[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=${PATH}:/home/users/igcmg/rebuild/bin/ |
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[16] | 95 | |
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[343] | 96 | #==================================================== |
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[421] | 97 | # Set lf95 environment |
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| 98 | #==================================================== |
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| 99 | . /usr/local/install/lf6481/bash_laheyfort_setup |
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| 100 | |
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| 101 | #==================================================== |
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[16] | 102 | # Host specific DIRECTORIES |
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| 103 | #==================================================== |
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| 104 | |
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| 105 | #==================================================== |
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[657] | 106 | #- MirrorlibIGCM for frontend |
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| 107 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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| 108 | |
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| 109 | #==================================================== |
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| 110 | #- libIGCM_POST for frontend |
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| 111 | typeset -r libIGCM_POST=${libIGCM} |
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| 112 | |
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| 113 | #==================================================== |
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[16] | 114 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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| 115 | typeset -r R_EXE="${MODIPSL}/bin" |
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| 116 | |
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| 117 | #==================================================== |
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| 118 | #- SUBMIT_DIR : submission dir |
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[256] | 119 | if [ X${PBS_O_WORKDIR} != X ] ; then |
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[1124] | 120 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PBS_O_WORKDIR}} |
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[256] | 121 | else |
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[1124] | 122 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PWD}} |
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[256] | 123 | fi |
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[657] | 124 | |
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[16] | 125 | #==================================================== |
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[725] | 126 | #- IN |
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[978] | 127 | typeset -r R_IN=${R_IN:=/home/orchideeshare/igcmg/IGCM} |
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[1180] | 128 | typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/home/orchideeshare/igcmg/IGCM} |
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[725] | 129 | |
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| 130 | #==================================================== |
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[16] | 131 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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[838] | 132 | if [ X${PBS_JOBID} != X ] ; then |
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| 133 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/scratch/$PBS_O_LOGNAME.$PBS_JOBID} |
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| 134 | else |
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[839] | 135 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/tmp/tmp$$} |
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[838] | 136 | fi |
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[16] | 137 | |
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| 138 | #==================================================== |
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[1179] | 139 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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[1186] | 140 | typeset -r OUTCOMMAND_PATH=/tmp |
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[1179] | 141 | |
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| 142 | #==================================================== |
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[16] | 143 | #- HOST_MPIRUN_COMMAND |
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| 144 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="time mpirun"} |
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| 145 | |
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[61] | 146 | #==================================================== |
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| 147 | #- Max number of arguments passed to nco operator or demigration command |
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| 148 | UNIX_MAX_LIMIT=360 |
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| 149 | |
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[657] | 150 | #==================================================== |
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[1180] | 151 | #- set PackDefault to false on obelix |
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| 152 | PackDefault=false |
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| 153 | |
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| 154 | #==================================================== |
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[657] | 155 | #- Number of core per node (max number of OpenMP task) |
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| 156 | NUM_COREPERNODE=1 |
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| 157 | |
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| 158 | #==================================================== |
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| 159 | #- Default number of MPI task for IPSL coupled model |
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| 160 | #- required for backward compatibility |
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| 161 | #- |
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| 162 | DEFAULT_NUM_PROC_OCE=1 |
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| 163 | DEFAULT_NUM_PROC_CPL=1 |
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| 164 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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| 165 | DEFAULT_NUM_PROC_TOTAL=${BATCH_NUM_PROC_TOT} |
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| 166 | |
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[16] | 167 | #D-#================================================== |
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[1057] | 168 | #D-function IGCM_sys_defineArchives |
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| 169 | #D-* Purpose: |
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| 170 | #D-* Define ARCHIVE : Dedicated to large files |
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| 171 | #D-* Define STORAGE : Dedicated to small/medium files |
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| 172 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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| 173 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) |
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| 174 | #D-* Define R_BUF : Output tree located on STORAGE hosting files waiting for rebuild or pack processes |
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| 175 | #D-* if SpaceName=TEST nothing special will hapen |
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[725] | 176 | #D-* Examples: |
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| 177 | #D- |
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[1057] | 178 | function IGCM_sys_defineArchives { |
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| 179 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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| 180 | |
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[1060] | 181 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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[1057] | 182 | #==================================================== |
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| 183 | #- ARCHIVE (dedicated to large files) |
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[1063] | 184 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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[1057] | 185 | else |
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| 186 | #==================================================== |
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| 187 | #- ARCHIVE (dedicated to large files) |
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[1063] | 188 | ARCHIVE=${ARCHIVE:=/home/scratch01/${LOGIN}} |
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[1057] | 189 | fi |
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| 190 | |
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[1060] | 191 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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[1057] | 192 | #==================================================== |
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| 193 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 194 | STORAGE=${config_UserChoices_STORAGE} |
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[1057] | 195 | else |
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| 196 | #==================================================== |
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| 197 | #- STORAGE (dedicated to small/medium files) |
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[1063] | 198 | STORAGE=${ARCHIVE} |
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[1057] | 199 | fi |
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| 200 | |
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| 201 | # ON OBELIX NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST |
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| 202 | |
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| 203 | #==================================================== |
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| 204 | #- R_OUT |
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[1063] | 205 | R_OUT=${ARCHIVE}/IGCM_OUT |
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[1057] | 206 | |
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| 207 | #==================================================== |
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| 208 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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[1063] | 209 | R_FIG=${STORAGE}/IGCM_OUT |
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[1057] | 210 | |
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| 211 | #==================================================== |
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| 212 | #- R_BUF (ONLY FOR double copy an scratch) |
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[1063] | 213 | R_BUF=${STORAGE}/IGCM_OUT |
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[1057] | 214 | |
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| 215 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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| 216 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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| 217 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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| 218 | |
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| 219 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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[725] | 220 | } |
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| 221 | |
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| 222 | #D-#================================================== |
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[37] | 223 | #D-function IGCM_sys_RshArchive |
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| 224 | #D-* Purpose: Archive rsh command |
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| 225 | #D-* Examples: |
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| 226 | #D- |
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| 227 | function IGCM_sys_RshArchive { |
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[657] | 228 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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| 229 | /bin/ksh <<-EOF |
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[40] | 230 | ${@} |
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| 231 | EOF |
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[811] | 232 | status=$? |
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| 233 | if [ ${status} -gt 0 ] ; then |
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| 234 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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[657] | 235 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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| 236 | fi |
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| 237 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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[37] | 238 | } |
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| 239 | |
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| 240 | #D-#================================================== |
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[1178] | 241 | #D-function IGCM_sys_RshArchive_NoError |
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| 242 | #D-* Purpose: Archive rsh command, without error |
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| 243 | #D-* used only in monitoring.job |
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| 244 | #D-* Examples: |
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| 245 | #D- |
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| 246 | function IGCM_sys_RshArchive_NoError { |
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| 247 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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| 248 | /bin/ksh <<-EOF |
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[1181] | 249 | ${@} 2> /dev/null |
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[1178] | 250 | EOF |
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| 251 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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| 252 | } |
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| 253 | |
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| 254 | #D-#================================================== |
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[16] | 255 | #D-function IGCM_sys_MkdirArchive |
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| 256 | #D-* Purpose: Mkdir on Archive |
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| 257 | #D-* Examples: |
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| 258 | #D- |
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| 259 | function IGCM_sys_MkdirArchive { |
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[657] | 260 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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| 261 | if ( $DEBUG_sys ) ; then |
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| 262 | echo "IGCM_sys_MkdirArchive :" $@ |
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| 263 | fi |
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[717] | 264 | #- creation de repertoire sur le serveur fichier |
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[657] | 265 | if [ ! -d ${1} ]; then |
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[1178] | 266 | \mkdir -p $1 |
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[811] | 267 | status=$? |
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| 268 | |
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| 269 | if [ ${status} -gt 0 ] ; then |
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| 270 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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[657] | 271 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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[16] | 272 | fi |
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[657] | 273 | fi |
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| 274 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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[16] | 275 | } |
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| 276 | |
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| 277 | #D-#================================================== |
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| 278 | #D-function IGCM_sys_TestDirArchive |
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| 279 | #D-* Purpose: Test Directory that must exists on Archive |
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| 280 | #D-* Examples: |
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| 281 | #D- |
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| 282 | function IGCM_sys_TestDirArchive { |
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[657] | 283 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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| 284 | if ( $DEBUG_sys ) ; then |
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| 285 | echo "IGCM_sys_TestDirArchive :" $@ |
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| 286 | fi |
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| 287 | typeset ExistFlag |
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| 288 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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| 289 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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| 290 | return ${ExistFlag} |
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[16] | 291 | } |
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| 292 | |
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| 293 | #D-#================================================== |
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[800] | 294 | #D-function IGCM_sys_IsFileArchived |
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[1180] | 295 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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[800] | 296 | #D-* Examples: |
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| 297 | #D- |
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| 298 | function IGCM_sys_IsFileArchived { |
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| 299 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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| 300 | if ( $DEBUG_sys ) ; then |
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| 301 | echo "IGCM_sys_IsFileArchived :" $@ |
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| 302 | fi |
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| 303 | typeset IsArchivedFlag |
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| 304 | # Never archived for this system |
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| 305 | IsArchivedFlag=1 |
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| 306 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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| 307 | |
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| 308 | return ${IsArchivedFlag} |
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| 309 | } |
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| 310 | |
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| 311 | #D-#================================================== |
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[16] | 312 | #D-function IGCM_sys_TestFileArchive |
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| 313 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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| 314 | #D-* Examples: |
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| 315 | #D- |
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| 316 | function IGCM_sys_TestFileArchive { |
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[657] | 317 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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| 318 | typeset ExistFlag |
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| 319 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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| 320 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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[67] | 321 | |
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[657] | 322 | return ${ExistFlag} |
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[67] | 323 | } |
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| 324 | |
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| 325 | #D-#================================================== |
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| 326 | #D-function IGCM_sys_CountFileArchive |
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| 327 | #D-* Purpose: Count files on Archive filesystem |
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| 328 | #D-* Examples: |
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| 329 | #D- |
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| 330 | function IGCM_sys_CountFileArchive { |
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[657] | 331 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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| 332 | ls ${@} 2>/dev/null | wc -l |
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| 333 | if [ $? -gt 0 ] ; then |
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| 334 | echo "IGCM_sys_CountFileArchive : erreur." |
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| 335 | fi |
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| 336 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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[16] | 337 | } |
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| 338 | |
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| 339 | #D-#================================================== |
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| 340 | #D-function IGCM_sys_Tree |
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| 341 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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| 342 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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| 343 | #D- |
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| 344 | function IGCM_sys_Tree { |
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[657] | 345 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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| 346 | if ( $DEBUG_sys ) ; then |
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| 347 | echo "IGCM_sys_Tree :" $@ |
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| 348 | fi |
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[16] | 349 | |
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[657] | 350 | \tree -f $@ |
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[16] | 351 | |
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[657] | 352 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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[16] | 353 | } |
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| 354 | |
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| 355 | #D-#================================================== |
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| 356 | #D-function IGCM_sys_Qsub |
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| 357 | #D-* Purpose: Qsub new job |
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| 358 | #D-* Examples: |
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| 359 | #D- |
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| 360 | function IGCM_sys_Qsub { |
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[657] | 361 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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| 362 | if ( $DEBUG_sys ) ; then |
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| 363 | echo "IGCM_sys_Qsub :" $@ |
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| 364 | fi |
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[923] | 365 | typeset options status |
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| 366 | options="-o ${SUBMIT_DIR}/${Script_Output}" |
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[1179] | 367 | /usr/local/bin/qsub ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[811] | 368 | status=$? |
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[949] | 369 | |
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[1179] | 370 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[811] | 371 | if [ ${status} -gt 0 ] ; then |
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[1180] | 372 | IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}" |
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[657] | 373 | IGCM_debug_Exit "IGCM_sys_Qsub" |
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[949] | 374 | else |
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[1179] | 375 | JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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[657] | 376 | fi |
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| 377 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
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[16] | 378 | } |
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| 379 | |
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| 380 | #D-#================================================== |
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| 381 | #D-function IGCM_sys_QsubPost |
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| 382 | #D-* Purpose: Qsub new job on scalaire |
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| 383 | #D-* Examples: |
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| 384 | #D- |
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| 385 | function IGCM_sys_QsubPost { |
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[657] | 386 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
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| 387 | if ( $DEBUG_sys ) ; then |
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| 388 | echo "IGCM_sys_QsubPost :" $@ |
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| 389 | fi |
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[923] | 390 | typeset options status |
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| 391 | options="-o ${POST_DIR}/${Script_Post_Output}.out -v ${listVarEnv}" |
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[1179] | 392 | /usr/local/bin/qsub ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[811] | 393 | status=$? |
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[949] | 394 | |
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[1179] | 395 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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[811] | 396 | if [ ${status} -gt 0 ] ; then |
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[923] | 397 | IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}" |
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[657] | 398 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
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[949] | 399 | else |
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[1179] | 400 | JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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[657] | 401 | fi |
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| 402 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
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[16] | 403 | } |
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| 404 | |
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| 405 | #D-************************* |
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[657] | 406 | #D- File transfer functions |
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[16] | 407 | #D-************************* |
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| 408 | #D- |
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| 409 | |
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| 410 | #D-#================================================== |
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[203] | 411 | #D-function IGCM_sys_RmRunDir |
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| 412 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
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| 413 | #D- scheduler will do the job) |
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| 414 | #D-* Examples: |
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| 415 | #D- |
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| 416 | function IGCM_sys_RmRunDir { |
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[1057] | 417 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
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[657] | 418 | if ( $DEBUG_sys ) ; then |
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| 419 | echo "IGCM_sys_RmRunDir :" $@ |
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[964] | 420 | echo "Dummy call, let the scheduler do that." |
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[657] | 421 | fi |
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| 422 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
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[203] | 423 | } |
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| 424 | |
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| 425 | #D-#================================================== |
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[16] | 426 | #D-function IGCM_sys_Put_Dir |
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| 427 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
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| 428 | #D-* Examples: |
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| 429 | #D- |
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| 430 | function IGCM_sys_Put_Dir { |
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[657] | 431 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
---|
| 432 | if ( $DEBUG_sys ) ; then |
---|
| 433 | echo "IGCM_sys_Put_Dir :" $@ |
---|
| 434 | fi |
---|
| 435 | if [ $DRYRUN = 0 ]; then |
---|
| 436 | if [ ! -d ${1} ] ; then |
---|
| 437 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
---|
| 438 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
| 439 | return |
---|
[16] | 440 | fi |
---|
| 441 | |
---|
[717] | 442 | typeset status |
---|
[16] | 443 | |
---|
[717] | 444 | # Only if we use rsync |
---|
| 445 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
---|
| 446 | # |
---|
| 447 | #USUAL WAY |
---|
[1179] | 448 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[717] | 449 | status=$? |
---|
[16] | 450 | |
---|
[717] | 451 | if [ ${status} -gt 0 ] ; then |
---|
[811] | 452 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
---|
[1179] | 453 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 454 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
---|
[16] | 455 | else |
---|
[1179] | 456 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[16] | 457 | fi |
---|
[657] | 458 | fi |
---|
| 459 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
[16] | 460 | } |
---|
| 461 | |
---|
| 462 | #D-#================================================== |
---|
| 463 | #D-function IGCM_sys_Get_Dir |
---|
[717] | 464 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
[16] | 465 | #D-* Examples: |
---|
| 466 | #D- |
---|
| 467 | function IGCM_sys_Get_Dir { |
---|
[657] | 468 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
| 469 | if ( $DEBUG_sys ) ; then |
---|
| 470 | echo "IGCM_sys_Get_Dir :" $@ |
---|
| 471 | fi |
---|
| 472 | if [ $DRYRUN = 0 ]; then |
---|
[1180] | 473 | typeset NB_ESSAI DELAI status i |
---|
| 474 | # number of tentative |
---|
| 475 | NB_ESSAI=3 |
---|
| 476 | # time delay between tentative |
---|
| 477 | DELAI=2 |
---|
[16] | 478 | |
---|
[1180] | 479 | # |
---|
| 480 | # USUAL WAY |
---|
| 481 | i=0 |
---|
| 482 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 483 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 484 | status=$? |
---|
| 485 | if [ ${status} -gt 0 ] ; then |
---|
| 486 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 487 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
| 488 | sleep $DELAI |
---|
| 489 | else |
---|
| 490 | break |
---|
| 491 | fi |
---|
| 492 | (( i = i + 1 )) |
---|
| 493 | done |
---|
[16] | 494 | |
---|
[717] | 495 | if [ ${status} -gt 0 ] ; then |
---|
[811] | 496 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
[1179] | 497 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 498 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
[16] | 499 | else |
---|
[1179] | 500 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[16] | 501 | fi |
---|
[657] | 502 | fi |
---|
| 503 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
[16] | 504 | } |
---|
| 505 | |
---|
| 506 | #D-#================================================== |
---|
| 507 | #D-function IGCM_sys_Put_Rest |
---|
[717] | 508 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
[282] | 509 | #D- File and target directory must exist. |
---|
[16] | 510 | #D-* Examples: |
---|
| 511 | #D- |
---|
| 512 | function IGCM_sys_Put_Rest { |
---|
[657] | 513 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
| 514 | if ( $DEBUG_sys ) ; then |
---|
| 515 | echo "IGCM_sys_Put_Rest :" $@ |
---|
| 516 | fi |
---|
| 517 | if [ $DRYRUN = 0 ]; then |
---|
| 518 | if [ ! -f ${1} ] ; then |
---|
| 519 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
| 520 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
[16] | 521 | fi |
---|
[717] | 522 | |
---|
| 523 | typeset status |
---|
| 524 | # |
---|
[1178] | 525 | # USUAL WAY |
---|
[1179] | 526 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[717] | 527 | status=$? |
---|
[16] | 528 | |
---|
[717] | 529 | # #RSYNC WITH NETWORK SSH CALL |
---|
[1179] | 530 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 531 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[16] | 532 | |
---|
[717] | 533 | # #RSYNC WITH NFS USE |
---|
[1179] | 534 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 535 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[16] | 536 | |
---|
[717] | 537 | # status=$? |
---|
| 538 | # IGCM_sys_Rsync_out $status |
---|
| 539 | |
---|
[1179] | 540 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[717] | 541 | # (( status=status+$? )) |
---|
| 542 | |
---|
| 543 | if [ ${status} -gt 0 ] ; then |
---|
[1180] | 544 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
[1178] | 545 | [ -f ${1} ] && ls -l ${1} |
---|
| 546 | [ -f ${2} ] && ls -l ${2} |
---|
| 547 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
[1179] | 548 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 549 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
| 550 | else |
---|
[1178] | 551 | |
---|
| 552 | if [ X${JobType} = XRUN ] ; then |
---|
| 553 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 554 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 555 | fi |
---|
| 556 | |
---|
[1179] | 557 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 558 | fi |
---|
| 559 | fi |
---|
| 560 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
| 561 | } |
---|
[16] | 562 | |
---|
[657] | 563 | #D-#================================================== |
---|
[16] | 564 | #D-function IGCM_sys_Put_Out |
---|
[717] | 565 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
[16] | 566 | #D-* Examples: |
---|
| 567 | #D- |
---|
| 568 | function IGCM_sys_Put_Out { |
---|
[657] | 569 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
| 570 | if ( $DEBUG_sys ) ; then |
---|
| 571 | echo "IGCM_sys_Put_Out :" $@ |
---|
| 572 | fi |
---|
[811] | 573 | |
---|
| 574 | typeset status |
---|
| 575 | |
---|
[657] | 576 | if [ $DRYRUN = 0 ]; then |
---|
[811] | 577 | if [ ! -f ${1} ] ; then |
---|
[657] | 578 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
| 579 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 580 | return 1 |
---|
[16] | 581 | fi |
---|
[719] | 582 | # |
---|
[811] | 583 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
| 584 | # |
---|
[657] | 585 | if [ X${JobType} = XRUN ] ; then |
---|
| 586 | if [ X${3} = X ] ; then |
---|
| 587 | IGCM_sys_Chmod 444 ${1} |
---|
| 588 | fi |
---|
| 589 | fi |
---|
[717] | 590 | # |
---|
[16] | 591 | |
---|
[1179] | 592 | echo ${RSYNC} ${RSYNC_opt} $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 593 | ${RSYNC} ${RSYNC_opt} $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[717] | 594 | status=$? |
---|
| 595 | IGCM_sys_Rsync_out $status |
---|
[16] | 596 | |
---|
[1179] | 597 | ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[717] | 598 | (( status=status+$? )) |
---|
[16] | 599 | |
---|
[717] | 600 | if [ ${status} -gt 0 ] ; then |
---|
[811] | 601 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : rsync failed error code ${status}" |
---|
[1179] | 602 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 603 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
[16] | 604 | else |
---|
[1179] | 605 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[16] | 606 | fi |
---|
[657] | 607 | fi |
---|
| 608 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 609 | return 0 |
---|
[16] | 610 | } |
---|
| 611 | |
---|
| 612 | #D-#================================================== |
---|
| 613 | #D-function IGCM_sys_Get |
---|
| 614 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
| 615 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
| 616 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
| 617 | function IGCM_sys_Get { |
---|
[657] | 618 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
[16] | 619 | |
---|
[811] | 620 | typeset DEST status dm_liste |
---|
[16] | 621 | |
---|
[657] | 622 | if ( $DEBUG_sys ) ; then |
---|
| 623 | echo "IGCM_sys_Get :" $@ |
---|
| 624 | fi |
---|
| 625 | if [ $DRYRUN -le 2 ]; then |
---|
| 626 | if [ X${1} = X'/l' ] ; then |
---|
| 627 | eval set +A dm_liste \${${2}} |
---|
| 628 | else |
---|
| 629 | dm_liste=${1} |
---|
[16] | 630 | fi |
---|
[657] | 631 | eval DEST=\${${#}} |
---|
[16] | 632 | |
---|
[717] | 633 | # test if the (first) file is present in the old computation : |
---|
[657] | 634 | IGCM_sys_TestFileArchive ${dm_liste[0]} |
---|
[717] | 635 | status=$? |
---|
| 636 | if [ ${status} -gt 0 ] ; then |
---|
[657] | 637 | echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." |
---|
| 638 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
[811] | 639 | return |
---|
[657] | 640 | fi |
---|
[16] | 641 | |
---|
[811] | 642 | #USUAL WAY |
---|
[1179] | 643 | \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
[811] | 644 | status=$? |
---|
[16] | 645 | |
---|
[811] | 646 | if [ ${status} -gt 0 ] ; then |
---|
| 647 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}" |
---|
[1179] | 648 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[657] | 649 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
[16] | 650 | else |
---|
[1179] | 651 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
[16] | 652 | fi |
---|
[657] | 653 | fi |
---|
| 654 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
[16] | 655 | } |
---|
| 656 | |
---|
| 657 | #D-#================================================== |
---|
[1131] | 658 | #D-function IGCM_sys_GetDate_Monitoring |
---|
| 659 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
| 660 | #D-* Examples: |
---|
| 661 | #D- |
---|
| 662 | function IGCM_sys_GetDate_Monitoring { |
---|
| 663 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
| 664 | if ( $DEBUG_sys ) ; then |
---|
| 665 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
| 666 | fi |
---|
| 667 | |
---|
| 668 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
| 669 | |
---|
| 670 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
| 671 | } |
---|
| 672 | |
---|
| 673 | #D-#================================================== |
---|
[343] | 674 | #D-function IGCM_sys_Dods_Rm |
---|
[717] | 675 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
[343] | 676 | #D-* Examples: |
---|
| 677 | #D- |
---|
| 678 | function IGCM_sys_Dods_Rm { |
---|
[657] | 679 | if ( $DEBUG_sys ) ; then |
---|
| 680 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
| 681 | fi |
---|
| 682 | return 0 |
---|
[343] | 683 | } |
---|
| 684 | |
---|
| 685 | #D-#================================================== |
---|
| 686 | #D-function IGCM_sys_Dods_Cp |
---|
[717] | 687 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
[343] | 688 | #D-* Examples: |
---|
| 689 | #D- |
---|
| 690 | function IGCM_sys_Dods_Cp { |
---|
[657] | 691 | if ( $DEBUG_sys ) ; then |
---|
| 692 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
| 693 | fi |
---|
| 694 | return 0 |
---|
[343] | 695 | } |
---|
| 696 | |
---|
| 697 | #D-#================================================== |
---|
[16] | 698 | #D-function IGCM_sys_Put_Dods |
---|
[811] | 699 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here |
---|
[16] | 700 | #D-* Examples: |
---|
| 701 | #D- |
---|
| 702 | function IGCM_sys_Put_Dods { |
---|
[657] | 703 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
| 704 | if ( $DEBUG_sys ) ; then |
---|
| 705 | echo "IGCM_sys_Put_Dods :" $@ |
---|
| 706 | fi |
---|
| 707 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
[16] | 708 | } |
---|
| 709 | |
---|
[657] | 710 | ############################################################## |
---|
| 711 | # REBUILD OPERATOR |
---|
[536] | 712 | |
---|
[811] | 713 | #D-#================================================== |
---|
[1163] | 714 | #D-function IGCM_sys_sync |
---|
| 715 | #D-* Purpose: flush buffer on disk (dummy function on Ada) |
---|
| 716 | #D-* Examples: |
---|
| 717 | #D- |
---|
| 718 | function IGCM_sys_sync { |
---|
| 719 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
| 720 | if ( $DEBUG_sys ) ; then |
---|
| 721 | echo "IGCM_sys_sync :" $@ |
---|
| 722 | echo "Dummy call, let the system do that." |
---|
| 723 | fi |
---|
| 724 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
| 725 | } |
---|
| 726 | |
---|
[657] | 727 | ############################################################ |
---|
| 728 | # Activate Running Environnment Variables |
---|
[536] | 729 | |
---|
[811] | 730 | #D-#================================================== |
---|
| 731 | #D-function IGCM_sys_desactiv_variables |
---|
| 732 | #D-* Purpose: set environement variables prior to execution |
---|
| 733 | #D-* Examples: |
---|
| 734 | #D- |
---|
[657] | 735 | function IGCM_sys_activ_variables { |
---|
| 736 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
| 737 | if ( $DEBUG_sys ) ; then |
---|
| 738 | echo "IGCM_sys_activ_variables" |
---|
| 739 | fi |
---|
[811] | 740 | |
---|
| 741 | # -------------------------------------------------------------------- |
---|
| 742 | #D- MPI specifications |
---|
| 743 | # -------------------------------------------------------------------- |
---|
| 744 | |
---|
| 745 | # -------------------------------------------------------------------- |
---|
| 746 | #D- Other specifications |
---|
| 747 | # -------------------------------------------------------------------- |
---|
| 748 | |
---|
[657] | 749 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
[16] | 750 | } |
---|
| 751 | |
---|
[657] | 752 | ############################################################ |
---|
| 753 | # Desactivate Running Environnment Variables |
---|
[16] | 754 | |
---|
[811] | 755 | #D-#================================================== |
---|
| 756 | #D-function IGCM_sys_desactiv_variables |
---|
| 757 | #D-* Purpose: unset environement variables after execution |
---|
| 758 | #D-* Examples: |
---|
| 759 | #D- |
---|
[657] | 760 | function IGCM_sys_desactiv_variables { |
---|
| 761 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
| 762 | if ( $DEBUG_sys ) ; then |
---|
| 763 | echo "IGCM_sys_desactiv_variables" |
---|
| 764 | fi |
---|
[811] | 765 | # -------------------------------------------------------------------- |
---|
| 766 | #D- MPI specifications |
---|
| 767 | # -------------------------------------------------------------------- |
---|
| 768 | |
---|
| 769 | # -------------------------------------------------------------------- |
---|
| 770 | #D- Other specifications |
---|
| 771 | # -------------------------------------------------------------------- |
---|
| 772 | |
---|
[657] | 773 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
| 774 | } |
---|
| 775 | |
---|
| 776 | ############################################################ |
---|
[800] | 777 | # Build MPI/OMP scripts run file (dummy function) |
---|
[657] | 778 | |
---|
[811] | 779 | #D-#================================================== |
---|
| 780 | #D-function IGCM_sys_build_run_file |
---|
| 781 | #D-* Purpose: build run file (deprecated) |
---|
| 782 | #D-* Examples: |
---|
| 783 | #D- |
---|
[657] | 784 | function IGCM_sys_build_run_file { |
---|
| 785 | |
---|
[664] | 786 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
[657] | 787 | |
---|
| 788 | } |
---|
| 789 | |
---|
| 790 | ############################################################ |
---|
| 791 | # Build MPI/OMP scripts |
---|
[811] | 792 | |
---|
| 793 | #D-#================================================== |
---|
| 794 | #D-function IGCM_sys_build_execution_scripts |
---|
| 795 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
| 796 | #D-* Examples: |
---|
| 797 | #D- |
---|
[657] | 798 | function IGCM_sys_build_execution_scripts |
---|
| 799 | { |
---|
| 800 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
| 801 | if ( $DEBUG_sys ) ; then |
---|
| 802 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
| 803 | fi |
---|
[1180] | 804 | |
---|
[657] | 805 | typeset nodes listnodes init_node start_num init_exec comp ExeNameIn ExeNameOut |
---|
| 806 | typeset node_num_current node_current comp_proc_mpi_loc comp_proc_omp_loc |
---|
| 807 | typeset num_corempi nombre_restant_node nombre_restant_comp |
---|
| 808 | |
---|
| 809 | if ( ${OK_PARA_MPMD} ) ; then |
---|
| 810 | |
---|
| 811 | if [ -f run_file ] ; then |
---|
| 812 | IGCM_sys_Rm -f run_file |
---|
[16] | 813 | fi |
---|
[657] | 814 | touch run_file |
---|
| 815 | |
---|
| 816 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 817 | |
---|
| 818 | # Hosts treatment |
---|
| 819 | |
---|
| 820 | ${HOST_MPIRUN_COMMAND} hostname | sort | uniq > hosts.tmp |
---|
| 821 | |
---|
| 822 | i=0 |
---|
| 823 | rm -f hosts |
---|
| 824 | IGCM_debug_Print 1 "sys Obelix, Hosts avaible :" |
---|
| 825 | for nodes in `cat hosts.tmp` ; do |
---|
| 826 | host[$i]=$nodes |
---|
| 827 | echo "${host[$i]} slots=1 max_slots=1" >> hosts |
---|
| 828 | IGCM_debug_Print 1 ${host[$i]} |
---|
| 829 | i=$((i+1)) |
---|
| 830 | done |
---|
| 831 | rm -f hosts.tmp |
---|
| 832 | |
---|
| 833 | listnodes=${host[*]} |
---|
| 834 | |
---|
| 835 | EXECUTION="${HOST_MPIRUN_COMMAND} -hostfile hosts" |
---|
| 836 | |
---|
| 837 | # Initialisation |
---|
| 838 | |
---|
| 839 | init_node=y |
---|
| 840 | node_num_current=0 |
---|
| 841 | start_num=0 |
---|
| 842 | init_exec=n |
---|
| 843 | |
---|
[1180] | 844 | # Build run_file |
---|
[657] | 845 | |
---|
[1180] | 846 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
| 847 | # the coupler ie oasis3 must be the first one |
---|
[657] | 848 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 849 | |
---|
| 850 | if [ "X${comp}" = "XCPL" ] ; then |
---|
| 851 | |
---|
| 852 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 853 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 854 | |
---|
| 855 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 856 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 857 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 858 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 859 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 860 | echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
| 861 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 862 | |
---|
| 863 | init_node=n |
---|
| 864 | |
---|
| 865 | (( nombre_restant_node = NUM_COREPERNODE - 1 )) |
---|
| 866 | node_num_current=0 |
---|
| 867 | node_current=${host[${node_num_current}]} |
---|
| 868 | |
---|
| 869 | EXECUTION="${EXECUTION} -H ${node_current} -np 1 ./script_${ExeNameOut}.ksh" |
---|
| 870 | |
---|
| 871 | init_exec=y |
---|
| 872 | start_num=1 |
---|
| 873 | |
---|
| 874 | fi |
---|
| 875 | |
---|
| 876 | done |
---|
| 877 | |
---|
| 878 | # Then loop on the components (except for oasis) |
---|
| 879 | |
---|
| 880 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 881 | |
---|
| 882 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 883 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 884 | |
---|
| 885 | # Only if we really have an executable for the component : |
---|
| 886 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
| 887 | |
---|
| 888 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 889 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 890 | |
---|
| 891 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 892 | # echo "set -vx" >> script_${ExeNameOut}.ksh |
---|
| 893 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 894 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 895 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 896 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 897 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 898 | echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK - ${start_num})) " >> script_${ExeNameOut}.ksh |
---|
| 899 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh |
---|
| 900 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 901 | |
---|
| 902 | node_num=0 |
---|
| 903 | |
---|
| 904 | # We define the number of MPI process to be assigned for the component |
---|
| 905 | |
---|
| 906 | nombre_restant_comp=${comp_proc_mpi_loc} |
---|
| 907 | |
---|
| 908 | # Loop on the allocated nodes |
---|
| 909 | |
---|
| 910 | for node in ${listnodes} ; do |
---|
| 911 | |
---|
| 912 | # We go to the current node |
---|
| 913 | if [ ${node_num} = ${node_num_current} ] ; then |
---|
| 914 | |
---|
| 915 | node_current=${host[${node_num_current}]} |
---|
| 916 | |
---|
| 917 | # If first time on the node : initialisation |
---|
| 918 | |
---|
| 919 | if [ ${init_node} = y ] ; then |
---|
| 920 | nombre_restant_node=${NUM_COREPERNODE} |
---|
| 921 | fi |
---|
| 922 | |
---|
| 923 | # Test on the number of OMP threads |
---|
| 924 | |
---|
| 925 | if [ ${comp_proc_omp_loc} -gt ${nombre_restant_node} ] ; then |
---|
| 926 | (( node_num = node_num + 1 )) |
---|
| 927 | node_num_current=${node_num} |
---|
| 928 | init_node=y |
---|
| 929 | continue |
---|
| 930 | fi |
---|
| 931 | |
---|
| 932 | # Number of MPI process to assign |
---|
| 933 | |
---|
| 934 | (( num_corempi = nombre_restant_node / comp_proc_omp_loc )) |
---|
| 935 | |
---|
| 936 | if [ ${num_corempi} -gt ${nombre_restant_comp} ] ; then |
---|
| 937 | num_corempi=${nombre_restant_comp} |
---|
| 938 | fi |
---|
| 939 | |
---|
| 940 | (( nombre_restant_node = nombre_restant_node - num_corempi * comp_proc_omp_loc )) |
---|
| 941 | (( nombre_restant_comp = nombre_restant_comp - num_corempi )) |
---|
| 942 | |
---|
| 943 | if [ ${init_exec} = y ] ; then |
---|
| 944 | EXECUTION="${EXECUTION} : -H ${node_current} -np ${num_corempi} ./script_${ExeNameOut}.ksh" |
---|
| 945 | else |
---|
| 946 | EXECUTION="${EXECUTION} -H ${node_current} -np ${num_corempi} ./script_${ExeNameOut}.ksh" |
---|
| 947 | init_exec=y |
---|
| 948 | fi |
---|
| 949 | |
---|
| 950 | (( start_num = num_corempi + start_num )) |
---|
| 951 | |
---|
| 952 | else |
---|
| 953 | |
---|
| 954 | (( node_num = node_num + 1 )) |
---|
| 955 | continue |
---|
| 956 | fi |
---|
| 957 | |
---|
| 958 | # Test on the number of core/process remaining on the node/component |
---|
| 959 | |
---|
| 960 | if [ ${nombre_restant_node} = 0 ] ; then |
---|
| 961 | (( node_num = node_num + 1 )) |
---|
| 962 | node_num_current=${node_num} |
---|
| 963 | init_node=y |
---|
| 964 | |
---|
| 965 | if [ ${nombre_restant_comp} = 0 ] ; then |
---|
| 966 | break 1 |
---|
| 967 | fi |
---|
| 968 | else |
---|
| 969 | |
---|
| 970 | node_num_current=${node_num} |
---|
| 971 | init_node=n |
---|
| 972 | |
---|
| 973 | if [ ${nombre_restant_comp} = 0 ] ; then |
---|
| 974 | break 1 |
---|
| 975 | fi |
---|
| 976 | fi |
---|
| 977 | done |
---|
| 978 | fi |
---|
| 979 | done |
---|
| 980 | |
---|
| 981 | else |
---|
| 982 | |
---|
[664] | 983 | # Then first loop on the components for the coupler ie oasis |
---|
[657] | 984 | |
---|
[664] | 985 | ## the coupler ie oasis must be the first one |
---|
| 986 | for comp in ${config_ListOfComponents[*]} ; do |
---|
[657] | 987 | |
---|
[664] | 988 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[657] | 989 | |
---|
| 990 | # for CPL component only |
---|
[664] | 991 | if [ "X${comp}" = "XCPL" ] ; then |
---|
| 992 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 993 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut} " >> run_file |
---|
| 994 | fi |
---|
| 995 | done |
---|
[657] | 996 | |
---|
[811] | 997 | # Then second loop on the components |
---|
[657] | 998 | |
---|
[664] | 999 | for comp in ${config_ListOfComponents[*]} ; do |
---|
[657] | 1000 | |
---|
[664] | 1001 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[657] | 1002 | |
---|
[664] | 1003 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
| 1004 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
| 1005 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 1006 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file |
---|
| 1007 | fi |
---|
| 1008 | done |
---|
| 1009 | IGCM_sys_Chmod u+x run_file |
---|
[657] | 1010 | |
---|
[664] | 1011 | EXECUTION="${HOST_MPIRUN_COMMAND} --app ./run_file" |
---|
[657] | 1012 | |
---|
[16] | 1013 | fi |
---|
| 1014 | |
---|
[657] | 1015 | else # Only one executable. launch it. |
---|
| 1016 | |
---|
[664] | 1017 | for comp in ${config_ListOfComponents[*]} ; do |
---|
[657] | 1018 | |
---|
[664] | 1019 | # Only if we really have an executable for the component : |
---|
| 1020 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1021 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
[657] | 1022 | |
---|
[664] | 1023 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1024 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1025 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 1026 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 1027 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1028 | fi |
---|
| 1029 | if ( ${OK_PARA_MPI} ) ; then |
---|
| 1030 | # Default : mpirun used if nb_proc gt 1 |
---|
| 1031 | # pour sortie out/err par process |
---|
| 1032 | # echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${OMPI_COMM_WORLD_RANK} 2>out_${ExeNameOut}.err.\${OMPI_COMM_WORLD_RANK}" >> script_${ExeNameOut}.ksh |
---|
| 1033 | echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1034 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1035 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
---|
| 1036 | else |
---|
| 1037 | # Default : mpirun is NOT used if nb_proc eq 1 |
---|
| 1038 | # pour sortie out/err par process |
---|
| 1039 | # echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
| 1040 | echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
| 1041 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1042 | EXECUTION="time ./script_${ExeNameOut}.ksh" |
---|
| 1043 | fi |
---|
[1002] | 1044 | |
---|
| 1045 | IGCM_debug_Print 1 "sys Obelix : script_${ExeNameOut}.ksh contains" |
---|
| 1046 | cat script_${ExeNameOut}.ksh |
---|
| 1047 | |
---|
[664] | 1048 | fi |
---|
[1180] | 1049 | |
---|
[664] | 1050 | done |
---|
[657] | 1051 | |
---|
| 1052 | fi |
---|
| 1053 | |
---|
[811] | 1054 | IGCM_debug_Print 1 "sys Obelix : execution command is" |
---|
| 1055 | IGCM_debug_Print 1 "$EXECUTION" |
---|
[657] | 1056 | |
---|
| 1057 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
[16] | 1058 | } |
---|
| 1059 | |
---|
[933] | 1060 | #D-#================================================== |
---|
| 1061 | #D-function IGCM_sys_check_path |
---|
| 1062 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
| 1063 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
| 1064 | #D-* Examples: |
---|
| 1065 | #D- |
---|
| 1066 | function IGCM_sys_check_path { |
---|
| 1067 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
| 1068 | if ( $DEBUG_sys ) ; then |
---|
| 1069 | echo "IGCM_sys_check_path" |
---|
| 1070 | fi |
---|
[811] | 1071 | |
---|
[933] | 1072 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then |
---|
| 1073 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
| 1074 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
[936] | 1075 | IGCM_debug_Exit "This will stop the job" |
---|
[933] | 1076 | fi |
---|
| 1077 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
| 1078 | } |
---|
| 1079 | |
---|
[811] | 1080 | #D-#================================================== |
---|
| 1081 | #D-function IGCM_sys_check_quota. Dummy call here |
---|
| 1082 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
| 1083 | #D-* Examples: |
---|
| 1084 | #D- |
---|
[657] | 1085 | function IGCM_sys_check_quota { |
---|
| 1086 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
| 1087 | if ( $DEBUG_sys ) ; then |
---|
| 1088 | echo "IGCM_sys_check_quota" |
---|
| 1089 | fi |
---|
| 1090 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
| 1091 | } |
---|
| 1092 | |
---|
[811] | 1093 | #D-#================================================== |
---|
[1124] | 1094 | #D-function IGCM_sys_GetJobID |
---|
| 1095 | #D-* Purpose: Check if job_name is currently |
---|
| 1096 | #D- running or in queue |
---|
| 1097 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
| 1098 | #D- |
---|
| 1099 | function IGCM_sys_GetJobID { |
---|
| 1100 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
| 1101 | if ( $DEBUG_sys ) ; then |
---|
| 1102 | echo "IGCM_sys_GetJobID" |
---|
| 1103 | fi |
---|
| 1104 | |
---|
| 1105 | # With -f option, the full job name is given in the last column |
---|
| 1106 | ID="$( qstat -u $2 | grep -w $1 | gawk '-F ' '{print $10}' )" |
---|
| 1107 | |
---|
| 1108 | eval ${3}=${ID} |
---|
| 1109 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
| 1110 | } |
---|
| 1111 | |
---|
| 1112 | #D-#================================================== |
---|
[811] | 1113 | #D-function IGCM_sys_CountJobInQueue |
---|
| 1114 | #D-* Purpose: Check if job_name is currently |
---|
| 1115 | #D- running or in queue |
---|
| 1116 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
| 1117 | #D- |
---|
| 1118 | function IGCM_sys_CountJobInQueue { |
---|
| 1119 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
| 1120 | if ( $DEBUG_sys ) ; then |
---|
| 1121 | echo "IGCM_sys_CountJobInQueue" |
---|
| 1122 | fi |
---|
| 1123 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
| 1124 | } |
---|