[1182] | 1 | #!/bin/ksh |
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| 2 | |
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| 3 | #************************************************************** |
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| 4 | # Author: Sebastien Denvil |
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| 5 | # Contact: Sebastien.Denvil__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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| 9 | # IPSL (2006) |
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| 10 | # This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC |
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| 11 | # |
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| 12 | #************************************************************** |
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| 13 | |
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| 14 | #========================================================= |
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| 15 | # The documentation of this file can be automatically generated |
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| 16 | # if you use the prefix #D- for comments to be extracted. |
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| 17 | # Extract with command: cat lib* | grep "^#D-" | cut -c "4-" |
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| 18 | #========================================================= |
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| 19 | |
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| 20 | #D-#================================================== |
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| 21 | #D-LibIGCM_sys for ciclad |
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| 22 | #D-#================================================== |
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| 23 | #D- |
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| 24 | #D- This ksh library if a layer under some usefull |
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| 25 | #D-environment variables and shell commands. |
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| 26 | #D-All those definitions depend on host particularities. |
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| 27 | #D-It manages a stack mechanism and test validity of operations. |
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| 28 | #D-All function described bellow must be prefixed by IGCM_sys. |
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| 29 | |
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| 30 | #==================================================== |
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| 31 | # libIGCM_sys PARAMETERS |
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| 32 | #==================================================== |
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| 33 | |
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| 34 | #==================================================== |
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| 35 | # set DEBUG_sys to true to output calls of function |
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| 36 | typeset -r DEBUG_sys=${DEBUG_sys:=true} |
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| 37 | |
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| 38 | #==================================================== |
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| 39 | # Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get) |
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| 40 | typeset -r DRYRUN=${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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| 45 | # | | Cp/Exe/param/files | | | | |
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| 46 | # | | Chmod Qsub | | | | |
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| 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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[1296] | 64 | # Host user names project maxCpuTime |
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[1182] | 65 | # $hostname ou hostname |
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| 66 | typeset HOST=${HOST:=$( hostname )} |
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| 67 | # $username ou whoami |
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| 68 | typeset LOGIN=${LOGIN:=$( whoami )} |
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| 69 | # $hostname of the MASTER job |
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| 70 | typeset MASTER=${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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[1182] | 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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| 81 | # Submit command |
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| 82 | typeset SUBMIT=${SUBMIT:=qsub} |
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| 83 | # rsync with path |
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| 84 | typeset -r RSYNC=/usr/bin/rsync |
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| 85 | # RSYNC_opt args to rsync |
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| 86 | typeset -r RSYNC_opt="-va" |
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| 87 | # ie storage filesystem |
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| 88 | typeset -r STOREHOST=${MASTER} |
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| 89 | |
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| 90 | #==================================================== |
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| 91 | # Access to module command |
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| 92 | #==================================================== |
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[1187] | 93 | . /usr/share/Modules/init/ksh |
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[1182] | 94 | |
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| 95 | #==================================================== |
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| 96 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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| 97 | #==================================================== |
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[1314] | 98 | if [ $CENTER == IPSL-ciclad ] ; then |
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| 99 | # At ciclad |
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| 100 | export PATH=${PATH}:/home/igcmg/rebuild/src_X64_CICLAD/modipsl_v2_2_3_netcdf4.2/bin/ |
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[1358] | 101 | module load python/2.7-anaconda > /dev/null 2>&1 |
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[1314] | 102 | . /home/igcmg/.atlas_env_ciclad_ksh |
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| 103 | else |
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| 104 | # At climserv use the same files stored at ciclad but adapt the path |
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| 105 | export PATH=${PATH}:/ciclad-home/igcmg/rebuild/src_X64_CICLAD/modipsl_v2_2_3_netcdf4.2/bin/ |
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[1358] | 106 | module load python/2.7-anaconda > /dev/null 2>&1 |
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[1314] | 107 | . /ciclad-home/igcmg/.atlas_env_ciclad_ksh |
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| 108 | fi |
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| 109 | |
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[1210] | 110 | [ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:" |
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| 111 | [ ! X${TaskType} = Xchecking ] && module list |
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[1208] | 112 | |
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[1182] | 113 | #==================================================== |
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| 114 | # Host specific DIRECTORIES |
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| 115 | #==================================================== |
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| 116 | |
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| 117 | #==================================================== |
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| 118 | #- MirrorlibIGCM for frontend |
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| 119 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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| 120 | |
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| 121 | #==================================================== |
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| 122 | #- libIGCM_POST for frontend |
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| 123 | typeset -r libIGCM_POST=${libIGCM} |
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| 124 | |
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| 125 | #==================================================== |
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| 126 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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| 127 | typeset -r R_EXE="${MODIPSL}/bin" |
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| 128 | |
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| 129 | #==================================================== |
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| 130 | #- SUBMIT_DIR : submission dir |
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| 131 | if [ X${PBS_O_WORKDIR} != X ] ; then |
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| 132 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PBS_O_WORKDIR}} |
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| 133 | else |
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| 134 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PWD}} |
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| 135 | fi |
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| 136 | |
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| 137 | #==================================================== |
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| 138 | #- IN |
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| 139 | typeset -r R_IN=${R_IN:=/prodigfs/ipslfs/igcmg/IGCM} |
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| 140 | typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/prodigfs/ipslfs/igcmg/IGCM} |
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| 141 | |
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| 142 | #==================================================== |
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| 143 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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| 144 | if [ X${PBS_JOBID} != X ] ; then |
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[1314] | 145 | if [ $CENTER == IPSL-ciclad ] ; then |
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| 146 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/data/${LOGIN}/RUN_DIR/${PBS_JOBID}_${$}} |
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| 147 | else |
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| 148 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/homedata/${LOGIN}/RUN_DIR/${PBS_JOBID}_${$}} |
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| 149 | fi |
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[1182] | 150 | else |
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| 151 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/tmp/tmp$$} |
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| 152 | fi |
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| 153 | |
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| 154 | #==================================================== |
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| 155 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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[1186] | 156 | typeset -r OUTCOMMAND_PATH=/tmp |
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[1182] | 157 | |
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| 158 | #==================================================== |
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| 159 | #- HOST_MPIRUN_COMMAND |
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| 160 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="time mpirun"} |
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| 161 | |
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| 162 | #==================================================== |
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| 163 | #- Max number of arguments passed to nco operator or demigration command |
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| 164 | UNIX_MAX_LIMIT=360 |
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| 165 | |
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| 166 | #==================================================== |
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| 167 | #- set PackDefault to false on ciclad |
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| 168 | PackDefault=false |
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| 169 | |
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| 170 | #==================================================== |
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| 171 | #- Default number of MPI task for IPSL coupled model |
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| 172 | #- required for backward compatibility |
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| 173 | #- |
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[1296] | 174 | DEFAULT_NUM_PROC_OCE=5 |
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[1182] | 175 | DEFAULT_NUM_PROC_CPL=1 |
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| 176 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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| 177 | |
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| 178 | #D-#================================================== |
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| 179 | #D-function IGCM_sys_defineArchives |
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| 180 | #D-* Purpose: |
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| 181 | #D-* Define ARCHIVE : Dedicated to large files |
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| 182 | #D-* Define STORAGE : Dedicated to small/medium files |
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| 183 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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| 184 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) |
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| 185 | #D-* Define R_BUF : Output tree located on STORAGE hosting files waiting for rebuild or pack processes |
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| 186 | #D-* if SpaceName=TEST nothing special will hapen |
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| 187 | #D-* Examples: |
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| 188 | #D- |
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| 189 | function IGCM_sys_defineArchives { |
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| 190 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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| 191 | |
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| 192 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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| 193 | #==================================================== |
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| 194 | #- ARCHIVE (dedicated to large files) |
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| 195 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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| 196 | else |
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| 197 | #==================================================== |
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| 198 | #- ARCHIVE (dedicated to large files) |
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[1314] | 199 | if [ $CENTER == IPSL-ciclad ] ; then |
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| 200 | # At ciclad |
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| 201 | ARCHIVE=${ARCHIVE:=/data/${LOGIN}} |
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| 202 | else |
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| 203 | # At climserv |
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| 204 | ARCHIVE=${ARCHIVE:=/homedata/${LOGIN}} |
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| 205 | fi |
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[1182] | 206 | fi |
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| 207 | |
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| 208 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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| 209 | #==================================================== |
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| 210 | #- STORAGE (dedicated to small/medium files) |
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| 211 | STORAGE=${config_UserChoices_STORAGE} |
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| 212 | else |
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| 213 | #==================================================== |
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| 214 | #- STORAGE (dedicated to small/medium files) |
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| 215 | STORAGE=${ARCHIVE} |
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| 216 | fi |
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| 217 | |
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| 218 | # ON CICLAD NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST |
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| 219 | |
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| 220 | #==================================================== |
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| 221 | #- R_OUT |
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| 222 | R_OUT=${ARCHIVE}/IGCM_OUT |
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| 223 | |
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| 224 | #==================================================== |
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| 225 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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| 226 | R_FIG=${STORAGE}/IGCM_OUT |
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| 227 | |
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| 228 | #==================================================== |
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| 229 | #- R_BUF (ONLY FOR double copy an scratch) |
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| 230 | R_BUF=${STORAGE}/IGCM_OUT |
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| 231 | |
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| 232 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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| 233 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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| 234 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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| 235 | |
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| 236 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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| 237 | } |
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| 238 | |
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| 239 | #D-#================================================== |
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| 240 | #D-function IGCM_sys_RshArchive |
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| 241 | #D-* Purpose: Archive rsh command |
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| 242 | #D-* Examples: |
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| 243 | #D- |
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| 244 | function IGCM_sys_RshArchive { |
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| 245 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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| 246 | /bin/ksh <<-EOF |
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| 247 | ${@} |
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| 248 | EOF |
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| 249 | status=$? |
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| 250 | if [ ${status} -gt 0 ] ; then |
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| 251 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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| 252 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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| 253 | fi |
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| 254 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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| 255 | } |
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| 256 | |
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| 257 | #D-#================================================== |
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| 258 | #D-function IGCM_sys_RshArchive_NoError |
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| 259 | #D-* Purpose: Archive rsh command, without error |
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| 260 | #D-* used only in monitoring.job |
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| 261 | #D-* Examples: |
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| 262 | #D- |
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| 263 | function IGCM_sys_RshArchive_NoError { |
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| 264 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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| 265 | /bin/ksh <<-EOF |
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| 266 | ${@} 2> /dev/null |
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| 267 | EOF |
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| 268 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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| 269 | } |
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| 270 | |
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| 271 | #D-#================================================== |
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| 272 | #D-function IGCM_sys_MkdirArchive |
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| 273 | #D-* Purpose: Mkdir on Archive |
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| 274 | #D-* Examples: |
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| 275 | #D- |
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| 276 | function IGCM_sys_MkdirArchive { |
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| 277 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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| 278 | if ( $DEBUG_sys ) ; then |
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| 279 | echo "IGCM_sys_MkdirArchive :" $@ |
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| 280 | fi |
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| 281 | #- creation de repertoire sur le serveur fichier |
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| 282 | if [ ! -d ${1} ]; then |
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| 283 | \mkdir -p $1 |
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| 284 | status=$? |
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| 285 | |
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| 286 | if [ ${status} -gt 0 ] ; then |
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| 287 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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| 288 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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| 289 | fi |
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| 290 | fi |
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| 291 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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| 292 | } |
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| 293 | |
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| 294 | #D-#================================================== |
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| 295 | #D-function IGCM_sys_TestDirArchive |
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| 296 | #D-* Purpose: Test Directory that must exists on Archive |
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| 297 | #D-* Examples: |
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| 298 | #D- |
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| 299 | function IGCM_sys_TestDirArchive { |
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| 300 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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| 301 | if ( $DEBUG_sys ) ; then |
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| 302 | echo "IGCM_sys_TestDirArchive :" $@ |
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| 303 | fi |
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| 304 | typeset ExistFlag |
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| 305 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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| 306 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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| 307 | return ${ExistFlag} |
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| 308 | } |
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| 309 | |
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| 310 | #D-#================================================== |
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| 311 | #D-function IGCM_sys_IsFileArchived |
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| 312 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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| 313 | #D-* Examples: |
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| 314 | #D- |
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| 315 | function IGCM_sys_IsFileArchived { |
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| 316 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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| 317 | if ( $DEBUG_sys ) ; then |
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| 318 | echo "IGCM_sys_IsFileArchived :" $@ |
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| 319 | fi |
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| 320 | typeset IsArchivedFlag |
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| 321 | # Never archived for this system |
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| 322 | IsArchivedFlag=1 |
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| 323 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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| 324 | |
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| 325 | return ${IsArchivedFlag} |
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| 326 | } |
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| 327 | |
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| 328 | #D-#================================================== |
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| 329 | #D-function IGCM_sys_TestFileArchive |
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| 330 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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| 331 | #D-* Examples: |
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| 332 | #D- |
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| 333 | function IGCM_sys_TestFileArchive { |
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| 334 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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| 335 | typeset ExistFlag |
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| 336 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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| 337 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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| 338 | |
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| 339 | return ${ExistFlag} |
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| 340 | } |
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| 341 | |
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| 342 | #D-#================================================== |
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| 343 | #D-function IGCM_sys_CountFileArchive |
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| 344 | #D-* Purpose: Count files on Archive filesystem |
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| 345 | #D-* Examples: |
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| 346 | #D- |
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| 347 | function IGCM_sys_CountFileArchive { |
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| 348 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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| 349 | ls ${@} 2>/dev/null | wc -l |
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| 350 | if [ $? -gt 0 ] ; then |
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| 351 | echo "IGCM_sys_CountFileArchive : erreur." |
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| 352 | fi |
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| 353 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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| 354 | } |
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| 355 | |
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| 356 | #D-#================================================== |
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| 357 | #D-function IGCM_sys_Tree |
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| 358 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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| 359 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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| 360 | #D- |
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| 361 | function IGCM_sys_Tree { |
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| 362 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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| 363 | if ( $DEBUG_sys ) ; then |
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| 364 | echo "IGCM_sys_Tree :" $@ |
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| 365 | fi |
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| 366 | |
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[1296] | 367 | \ls -lR ${@} |
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[1182] | 368 | |
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| 369 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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| 370 | } |
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| 371 | |
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| 372 | #D-#================================================== |
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| 373 | #D-function IGCM_sys_Qsub |
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| 374 | #D-* Purpose: Qsub new job |
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| 375 | #D-* Examples: |
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| 376 | #D- |
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| 377 | function IGCM_sys_Qsub { |
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| 378 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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| 379 | if ( $DEBUG_sys ) ; then |
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| 380 | echo "IGCM_sys_Qsub :" $@ |
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| 381 | fi |
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| 382 | typeset options status |
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| 383 | options="-o ${SUBMIT_DIR}/${Script_Output}" |
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[1188] | 384 | /usr/bin/qsub ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[1182] | 385 | status=$? |
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| 386 | |
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| 387 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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| 388 | if [ ${status} -gt 0 ] ; then |
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| 389 | IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}" |
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| 390 | IGCM_debug_Exit "IGCM_sys_Qsub" |
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| 391 | else |
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| 392 | JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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| 393 | fi |
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| 394 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
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| 395 | } |
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| 396 | |
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| 397 | #D-#================================================== |
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| 398 | #D-function IGCM_sys_QsubPost |
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| 399 | #D-* Purpose: Qsub new job on scalaire |
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| 400 | #D-* Examples: |
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| 401 | #D- |
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| 402 | function IGCM_sys_QsubPost { |
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| 403 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
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| 404 | if ( $DEBUG_sys ) ; then |
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| 405 | echo "IGCM_sys_QsubPost :" $@ |
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| 406 | fi |
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| 407 | typeset options status |
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| 408 | options="-o ${POST_DIR}/${Script_Post_Output}.out -v ${listVarEnv}" |
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[1188] | 409 | /usr/bin/qsub ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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[1182] | 410 | status=$? |
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| 411 | |
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| 412 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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| 413 | if [ ${status} -gt 0 ] ; then |
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| 414 | IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}" |
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| 415 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
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| 416 | else |
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| 417 | JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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| 418 | fi |
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| 419 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
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| 420 | } |
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| 421 | |
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| 422 | #D-************************* |
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| 423 | #D- File transfer functions |
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| 424 | #D-************************* |
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| 425 | #D- |
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| 426 | |
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| 427 | #D-#================================================== |
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| 428 | #D-function IGCM_sys_RmRunDir |
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| 429 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
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| 430 | #D- scheduler will do the job) |
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| 431 | #D-* Examples: |
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| 432 | #D- |
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| 433 | function IGCM_sys_RmRunDir { |
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| 434 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
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| 435 | if ( $DEBUG_sys ) ; then |
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| 436 | echo "IGCM_sys_RmRunDir :" $@ |
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| 437 | fi |
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| 438 | |
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| 439 | typeset status |
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| 440 | |
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| 441 | echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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| 442 | \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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| 443 | status=$? |
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| 444 | |
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| 445 | if [ ${status} -gt 0 ] ; then |
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| 446 | IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}." |
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| 447 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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| 448 | IGCM_debug_Exit "IGCM_sys_RmRunDir" |
---|
| 449 | else |
---|
| 450 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 451 | fi |
---|
| 452 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
---|
| 453 | } |
---|
| 454 | |
---|
| 455 | #D-#================================================== |
---|
| 456 | #D-function IGCM_sys_Put_Dir |
---|
| 457 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
---|
| 458 | #D-* Examples: |
---|
| 459 | #D- |
---|
| 460 | function IGCM_sys_Put_Dir { |
---|
| 461 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
---|
| 462 | if ( $DEBUG_sys ) ; then |
---|
| 463 | echo "IGCM_sys_Put_Dir :" $@ |
---|
| 464 | fi |
---|
| 465 | if [ $DRYRUN = 0 ]; then |
---|
| 466 | if [ ! -d ${1} ] ; then |
---|
| 467 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
---|
| 468 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
| 469 | return |
---|
| 470 | fi |
---|
| 471 | |
---|
| 472 | typeset status |
---|
| 473 | |
---|
| 474 | # Only if we use rsync |
---|
| 475 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
---|
| 476 | # |
---|
| 477 | #USUAL WAY |
---|
| 478 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 479 | status=$? |
---|
| 480 | |
---|
| 481 | if [ ${status} -gt 0 ] ; then |
---|
| 482 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
---|
| 483 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 484 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
---|
| 485 | else |
---|
| 486 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 487 | fi |
---|
| 488 | fi |
---|
| 489 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
| 490 | } |
---|
| 491 | |
---|
| 492 | #D-#================================================== |
---|
| 493 | #D-function IGCM_sys_Get_Dir |
---|
| 494 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
| 495 | #D-* Examples: |
---|
| 496 | #D- |
---|
| 497 | function IGCM_sys_Get_Dir { |
---|
| 498 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
| 499 | if ( $DEBUG_sys ) ; then |
---|
| 500 | echo "IGCM_sys_Get_Dir :" $@ |
---|
| 501 | fi |
---|
| 502 | if [ $DRYRUN = 0 ]; then |
---|
| 503 | typeset NB_ESSAI DELAI status i |
---|
| 504 | # number of tentative |
---|
| 505 | NB_ESSAI=3 |
---|
| 506 | # time delay between tentative |
---|
| 507 | DELAI=2 |
---|
| 508 | |
---|
| 509 | # |
---|
| 510 | # USUAL WAY |
---|
| 511 | i=0 |
---|
| 512 | while [ $i -lt $NB_ESSAI ] ; do |
---|
| 513 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 514 | status=$? |
---|
| 515 | if [ ${status} -gt 0 ] ; then |
---|
| 516 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
| 517 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
| 518 | sleep $DELAI |
---|
| 519 | else |
---|
| 520 | break |
---|
| 521 | fi |
---|
| 522 | (( i = i + 1 )) |
---|
| 523 | done |
---|
| 524 | |
---|
| 525 | if [ ${status} -gt 0 ] ; then |
---|
| 526 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
| 527 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 528 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
| 529 | else |
---|
| 530 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 531 | fi |
---|
| 532 | fi |
---|
| 533 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
| 534 | } |
---|
| 535 | |
---|
| 536 | #D-#================================================== |
---|
| 537 | #D-function IGCM_sys_Put_Rest |
---|
| 538 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
| 539 | #D- File and target directory must exist. |
---|
| 540 | #D-* Examples: |
---|
| 541 | #D- |
---|
| 542 | function IGCM_sys_Put_Rest { |
---|
| 543 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
| 544 | if ( $DEBUG_sys ) ; then |
---|
| 545 | echo "IGCM_sys_Put_Rest :" $@ |
---|
| 546 | fi |
---|
| 547 | if [ $DRYRUN = 0 ]; then |
---|
| 548 | if [ ! -f ${1} ] ; then |
---|
| 549 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
| 550 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
| 551 | fi |
---|
| 552 | |
---|
| 553 | typeset status |
---|
| 554 | # |
---|
| 555 | # USUAL WAY |
---|
| 556 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 557 | status=$? |
---|
| 558 | |
---|
| 559 | # #RSYNC WITH NETWORK SSH CALL |
---|
| 560 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 561 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 562 | |
---|
| 563 | # #RSYNC WITH NFS USE |
---|
| 564 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 565 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 566 | |
---|
| 567 | # status=$? |
---|
| 568 | # IGCM_sys_Rsync_out $status |
---|
| 569 | |
---|
| 570 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 571 | # (( status=status+$? )) |
---|
| 572 | |
---|
| 573 | if [ ${status} -gt 0 ] ; then |
---|
| 574 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
| 575 | [ -f ${1} ] && ls -l ${1} |
---|
| 576 | [ -f ${2} ] && ls -l ${2} |
---|
| 577 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
| 578 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 579 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
| 580 | else |
---|
| 581 | |
---|
| 582 | if [ X${JobType} = XRUN ] ; then |
---|
| 583 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
| 584 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
| 585 | fi |
---|
| 586 | |
---|
| 587 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 588 | fi |
---|
| 589 | fi |
---|
| 590 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
| 591 | } |
---|
| 592 | |
---|
| 593 | #D-#================================================== |
---|
| 594 | #D-function IGCM_sys_Put_Out |
---|
| 595 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
| 596 | #D-* Examples: |
---|
| 597 | #D- |
---|
| 598 | function IGCM_sys_Put_Out { |
---|
| 599 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
| 600 | if ( $DEBUG_sys ) ; then |
---|
| 601 | echo "IGCM_sys_Put_Out :" $@ |
---|
| 602 | fi |
---|
| 603 | |
---|
| 604 | typeset status |
---|
| 605 | |
---|
| 606 | if [ $DRYRUN = 0 ]; then |
---|
| 607 | if [ ! -f ${1} ] ; then |
---|
| 608 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
| 609 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 610 | return 1 |
---|
| 611 | fi |
---|
| 612 | # |
---|
| 613 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
| 614 | # |
---|
| 615 | if [ X${JobType} = XRUN ] ; then |
---|
| 616 | if [ X${3} = X ] ; then |
---|
| 617 | IGCM_sys_Chmod 444 ${1} |
---|
| 618 | fi |
---|
| 619 | fi |
---|
| 620 | # |
---|
| 621 | |
---|
| 622 | echo ${RSYNC} ${RSYNC_opt} $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 623 | ${RSYNC} ${RSYNC_opt} $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 624 | status=$? |
---|
| 625 | IGCM_sys_Rsync_out $status |
---|
| 626 | |
---|
| 627 | ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 628 | (( status=status+$? )) |
---|
| 629 | |
---|
| 630 | if [ ${status} -gt 0 ] ; then |
---|
| 631 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : rsync failed error code ${status}" |
---|
| 632 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 633 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
| 634 | else |
---|
| 635 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 636 | fi |
---|
| 637 | fi |
---|
| 638 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
| 639 | return 0 |
---|
| 640 | } |
---|
| 641 | |
---|
| 642 | #D-#================================================== |
---|
| 643 | #D-function IGCM_sys_Get |
---|
| 644 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
| 645 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
| 646 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
| 647 | function IGCM_sys_Get { |
---|
| 648 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
| 649 | |
---|
| 650 | typeset DEST status dm_liste |
---|
| 651 | |
---|
| 652 | if ( $DEBUG_sys ) ; then |
---|
| 653 | echo "IGCM_sys_Get :" $@ |
---|
| 654 | fi |
---|
| 655 | if [ $DRYRUN -le 2 ]; then |
---|
| 656 | if [ X${1} = X'/l' ] ; then |
---|
| 657 | eval set +A dm_liste \${${2}} |
---|
| 658 | else |
---|
| 659 | dm_liste=${1} |
---|
| 660 | fi |
---|
| 661 | eval DEST=\${${#}} |
---|
| 662 | |
---|
| 663 | # test if the (first) file is present in the old computation : |
---|
| 664 | IGCM_sys_TestFileArchive ${dm_liste[0]} |
---|
| 665 | status=$? |
---|
| 666 | if [ ${status} -gt 0 ] ; then |
---|
| 667 | echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." |
---|
| 668 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 669 | return |
---|
| 670 | fi |
---|
| 671 | |
---|
| 672 | #USUAL WAY |
---|
| 673 | \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 674 | status=$? |
---|
| 675 | |
---|
| 676 | if [ ${status} -gt 0 ] ; then |
---|
| 677 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}" |
---|
| 678 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 679 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
| 680 | else |
---|
| 681 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 682 | fi |
---|
| 683 | fi |
---|
| 684 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
| 685 | } |
---|
| 686 | |
---|
| 687 | #D-#================================================== |
---|
| 688 | #D-function IGCM_sys_GetDate_Monitoring |
---|
| 689 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
| 690 | #D-* Examples: |
---|
| 691 | #D- |
---|
| 692 | function IGCM_sys_GetDate_Monitoring { |
---|
| 693 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
| 694 | if ( $DEBUG_sys ) ; then |
---|
| 695 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
| 696 | fi |
---|
| 697 | |
---|
| 698 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
| 699 | |
---|
| 700 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
| 701 | } |
---|
| 702 | |
---|
| 703 | #D-#================================================== |
---|
| 704 | #D-function IGCM_sys_Dods_Rm |
---|
| 705 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
| 706 | #D-* Examples: |
---|
| 707 | #D- |
---|
| 708 | function IGCM_sys_Dods_Rm { |
---|
| 709 | if ( $DEBUG_sys ) ; then |
---|
| 710 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
| 711 | fi |
---|
| 712 | return 0 |
---|
| 713 | } |
---|
| 714 | |
---|
| 715 | #D-#================================================== |
---|
| 716 | #D-function IGCM_sys_Dods_Cp |
---|
| 717 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
| 718 | #D-* Examples: |
---|
| 719 | #D- |
---|
| 720 | function IGCM_sys_Dods_Cp { |
---|
| 721 | if ( $DEBUG_sys ) ; then |
---|
| 722 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
| 723 | fi |
---|
| 724 | return 0 |
---|
| 725 | } |
---|
| 726 | |
---|
| 727 | #D-#================================================== |
---|
| 728 | #D-function IGCM_sys_Put_Dods |
---|
| 729 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here |
---|
| 730 | #D-* Examples: |
---|
| 731 | #D- |
---|
| 732 | function IGCM_sys_Put_Dods { |
---|
| 733 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
| 734 | if ( $DEBUG_sys ) ; then |
---|
| 735 | echo "IGCM_sys_Put_Dods :" $@ |
---|
| 736 | fi |
---|
| 737 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
| 738 | } |
---|
| 739 | |
---|
| 740 | ############################################################## |
---|
| 741 | # REBUILD OPERATOR |
---|
| 742 | |
---|
| 743 | #D-#================================================== |
---|
| 744 | #D-function IGCM_sys_sync |
---|
[1296] | 745 | #D-* Purpose: flush buffer on disk (dummy function on Ciclad) |
---|
[1182] | 746 | #D-* Examples: |
---|
| 747 | #D- |
---|
| 748 | function IGCM_sys_sync { |
---|
| 749 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
| 750 | if ( $DEBUG_sys ) ; then |
---|
| 751 | echo "IGCM_sys_sync :" $@ |
---|
| 752 | echo "Dummy call, let the system do that." |
---|
| 753 | fi |
---|
| 754 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
| 755 | } |
---|
| 756 | |
---|
| 757 | ############################################################ |
---|
| 758 | # Activate Running Environnment Variables |
---|
| 759 | |
---|
| 760 | #D-#================================================== |
---|
[1239] | 761 | #D-function IGCM_sys_activ_variables |
---|
[1182] | 762 | #D-* Purpose: set environement variables prior to execution |
---|
| 763 | #D-* Examples: |
---|
| 764 | #D- |
---|
| 765 | function IGCM_sys_activ_variables { |
---|
| 766 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
| 767 | if ( $DEBUG_sys ) ; then |
---|
| 768 | echo "IGCM_sys_activ_variables" |
---|
| 769 | fi |
---|
| 770 | |
---|
| 771 | # -------------------------------------------------------------------- |
---|
| 772 | #D- MPI specifications |
---|
| 773 | # -------------------------------------------------------------------- |
---|
| 774 | |
---|
| 775 | # -------------------------------------------------------------------- |
---|
| 776 | #D- Other specifications |
---|
| 777 | # -------------------------------------------------------------------- |
---|
| 778 | |
---|
| 779 | ulimit -s unlimited |
---|
| 780 | |
---|
| 781 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
| 782 | } |
---|
| 783 | |
---|
| 784 | ############################################################ |
---|
| 785 | # Desactivate Running Environnment Variables |
---|
| 786 | |
---|
| 787 | #D-#================================================== |
---|
| 788 | #D-function IGCM_sys_desactiv_variables |
---|
| 789 | #D-* Purpose: unset environement variables after execution |
---|
| 790 | #D-* Examples: |
---|
| 791 | #D- |
---|
| 792 | function IGCM_sys_desactiv_variables { |
---|
| 793 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
| 794 | if ( $DEBUG_sys ) ; then |
---|
| 795 | echo "IGCM_sys_desactiv_variables" |
---|
| 796 | fi |
---|
| 797 | # -------------------------------------------------------------------- |
---|
| 798 | #D- MPI specifications |
---|
| 799 | # -------------------------------------------------------------------- |
---|
| 800 | |
---|
| 801 | # -------------------------------------------------------------------- |
---|
| 802 | #D- Other specifications |
---|
| 803 | # -------------------------------------------------------------------- |
---|
| 804 | |
---|
| 805 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
| 806 | } |
---|
| 807 | |
---|
| 808 | ############################################################ |
---|
[1239] | 809 | # Update job headers to be used by the scheduler |
---|
| 810 | |
---|
| 811 | #D-#================================================== |
---|
| 812 | #D-function IGCM_sys_updateHeaders |
---|
| 813 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
| 814 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
| 815 | #D- |
---|
| 816 | function IGCM_sys_updateHeaders { |
---|
| 817 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
| 818 | if ( $DEBUG_sys ) ; then |
---|
| 819 | echo "IGCM_sys_updateHeaders" |
---|
| 820 | fi |
---|
| 821 | typeset file |
---|
| 822 | file=$1 |
---|
| 823 | |
---|
| 824 | if [ ${executionType} -eq 1 ] ; then |
---|
| 825 | # MPMD + MPI |
---|
| 826 | sed -e "/::openMPthreads::/d" \ |
---|
| 827 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 828 | ${file} > ${file}.tmp |
---|
| 829 | |
---|
| 830 | elif [ ${executionType} -eq 2 ] ; then |
---|
| 831 | # MPMD + MPI + OMP |
---|
| 832 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 833 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
| 834 | ${file} > ${file}.tmp |
---|
| 835 | |
---|
| 836 | elif [ ${executionType} -eq 3 ] ; then |
---|
| 837 | # SPMD + MPI/OMP |
---|
| 838 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 839 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 840 | ${file} > ${file}.tmp |
---|
| 841 | |
---|
| 842 | elif [ ${executionType} -eq 4 ] ; then |
---|
| 843 | # SPMD + MPI only |
---|
| 844 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
| 845 | -e "/::openMPthreads::/d" \ |
---|
| 846 | ${file} > ${file}.tmp |
---|
| 847 | |
---|
| 848 | elif [ ${executionType} -eq 5 ] ; then |
---|
| 849 | # SPMD + OMP only |
---|
| 850 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
| 851 | -e "/::JobNumProcTot::/d" \ |
---|
| 852 | ${file} > ${file}.tmp |
---|
| 853 | |
---|
| 854 | elif [ ${executionType} -eq 6 ] ; then |
---|
| 855 | # SEQUENTIAL THEN |
---|
| 856 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
| 857 | -e "/::openMPthreads::/d" \ |
---|
| 858 | ${file} > ${file}.tmp |
---|
| 859 | |
---|
| 860 | fi |
---|
| 861 | |
---|
| 862 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
| 863 | |
---|
| 864 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
| 865 | } |
---|
| 866 | |
---|
| 867 | ############################################################ |
---|
[1182] | 868 | # Build MPI/OMP scripts run file (dummy function) |
---|
| 869 | |
---|
| 870 | #D-#================================================== |
---|
| 871 | #D-function IGCM_sys_build_run_file |
---|
| 872 | #D-* Purpose: build run file (deprecated) |
---|
| 873 | #D-* Examples: |
---|
| 874 | #D- |
---|
| 875 | function IGCM_sys_build_run_file { |
---|
| 876 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
| 877 | } |
---|
| 878 | |
---|
| 879 | ############################################################ |
---|
| 880 | # Build MPI/OMP scripts |
---|
| 881 | |
---|
| 882 | #D-#================================================== |
---|
| 883 | #D-function IGCM_sys_build_execution_scripts |
---|
| 884 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
| 885 | #D-* Examples: |
---|
| 886 | #D- |
---|
| 887 | function IGCM_sys_build_execution_scripts |
---|
| 888 | { |
---|
| 889 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
| 890 | if ( $DEBUG_sys ) ; then |
---|
| 891 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
| 892 | fi |
---|
| 893 | |
---|
[1296] | 894 | EXECUTION=${HOST_MPIRUN_COMMAND} |
---|
[1182] | 895 | |
---|
[1296] | 896 | # MPMD mode |
---|
[1182] | 897 | if ( ${OK_PARA_MPMD} ) ; then |
---|
| 898 | |
---|
[1296] | 899 | # Only MPI (MPMD) |
---|
| 900 | if ( ! ${OK_PARA_OMP} ) ; then |
---|
[1182] | 901 | |
---|
[1296] | 902 | if [ -f run_file ] ; then |
---|
| 903 | IGCM_sys_Rm -f run_file |
---|
| 904 | fi |
---|
| 905 | touch run_file |
---|
[1182] | 906 | |
---|
[1296] | 907 | # Build run_file |
---|
| 908 | |
---|
| 909 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
| 910 | # the coupler ie oasis3 must be the first one |
---|
| 911 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 912 | |
---|
| 913 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 914 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 915 | |
---|
| 916 | # for CPL component only |
---|
| 917 | if [ "X${comp}" = "XCPL" ] && [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
| 918 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 919 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 920 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut} " >> run_file |
---|
| 921 | fi |
---|
| 922 | done |
---|
| 923 | |
---|
| 924 | # Then second loop on the components |
---|
| 925 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 926 | |
---|
| 927 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 928 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 929 | |
---|
| 930 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
| 931 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
| 932 | |
---|
| 933 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 934 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 935 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file |
---|
| 936 | fi |
---|
| 937 | done |
---|
| 938 | |
---|
| 939 | EXECUTION="${HOST_MPIRUN_COMMAND} --app ./run_file" |
---|
| 940 | |
---|
| 941 | IGCM_sys_Chmod u+x run_file |
---|
| 942 | if ( $DEBUG_sys ) ; then |
---|
| 943 | echo "run_file contains : " |
---|
| 944 | cat run_file |
---|
| 945 | fi |
---|
| 946 | |
---|
| 947 | # MPI-OpenMP (MPMD) |
---|
| 948 | else |
---|
| 949 | |
---|
[1182] | 950 | # Hosts treatment |
---|
| 951 | ${HOST_MPIRUN_COMMAND} hostname | sort | uniq > hosts.tmp |
---|
| 952 | |
---|
| 953 | i=0 |
---|
| 954 | rm -f hosts |
---|
[1296] | 955 | IGCM_debug_Print 1 "sys Ciclad, Hosts available :" |
---|
[1182] | 956 | for nodes in `cat hosts.tmp` ; do |
---|
| 957 | host[$i]=$nodes |
---|
| 958 | echo "${host[$i]} slots=1 max_slots=1" >> hosts |
---|
| 959 | IGCM_debug_Print 1 ${host[$i]} |
---|
| 960 | i=$((i+1)) |
---|
| 961 | done |
---|
| 962 | rm -f hosts.tmp |
---|
| 963 | |
---|
| 964 | listnodes=${host[*]} |
---|
| 965 | |
---|
| 966 | EXECUTION="${HOST_MPIRUN_COMMAND} -hostfile hosts" |
---|
| 967 | |
---|
| 968 | # Initialisation |
---|
[1296] | 969 | rank=0 |
---|
| 970 | current_core=0 |
---|
| 971 | core_per_node=8 |
---|
[1182] | 972 | init_exec=n |
---|
| 973 | |
---|
[1296] | 974 | # Loop on the components |
---|
[1182] | 975 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 976 | |
---|
[1296] | 977 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
| 978 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
[1182] | 979 | |
---|
[1296] | 980 | # Not possible if oasis has an executable (i.e old version of oasis3) |
---|
| 981 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
---|
| 982 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
---|
| 983 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
---|
| 984 | IGCM_debug_Verif_Exit |
---|
[1182] | 985 | fi |
---|
| 986 | |
---|
| 987 | # Only if we really have an executable for the component : |
---|
[1296] | 988 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
[1182] | 989 | |
---|
| 990 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
| 991 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
| 992 | |
---|
| 993 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 994 | echo "" >> script_${ExeNameOut}.ksh |
---|
[1296] | 995 | if [ ${comp_proc_omp_loc} -gt 1 ] ; then |
---|
| 996 | |
---|
| 997 | # Check if the number of threads is correct |
---|
| 998 | case ${comp_proc_omp_loc} in |
---|
[1299] | 999 | 2|4|8) |
---|
[1296] | 1000 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
---|
| 1001 | ;; |
---|
| 1002 | *) |
---|
| 1003 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
| 1004 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
[1299] | 1005 | IGCM_debug_Print 2 "Only 2,4,8 as number of OMP threads are possible " |
---|
[1296] | 1006 | IGCM_debug_Verif_Exit |
---|
| 1007 | ;; |
---|
| 1008 | esac |
---|
| 1009 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
| 1010 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
| 1011 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
| 1012 | echo "export OMP_STACKSIZE=200M" >> script_${ExeNameOut}.ksh |
---|
| 1013 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
| 1014 | fi |
---|
[1318] | 1015 | |
---|
[1317] | 1016 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
[1318] | 1017 | echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK )) " >> script_${ExeNameOut}.ksh |
---|
| 1018 | echo "MYMPIRANK=\$(printf '%3.3d\n' \${MYMPIRANK})" >> script_${ExeNameOut}.ksh |
---|
| 1019 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh |
---|
[1182] | 1020 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1021 | |
---|
[1296] | 1022 | if [ ${init_exec} = y ] ; then |
---|
| 1023 | EXECUTION="${EXECUTION} : -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
| 1024 | else |
---|
| 1025 | EXECUTION="${EXECUTION} -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
| 1026 | init_exec=y |
---|
| 1027 | fi |
---|
[1182] | 1028 | |
---|
[1296] | 1029 | # Build rankfile : method used to assign cores and nodes for the MPI process |
---|
| 1030 | # Ex : |
---|
| 1031 | #rank 0=curie5296 slot=0,1,2,3 |
---|
| 1032 | #rank 1=curie5296 slot=4,5,6,7 |
---|
| 1033 | # Example of final command : |
---|
| 1034 | # mpirun -hostfile hosts -rankfile rankfile -np 27 ./script_lmdz.x.ksh : -np 5 ./script_opa.xx.ksh |
---|
| 1035 | # with script_lmdz.x.ksh : |
---|
| 1036 | # #!/bin/ksh |
---|
| 1037 | #export OMP_STACKSIZE=200M |
---|
| 1038 | #export OMP_NUM_THREADS=4 |
---|
| 1039 | #./lmdz.x |
---|
[1182] | 1040 | |
---|
[1296] | 1041 | for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do |
---|
| 1042 | (( index_host = current_core / core_per_node )) |
---|
| 1043 | host_value=${host[${index_host}]} |
---|
| 1044 | (( slot = current_core % core_per_node )) |
---|
| 1045 | virg="," |
---|
| 1046 | string_final="" |
---|
| 1047 | for index in `seq $slot $(($slot+$comp_proc_omp_loc-1))`; do |
---|
| 1048 | string=$index$virg |
---|
| 1049 | string_final=$string_final$string |
---|
| 1050 | done |
---|
| 1051 | string_final=$( echo $string_final | sed "s/.$//" ) |
---|
| 1052 | echo "rank $rank=$host_value slot=$string_final" >> rankfile |
---|
| 1053 | (( rank = rank + 1 )) |
---|
| 1054 | (( current_core = current_core + comp_proc_omp_loc )) |
---|
[1182] | 1055 | done |
---|
| 1056 | fi |
---|
| 1057 | done |
---|
| 1058 | fi |
---|
| 1059 | |
---|
[1296] | 1060 | # Only one executable (SPMD mode). |
---|
| 1061 | else |
---|
[1182] | 1062 | |
---|
| 1063 | for comp in ${config_ListOfComponents[*]} ; do |
---|
| 1064 | |
---|
| 1065 | # Only if we really have an executable for the component : |
---|
| 1066 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
| 1067 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
| 1068 | |
---|
| 1069 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
| 1070 | echo "" >> script_${ExeNameOut}.ksh |
---|
| 1071 | if ( ${OK_PARA_OMP} ) ; then |
---|
| 1072 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
[1293] | 1073 | echo "export OMP_STACKSIZE=200M" >> script_${ExeNameOut}.ksh |
---|
| 1074 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
[1182] | 1075 | fi |
---|
| 1076 | if ( ${OK_PARA_MPI} ) ; then |
---|
| 1077 | # Default : mpirun used if nb_proc gt 1 |
---|
| 1078 | # pour sortie out/err par process |
---|
[1317] | 1079 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${OMPI_COMM_WORLD_RANK} 2>out_${ExeNameOut}.err.\${OMPI_COMM_WORLD_RANK}" >> script_${ExeNameOut}.ksh |
---|
| 1080 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
[1182] | 1081 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1082 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
---|
| 1083 | else |
---|
| 1084 | # Default : mpirun is NOT used if nb_proc eq 1 |
---|
| 1085 | # pour sortie out/err par process |
---|
[1317] | 1086 | echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
| 1087 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
[1182] | 1088 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
| 1089 | EXECUTION="time ./script_${ExeNameOut}.ksh" |
---|
| 1090 | fi |
---|
| 1091 | |
---|
| 1092 | IGCM_debug_Print 1 "sys Ciclad : script_${ExeNameOut}.ksh contains" |
---|
| 1093 | cat script_${ExeNameOut}.ksh |
---|
| 1094 | |
---|
| 1095 | fi |
---|
| 1096 | |
---|
| 1097 | done |
---|
| 1098 | |
---|
| 1099 | fi |
---|
| 1100 | |
---|
| 1101 | IGCM_debug_Print 1 "sys Ciclad : execution command is" |
---|
| 1102 | IGCM_debug_Print 1 "$EXECUTION" |
---|
| 1103 | |
---|
| 1104 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
| 1105 | } |
---|
| 1106 | |
---|
| 1107 | #D-#================================================== |
---|
| 1108 | #D-function IGCM_sys_check_path |
---|
| 1109 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
| 1110 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
| 1111 | #D-* Examples: |
---|
| 1112 | #D- |
---|
| 1113 | function IGCM_sys_check_path { |
---|
| 1114 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
| 1115 | if ( $DEBUG_sys ) ; then |
---|
| 1116 | echo "IGCM_sys_check_path" |
---|
| 1117 | fi |
---|
| 1118 | |
---|
| 1119 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then |
---|
| 1120 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
| 1121 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
| 1122 | IGCM_debug_Exit "This will stop the job" |
---|
| 1123 | fi |
---|
| 1124 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
| 1125 | } |
---|
| 1126 | |
---|
| 1127 | #D-#================================================== |
---|
| 1128 | #D-function IGCM_sys_check_quota. Dummy call here |
---|
| 1129 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
| 1130 | #D-* Examples: |
---|
| 1131 | #D- |
---|
| 1132 | function IGCM_sys_check_quota { |
---|
| 1133 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
| 1134 | if ( $DEBUG_sys ) ; then |
---|
| 1135 | echo "IGCM_sys_check_quota" |
---|
| 1136 | fi |
---|
| 1137 | |
---|
| 1138 | # TO BE IMPLEMENTED |
---|
| 1139 | |
---|
| 1140 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
| 1141 | } |
---|
| 1142 | |
---|
| 1143 | #D-#================================================== |
---|
[1286] | 1144 | #D-function IGCM_sys_projectAccounting |
---|
| 1145 | #D-* Purpose: store project accounting information in a file |
---|
| 1146 | #D-* Examples: |
---|
| 1147 | #D- |
---|
| 1148 | function IGCM_sys_projectAccounting { |
---|
| 1149 | IGCM_debug_PushStack "IGCM_sys_projectAccounting" |
---|
| 1150 | if ( $DEBUG_sys ) ; then |
---|
| 1151 | echo "IGCM_sys_check_quota" |
---|
| 1152 | fi |
---|
| 1153 | |
---|
| 1154 | touch $1 |
---|
| 1155 | |
---|
| 1156 | IGCM_debug_PopStack "IGCM_sys_projectAccounting" |
---|
| 1157 | } |
---|
| 1158 | |
---|
| 1159 | #D-#================================================== |
---|
[1244] | 1160 | #D-function IGCM_sys_getJobSchedulerID |
---|
| 1161 | #D-* Purpose: Get the job ID during execution |
---|
| 1162 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
| 1163 | #D- |
---|
| 1164 | function IGCM_sys_getJobSchedulerID { |
---|
| 1165 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
| 1166 | if ( $DEBUG_sys ) ; then |
---|
| 1167 | echo "IGCM_sys_getJobSchedulerID" |
---|
| 1168 | fi |
---|
| 1169 | |
---|
| 1170 | eval ${1}=$( echo ${PBS_JOBID} | awk -F. '{print $1}' ) |
---|
| 1171 | |
---|
| 1172 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
| 1173 | } |
---|
| 1174 | |
---|
| 1175 | #D-#================================================== |
---|
[1182] | 1176 | #D-function IGCM_sys_GetJobID |
---|
[1244] | 1177 | #D-* Purpose: Get the job ID from the JobName |
---|
[1182] | 1178 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
| 1179 | #D- |
---|
| 1180 | function IGCM_sys_GetJobID { |
---|
| 1181 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
| 1182 | if ( $DEBUG_sys ) ; then |
---|
| 1183 | echo "IGCM_sys_GetJobID" |
---|
| 1184 | fi |
---|
| 1185 | |
---|
| 1186 | # With -f option, the full job name is given in the last column |
---|
| 1187 | ID="$( qstat -u $2 | grep -w $1 | gawk '-F ' '{print $10}' )" |
---|
| 1188 | |
---|
| 1189 | eval ${3}=${ID} |
---|
| 1190 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
| 1191 | } |
---|
| 1192 | |
---|
| 1193 | #D-#================================================== |
---|
| 1194 | #D-function IGCM_sys_CountJobInQueue |
---|
[1244] | 1195 | #D-* Purpose: Count number of users job |
---|
[1182] | 1196 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
| 1197 | #D- |
---|
| 1198 | function IGCM_sys_CountJobInQueue { |
---|
| 1199 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
| 1200 | if ( $DEBUG_sys ) ; then |
---|
| 1201 | echo "IGCM_sys_CountJobInQueue" |
---|
| 1202 | fi |
---|
| 1203 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
| 1204 | } |
---|
[1272] | 1205 | |
---|
| 1206 | #D-#================================================== |
---|
| 1207 | #D-function IGCM_sys_atlas |
---|
| 1208 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
---|
| 1209 | #D-* Examples: |
---|
| 1210 | #D- |
---|
| 1211 | function IGCM_sys_atlas { |
---|
| 1212 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
---|
| 1213 | if ( $DEBUG_sys ) ; then |
---|
| 1214 | echo "IGCM_sys_atlas :" $@ |
---|
| 1215 | fi |
---|
| 1216 | |
---|
| 1217 | typeset status |
---|
| 1218 | |
---|
| 1219 | \atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
| 1220 | status=$? |
---|
| 1221 | if [ ${status} -gt 0 ] ; then |
---|
| 1222 | echo "IGCM_sys_atlas : error code ${status}" |
---|
| 1223 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1224 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
| 1225 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1226 | return 1 |
---|
| 1227 | else |
---|
| 1228 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1229 | return 0 |
---|
| 1230 | fi |
---|
| 1231 | |
---|
| 1232 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
| 1233 | } |
---|
| 1234 | |
---|