[657] | 1 | #!/bin/ksh |
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[16] | 2 | |
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| 3 | #************************************************************** |
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| 4 | # Author: Sebastien Denvil, Martial Mancip, Christian Laguerre |
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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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[16] | 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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[657] | 11 | # |
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[16] | 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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[657] | 16 | # if you use the prefix #D- for comments to be extracted. |
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[16] | 17 | # Extract with command: cat lib* | grep "^#D-" | cut -c "4-" |
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| 18 | #========================================================= |
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| 19 | |
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| 20 | #D-#================================================== |
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| 21 | #D-LibIGCM_sys for obelix |
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| 22 | #D-#================================================== |
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| 23 | #D- |
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[657] | 24 | #D- This ksh library if a layer under some usefull |
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[16] | 25 | #D-environment variables and shell commands. |
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| 26 | #D-All those definitions depend on host particularities. |
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| 27 | #D-It manages a stack mechanism and test validity of operations. |
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| 28 | #D-All function described bellow must be prefixed by IGCM_sys. |
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| 29 | |
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| 30 | #==================================================== |
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| 31 | # libIGCM_sys PARAMETERS |
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| 32 | #==================================================== |
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| 33 | |
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[343] | 34 | #==================================================== |
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[16] | 35 | # set DEBUG_sys to true to output calls of function |
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| 36 | typeset -r DEBUG_sys=${DEBUG_sys:=true} |
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| 37 | |
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[343] | 38 | #==================================================== |
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[16] | 39 | # Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get) |
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| 40 | typeset -r DRYRUN=${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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[16] | 47 | # ------------------------------------------------------------------------------------- |
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| 48 | # | 0 | yes | yes | yes | yes | |
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| 49 | # ------------------------------------------------------------------------------------- |
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| 50 | # | 1 | yes | yes | yes | no | |
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| 51 | # ------------------------------------------------------------------------------------- |
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| 52 | # | 2 | yes | yes | no | no | |
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| 53 | # ------------------------------------------------------------------------------------- |
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| 54 | # | 3 | yes | no | no | no | |
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| 55 | # ------------------------------------------------------------------------------------- |
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| 56 | |
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| 57 | #===================================================== |
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| 58 | # Global Variables : |
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| 59 | #===================================================== |
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| 60 | # Language : "fr" or "en" |
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| 61 | typeset -r MYLANG="fr" |
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| 62 | |
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| 63 | #===================================================== |
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[657] | 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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[16] | 67 | # $username ou whoami |
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[1180] | 68 | typeset LOGIN=${LOGIN:=$( whoami )} |
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[657] | 69 | # $hostname of the MASTER job |
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[742] | 70 | typeset MASTER=${MASTER:=$( hostname )} |
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[1201] | 71 | # project name |
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| 72 | typeset PROJECT=NONE |
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| 73 | # jobWarningDelay in seconds |
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| 74 | typeset jobWarningDelay=${PBS_WALLTIME} |
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[16] | 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=${SUBMIT:=qsub} |
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[16] | 83 | # rsync with path |
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| 84 | typeset -r RSYNC=/usr/bin/rsync |
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| 85 | # RSYNC_opt args to rsync |
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[282] | 86 | typeset -r RSYNC_opt="-va" |
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[657] | 87 | # ie storage filesystem |
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| 88 | typeset -r STOREHOST=${MASTER} |
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[16] | 89 | |
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| 90 | #==================================================== |
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[1180] | 91 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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[305] | 92 | #==================================================== |
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[1097] | 93 | . /home/users/igcmg/.atlas_env_asterix_ksh |
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[1180] | 94 | export PATH=${PATH}:/home/users/igcmg/rebuild/bin/ |
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[16] | 95 | |
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[343] | 96 | #==================================================== |
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[16] | 97 | # Host specific DIRECTORIES |
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| 98 | #==================================================== |
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| 99 | |
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| 100 | #==================================================== |
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[657] | 101 | #- MirrorlibIGCM for frontend |
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| 102 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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| 103 | |
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| 104 | #==================================================== |
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| 105 | #- libIGCM_POST for frontend |
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| 106 | typeset -r libIGCM_POST=${libIGCM} |
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| 107 | |
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| 108 | #==================================================== |
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[16] | 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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| 113 | #- SUBMIT_DIR : submission dir |
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[256] | 114 | if [ X${PBS_O_WORKDIR} != X ] ; then |
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[1124] | 115 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PBS_O_WORKDIR}} |
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[256] | 116 | else |
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[1124] | 117 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PWD}} |
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[256] | 118 | fi |
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[657] | 119 | |
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[16] | 120 | #==================================================== |
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[725] | 121 | #- IN |
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[978] | 122 | typeset -r R_IN=${R_IN:=/home/orchideeshare/igcmg/IGCM} |
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[1180] | 123 | typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/home/orchideeshare/igcmg/IGCM} |
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[725] | 124 | |
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| 125 | #==================================================== |
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[16] | 126 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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[838] | 127 | if [ X${PBS_JOBID} != X ] ; then |
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| 128 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/scratch/$PBS_O_LOGNAME.$PBS_JOBID} |
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| 129 | else |
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[839] | 130 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/tmp/tmp$$} |
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[838] | 131 | fi |
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[16] | 132 | |
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| 133 | #==================================================== |
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[1179] | 134 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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[1186] | 135 | typeset -r OUTCOMMAND_PATH=/tmp |
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[1179] | 136 | |
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| 137 | #==================================================== |
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[16] | 138 | #- HOST_MPIRUN_COMMAND |
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| 139 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="time mpirun"} |
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| 140 | |
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[61] | 141 | #==================================================== |
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| 142 | #- Max number of arguments passed to nco operator or demigration command |
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| 143 | UNIX_MAX_LIMIT=360 |
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| 144 | |
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[657] | 145 | #==================================================== |
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[1180] | 146 | #- set PackDefault to false on obelix |
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| 147 | PackDefault=false |
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| 148 | |
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| 149 | #==================================================== |
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[657] | 150 | #- Number of core per node (max number of OpenMP task) |
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[1260] | 151 | NUM_COREPERNODE=4 |
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[657] | 152 | |
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| 153 | #==================================================== |
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| 154 | #- Default number of MPI task for IPSL coupled model |
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| 155 | #- required for backward compatibility |
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| 156 | #- |
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| 157 | DEFAULT_NUM_PROC_OCE=1 |
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| 158 | DEFAULT_NUM_PROC_CPL=1 |
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| 159 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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| 160 | |
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[16] | 161 | #D-#================================================== |
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[1057] | 162 | #D-function IGCM_sys_defineArchives |
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| 163 | #D-* Purpose: |
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| 164 | #D-* Define ARCHIVE : Dedicated to large files |
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| 165 | #D-* Define STORAGE : Dedicated to small/medium files |
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| 166 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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| 167 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) |
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| 168 | #D-* Define R_BUF : Output tree located on STORAGE hosting files waiting for rebuild or pack processes |
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| 169 | #D-* if SpaceName=TEST nothing special will hapen |
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[725] | 170 | #D-* Examples: |
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| 171 | #D- |
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[1057] | 172 | function IGCM_sys_defineArchives { |
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| 173 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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| 174 | |
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[1060] | 175 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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[1057] | 176 | #==================================================== |
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| 177 | #- ARCHIVE (dedicated to large files) |
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[1063] | 178 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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[1057] | 179 | else |
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| 180 | #==================================================== |
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| 181 | #- ARCHIVE (dedicated to large files) |
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[1063] | 182 | ARCHIVE=${ARCHIVE:=/home/scratch01/${LOGIN}} |
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[1057] | 183 | fi |
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| 184 | |
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[1060] | 185 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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[1057] | 186 | #==================================================== |
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| 187 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 188 | STORAGE=${config_UserChoices_STORAGE} |
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[1057] | 189 | else |
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| 190 | #==================================================== |
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| 191 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 192 | STORAGE=${ARCHIVE} |
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[1057] | 193 | fi |
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| 194 | |
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| 195 | # ON OBELIX NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST |
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| 196 | |
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| 197 | #==================================================== |
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| 198 | #- R_OUT |
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[1063] | 199 | R_OUT=${ARCHIVE}/IGCM_OUT |
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[1057] | 200 | |
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| 201 | #==================================================== |
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| 202 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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[1063] | 203 | R_FIG=${STORAGE}/IGCM_OUT |
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[1057] | 204 | |
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| 205 | #==================================================== |
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| 206 | #- R_BUF (ONLY FOR double copy an scratch) |
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[1063] | 207 | R_BUF=${STORAGE}/IGCM_OUT |
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[1057] | 208 | |
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| 209 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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| 210 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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| 211 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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| 212 | |
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| 213 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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[725] | 214 | } |
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| 215 | |
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| 216 | #D-#================================================== |
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[37] | 217 | #D-function IGCM_sys_RshArchive |
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| 218 | #D-* Purpose: Archive rsh command |
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| 219 | #D-* Examples: |
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| 220 | #D- |
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| 221 | function IGCM_sys_RshArchive { |
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[657] | 222 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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| 223 | /bin/ksh <<-EOF |
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[40] | 224 | ${@} |
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| 225 | EOF |
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[811] | 226 | status=$? |
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| 227 | if [ ${status} -gt 0 ] ; then |
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| 228 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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[657] | 229 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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| 230 | fi |
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| 231 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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[37] | 232 | } |
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| 233 | |
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| 234 | #D-#================================================== |
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[1178] | 235 | #D-function IGCM_sys_RshArchive_NoError |
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| 236 | #D-* Purpose: Archive rsh command, without error |
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| 237 | #D-* used only in monitoring.job |
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| 238 | #D-* Examples: |
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| 239 | #D- |
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| 240 | function IGCM_sys_RshArchive_NoError { |
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| 241 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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| 242 | /bin/ksh <<-EOF |
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[1181] | 243 | ${@} 2> /dev/null |
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[1178] | 244 | EOF |
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| 245 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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| 246 | } |
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| 247 | |
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| 248 | #D-#================================================== |
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[16] | 249 | #D-function IGCM_sys_MkdirArchive |
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| 250 | #D-* Purpose: Mkdir on Archive |
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| 251 | #D-* Examples: |
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| 252 | #D- |
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| 253 | function IGCM_sys_MkdirArchive { |
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[657] | 254 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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| 255 | if ( $DEBUG_sys ) ; then |
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| 256 | echo "IGCM_sys_MkdirArchive :" $@ |
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| 257 | fi |
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[717] | 258 | #- creation de repertoire sur le serveur fichier |
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[657] | 259 | if [ ! -d ${1} ]; then |
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[1178] | 260 | \mkdir -p $1 |
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[811] | 261 | status=$? |
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| 262 | |
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| 263 | if [ ${status} -gt 0 ] ; then |
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| 264 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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[657] | 265 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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[16] | 266 | fi |
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[657] | 267 | fi |
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| 268 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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[16] | 269 | } |
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| 270 | |
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| 271 | #D-#================================================== |
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| 272 | #D-function IGCM_sys_TestDirArchive |
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| 273 | #D-* Purpose: Test Directory that must exists on Archive |
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| 274 | #D-* Examples: |
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| 275 | #D- |
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| 276 | function IGCM_sys_TestDirArchive { |
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[657] | 277 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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| 278 | if ( $DEBUG_sys ) ; then |
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| 279 | echo "IGCM_sys_TestDirArchive :" $@ |
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| 280 | fi |
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| 281 | typeset ExistFlag |
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| 282 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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| 283 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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| 284 | return ${ExistFlag} |
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[16] | 285 | } |
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| 286 | |
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| 287 | #D-#================================================== |
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[800] | 288 | #D-function IGCM_sys_IsFileArchived |
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[1180] | 289 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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[800] | 290 | #D-* Examples: |
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| 291 | #D- |
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| 292 | function IGCM_sys_IsFileArchived { |
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| 293 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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| 294 | if ( $DEBUG_sys ) ; then |
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| 295 | echo "IGCM_sys_IsFileArchived :" $@ |
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| 296 | fi |
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| 297 | typeset IsArchivedFlag |
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| 298 | # Never archived for this system |
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| 299 | IsArchivedFlag=1 |
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| 300 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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| 301 | |
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| 302 | return ${IsArchivedFlag} |
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| 303 | } |
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| 304 | |
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| 305 | #D-#================================================== |
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[16] | 306 | #D-function IGCM_sys_TestFileArchive |
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| 307 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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| 308 | #D-* Examples: |
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| 309 | #D- |
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| 310 | function IGCM_sys_TestFileArchive { |
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[657] | 311 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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| 312 | typeset ExistFlag |
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| 313 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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| 314 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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[67] | 315 | |
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[657] | 316 | return ${ExistFlag} |
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[67] | 317 | } |
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| 318 | |
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| 319 | #D-#================================================== |
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| 320 | #D-function IGCM_sys_CountFileArchive |
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| 321 | #D-* Purpose: Count files on Archive filesystem |
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| 322 | #D-* Examples: |
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| 323 | #D- |
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| 324 | function IGCM_sys_CountFileArchive { |
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[657] | 325 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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| 326 | ls ${@} 2>/dev/null | wc -l |
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| 327 | if [ $? -gt 0 ] ; then |
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| 328 | echo "IGCM_sys_CountFileArchive : erreur." |
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| 329 | fi |
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| 330 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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[16] | 331 | } |
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| 332 | |
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| 333 | #D-#================================================== |
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| 334 | #D-function IGCM_sys_Tree |
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| 335 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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| 336 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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| 337 | #D- |
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| 338 | function IGCM_sys_Tree { |
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[657] | 339 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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| 340 | if ( $DEBUG_sys ) ; then |
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| 341 | echo "IGCM_sys_Tree :" $@ |
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| 342 | fi |
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[16] | 343 | |
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[657] | 344 | \tree -f $@ |
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[16] | 345 | |
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[657] | 346 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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[16] | 347 | } |
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| 348 | |
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| 349 | #D-#================================================== |
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| 350 | #D-function IGCM_sys_Qsub |
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| 351 | #D-* Purpose: Qsub new job |
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| 352 | #D-* Examples: |
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| 353 | #D- |
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| 354 | function IGCM_sys_Qsub { |
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[657] | 355 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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| 356 | if ( $DEBUG_sys ) ; then |
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| 357 | echo "IGCM_sys_Qsub :" $@ |
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| 358 | fi |
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[923] | 359 | typeset options status |
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| 360 | options="-o ${SUBMIT_DIR}/${Script_Output}" |
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[1179] | 361 | /usr/local/bin/qsub ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[811] | 362 | status=$? |
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[949] | 363 | |
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[1179] | 364 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[811] | 365 | if [ ${status} -gt 0 ] ; then |
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[1180] | 366 | IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}" |
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[657] | 367 | IGCM_debug_Exit "IGCM_sys_Qsub" |
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[949] | 368 | else |
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[1179] | 369 | JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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[657] | 370 | fi |
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| 371 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
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[16] | 372 | } |
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| 373 | |
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| 374 | #D-#================================================== |
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| 375 | #D-function IGCM_sys_QsubPost |
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| 376 | #D-* Purpose: Qsub new job on scalaire |
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| 377 | #D-* Examples: |
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| 378 | #D- |
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| 379 | function IGCM_sys_QsubPost { |
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[657] | 380 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
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| 381 | if ( $DEBUG_sys ) ; then |
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| 382 | echo "IGCM_sys_QsubPost :" $@ |
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| 383 | fi |
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[923] | 384 | typeset options status |
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| 385 | options="-o ${POST_DIR}/${Script_Post_Output}.out -v ${listVarEnv}" |
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[1179] | 386 | /usr/local/bin/qsub ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[811] | 387 | status=$? |
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[949] | 388 | |
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[1179] | 389 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[811] | 390 | if [ ${status} -gt 0 ] ; then |
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[923] | 391 | IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}" |
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[657] | 392 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
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[949] | 393 | else |
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[1179] | 394 | JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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[657] | 395 | fi |
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| 396 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
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[16] | 397 | } |
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| 398 | |
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| 399 | #D-************************* |
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[657] | 400 | #D- File transfer functions |
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[16] | 401 | #D-************************* |
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| 402 | #D- |
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| 403 | |
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| 404 | #D-#================================================== |
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[203] | 405 | #D-function IGCM_sys_RmRunDir |
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| 406 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
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| 407 | #D- scheduler will do the job) |
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| 408 | #D-* Examples: |
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| 409 | #D- |
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| 410 | function IGCM_sys_RmRunDir { |
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[1057] | 411 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
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[657] | 412 | if ( $DEBUG_sys ) ; then |
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| 413 | echo "IGCM_sys_RmRunDir :" $@ |
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[964] | 414 | echo "Dummy call, let the scheduler do that." |
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[657] | 415 | fi |
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| 416 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
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[203] | 417 | } |
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| 418 | |
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| 419 | #D-#================================================== |
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[16] | 420 | #D-function IGCM_sys_Put_Dir |
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| 421 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
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| 422 | #D-* Examples: |
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| 423 | #D- |
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| 424 | function IGCM_sys_Put_Dir { |
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[657] | 425 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
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| 426 | if ( $DEBUG_sys ) ; then |
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| 427 | echo "IGCM_sys_Put_Dir :" $@ |
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| 428 | fi |
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| 429 | if [ $DRYRUN = 0 ]; then |
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| 430 | if [ ! -d ${1} ] ; then |
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| 431 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
---|
| 432 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
| 433 | return |
---|
[16] | 434 | fi |
---|
| 435 | |
---|
[717] | 436 | typeset status |
---|
[16] | 437 | |
---|
[717] | 438 | # Only if we use rsync |
---|
| 439 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
---|
| 440 | # |
---|
| 441 | #USUAL WAY |
---|
[1179] | 442 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[717] | 443 | status=$? |
---|
[16] | 444 | |
---|
[717] | 445 | if [ ${status} -gt 0 ] ; then |
---|
[811] | 446 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
---|
[1179] | 447 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 448 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
---|
[16] | 449 | else |
---|
[1179] | 450 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[16] | 451 | fi |
---|
[657] | 452 | fi |
---|
| 453 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
[16] | 454 | } |
---|
| 455 | |
---|
| 456 | #D-#================================================== |
---|
| 457 | #D-function IGCM_sys_Get_Dir |
---|
[717] | 458 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
[16] | 459 | #D-* Examples: |
---|
| 460 | #D- |
---|
| 461 | function IGCM_sys_Get_Dir { |
---|
[657] | 462 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
| 463 | if ( $DEBUG_sys ) ; then |
---|
| 464 | echo "IGCM_sys_Get_Dir :" $@ |
---|
| 465 | fi |
---|
| 466 | if [ $DRYRUN = 0 ]; then |
---|
[1180] | 467 | typeset NB_ESSAI DELAI status i |
---|
| 468 | # number of tentative |
---|
| 469 | NB_ESSAI=3 |
---|
| 470 | # time delay between tentative |
---|
| 471 | DELAI=2 |
---|
[16] | 472 | |
---|
[1180] | 473 | # |
---|
| 474 | # USUAL WAY |
---|
| 475 | i=0 |
---|
| 476 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 477 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 478 | status=$? |
---|
| 479 | if [ ${status} -gt 0 ] ; then |
---|
| 480 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 481 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
| 482 | sleep $DELAI |
---|
| 483 | else |
---|
| 484 | break |
---|
| 485 | fi |
---|
| 486 | (( i = i + 1 )) |
---|
| 487 | done |
---|
[16] | 488 | |
---|
[717] | 489 | if [ ${status} -gt 0 ] ; then |
---|
[811] | 490 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
[1179] | 491 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 492 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
[16] | 493 | else |
---|
[1179] | 494 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[16] | 495 | fi |
---|
[657] | 496 | fi |
---|
| 497 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
[16] | 498 | } |
---|
| 499 | |
---|
| 500 | #D-#================================================== |
---|
| 501 | #D-function IGCM_sys_Put_Rest |
---|
[717] | 502 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
[282] | 503 | #D- File and target directory must exist. |
---|
[16] | 504 | #D-* Examples: |
---|
| 505 | #D- |
---|
| 506 | function IGCM_sys_Put_Rest { |
---|
[657] | 507 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
| 508 | if ( $DEBUG_sys ) ; then |
---|
| 509 | echo "IGCM_sys_Put_Rest :" $@ |
---|
| 510 | fi |
---|
| 511 | if [ $DRYRUN = 0 ]; then |
---|
| 512 | if [ ! -f ${1} ] ; then |
---|
| 513 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
| 514 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
[16] | 515 | fi |
---|
[717] | 516 | |
---|
| 517 | typeset status |
---|
| 518 | # |
---|
[1178] | 519 | # USUAL WAY |
---|
[1179] | 520 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[717] | 521 | status=$? |
---|
[16] | 522 | |
---|
[717] | 523 | # #RSYNC WITH NETWORK SSH CALL |
---|
[1179] | 524 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 525 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[16] | 526 | |
---|
[717] | 527 | # #RSYNC WITH NFS USE |
---|
[1179] | 528 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 529 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[16] | 530 | |
---|
[717] | 531 | # status=$? |
---|
| 532 | # IGCM_sys_Rsync_out $status |
---|
| 533 | |
---|
[1179] | 534 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[717] | 535 | # (( status=status+$? )) |
---|
| 536 | |
---|
| 537 | if [ ${status} -gt 0 ] ; then |
---|
[1180] | 538 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
[1178] | 539 | [ -f ${1} ] && ls -l ${1} |
---|
| 540 | [ -f ${2} ] && ls -l ${2} |
---|
| 541 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
[1179] | 542 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 543 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
| 544 | else |
---|
[1178] | 545 | |
---|
| 546 | if [ X${JobType} = XRUN ] ; then |
---|
| 547 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 548 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 549 | fi |
---|
| 550 | |
---|
[1179] | 551 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 552 | fi |
---|
| 553 | fi |
---|
| 554 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
| 555 | } |
---|
[16] | 556 | |
---|
[657] | 557 | #D-#================================================== |
---|
[16] | 558 | #D-function IGCM_sys_Put_Out |
---|
[717] | 559 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
[16] | 560 | #D-* Examples: |
---|
| 561 | #D- |
---|
| 562 | function IGCM_sys_Put_Out { |
---|
[657] | 563 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
| 564 | if ( $DEBUG_sys ) ; then |
---|
| 565 | echo "IGCM_sys_Put_Out :" $@ |
---|
| 566 | fi |
---|
[811] | 567 | |
---|
| 568 | typeset status |
---|
| 569 | |
---|
[657] | 570 | if [ $DRYRUN = 0 ]; then |
---|
[811] | 571 | if [ ! -f ${1} ] ; then |
---|
[657] | 572 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
| 573 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 574 | return 1 |
---|
[16] | 575 | fi |
---|
[719] | 576 | # |
---|
[811] | 577 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
| 578 | # |
---|
[657] | 579 | if [ X${JobType} = XRUN ] ; then |
---|
| 580 | if [ X${3} = X ] ; then |
---|
| 581 | IGCM_sys_Chmod 444 ${1} |
---|
| 582 | fi |
---|
| 583 | fi |
---|
[717] | 584 | # |
---|
[16] | 585 | |
---|
[1179] | 586 | echo ${RSYNC} ${RSYNC_opt} $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 587 | ${RSYNC} ${RSYNC_opt} $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[717] | 588 | status=$? |
---|
| 589 | IGCM_sys_Rsync_out $status |
---|
[16] | 590 | |
---|
[1179] | 591 | ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[717] | 592 | (( status=status+$? )) |
---|
[16] | 593 | |
---|
[717] | 594 | if [ ${status} -gt 0 ] ; then |
---|
[811] | 595 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : rsync failed error code ${status}" |
---|
[1179] | 596 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 597 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
[16] | 598 | else |
---|
[1179] | 599 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[16] | 600 | fi |
---|
[657] | 601 | fi |
---|
| 602 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 603 | return 0 |
---|
[16] | 604 | } |
---|
| 605 | |
---|
| 606 | #D-#================================================== |
---|
| 607 | #D-function IGCM_sys_Get |
---|
| 608 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
| 609 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
| 610 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
| 611 | function IGCM_sys_Get { |
---|
[657] | 612 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
[16] | 613 | |
---|
[811] | 614 | typeset DEST status dm_liste |
---|
[16] | 615 | |
---|
[657] | 616 | if ( $DEBUG_sys ) ; then |
---|
| 617 | echo "IGCM_sys_Get :" $@ |
---|
| 618 | fi |
---|
| 619 | if [ $DRYRUN -le 2 ]; then |
---|
| 620 | if [ X${1} = X'/l' ] ; then |
---|
| 621 | eval set +A dm_liste \${${2}} |
---|
| 622 | else |
---|
| 623 | dm_liste=${1} |
---|
[16] | 624 | fi |
---|
[657] | 625 | eval DEST=\${${#}} |
---|
[16] | 626 | |
---|
[717] | 627 | # test if the (first) file is present in the old computation : |
---|
[657] | 628 | IGCM_sys_TestFileArchive ${dm_liste[0]} |
---|
[717] | 629 | status=$? |
---|
| 630 | if [ ${status} -gt 0 ] ; then |
---|
[657] | 631 | echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." |
---|
| 632 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
[811] | 633 | return |
---|
[657] | 634 | fi |
---|
[16] | 635 | |
---|
[811] | 636 | #USUAL WAY |
---|
[1179] | 637 | \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[811] | 638 | status=$? |
---|
[16] | 639 | |
---|
[811] | 640 | if [ ${status} -gt 0 ] ; then |
---|
| 641 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}" |
---|
[1179] | 642 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 643 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
[16] | 644 | else |
---|
[1179] | 645 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[16] | 646 | fi |
---|
[657] | 647 | fi |
---|
| 648 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
[16] | 649 | } |
---|
| 650 | |
---|
| 651 | #D-#================================================== |
---|
[1131] | 652 | #D-function IGCM_sys_GetDate_Monitoring |
---|
| 653 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
| 654 | #D-* Examples: |
---|
| 655 | #D- |
---|
| 656 | function IGCM_sys_GetDate_Monitoring { |
---|
| 657 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
| 658 | if ( $DEBUG_sys ) ; then |
---|
| 659 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
| 660 | fi |
---|
| 661 | |
---|
| 662 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
| 663 | |
---|
| 664 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
| 665 | } |
---|
| 666 | |
---|
| 667 | #D-#================================================== |
---|
[343] | 668 | #D-function IGCM_sys_Dods_Rm |
---|
[717] | 669 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
[343] | 670 | #D-* Examples: |
---|
| 671 | #D- |
---|
| 672 | function IGCM_sys_Dods_Rm { |
---|
[657] | 673 | if ( $DEBUG_sys ) ; then |
---|
| 674 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
| 675 | fi |
---|
| 676 | return 0 |
---|
[343] | 677 | } |
---|
| 678 | |
---|
| 679 | #D-#================================================== |
---|
| 680 | #D-function IGCM_sys_Dods_Cp |
---|
[717] | 681 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
[343] | 682 | #D-* Examples: |
---|
| 683 | #D- |
---|
| 684 | function IGCM_sys_Dods_Cp { |
---|
[657] | 685 | if ( $DEBUG_sys ) ; then |
---|
| 686 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
| 687 | fi |
---|
| 688 | return 0 |
---|
[343] | 689 | } |
---|
| 690 | |
---|
| 691 | #D-#================================================== |
---|
[16] | 692 | #D-function IGCM_sys_Put_Dods |
---|
[811] | 693 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here |
---|
[16] | 694 | #D-* Examples: |
---|
| 695 | #D- |
---|
| 696 | function IGCM_sys_Put_Dods { |
---|
[657] | 697 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
| 698 | if ( $DEBUG_sys ) ; then |
---|
| 699 | echo "IGCM_sys_Put_Dods :" $@ |
---|
| 700 | fi |
---|
| 701 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
[16] | 702 | } |
---|
| 703 | |
---|
[657] | 704 | ############################################################## |
---|
| 705 | # REBUILD OPERATOR |
---|
[536] | 706 | |
---|
[811] | 707 | #D-#================================================== |
---|
[1163] | 708 | #D-function IGCM_sys_sync |
---|
| 709 | #D-* Purpose: flush buffer on disk (dummy function on Ada) |
---|
| 710 | #D-* Examples: |
---|
| 711 | #D- |
---|
| 712 | function IGCM_sys_sync { |
---|
| 713 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
| 714 | if ( $DEBUG_sys ) ; then |
---|
| 715 | echo "IGCM_sys_sync :" $@ |
---|
| 716 | echo "Dummy call, let the system do that." |
---|
| 717 | fi |
---|
| 718 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
| 719 | } |
---|
| 720 | |
---|
[657] | 721 | ############################################################ |
---|
| 722 | # Activate Running Environnment Variables |
---|
[536] | 723 | |
---|
[811] | 724 | #D-#================================================== |
---|
[1239] | 725 | #D-function IGCM_sys_activ_variables |
---|
[811] | 726 | #D-* Purpose: set environement variables prior to execution |
---|
| 727 | #D-* Examples: |
---|
| 728 | #D- |
---|
[657] | 729 | function IGCM_sys_activ_variables { |
---|
| 730 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
| 731 | if ( $DEBUG_sys ) ; then |
---|
| 732 | echo "IGCM_sys_activ_variables" |
---|
| 733 | fi |
---|
[811] | 734 | |
---|
| 735 | # -------------------------------------------------------------------- |
---|
| 736 | #D- MPI specifications |
---|
| 737 | # -------------------------------------------------------------------- |
---|
| 738 | |
---|
| 739 | # -------------------------------------------------------------------- |
---|
| 740 | #D- Other specifications |
---|
| 741 | # -------------------------------------------------------------------- |
---|
| 742 | |
---|
[657] | 743 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
[16] | 744 | } |
---|
| 745 | |
---|
[657] | 746 | ############################################################ |
---|
| 747 | # Desactivate Running Environnment Variables |
---|
[16] | 748 | |
---|
[811] | 749 | #D-#================================================== |
---|
| 750 | #D-function IGCM_sys_desactiv_variables |
---|
| 751 | #D-* Purpose: unset environement variables after execution |
---|
| 752 | #D-* Examples: |
---|
| 753 | #D- |
---|
[657] | 754 | function IGCM_sys_desactiv_variables { |
---|
| 755 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
| 756 | if ( $DEBUG_sys ) ; then |
---|
| 757 | echo "IGCM_sys_desactiv_variables" |
---|
| 758 | fi |
---|
[811] | 759 | # -------------------------------------------------------------------- |
---|
| 760 | #D- MPI specifications |
---|
| 761 | # -------------------------------------------------------------------- |
---|
| 762 | |
---|
| 763 | # -------------------------------------------------------------------- |
---|
| 764 | #D- Other specifications |
---|
| 765 | # -------------------------------------------------------------------- |
---|
| 766 | |
---|
[657] | 767 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
| 768 | } |
---|
| 769 | |
---|
| 770 | ############################################################ |
---|
[1239] | 771 | # Update job headers to be used by the scheduler |
---|
| 772 | |
---|
| 773 | #D-#================================================== |
---|
| 774 | #D-function IGCM_sys_updateHeaders |
---|
| 775 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
| 776 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
| 777 | #D- |
---|
| 778 | function IGCM_sys_updateHeaders { |
---|
| 779 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
| 780 | if ( $DEBUG_sys ) ; then |
---|
| 781 | echo "IGCM_sys_updateHeaders" |
---|
| 782 | fi |
---|
| 783 | typeset file |
---|
| 784 | file=$1 |
---|
| 785 | |
---|
| 786 | if [ ${executionType} -eq 1 ] ; then |
---|
| 787 | # MPMD + MPI |
---|
| 788 | sed -e "/::openMPthreads::/d" \ |
---|
| 789 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 790 | ${file} > ${file}.tmp |
---|
| 791 | |
---|
| 792 | elif [ ${executionType} -eq 2 ] ; then |
---|
| 793 | # MPMD + MPI + OMP |
---|
| 794 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 795 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 796 | ${file} > ${file}.tmp |
---|
| 797 | |
---|
| 798 | elif [ ${executionType} -eq 3 ] ; then |
---|
| 799 | # SPMD + MPI/OMP |
---|
| 800 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 801 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 802 | ${file} > ${file}.tmp |
---|
| 803 | |
---|
| 804 | elif [ ${executionType} -eq 4 ] ; then |
---|
| 805 | # SPMD + MPI only |
---|
| 806 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 807 | -e "/::openMPthreads::/d" \ |
---|
| 808 | ${file} > ${file}.tmp |
---|
| 809 | |
---|
| 810 | elif [ ${executionType} -eq 5 ] ; then |
---|
| 811 | # SPMD + OMP only |
---|
| 812 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 813 | -e "/::JobNumProcTot::/d" \ |
---|
| 814 | ${file} > ${file}.tmp |
---|
| 815 | |
---|
| 816 | elif [ ${executionType} -eq 6 ] ; then |
---|
| 817 | # SEQUENTIAL THEN |
---|
| 818 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
| 819 | -e "/::openMPthreads::/d" \ |
---|
| 820 | ${file} > ${file}.tmp |
---|
| 821 | |
---|
| 822 | fi |
---|
| 823 | |
---|
| 824 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
| 825 | |
---|
| 826 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
| 827 | } |
---|
| 828 | |
---|
| 829 | ############################################################ |
---|
[800] | 830 | # Build MPI/OMP scripts run file (dummy function) |
---|
[657] | 831 | |
---|
[811] | 832 | #D-#================================================== |
---|
| 833 | #D-function IGCM_sys_build_run_file |
---|
| 834 | #D-* Purpose: build run file (deprecated) |
---|
| 835 | #D-* Examples: |
---|
| 836 | #D- |
---|
[657] | 837 | function IGCM_sys_build_run_file { |
---|
| 838 | |
---|
[664] | 839 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
[657] | 840 | |
---|
| 841 | } |
---|
| 842 | |
---|
| 843 | ############################################################ |
---|
| 844 | # Build MPI/OMP scripts |
---|
[811] | 845 | |
---|
| 846 | #D-#================================================== |
---|
| 847 | #D-function IGCM_sys_build_execution_scripts |
---|
| 848 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
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| 849 | #D-* Examples: |
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| 850 | #D- |
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[657] | 851 | function IGCM_sys_build_execution_scripts |
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| 852 | { |
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| 853 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
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| 854 | if ( $DEBUG_sys ) ; then |
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| 855 | echo "IGCM_sys_build_execution_scripts " $@ |
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| 856 | fi |
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[1180] | 857 | |
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[657] | 858 | typeset nodes listnodes init_node start_num init_exec comp ExeNameIn ExeNameOut |
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| 859 | typeset node_num_current node_current comp_proc_mpi_loc comp_proc_omp_loc |
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| 860 | typeset num_corempi nombre_restant_node nombre_restant_comp |
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| 861 | |
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| 862 | if ( ${OK_PARA_MPMD} ) ; then |
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| 863 | |
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| 864 | if [ -f run_file ] ; then |
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| 865 | IGCM_sys_Rm -f run_file |
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[16] | 866 | fi |
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[657] | 867 | touch run_file |
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| 868 | |
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| 869 | if ( ${OK_PARA_OMP} ) ; then |
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| 870 | |
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| 871 | # Hosts treatment |
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| 872 | |
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| 873 | ${HOST_MPIRUN_COMMAND} hostname | sort | uniq > hosts.tmp |
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| 874 | |
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| 875 | i=0 |
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| 876 | rm -f hosts |
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| 877 | IGCM_debug_Print 1 "sys Obelix, Hosts avaible :" |
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| 878 | for nodes in `cat hosts.tmp` ; do |
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| 879 | host[$i]=$nodes |
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| 880 | echo "${host[$i]} slots=1 max_slots=1" >> hosts |
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| 881 | IGCM_debug_Print 1 ${host[$i]} |
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| 882 | i=$((i+1)) |
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| 883 | done |
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| 884 | rm -f hosts.tmp |
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| 885 | |
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| 886 | listnodes=${host[*]} |
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| 887 | |
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| 888 | EXECUTION="${HOST_MPIRUN_COMMAND} -hostfile hosts" |
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| 889 | |
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| 890 | # Initialisation |
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| 891 | |
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| 892 | init_node=y |
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| 893 | node_num_current=0 |
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| 894 | start_num=0 |
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| 895 | init_exec=n |
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| 896 | |
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[1180] | 897 | # Build run_file |
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[657] | 898 | |
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[1180] | 899 | # First loop on the components for the coupler ie oasis (only if oasis3) |
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| 900 | # the coupler ie oasis3 must be the first one |
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[657] | 901 | for comp in ${config_ListOfComponents[*]} ; do |
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| 902 | |
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| 903 | if [ "X${comp}" = "XCPL" ] ; then |
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| 904 | |
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| 905 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
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| 906 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
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| 907 | |
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| 908 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
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| 909 | echo "" >> script_${ExeNameOut}.ksh |
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| 910 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
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| 911 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
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| 912 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
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| 913 | echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
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| 914 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
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| 915 | |
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| 916 | init_node=n |
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| 917 | |
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| 918 | (( nombre_restant_node = NUM_COREPERNODE - 1 )) |
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| 919 | node_num_current=0 |
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| 920 | node_current=${host[${node_num_current}]} |
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| 921 | |
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| 922 | EXECUTION="${EXECUTION} -H ${node_current} -np 1 ./script_${ExeNameOut}.ksh" |
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| 923 | |
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| 924 | init_exec=y |
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| 925 | start_num=1 |
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| 926 | |
---|
| 927 | fi |
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| 928 | |
---|
| 929 | done |
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| 930 | |
---|
| 931 | # Then loop on the components (except for oasis) |
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| 932 | |
---|
| 933 | for comp in ${config_ListOfComponents[*]} ; do |
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| 934 | |
---|
| 935 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
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| 936 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
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| 937 | |
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| 938 | # Only if we really have an executable for the component : |
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| 939 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
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| 940 | |
---|
| 941 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
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| 942 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
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| 943 | |
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| 944 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
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| 945 | # echo "set -vx" >> script_${ExeNameOut}.ksh |
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| 946 | echo "" >> script_${ExeNameOut}.ksh |
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| 947 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
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| 948 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
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| 949 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
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| 950 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
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| 951 | echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK - ${start_num})) " >> script_${ExeNameOut}.ksh |
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| 952 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh |
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| 953 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
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| 954 | |
---|
| 955 | node_num=0 |
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| 956 | |
---|
| 957 | # We define the number of MPI process to be assigned for the component |
---|
| 958 | |
---|
| 959 | nombre_restant_comp=${comp_proc_mpi_loc} |
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| 960 | |
---|
| 961 | # Loop on the allocated nodes |
---|
| 962 | |
---|
| 963 | for node in ${listnodes} ; do |
---|
| 964 | |
---|
| 965 | # We go to the current node |
---|
| 966 | if [ ${node_num} = ${node_num_current} ] ; then |
---|
| 967 | |
---|
| 968 | node_current=${host[${node_num_current}]} |
---|
| 969 | |
---|
| 970 | # If first time on the node : initialisation |
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| 971 | |
---|
| 972 | if [ ${init_node} = y ] ; then |
---|
| 973 | nombre_restant_node=${NUM_COREPERNODE} |
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| 974 | fi |
---|
| 975 | |
---|
| 976 | # Test on the number of OMP threads |
---|
| 977 | |
---|
| 978 | if [ ${comp_proc_omp_loc} -gt ${nombre_restant_node} ] ; then |
---|
| 979 | (( node_num = node_num + 1 )) |
---|
| 980 | node_num_current=${node_num} |
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| 981 | init_node=y |
---|
| 982 | continue |
---|
| 983 | fi |
---|
| 984 | |
---|
| 985 | # Number of MPI process to assign |
---|
| 986 | |
---|
| 987 | (( num_corempi = nombre_restant_node / comp_proc_omp_loc )) |
---|
| 988 | |
---|
| 989 | if [ ${num_corempi} -gt ${nombre_restant_comp} ] ; then |
---|
| 990 | num_corempi=${nombre_restant_comp} |
---|
| 991 | fi |
---|
| 992 | |
---|
| 993 | (( nombre_restant_node = nombre_restant_node - num_corempi * comp_proc_omp_loc )) |
---|
| 994 | (( nombre_restant_comp = nombre_restant_comp - num_corempi )) |
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| 995 | |
---|
| 996 | if [ ${init_exec} = y ] ; then |
---|
| 997 | EXECUTION="${EXECUTION} : -H ${node_current} -np ${num_corempi} ./script_${ExeNameOut}.ksh" |
---|
| 998 | else |
---|
| 999 | EXECUTION="${EXECUTION} -H ${node_current} -np ${num_corempi} ./script_${ExeNameOut}.ksh" |
---|
| 1000 | init_exec=y |
---|
| 1001 | fi |
---|
| 1002 | |
---|
| 1003 | (( start_num = num_corempi + start_num )) |
---|
| 1004 | |
---|
| 1005 | else |
---|
| 1006 | |
---|
| 1007 | (( node_num = node_num + 1 )) |
---|
| 1008 | continue |
---|
| 1009 | fi |
---|
| 1010 | |
---|
| 1011 | # Test on the number of core/process remaining on the node/component |
---|
| 1012 | |
---|
| 1013 | if [ ${nombre_restant_node} = 0 ] ; then |
---|
| 1014 | (( node_num = node_num + 1 )) |
---|
| 1015 | node_num_current=${node_num} |
---|
| 1016 | init_node=y |
---|
| 1017 | |
---|
| 1018 | if [ ${nombre_restant_comp} = 0 ] ; then |
---|
| 1019 | break 1 |
---|
| 1020 | fi |
---|
| 1021 | else |
---|
| 1022 | |
---|
| 1023 | node_num_current=${node_num} |
---|
| 1024 | init_node=n |
---|
| 1025 | |
---|
| 1026 | if [ ${nombre_restant_comp} = 0 ] ; then |
---|
| 1027 | break 1 |
---|
| 1028 | fi |
---|
| 1029 | fi |
---|
| 1030 | done |
---|
| 1031 | fi |
---|
| 1032 | done |
---|
| 1033 | |
---|
| 1034 | else |
---|
| 1035 | |
---|
[664] | 1036 | # Then first loop on the components for the coupler ie oasis |
---|
[657] | 1037 | |
---|
[664] | 1038 | ## the coupler ie oasis must be the first one |
---|
| 1039 | for comp in ${config_ListOfComponents[*]} ; do |
---|
[657] | 1040 | |
---|
[664] | 1041 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[657] | 1042 | |
---|
| 1043 | # for CPL component only |
---|
[664] | 1044 | if [ "X${comp}" = "XCPL" ] ; then |
---|
| 1045 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1046 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut} " >> run_file |
---|
| 1047 | fi |
---|
| 1048 | done |
---|
[657] | 1049 | |
---|
[811] | 1050 | # Then second loop on the components |
---|
[657] | 1051 | |
---|
[664] | 1052 | for comp in ${config_ListOfComponents[*]} ; do |
---|
[657] | 1053 | |
---|
[664] | 1054 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[657] | 1055 | |
---|
[664] | 1056 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
| 1057 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
| 1058 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1059 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file |
---|
| 1060 | fi |
---|
| 1061 | done |
---|
| 1062 | IGCM_sys_Chmod u+x run_file |
---|
[657] | 1063 | |
---|
[664] | 1064 | EXECUTION="${HOST_MPIRUN_COMMAND} --app ./run_file" |
---|
[657] | 1065 | |
---|
[16] | 1066 | fi |
---|
| 1067 | |
---|
[657] | 1068 | else # Only one executable. launch it. |
---|
| 1069 | |
---|
[664] | 1070 | for comp in ${config_ListOfComponents[*]} ; do |
---|
[657] | 1071 | |
---|
[664] | 1072 | # Only if we really have an executable for the component : |
---|
| 1073 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1074 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
[657] | 1075 | |
---|
[664] | 1076 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1077 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1078 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 1079 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 1080 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1081 | fi |
---|
| 1082 | if ( ${OK_PARA_MPI} ) ; then |
---|
| 1083 | # Default : mpirun used if nb_proc gt 1 |
---|
| 1084 | # pour sortie out/err par process |
---|
| 1085 | # echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${OMPI_COMM_WORLD_RANK} 2>out_${ExeNameOut}.err.\${OMPI_COMM_WORLD_RANK}" >> script_${ExeNameOut}.ksh |
---|
| 1086 | echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1087 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1088 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
---|
| 1089 | else |
---|
| 1090 | # Default : mpirun is NOT used if nb_proc eq 1 |
---|
| 1091 | # pour sortie out/err par process |
---|
| 1092 | # echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
| 1093 | echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1094 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1095 | EXECUTION="time ./script_${ExeNameOut}.ksh" |
---|
| 1096 | fi |
---|
[1002] | 1097 | |
---|
| 1098 | IGCM_debug_Print 1 "sys Obelix : script_${ExeNameOut}.ksh contains" |
---|
| 1099 | cat script_${ExeNameOut}.ksh |
---|
| 1100 | |
---|
[664] | 1101 | fi |
---|
[1180] | 1102 | |
---|
[664] | 1103 | done |
---|
[657] | 1104 | |
---|
| 1105 | fi |
---|
| 1106 | |
---|
[811] | 1107 | IGCM_debug_Print 1 "sys Obelix : execution command is" |
---|
| 1108 | IGCM_debug_Print 1 "$EXECUTION" |
---|
[657] | 1109 | |
---|
| 1110 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
[16] | 1111 | } |
---|
| 1112 | |
---|
[933] | 1113 | #D-#================================================== |
---|
| 1114 | #D-function IGCM_sys_check_path |
---|
| 1115 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
| 1116 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
| 1117 | #D-* Examples: |
---|
| 1118 | #D- |
---|
| 1119 | function IGCM_sys_check_path { |
---|
| 1120 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
| 1121 | if ( $DEBUG_sys ) ; then |
---|
| 1122 | echo "IGCM_sys_check_path" |
---|
| 1123 | fi |
---|
[811] | 1124 | |
---|
[933] | 1125 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then |
---|
| 1126 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
| 1127 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
[936] | 1128 | IGCM_debug_Exit "This will stop the job" |
---|
[933] | 1129 | fi |
---|
| 1130 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
| 1131 | } |
---|
| 1132 | |
---|
[811] | 1133 | #D-#================================================== |
---|
| 1134 | #D-function IGCM_sys_check_quota. Dummy call here |
---|
| 1135 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
| 1136 | #D-* Examples: |
---|
| 1137 | #D- |
---|
[657] | 1138 | function IGCM_sys_check_quota { |
---|
| 1139 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
| 1140 | if ( $DEBUG_sys ) ; then |
---|
| 1141 | echo "IGCM_sys_check_quota" |
---|
| 1142 | fi |
---|
| 1143 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
| 1144 | } |
---|
| 1145 | |
---|
[811] | 1146 | #D-#================================================== |
---|
[1244] | 1147 | #D-function IGCM_sys_getJobSchedulerID |
---|
| 1148 | #D-* Purpose: Get the job ID during execution |
---|
| 1149 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
| 1150 | #D- |
---|
| 1151 | function IGCM_sys_getJobSchedulerID { |
---|
| 1152 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
| 1153 | if ( $DEBUG_sys ) ; then |
---|
| 1154 | echo "IGCM_sys_getJobSchedulerID" |
---|
| 1155 | fi |
---|
| 1156 | |
---|
| 1157 | eval ${1}=$( echo ${PBS_JOBID} | awk -F. '{print $1}' ) |
---|
| 1158 | |
---|
| 1159 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
| 1160 | } |
---|
| 1161 | |
---|
| 1162 | #D-#================================================== |
---|
[1124] | 1163 | #D-function IGCM_sys_GetJobID |
---|
[1244] | 1164 | #D-* Purpose: Get the job ID from the JobName |
---|
[1124] | 1165 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
| 1166 | #D- |
---|
| 1167 | function IGCM_sys_GetJobID { |
---|
| 1168 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
| 1169 | if ( $DEBUG_sys ) ; then |
---|
| 1170 | echo "IGCM_sys_GetJobID" |
---|
| 1171 | fi |
---|
| 1172 | |
---|
| 1173 | # With -f option, the full job name is given in the last column |
---|
| 1174 | ID="$( qstat -u $2 | grep -w $1 | gawk '-F ' '{print $10}' )" |
---|
| 1175 | |
---|
| 1176 | eval ${3}=${ID} |
---|
| 1177 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
| 1178 | } |
---|
| 1179 | |
---|
| 1180 | #D-#================================================== |
---|
[811] | 1181 | #D-function IGCM_sys_CountJobInQueue |
---|
[1244] | 1182 | #D-* Purpose: Count number of users job |
---|
[811] | 1183 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
| 1184 | #D- |
---|
| 1185 | function IGCM_sys_CountJobInQueue { |
---|
| 1186 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
| 1187 | if ( $DEBUG_sys ) ; then |
---|
| 1188 | echo "IGCM_sys_CountJobInQueue" |
---|
| 1189 | fi |
---|
| 1190 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
| 1191 | } |
---|