[622] | 1 | #-Q- curie ###################### |
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| 2 | #-Q- curie ## CURIE TGCC/CEA ## |
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| 3 | #-Q- curie ###################### |
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[837] | 4 | #-Q- curie #MSUB -r PACKOUTPUT # Nom du job |
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[1468] | 5 | #-Q- curie #MSUB -o PACKOUTPUT.out_%I |
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| 6 | #-Q- curie #MSUB -e PACKOUTPUT.out_%I |
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[622] | 7 | #-Q- curie #MSUB -n 1 # Reservation du processus |
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[880] | 8 | #-Q- curie #MSUB -T 36000 # Limite de temps elapsed du job |
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[1154] | 9 | #-Q- curie #MSUB -q ::default_node:: |
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[1274] | 10 | #-Q- curie #MSUB -c ::default_core:: |
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[704] | 11 | #-Q- curie #MSUB -Q normal |
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[837] | 12 | #-Q- curie #MSUB -A ::default_project:: |
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[681] | 13 | #-Q- curie set +x |
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[1433] | 14 | #-Q- irene ###################### |
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| 15 | #-Q- irene ## IRENE TGCC/CEA ## |
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| 16 | #-Q- irene ###################### |
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| 17 | #-Q- irene #MSUB -r PACKOUTPUT # Job name |
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[1468] | 18 | #-Q- irene #MSUB -o PACKOUTPUT.out_%I |
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| 19 | #-Q- irene #MSUB -e PACKOUTPUT.out_%I |
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[1433] | 20 | #-Q- irene #MSUB -n 1 # Number of cores |
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| 21 | #-Q- irene #MSUB -T 36000 # Maximum elapsed time |
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[1468] | 22 | #-Q- irene #MSUB -q ::default_node:: |
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[1465] | 23 | #-Q- irene #MSUB -c ::default_core:: |
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[1433] | 24 | #-Q- irene #MSUB -Q normal |
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[1468] | 25 | #-Q- irene #MSUB -A ::default_post_project:: |
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[1460] | 26 | #-Q- irene #MSUB -m store,work,scratch |
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[1433] | 27 | #-Q- irene set +x |
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[1491] | 28 | #-Q- jeanzay #!/bin/ksh |
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| 29 | #-Q- jeanzay ###################### |
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| 30 | #-Q- jeanzay ## JEANZAY IDRIS ## |
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| 31 | #-Q- jeanzay ###################### |
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| 32 | #-Q- jeanzay #SBATCH --job-name=PACKOUTPUT # Job Name |
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[1501] | 33 | #-Q- jeanzay #SBATCH --output=PACKOUTPUT.out_%J # standard output |
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| 34 | #-Q- jeanzay #SBATCH --error=PACKOUTPUT.out_%J # error output |
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[1494] | 35 | #-Q- jeanzay #SBATCH -N 1 # Number of core |
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| 36 | #-Q- jeanzay #SBATCH --partition=prepost # Post-processing partition |
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[1491] | 37 | #-Q- jeanzay #SBATCH --time=10:00:00 # Wall clock limit (seconds) |
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| 38 | #-Q- jeanzay #SBATCH --account ::default_project::@cpu |
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| 39 | #-Q- jeanzay set +x |
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[770] | 40 | #-Q- ada #!/bin/ksh |
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| 41 | #-Q- ada ####################### |
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[929] | 42 | #-Q- ada ## ADA IDRIS ## |
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[770] | 43 | #-Q- ada ####################### |
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[1409] | 44 | #-Q- ada # @ job_type = mpich |
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[848] | 45 | #-Q- ada # @ requirements = (Feature == "prepost") |
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[770] | 46 | #-Q- ada # Temps Elapsed max. d'une requete hh:mm:ss |
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| 47 | #-Q- ada # @ wall_clock_limit = 10:00:00 |
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[1334] | 48 | #-Q- ada # Memory required for ncrcat |
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| 49 | #-Q- ada # @ as_limit = 30Gb |
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[770] | 50 | #-Q- ada # Nom du travail LoadLeveler |
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| 51 | #-Q- ada # @ job_name = PACKOUTPUT |
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| 52 | #-Q- ada # Fichier de sortie standard du travail |
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| 53 | #-Q- ada # @ output = $(job_name).$(jobid) |
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| 54 | #-Q- ada # Fichier de sortie d'erreur du travail |
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| 55 | #-Q- ada # @ error = $(job_name).$(jobid) |
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| 56 | #-Q- ada # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.) |
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| 57 | #-Q- ada # @ notification = error |
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[1290] | 58 | #-Q- ada # @ environment = $DEBUG_debug ; $BigBrother ; $postProcessingStopLevel ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $POST_DIR ; $Script_Post_Output ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER ; wall_clock_limit=$(wall_clock_limit) |
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[770] | 59 | #-Q- ada # @ queue |
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[583] | 60 | #-Q- lxiv8 ###################### |
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| 61 | #-Q- lxiv8 ## OBELIX LSCE ## |
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| 62 | #-Q- lxiv8 ###################### |
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| 63 | #-Q- lxiv8 #PBS -N PACKOUTPUT |
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| 64 | #-Q- lxiv8 #PBS -m a |
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| 65 | #-Q- lxiv8 #PBS -j oe |
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| 66 | #-Q- lxiv8 #PBS -q medium |
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| 67 | #-Q- lxiv8 #PBS -o PACKOUTPUT.$$ |
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| 68 | #-Q- lxiv8 #PBS -S /bin/ksh |
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[1184] | 69 | #-Q- ifort_CICLAD ###################### |
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| 70 | #-Q- ifort_CICLAD ## CICLAD IPSL ## |
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| 71 | #-Q- ifort_CICLAD ###################### |
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| 72 | #-Q- ifort_CICLAD #PBS -N PACKOUTPUT |
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| 73 | #-Q- ifort_CICLAD #PBS -m a |
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| 74 | #-Q- ifort_CICLAD #PBS -j oe |
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| 75 | #-Q- ifort_CICLAD #PBS -q std |
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| 76 | #-Q- ifort_CICLAD #PBS -S /bin/ksh |
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[583] | 77 | #-Q- default #!/bin/ksh |
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| 78 | #-Q- default ################## |
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| 79 | #-Q- default ## DEFAULT HOST ## |
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| 80 | #-Q- default ################## |
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| 81 | |
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| 82 | #************************************************************** |
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| 83 | # Author: Sebastien Denvil |
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| 84 | # Contact: Sebastien.Denvil__at__ipsl.jussieu.fr |
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| 85 | # $Revision:: $ Revision of last commit |
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| 86 | # $Author:: $ Author of last commit |
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| 87 | # $Date:: $ Date of last commit |
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| 88 | # IPSL (2006) |
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| 89 | # This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC |
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| 90 | # |
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| 91 | #************************************************************** |
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| 92 | |
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| 93 | #set -eu |
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| 94 | #set -vx |
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| 95 | |
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| 96 | date |
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| 97 | |
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[1356] | 98 | #D- Task type DO NOT CHANGE (computing, post-processing or checking) |
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[712] | 99 | TaskType=post-processing |
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| 100 | |
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[583] | 101 | ######################################################################## |
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| 102 | |
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| 103 | #D- Flag to determine if this job in a standalone mode |
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| 104 | #D- Default : value from AA_job if any |
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| 105 | StandAlone=${StandAlone:=true} |
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| 106 | |
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| 107 | #D- Path to libIGCM |
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| 108 | #D- Default : value from AA_job if any |
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| 109 | # WARNING For StandAlone use : To run this script on some machine (ulam and cesium) |
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| 110 | # WARNING you must check MirrorlibIGCM variable in sys library. |
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| 111 | # WARNING If this variable is true, you must use libIGCM_POST path instead |
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| 112 | # WARNING of your running libIGCM directory. |
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| 113 | libIGCM=${libIGCM:=::modipsl::/libIGCM} |
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| 114 | |
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| 115 | #-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer. |
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[928] | 116 | MASTER=${MASTER:=ada|curie} |
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[583] | 117 | |
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| 118 | #D- Flag to determine begin date for restart pack |
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| 119 | #D- Default : value from AA_job if any |
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| 120 | DateBegin=${DateBegin:=20000101} |
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| 121 | |
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| 122 | #D- Flag to determine end date for restart pack |
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| 123 | #D- Default : value from AA_job if any |
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| 124 | DateEnd=${DateEnd:=20691231} |
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| 125 | |
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| 126 | #D- Flag to determine pack period |
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| 127 | #D- Default : value from AA_job if any |
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| 128 | PeriodPack=${PeriodPack:=10Y} |
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| 129 | |
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| 130 | #D- Uncomment to run interactively |
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| 131 | #D- For testing purpose, will be remove |
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| 132 | #SUBMIT_DIR=${PWD} |
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| 133 | #RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test |
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| 134 | |
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| 135 | #D- Increased verbosity (1, 2, 3) |
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| 136 | #D- Default : value from AA_job if any |
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| 137 | Verbosity=${Verbosity:=3} |
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| 138 | |
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| 139 | #D- Low level debug : to bypass lib test checks and stack construction |
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| 140 | #D- Default : value from AA_job if any |
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| 141 | DEBUG_debug=${DEBUG_debug:=false} |
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| 142 | |
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| 143 | ######################################################################## |
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| 144 | |
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| 145 | . ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh |
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| 146 | . ${libIGCM}/libIGCM_card/libIGCM_card.ksh |
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| 147 | . ${libIGCM}/libIGCM_date/libIGCM_date.ksh |
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| 148 | #------- |
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| 149 | . ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh |
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[731] | 150 | . ${libIGCM}/libIGCM_config/libIGCM_config.ksh |
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[583] | 151 | . ${libIGCM}/libIGCM_post/libIGCM_post.ksh |
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[832] | 152 | #------- |
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[1192] | 153 | RUN_DIR=${RUN_DIR_PATH} |
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| 154 | IGCM_sys_MkdirWork ${RUN_DIR} |
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| 155 | IGCM_sys_Cd ${RUN_DIR} |
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| 156 | #------- |
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[832] | 157 | ( ${DEBUG_debug} ) && IGCM_debug_Check |
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| 158 | ( ${DEBUG_debug} ) && IGCM_card_Check |
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| 159 | ( ${DEBUG_debug} ) && IGCM_date_Check |
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[583] | 160 | |
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| 161 | ######################################################################## |
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| 162 | |
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| 163 | #set -vx |
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| 164 | |
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| 165 | # ------------------------------------------------------------------ |
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| 166 | # Test if all was right before proceeding further |
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| 167 | # ------------------------------------------------------------------ |
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[1206] | 168 | IGCM_debug_Verif_Exit |
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[583] | 169 | |
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| 170 | if [ ${StandAlone} = true ] ; then |
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| 171 | CARD_DIR=${SUBMIT_DIR} |
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| 172 | else |
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[647] | 173 | CARD_DIR=${RUN_DIR_PATH} |
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[640] | 174 | IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH} |
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| 175 | IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card ${RUN_DIR_PATH} |
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| 176 | IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP ${RUN_DIR_PATH} |
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| 177 | IGCM_sys_Get_Master ${SUBMIT_DIR}/POST ${RUN_DIR_PATH} |
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[583] | 178 | fi |
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| 179 | |
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[727] | 180 | #================================== |
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[583] | 181 | # First of all |
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| 182 | # |
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[727] | 183 | # Read libIGCM compatibility version in config.card |
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| 184 | # Read UserChoices section |
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| 185 | # Read Ensemble section |
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| 186 | # Read Post section |
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| 187 | # Define all netcdf output directories |
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| 188 | #================================== |
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| 189 | IGCM_config_CommonConfiguration ${CARD_DIR}/config.card |
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[583] | 190 | |
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[1198] | 191 | # ------------------------------------------------------------------ |
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| 192 | # Activate BigBrother so as to supervise this job |
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| 193 | # ------------------------------------------------------------------ |
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| 194 | IGCM_debug_BigBro_Initialize |
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| 195 | |
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[727] | 196 | #================================== |
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| 197 | # Read ListOfComponents section |
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| 198 | # to drive the loop over find |
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| 199 | IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents |
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[1198] | 200 | |
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| 201 | #================================== |
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| 202 | # Test and set up directories |
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| 203 | #================================== |
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[583] | 204 | IGCM_sys_TestDirArchive ${R_SAVE} |
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| 205 | [ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive" |
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| 206 | |
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| 207 | # Where to store used file list /!\ TEMPORARY /!\ |
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| 208 | STORE_DEBUG=${R_SAVE}/DEBUG |
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| 209 | |
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| 210 | # Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure) |
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| 211 | JobName=${config_UserChoices_JobName} |
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[590] | 212 | echo $JobName $DateBegin $DateEnd |
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[583] | 213 | |
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| 214 | # ------------------------------------------------------------------ |
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| 215 | # Test if all was right before proceeding further |
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| 216 | # ------------------------------------------------------------------ |
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[1206] | 217 | IGCM_debug_Verif_Exit |
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[583] | 218 | |
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[641] | 219 | IGCM_debug_Print 1 "Check coherence between PackFrequency and PeriodLength" |
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| 220 | IGCM_post_CheckModuloFrequency PeriodPack config_UserChoices_PeriodLength NbPeriodPerFrequency |
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| 221 | # ------------------------------------------------------------------ |
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| 222 | # Test if all was right before proceeding further |
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| 223 | # ------------------------------------------------------------------ |
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[1206] | 224 | IGCM_debug_Verif_Exit |
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[641] | 225 | |
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| 226 | IGCM_debug_Print 1 "We must process ${NbPeriodPerFrequency} files for each pack" |
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| 227 | |
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[583] | 228 | # Init loop |
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| 229 | date_begin_pack=${DateBegin} |
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| 230 | date_end_simulation=${DateEnd} |
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| 231 | number_pack=1 |
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| 232 | |
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| 233 | IGCM_debug_PrintVariables 3 date_begin_pack |
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| 234 | IGCM_debug_PrintVariables 3 date_end_simulation |
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| 235 | |
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| 236 | while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do |
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| 237 | |
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| 238 | IGCM_debug_PrintVariables 3 number_pack |
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[590] | 239 | DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} ) |
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[583] | 240 | date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) ) |
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| 241 | |
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| 242 | for comp in ${config_ListOfComponents[*]} ; do |
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[584] | 243 | dirList=$( find ${R_BUFR}/${comp}/Output -maxdepth 1 -mindepth 1 -type d ) |
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| 244 | for dir in ${dirList} ; do |
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[583] | 245 | # dirID is like ATM.Output.MO |
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| 246 | dirID=$( echo $dir | sed "s:${R_BUFR}/::" | sed "s:/:.:g" ) |
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| 247 | # Sort what's in the directory |
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| 248 | find ${dir} -type f -name "${JobName}*.nc" -ls | sort -k 11 > liste_files.${dirID}.txt |
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| 249 | # How much file type. Example : 1M_histmthCOSP.nc, 1M_histmth.nc, 1M_histmthNMC.nc, 1M_paramLMDZ_phy.nc |
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| 250 | # /!\ fileType include the .nc extension /!\ |
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| 251 | fileType=$( gawk '{print $11}' liste_files.${dirID}.txt | gawk -F$dir/ '{print $2}' | sed "s:${JobName}_[0-9]\{8,9\}_[0-9]\{8,9\}_::g" | sort | uniq ) |
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| 252 | # Loop over the file type and pack them when in between date_begin_pack and date_end_pack |
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| 253 | for myType in ${fileType} ; do |
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[590] | 254 | grep ${myType} liste_files.${dirID}.txt > liste_files.${dirID}.${myType}.txt |
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| 255 | nbfile=0 |
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| 256 | for file in $( gawk '{print $11}' liste_files.${dirID}.${myType}.txt ); do |
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| 257 | extract_date_file=$( echo ${file} | sed -e "s/.*${JobName}_[0-9]*_//" ) |
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| 258 | date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' ) |
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| 259 | # echo pack n°${number_pack} ${date_file} ${date_begin_pack} ${date_end_pack} |
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| 260 | if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then |
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[617] | 261 | echo ${file} >> liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt |
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| 262 | ncdump -h ${file} | grep -E 'float|double' | cut -f 1 -d '(' | cut -f 2 -d ' ' >> liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt |
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[590] | 263 | (( nbfile = nbfile + 1 )) |
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| 264 | fi |
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| 265 | done |
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[656] | 266 | |
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[718] | 267 | if [ ${nbfile} = 0 ] ; then |
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| 268 | IGCM_debug_Print 1 "We found no file to process" |
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[656] | 269 | IGCM_debug_Print 1 "We should have found ${NbPeriodPerFrequency} files" |
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[718] | 270 | IGCM_debug_Print 1 "As some files can be produced only for some selected period we consider we can move to the next file type" |
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[656] | 271 | continue |
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| 272 | fi |
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| 273 | |
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[653] | 274 | # Select list of variables to work with |
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| 275 | list_var=$( cat liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt | sort | uniq -c | awk -v nbfile=$nbfile '{if ($1 != nbfile) {print $2}}' | paste -s -d ',' ) |
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| 276 | liste_file_tmp=$( for i in $( cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ) ; do basename $i ; done ) |
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| 277 | # Create packed files |
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| 278 | IGCM_debug_Print 1 "Ncrcat ongoing for ${dir} and ${myType}" |
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[641] | 279 | if [ ! ${nbfile} = ${NbPeriodPerFrequency} ] ; then |
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| 280 | IGCM_debug_Print 1 "Number of files to process is not equal to what it should be" |
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[653] | 281 | IGCM_debug_Print 1 "We found ${nbfile} files and it should have been ${NbPeriodPerFrequency} files" |
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[641] | 282 | IGCM_debug_Exit "ERROR in number of files to process. STOP HERE INCLUDING THE COMPUTING JOB" |
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| 283 | IGCM_debug_Verif_Exit |
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| 284 | fi |
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[590] | 285 | output=${JobName}_${date_begin_pack}_${date_end_pack}_${myType} |
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[617] | 286 | #cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs ncrcat -v ${list_var} -o ${output} |
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[590] | 287 | if [ X${list_var} = X ] ; then |
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| 288 | IGCM_sys_ncrcat -p ${dir} ${liste_file_tmp} --output ${output} |
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| 289 | else |
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| 290 | IGCM_sys_ncrcat -x -v ${list_var} -p ${dir} ${liste_file_tmp} --output ${output} |
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| 291 | fi |
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| 292 | # ------------------------------------------------------------------ |
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[583] | 293 | # Test if all was right before proceeding further |
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| 294 | # ------------------------------------------------------------------ |
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[1206] | 295 | IGCM_debug_Verif_Exit |
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[583] | 296 | # Save it |
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[590] | 297 | IGCM_sys_Put_Out ${output} ${R_SAVE}/$( echo $dir | sed "s:${R_BUFR}/::" )/${output} |
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[699] | 298 | # Clean file produced by ncrcat |
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| 299 | IGCM_sys_Rm ${output} |
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[590] | 300 | # ------------------------------------------------------------------ |
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[583] | 301 | # Test if all was right before proceeding further |
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| 302 | # ------------------------------------------------------------------ |
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[1206] | 303 | IGCM_debug_Verif_Exit |
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[583] | 304 | # Clean files used by ncrcat |
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[617] | 305 | cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs rm |
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[583] | 306 | # Save the list of files that has been pack (ncrcat) |
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[632] | 307 | #mv liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG} |
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[590] | 308 | IGCM_debug_Print 1 "Ncrcat and cleaning done for ${dir} and ${myType}" |
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[785] | 309 | echo |
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[583] | 310 | done |
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| 311 | done |
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| 312 | done |
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| 313 | (( number_pack = number_pack + 1 )) |
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| 314 | # Add 1 day to date_end_pack to have the new date_begin_pack |
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| 315 | date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 ) |
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| 316 | done |
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[590] | 317 | |
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[628] | 318 | # Flush post-processing submission |
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| 319 | if [ -f ${R_BUFR}/FlushPost_${DateEnd}.ksh ] ; then |
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| 320 | . ${R_BUFR}/FlushPost_${DateEnd}.ksh |
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| 321 | IGCM_FlushPost |
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| 322 | #IGCM_sys_Rm -f ${R_BUFR}/FlushPost_${DateEnd}.ksh |
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| 323 | fi |
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| 324 | |
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[590] | 325 | # Clean RUN_DIR_PATH (necessary for cesium and titane only) |
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| 326 | IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH} |
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| 327 | |
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[1198] | 328 | # ------------------------------------------------------------------ |
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| 329 | # Finalize BigBrother to inform that the jobs end |
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| 330 | # ------------------------------------------------------------------ |
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| 331 | IGCM_debug_BigBro_Finalize |
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| 332 | |
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[590] | 333 | date |
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