( $DEBUG_sys ) ; then |
---|
| 713 | echo "IGCM_sys_activ_variables" |
---|
| 714 | fi |
---|
[811] | 715 | |
---|
| 716 | # -------------------------------------------------------------------- |
---|
| 717 | #D- MPI specifications |
---|
| 718 | # -------------------------------------------------------------------- |
---|
| 719 | |
---|
| 720 | # -------------------------------------------------------------------- |
---|
| 721 | #D- Other specifications |
---|
| 722 | # -------------------------------------------------------------------- |
---|
| 723 | |
---|
[664] | 724 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
[2] | 725 | } |
---|
| 726 | |
---|
[664] | 727 | ############################################################ |
---|
| 728 | # Desactivate Running Environnment Variables |
---|
[2] | 729 | |
---|
[811] | 730 | #D-#================================================== |
---|
| 731 | #D-function IGCM_sys_desactiv_variables |
---|
| 732 | #D-* Purpose: unset environement variables after execution |
---|
| 733 | #D-* Examples: |
---|
| 734 | #D- |
---|
[664] | 735 | function IGCM_sys_desactiv_variables { |
---|
| 736 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
| 737 | if ( $DEBUG_sys ) ; then |
---|
| 738 | echo "IGCM_sys_desactiv_variables" |
---|
| 739 | fi |
---|
[811] | 740 | # -------------------------------------------------------------------- |
---|
| 741 | #D- MPI specifications |
---|
| 742 | # -------------------------------------------------------------------- |
---|
| 743 | |
---|
| 744 | # -------------------------------------------------------------------- |
---|
| 745 | #D- Other specifications |
---|
| 746 | # -------------------------------------------------------------------- |
---|
| 747 | |
---|
[664] | 748 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
| 749 | } |
---|
| 750 | |
---|
| 751 | ############################################################ |
---|
[1239] | 752 | # Update job headers to be used by the scheduler |
---|
| 753 | |
---|
| 754 | #D-#================================================== |
---|
| 755 | #D-function IGCM_sys_updateHeaders |
---|
| 756 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
| 757 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
| 758 | #D- |
---|
| 759 | function IGCM_sys_updateHeaders { |
---|
| 760 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
| 761 | if ( $DEBUG_sys ) ; then |
---|
| 762 | echo "IGCM_sys_updateHeaders" |
---|
| 763 | fi |
---|
| 764 | typeset file |
---|
| 765 | file=$1 |
---|
| 766 | |
---|
| 767 | if [ ${executionType} -eq 1 ] ; then |
---|
| 768 | # MPMD + MPI |
---|
| 769 | sed -e "/::openMPthreads::/d" \ |
---|
| 770 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 771 | ${file} > ${file}.tmp |
---|
| 772 | |
---|
| 773 | elif [ ${executionType} -eq 2 ] ; then |
---|
| 774 | # MPMD + MPI + OMP |
---|
| 775 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 776 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 777 | ${file} > ${file}.tmp |
---|
| 778 | |
---|
| 779 | elif [ ${executionType} -eq 3 ] ; then |
---|
| 780 | # SPMD + MPI/OMP |
---|
| 781 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 782 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 783 | ${file} > ${file}.tmp |
---|
| 784 | |
---|
| 785 | elif [ ${executionType} -eq 4 ] ; then |
---|
| 786 | # SPMD + MPI only |
---|
| 787 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 788 | -e "/::openMPthreads::/d" \ |
---|
| 789 | ${file} > ${file}.tmp |
---|
| 790 | |
---|
| 791 | elif [ ${executionType} -eq 5 ] ; then |
---|
| 792 | # SPMD + OMP only |
---|
| 793 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 794 | -e "/::JobNumProcTot::/d" \ |
---|
| 795 | ${file} > ${file}.tmp |
---|
| 796 | |
---|
| 797 | elif [ ${executionType} -eq 6 ] ; then |
---|
| 798 | # SEQUENTIAL THEN |
---|
| 799 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
| 800 | -e "/::openMPthreads::/d" \ |
---|
| 801 | ${file} > ${file}.tmp |
---|
| 802 | |
---|
| 803 | fi |
---|
| 804 | |
---|
| 805 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
| 806 | |
---|
| 807 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
| 808 | } |
---|
| 809 | |
---|
| 810 | ############################################################ |
---|
[800] | 811 | # Build MPI/OMP scripts run file (dummy function) |
---|
[664] | 812 | |
---|
[811] | 813 | #D-#================================================== |
---|
| 814 | #D-function IGCM_sys_build_run_file |
---|
| 815 | #D-* Purpose: build run file (deprecated) |
---|
| 816 | #D-* Examples: |
---|
| 817 | #D- |
---|
[664] | 818 | function IGCM_sys_build_run_file { |
---|
| 819 | |
---|
| 820 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
| 821 | |
---|
| 822 | } |
---|
| 823 | |
---|
| 824 | ############################################################ |
---|
| 825 | # Build MPI/OMP scripts |
---|
[811] | 826 | |
---|
| 827 | #D-#================================================== |
---|
| 828 | #D-function IGCM_sys_build_execution_scripts |
---|
| 829 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
| 830 | #D-* Examples: |
---|
| 831 | #D- |
---|
[664] | 832 | function IGCM_sys_build_execution_scripts |
---|
| 833 | { |
---|
| 834 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
| 835 | if ( $DEBUG_sys ) ; then |
---|
| 836 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
| 837 | fi |
---|
[1180] | 838 | |
---|
[664] | 839 | typeset nodes listnodes init_node start_num init_exec comp ExeNameIn ExeNameOut |
---|
| 840 | typeset node_num_current node_current comp_proc_mpi_loc comp_proc_omp_loc |
---|
| 841 | typeset num_corempi nombre_restant_node nombre_restant_comp |
---|
| 842 | |
---|
| 843 | if ( ${OK_PARA_MPMD} ) ; then |
---|
| 844 | |
---|
| 845 | if [ -f run_file ] ; then |
---|
| 846 | IGCM_sys_Rm -f run_file |
---|
[2] | 847 | fi |
---|
[664] | 848 | touch run_file |
---|
| 849 | |
---|
| 850 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 851 | |
---|
| 852 | # Hosts treatment |
---|
| 853 | |
---|
| 854 | ${HOST_MPIRUN_COMMAND} hostname | sort | uniq > hosts.tmp |
---|
| 855 | |
---|
| 856 | i=0 |
---|
| 857 | rm -f hosts |
---|
| 858 | IGCM_debug_Print 1 "sys $( hostname ), Hosts avaible :" |
---|
| 859 | for nodes in `cat hosts.tmp` ; do |
---|
| 860 | host[$i]=$nodes |
---|
| 861 | echo "${host[$i]} slots=1 max_slots=1" >> hosts |
---|
| 862 | IGCM_debug_Print 1 ${host[$i]} |
---|
| 863 | i=$((i+1)) |
---|
| 864 | done |
---|
| 865 | rm -f hosts.tmp |
---|
| 866 | |
---|
| 867 | listnodes=${host[*]} |
---|
| 868 | |
---|
| 869 | EXECUTION="${HOST_MPIRUN_COMMAND} -hostfile hosts" |
---|
| 870 | |
---|
| 871 | # Initialisation |
---|
| 872 | |
---|
| 873 | init_node=y |
---|
| 874 | node_num_current=0 |
---|
| 875 | start_num=0 |
---|
| 876 | init_exec=n |
---|
| 877 | |
---|
[1180] | 878 | # Build run_file |
---|
[664] | 879 | |
---|
[1180] | 880 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
| 881 | # the coupler ie oasis3 must be the first one |
---|
[664] | 882 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 883 | |
---|
| 884 | if [ "X${comp}" = "XCPL" ] ; then |
---|
| 885 | |
---|
| 886 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 887 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 888 | |
---|
| 889 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 890 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 891 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 892 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 893 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 894 | echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
| 895 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 896 | |
---|
| 897 | init_node=n |
---|
| 898 | |
---|
| 899 | (( nombre_restant_node = NUM_COREPERNODE - 1 )) |
---|
| 900 | node_num_current=0 |
---|
| 901 | node_current=${host[${node_num_current}]} |
---|
| 902 | |
---|
| 903 | EXECUTION="${EXECUTION} -H ${node_current} -np 1 ./script_${ExeNameOut}.ksh" |
---|
| 904 | |
---|
| 905 | init_exec=y |
---|
| 906 | start_num=1 |
---|
| 907 | |
---|
| 908 | fi |
---|
| 909 | |
---|
| 910 | done |
---|
| 911 | |
---|
| 912 | # Then loop on the components (except for oasis) |
---|
| 913 | |
---|
| 914 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 915 | |
---|
| 916 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 917 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 918 | |
---|
| 919 | # Only if we really have an executable for the component : |
---|
| 920 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
| 921 | |
---|
| 922 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 923 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 924 | |
---|
| 925 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 926 | # echo "set -vx" >> script_${ExeNameOut}.ksh |
---|
| 927 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 928 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 929 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 930 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 931 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 932 | echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK - ${start_num})) " >> script_${ExeNameOut}.ksh |
---|
| 933 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh |
---|
| 934 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 935 | |
---|
| 936 | node_num=0 |
---|
| 937 | |
---|
| 938 | # We define the number of MPI process to be assigned for the component |
---|
| 939 | |
---|
| 940 | nombre_restant_comp=${comp_proc_mpi_loc} |
---|
| 941 | |
---|
| 942 | # Loop on the allocated nodes |
---|
| 943 | |
---|
| 944 | for node in ${listnodes} ; do |
---|
| 945 | |
---|
| 946 | # We go to the current node |
---|
| 947 | if [ ${node_num} = ${node_num_current} ] ; then |
---|
| 948 | |
---|
| 949 | node_current=${host[${node_num_current}]} |
---|
| 950 | |
---|
| 951 | # If first time on the node : initialisation |
---|
| 952 | |
---|
| 953 | if [ ${init_node} = y ] ; then |
---|
| 954 | nombre_restant_node=${NUM_COREPERNODE} |
---|
| 955 | fi |
---|
| 956 | |
---|
| 957 | # Test on the number of OMP threads |
---|
| 958 | |
---|
| 959 | if [ ${comp_proc_omp_loc} -gt ${nombre_restant_node} ] ; then |
---|
| 960 | (( node_num = node_num + 1 )) |
---|
| 961 | node_num_current=${node_num} |
---|
| 962 | init_node=y |
---|
| 963 | continue |
---|
| 964 | fi |
---|
| 965 | |
---|
| 966 | # Number of MPI process to assign |
---|
| 967 | |
---|
| 968 | (( num_corempi = nombre_restant_node / comp_proc_omp_loc )) |
---|
| 969 | |
---|
| 970 | if [ ${num_corempi} -gt ${nombre_restant_comp} ] ; then |
---|
| 971 | num_corempi=${nombre_restant_comp} |
---|
| 972 | fi |
---|
| 973 | |
---|
| 974 | (( nombre_restant_node = nombre_restant_node - num_corempi * comp_proc_omp_loc )) |
---|
| 975 | (( nombre_restant_comp = nombre_restant_comp - num_corempi )) |
---|
| 976 | |
---|
| 977 | if [ ${init_exec} = y ] ; then |
---|
| 978 | EXECUTION="${EXECUTION} : -H ${node_current} -np ${num_corempi} ./script_${ExeNameOut}.ksh" |
---|
| 979 | else |
---|
| 980 | EXECUTION="${EXECUTION} -H ${node_current} -np ${num_corempi} ./script_${ExeNameOut}.ksh" |
---|
| 981 | init_exec=y |
---|
| 982 | fi |
---|
| 983 | |
---|
| 984 | (( start_num = num_corempi + start_num )) |
---|
| 985 | |
---|
| 986 | else |
---|
| 987 | |
---|
| 988 | (( node_num = node_num + 1 )) |
---|
| 989 | continue |
---|
| 990 | fi |
---|
| 991 | |
---|
| 992 | # Test on the number of core/process remaining on the node/component |
---|
| 993 | |
---|
| 994 | if [ ${nombre_restant_node} = 0 ] ; then |
---|
| 995 | (( node_num = node_num + 1 )) |
---|
| 996 | node_num_current=${node_num} |
---|
| 997 | init_node=y |
---|
| 998 | |
---|
| 999 | if [ ${nombre_restant_comp} = 0 ] ; then |
---|
| 1000 | break 1 |
---|
| 1001 | fi |
---|
| 1002 | else |
---|
| 1003 | |
---|
| 1004 | node_num_current=${node_num} |
---|
| 1005 | init_node=n |
---|
| 1006 | |
---|
| 1007 | if [ ${nombre_restant_comp} = 0 ] ; then |
---|
| 1008 | break 1 |
---|
| 1009 | fi |
---|
| 1010 | fi |
---|
| 1011 | done |
---|
| 1012 | fi |
---|
| 1013 | done |
---|
| 1014 | |
---|
| 1015 | else |
---|
| 1016 | |
---|
| 1017 | # Then first loop on the components for the coupler ie oasis |
---|
| 1018 | |
---|
| 1019 | ## the coupler ie oasis must be the first one |
---|
| 1020 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1021 | |
---|
| 1022 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1023 | |
---|
| 1024 | # for CPL component only |
---|
| 1025 | if [ "X${comp}" = "XCPL" ] ; then |
---|
| 1026 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1027 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut} " >> run_file |
---|
| 1028 | fi |
---|
| 1029 | done |
---|
| 1030 | |
---|
| 1031 | # Then second loop on the components |
---|
| 1032 | |
---|
| 1033 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1034 | |
---|
| 1035 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1036 | |
---|
| 1037 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
| 1038 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
| 1039 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1040 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file |
---|
| 1041 | fi |
---|
| 1042 | done |
---|
| 1043 | IGCM_sys_Chmod u+x run_file |
---|
| 1044 | |
---|
| 1045 | EXECUTION="${HOST_MPIRUN_COMMAND} --app ./run_file" |
---|
| 1046 | |
---|
[2] | 1047 | fi |
---|
| 1048 | |
---|
[664] | 1049 | else # Only one executable. launch it. |
---|
| 1050 | |
---|
| 1051 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1052 | |
---|
| 1053 | # Only if we really have an executable for the component : |
---|
| 1054 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1055 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
| 1056 | |
---|
| 1057 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1058 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1059 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 1060 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 1061 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1062 | fi |
---|
| 1063 | if ( ${OK_PARA_MPI} ) ; then |
---|
| 1064 | # Default : mpirun used if nb_proc gt 1 |
---|
| 1065 | # pour sortie out/err par process |
---|
| 1066 | # echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${OMPI_COMM_WORLD_RANK} 2>out_${ExeNameOut}.err.\${OMPI_COMM_WORLD_RANK}" >> script_${ExeNameOut}.ksh |
---|
| 1067 | echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1068 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1069 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
---|
| 1070 | else |
---|
| 1071 | # Default : mpirun is NOT used if nb_proc eq 1 |
---|
| 1072 | # pour sortie out/err par process |
---|
| 1073 | # echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
| 1074 | echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1075 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1076 | EXECUTION="time ./script_${ExeNameOut}.ksh" |
---|
| 1077 | fi |
---|
[1178] | 1078 | |
---|
| 1079 | IGCM_debug_Print 1 "sys $( hostname ) : script_${ExeNameOut}.ksh contains" |
---|
| 1080 | cat script_${ExeNameOut}.ksh |
---|
| 1081 | |
---|
[664] | 1082 | fi |
---|
[1180] | 1083 | |
---|
[664] | 1084 | done |
---|
| 1085 | |
---|
| 1086 | fi |
---|
| 1087 | |
---|
[811] | 1088 | IGCM_debug_Print 1 "sys $( hostname ) : execution command is" |
---|
| 1089 | IGCM_debug_Print 1 "$EXECUTION" |
---|
[664] | 1090 | |
---|
| 1091 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
[2] | 1092 | } |
---|
| 1093 | |
---|
[933] | 1094 | #D-#================================================== |
---|
| 1095 | #D-function IGCM_sys_check_path |
---|
| 1096 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
| 1097 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
| 1098 | #D-* Examples: |
---|
| 1099 | #D- |
---|
| 1100 | function IGCM_sys_check_path { |
---|
| 1101 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
| 1102 | if ( $DEBUG_sys ) ; then |
---|
| 1103 | echo "IGCM_sys_check_path" |
---|
| 1104 | fi |
---|
[811] | 1105 | |
---|
[933] | 1106 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then |
---|
| 1107 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
| 1108 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
[936] | 1109 | IGCM_debug_Exit "This will stop the job" |
---|
[933] | 1110 | fi |
---|
| 1111 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
| 1112 | } |
---|
| 1113 | |
---|
[811] | 1114 | #D-#================================================== |
---|
| 1115 | #D-function IGCM_sys_check_quota. Dummy call here |
---|
| 1116 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
| 1117 | #D-* Examples: |
---|
| 1118 | #D- |
---|
[664] | 1119 | function IGCM_sys_check_quota { |
---|
| 1120 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
| 1121 | if ( $DEBUG_sys ) ; then |
---|
| 1122 | echo "IGCM_sys_check_quota" |
---|
| 1123 | fi |
---|
| 1124 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
| 1125 | } |
---|
| 1126 | |
---|
[811] | 1127 | #D-#================================================== |
---|
[1244] | 1128 | #D-function IGCM_sys_getJobSchedulerID |
---|
| 1129 | #D-* Purpose: Get the job ID during execution |
---|
| 1130 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
| 1131 | #D- |
---|
| 1132 | function IGCM_sys_getJobSchedulerID { |
---|
| 1133 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
| 1134 | if ( $DEBUG_sys ) ; then |
---|
| 1135 | echo "IGCM_sys_getJobSchedulerID" |
---|
| 1136 | fi |
---|
| 1137 | |
---|
| 1138 | eval ${1}="N/A" |
---|
| 1139 | |
---|
| 1140 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
| 1141 | } |
---|
| 1142 | |
---|
| 1143 | #D-#================================================== |
---|
[811] | 1144 | #D-function IGCM_sys_CountJobInQueue |
---|
[1244] | 1145 | #D-* Purpose: Count number of users job |
---|
[811] | 1146 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
| 1147 | #D- |
---|
| 1148 | function IGCM_sys_CountJobInQueue { |
---|
| 1149 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
| 1150 | if ( $DEBUG_sys ) ; then |
---|
| 1151 | echo "IGCM_sys_CountJobInQueue" |
---|
| 1152 | fi |
---|
| 1153 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
| 1154 | } |
---|
[1272] | 1155 | |
---|
| 1156 | #D-#================================================== |
---|
| 1157 | #D-function IGCM_sys_atlas |
---|
| 1158 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
---|
| 1159 | #D-* Examples: |
---|
| 1160 | #D- |
---|
| 1161 | function IGCM_sys_atlas { |
---|
| 1162 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
---|
| 1163 | if ( $DEBUG_sys ) ; then |
---|
| 1164 | echo "IGCM_sys_atlas :" $@ |
---|
| 1165 | fi |
---|
| 1166 | |
---|
| 1167 | typeset status |
---|
| 1168 | |
---|
| 1169 | \atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 1170 | status=$? |
---|
| 1171 | if [ ${status} -gt 0 ] ; then |
---|
| 1172 | echo "IGCM_sys_atlas : error code ${status}" |
---|
| 1173 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1174 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1175 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1176 | return 1 |
---|
| 1177 | else |
---|
| 1178 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1179 | return 0 |
---|
| 1180 | fi |
---|
| 1181 | |
---|
| 1182 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1183 | } |
---|
| 1184 | |
---|