[583] | 1 | #-Q- cesium #!/bin/ksh |
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| 2 | #-Q- cesium ###################### |
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| 3 | #-Q- cesium ## CESIUM CEA ## |
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| 4 | #-Q- cesium ###################### |
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[590] | 5 | #-Q- cesium #MSUB -r PACKOUTPUT # Nom du job |
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[583] | 6 | #-Q- cesium #MSUB -N 1 # Reservation du noeud |
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| 7 | #-Q- cesium #MSUB -n 1 # Reservation du processus |
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| 8 | #-Q- cesium #MSUB -T 86400 # Limite de temps elapsed du job |
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| 9 | #-Q- cesium #MSUB -E "-j o" |
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| 10 | #-Q- cesium #MSUB -E "-S /bin/ksh" |
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| 11 | #-Q- platine #!/usr/bin/ksh |
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| 12 | #-Q- platine ################### |
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| 13 | #-Q- platine ## PLATINE CEA ## |
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| 14 | #-Q- platine ################### |
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| 15 | #-Q- platine #BSUB -J PACKOUTPUT # Nom du job |
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| 16 | #-Q- platine #BSUB -N # message a la fin du job |
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| 17 | #-Q- platine #BSUB -n 1 # reservation des processeurs pour le job |
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| 18 | #-Q- platine #BSUB -W 4:00 # Limite temps |
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| 19 | #-Q- platine #BSUB -q post # Passage en queue post |
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| 20 | #-Q- platine #BSUB -L /bin/ksh |
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| 21 | #-Q- sx8brodie #!/bin/ksh |
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| 22 | #-Q- sx8brodie ####################### |
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| 23 | #-Q- sx8brodie ## SX8BRODIE IDRIS ## |
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| 24 | #-Q- sx8brodie ####################### |
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| 25 | #-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss |
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| 26 | #-Q- sx8brodie # @ wall_clock_limit = 10:00:00 |
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| 27 | #-Q- sx8brodie # Nom du travail LoadLeveler |
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| 28 | #-Q- sx8brodie # @ job_name = PACKOUTPUT |
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[590] | 29 | #-Q- sx8brodie # Fichier de sortie standard du travail |
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[583] | 30 | #-Q- sx8brodie # @ output = $(job_name).$(jobid) |
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| 31 | #-Q- sx8brodie # Fichier de sortie d'erreur du travail |
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| 32 | #-Q- sx8brodie # @ error = $(job_name).$(jobid) |
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| 33 | #-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.) |
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| 34 | #-Q- sx8brodie # @ notification = error |
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| 35 | #-Q- sx8brodie # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER |
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| 36 | #-Q- sx8brodie # @ queue |
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| 37 | #-Q- aix6 #!/bin/ksh |
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| 38 | #-Q- aix6 ####################### |
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| 39 | #-Q- aix6 ## VARGAS IDRIS ## |
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| 40 | #-Q- aix6 ####################### |
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| 41 | #-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss |
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| 42 | #-Q- aix6 # @ wall_clock_limit = 10:00:00 |
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| 43 | #-Q- aix6 # Nom du travail LoadLeveler |
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| 44 | #-Q- aix6 # @ job_name = PACKOUTPUT |
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| 45 | #-Q- aix6 # Fichier de sortie standard du travail |
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| 46 | #-Q- aix6 # @ output = $(job_name).$(jobid) |
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| 47 | #-Q- aix6 # Fichier de sortie d'erreur du travail |
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| 48 | #-Q- aix6 # @ error = $(job_name).$(jobid) |
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| 49 | #-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.) |
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| 50 | #-Q- aix6 # @ notification = error |
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| 51 | #-Q- aix6 # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER |
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| 52 | #-Q- aix6 # @ queue |
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| 53 | #-Q- ulam #!/bin/ksh |
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| 54 | #-Q- ulam ####################### |
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| 55 | #-Q- ulam ## VARGAS IDRIS ## |
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| 56 | #-Q- ulam ####################### |
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| 57 | #-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss |
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| 58 | #-Q- ulam # @ wall_clock_limit = 10:00:00 |
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| 59 | #-Q- ulam # Nom du travail LoadLeveler |
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| 60 | #-Q- ulam # @ job_name = PACKOUTPUT |
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| 61 | #-Q- ulam # Fichier de sortie standard du travail |
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| 62 | #-Q- ulam # @ output = $(job_name).$(jobid) |
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| 63 | #-Q- ulam # Fichier de sortie d'erreur du travail |
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| 64 | #-Q- ulam # @ error = $(job_name).$(jobid) |
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| 65 | #-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.) |
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| 66 | #-Q- ulam # @ notification = error |
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| 67 | #-Q- ulam # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER |
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| 68 | #-Q- ulam # @ queue |
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| 69 | #-Q- sx8mercure #!/bin/ksh |
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| 70 | #-Q- sx8mercure ###################### |
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| 71 | #-Q- sx8mercure ## SX8MERCURE CEA ## |
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| 72 | #-Q- sx8mercure ###################### |
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| 73 | #-Q- sx8mercure #PBS -N PACKOUTPUT # Nom du job |
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| 74 | #-Q- sx8mercure #PBS -j o # regroupement des stdout et stderr |
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| 75 | #-Q- sx8mercure #PBS -S /usr/bin/ksh # shell de soumission |
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| 76 | #-Q- sx8mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go |
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| 77 | #-Q- sx8mercure #PBS -l cputim_job=24:00:00 # Limite temps a 1 heures |
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| 78 | #-Q- sx8mercure #PBS -q scalaire |
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| 79 | #-Q- sx9mercure #!/bin/ksh |
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| 80 | #-Q- sx9mercure ###################### |
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[597] | 81 | #-Q- sx9mercure ## SX9MERCURE CCRT ## |
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[583] | 82 | #-Q- sx9mercure ###################### |
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[597] | 83 | #-Q- sx9mercure #PBS -N PACKOUTPUT # Nom du job |
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| 84 | #-Q- sx9mercure #PBS -j o # regroupement des stdout et stderr |
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| 85 | #-Q- sx9mercure #PBS -S /usr/bin/ksh # shell de soumission |
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| 86 | #-Q- sx9mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go |
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[605] | 87 | #-Q- sx9mercure #PBS -l elapstim_req=24:00:00 # Limite temps a 1 heures |
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[597] | 88 | #-Q- sx9mercure #PBS -q scalaire |
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[583] | 89 | #-Q- titane #!/bin/ksh |
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| 90 | #-Q- titane ###################### |
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| 91 | #-Q- titane ## TITANE CEA ## |
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| 92 | #-Q- titane ###################### |
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[590] | 93 | #-Q- titane #MSUB -r PACKOUTPUT # Nom du job |
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[583] | 94 | #-Q- titane #MSUB -eo |
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| 95 | #-Q- titane #MSUB -n 1 # Reservation du processus |
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| 96 | #-Q- titane #MSUB -T 86400 # Limite de temps elapsed du job |
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| 97 | #-Q- titane #MSUB -q mono |
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| 98 | #-Q- lxiv8 ###################### |
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| 99 | #-Q- lxiv8 ## OBELIX LSCE ## |
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| 100 | #-Q- lxiv8 ###################### |
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| 101 | #-Q- lxiv8 #PBS -N PACKOUTPUT |
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| 102 | #-Q- lxiv8 #PBS -m a |
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| 103 | #-Q- lxiv8 #PBS -j oe |
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| 104 | #-Q- lxiv8 #PBS -q medium |
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| 105 | #-Q- lxiv8 #PBS -o PACKOUTPUT.$$ |
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| 106 | #-Q- lxiv8 #PBS -S /bin/ksh |
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| 107 | #-Q- default #!/bin/ksh |
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| 108 | #-Q- default ################## |
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| 109 | #-Q- default ## DEFAULT HOST ## |
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| 110 | #-Q- default ################## |
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| 111 | |
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| 112 | #************************************************************** |
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| 113 | # Author: Sebastien Denvil |
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| 114 | # Contact: Sebastien.Denvil__at__ipsl.jussieu.fr |
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| 115 | # $Revision:: $ Revision of last commit |
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| 116 | # $Author:: $ Author of last commit |
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| 117 | # $Date:: $ Date of last commit |
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| 118 | # IPSL (2006) |
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| 119 | # This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC |
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| 120 | # |
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| 121 | #************************************************************** |
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| 122 | |
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| 123 | #set -eu |
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| 124 | #set -vx |
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| 125 | |
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| 126 | date |
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| 127 | |
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| 128 | ######################################################################## |
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| 129 | |
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| 130 | #D- Flag to determine if this job in a standalone mode |
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| 131 | #D- Default : value from AA_job if any |
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| 132 | StandAlone=${StandAlone:=true} |
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| 133 | |
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| 134 | #D- Path to libIGCM |
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| 135 | #D- Default : value from AA_job if any |
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| 136 | # WARNING For StandAlone use : To run this script on some machine (ulam and cesium) |
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| 137 | # WARNING you must check MirrorlibIGCM variable in sys library. |
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| 138 | # WARNING If this variable is true, you must use libIGCM_POST path instead |
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| 139 | # WARNING of your running libIGCM directory. |
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| 140 | libIGCM=${libIGCM:=::modipsl::/libIGCM} |
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| 141 | |
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| 142 | #-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer. |
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| 143 | MASTER=${MASTER:=mercure|titane|brodie|vargas} |
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| 144 | |
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| 145 | #D- Flag to determine begin date for restart pack |
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| 146 | #D- Default : value from AA_job if any |
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| 147 | DateBegin=${DateBegin:=20000101} |
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| 148 | |
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| 149 | #D- Flag to determine end date for restart pack |
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| 150 | #D- Default : value from AA_job if any |
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| 151 | DateEnd=${DateEnd:=20691231} |
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| 152 | |
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| 153 | #D- Flag to determine pack period |
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| 154 | #D- Default : value from AA_job if any |
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| 155 | PeriodPack=${PeriodPack:=10Y} |
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| 156 | |
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| 157 | #D- Uncomment to run interactively |
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| 158 | #D- For testing purpose, will be remove |
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| 159 | #SUBMIT_DIR=${PWD} |
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| 160 | #RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test |
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| 161 | |
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| 162 | #D- Increased verbosity (1, 2, 3) |
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| 163 | #D- Default : value from AA_job if any |
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| 164 | Verbosity=${Verbosity:=3} |
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| 165 | |
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| 166 | #D- Low level debug : to bypass lib test checks and stack construction |
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| 167 | #D- Default : value from AA_job if any |
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| 168 | DEBUG_debug=${DEBUG_debug:=false} |
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| 169 | |
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| 170 | ######################################################################## |
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| 171 | |
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| 172 | . ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh |
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| 173 | ( ${DEBUG_debug} ) && IGCM_debug_Check |
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| 174 | . ${libIGCM}/libIGCM_card/libIGCM_card.ksh |
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| 175 | ( ${DEBUG_debug} ) && IGCM_card_Check |
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| 176 | . ${libIGCM}/libIGCM_date/libIGCM_date.ksh |
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| 177 | ( ${DEBUG_debug} ) && IGCM_date_Check |
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| 178 | #------- |
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| 179 | . ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh |
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| 180 | . ${libIGCM}/libIGCM_post/libIGCM_post.ksh |
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| 181 | |
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| 182 | ######################################################################## |
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| 183 | |
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| 184 | #set -vx |
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| 185 | |
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| 186 | RUN_DIR=${RUN_DIR_PATH} |
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| 187 | IGCM_sys_MkdirWork ${RUN_DIR} |
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| 188 | IGCM_sys_Cd ${RUN_DIR} |
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| 189 | |
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| 190 | # ------------------------------------------------------------------ |
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| 191 | # Test if all was right before proceeding further |
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| 192 | # ------------------------------------------------------------------ |
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| 193 | IGCM_debug_Verif_Exit_Post |
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| 194 | |
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| 195 | if [ ${StandAlone} = true ] ; then |
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| 196 | CARD_DIR=${SUBMIT_DIR} |
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| 197 | else |
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| 198 | CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} ) |
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| 199 | IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH} |
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| 200 | fi |
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| 201 | |
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[590] | 202 | #==================================================== |
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[583] | 203 | # First of all |
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| 204 | # |
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[590] | 205 | # Read config.card |
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[583] | 206 | |
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| 207 | IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card UserChoices |
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| 208 | typeset option |
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| 209 | for option in ${config_UserChoices[*]} ; do |
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| 210 | IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option} |
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| 211 | done |
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| 212 | # |
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| 213 | echo |
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| 214 | IGCM_debug_Print 1 "DefineArrayFromOption : config_UserChoices" |
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| 215 | IGCM_debug_PrintVariables 3 config_UserChoices_JobName |
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| 216 | IGCM_debug_PrintVariables 3 config_UserChoices_LongName |
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| 217 | IGCM_debug_PrintVariables 3 config_UserChoices_TagName |
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| 218 | IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName |
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| 219 | IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName |
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| 220 | IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType |
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| 221 | IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin |
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| 222 | IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd |
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| 223 | IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength |
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| 224 | echo |
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| 225 | |
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| 226 | # Get ListOfComponents to drive the loop over find |
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| 227 | IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents |
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| 228 | |
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| 229 | #==================================================== |
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| 230 | #R_SAVE : Job output storage directory |
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| 231 | #R_BUFR : Job output buffered directory |
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| 232 | |
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| 233 | if ( [ ! X${config_UserChoices_SpaceName} = X ] && [ ! X${config_UserChoices_ExperimentName} = X ] ) ; then |
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| 234 | FreeName=$( echo ${config_UserChoices_JobName} | sed 's/.*_//' ) |
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| 235 | R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName} |
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| 236 | R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName} |
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| 237 | else |
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| 238 | R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_JobName} |
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| 239 | R_BUFR=${R_BUF}/${config_UserChoices_TagName}/${config_UserChoices_JobName} |
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| 240 | fi |
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| 241 | IGCM_sys_TestDirArchive ${R_SAVE} |
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| 242 | [ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive" |
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| 243 | |
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| 244 | # Where to store used file list /!\ TEMPORARY /!\ |
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| 245 | STORE_DEBUG=${R_SAVE}/DEBUG |
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| 246 | |
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| 247 | # Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure) |
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| 248 | JobName=${config_UserChoices_JobName} |
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[590] | 249 | echo $JobName $DateBegin $DateEnd |
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[583] | 250 | |
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| 251 | # ------------------------------------------------------------------ |
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| 252 | # Test if all was right before proceeding further |
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| 253 | # ------------------------------------------------------------------ |
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| 254 | IGCM_debug_Verif_Exit_Post |
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| 255 | |
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| 256 | # Init loop |
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| 257 | date_begin_pack=${DateBegin} |
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| 258 | date_end_simulation=${DateEnd} |
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| 259 | number_pack=1 |
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| 260 | |
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| 261 | IGCM_debug_PrintVariables 3 date_begin_pack |
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| 262 | IGCM_debug_PrintVariables 3 date_end_simulation |
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| 263 | |
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| 264 | while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do |
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| 265 | |
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| 266 | IGCM_debug_PrintVariables 3 number_pack |
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[590] | 267 | DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} ) |
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[583] | 268 | date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) ) |
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| 269 | |
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| 270 | for comp in ${config_ListOfComponents[*]} ; do |
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[584] | 271 | dirList=$( find ${R_BUFR}/${comp}/Output -maxdepth 1 -mindepth 1 -type d ) |
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| 272 | for dir in ${dirList} ; do |
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[583] | 273 | # dirID is like ATM.Output.MO |
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| 274 | dirID=$( echo $dir | sed "s:${R_BUFR}/::" | sed "s:/:.:g" ) |
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| 275 | # Sort what's in the directory |
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| 276 | find ${dir} -type f -name "${JobName}*.nc" -ls | sort -k 11 > liste_files.${dirID}.txt |
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| 277 | # How much file type. Example : 1M_histmthCOSP.nc, 1M_histmth.nc, 1M_histmthNMC.nc, 1M_paramLMDZ_phy.nc |
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| 278 | # /!\ fileType include the .nc extension /!\ |
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| 279 | fileType=$( 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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| 280 | # Loop over the file type and pack them when in between date_begin_pack and date_end_pack |
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| 281 | for myType in ${fileType} ; do |
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[590] | 282 | grep ${myType} liste_files.${dirID}.txt > liste_files.${dirID}.${myType}.txt |
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| 283 | nbfile=0 |
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| 284 | for file in $( gawk '{print $11}' liste_files.${dirID}.${myType}.txt ); do |
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| 285 | extract_date_file=$( echo ${file} | sed -e "s/.*${JobName}_[0-9]*_//" ) |
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| 286 | date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' ) |
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| 287 | # echo pack n°${number_pack} ${date_file} ${date_begin_pack} ${date_end_pack} |
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| 288 | if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then |
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| 289 | echo ${file} >> liste_pack_${myType}_${number_pack}.txt |
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| 290 | ncdump -h ${file} | grep -E 'float|double' | cut -f 1 -d '(' | cut -f 2 -d ' ' >> liste_variables_${myType}_${number_pack}.txt |
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| 291 | (( nbfile = nbfile + 1 )) |
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| 292 | fi |
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| 293 | done |
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| 294 | # Select list of variables to work with |
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| 295 | list_var=$( cat liste_variables_${myType}_${number_pack}.txt | sort | uniq -c | awk -v nbfile=$nbfile '{if ($1 != nbfile) {print $2}}' | paste -s -d ',' ) |
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| 296 | liste_file_tmp=$( for i in $( cat liste_pack_${myType}_${number_pack}.txt ) ; do basename $i ; done ) |
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| 297 | # Create packed files |
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| 298 | IGCM_debug_Print 1 "Ncrcat ongoing for ${dir} and ${myType}" |
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| 299 | output=${JobName}_${date_begin_pack}_${date_end_pack}_${myType} |
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| 300 | #cat liste_pack_${myType}_${number_pack}.txt | xargs ncrcat -v ${list_var} -o ${output} |
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| 301 | if [ X${list_var} = X ] ; then |
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| 302 | IGCM_sys_ncrcat -p ${dir} ${liste_file_tmp} --output ${output} |
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| 303 | else |
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| 304 | IGCM_sys_ncrcat -x -v ${list_var} -p ${dir} ${liste_file_tmp} --output ${output} |
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| 305 | fi |
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| 306 | # ------------------------------------------------------------------ |
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[583] | 307 | # Test if all was right before proceeding further |
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| 308 | # ------------------------------------------------------------------ |
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[590] | 309 | IGCM_debug_Verif_Exit_Post |
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[583] | 310 | # Save it |
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[590] | 311 | IGCM_sys_Put_Out ${output} ${R_SAVE}/$( echo $dir | sed "s:${R_BUFR}/::" )/${output} |
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| 312 | # ------------------------------------------------------------------ |
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[583] | 313 | # Test if all was right before proceeding further |
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| 314 | # ------------------------------------------------------------------ |
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[590] | 315 | IGCM_debug_Verif_Exit_Post |
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[583] | 316 | # Clean file produced by ncrcat |
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[590] | 317 | IGCM_sys_Rm ${output} |
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[583] | 318 | # Clean files used by ncrcat |
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[590] | 319 | cat liste_pack_${myType}_${number_pack}.txt | xargs rm |
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[583] | 320 | # Save the list of files that has been pack (ncrcat) |
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[590] | 321 | mv liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG} |
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| 322 | IGCM_debug_Print 1 "Ncrcat and cleaning done for ${dir} and ${myType}" |
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[583] | 323 | done |
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| 324 | done |
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| 325 | done |
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| 326 | (( number_pack = number_pack + 1 )) |
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| 327 | # Add 1 day to date_end_pack to have the new date_begin_pack |
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| 328 | date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 ) |
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| 329 | done |
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[590] | 330 | |
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| 331 | # Clean RUN_DIR_PATH (necessary for cesium and titane only) |
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| 332 | IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH} |
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| 333 | |
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| 334 | date |
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