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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5 | #-Q- cesium #MSUB -r PACKOUTPUT # Nom du job |
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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- curie ###################### |
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12 | #-Q- curie ## CURIE TGCC/CEA ## |
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13 | #-Q- curie ###################### |
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14 | #-Q- curie #MSUB -r PACKOUTPUT # Nom du job |
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15 | #-Q- curie #MSUB -eo |
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16 | #-Q- curie #MSUB -n 1 # Reservation du processus |
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17 | #-Q- curie #MSUB -T 86400 # Limite de temps elapsed du job |
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18 | #-Q- curie #MSUB -q xlarge |
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19 | #-Q- curie #MSUB -Q normal |
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20 | #-Q- curie set +x |
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21 | #-Q- platine #!/usr/bin/ksh |
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22 | #-Q- platine ################### |
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23 | #-Q- platine ## PLATINE CEA ## |
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24 | #-Q- platine ################### |
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25 | #-Q- platine #BSUB -J PACKOUTPUT # Nom du job |
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26 | #-Q- platine #BSUB -N # message a la fin du job |
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27 | #-Q- platine #BSUB -n 1 # reservation des processeurs pour le job |
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28 | #-Q- platine #BSUB -W 4:00 # Limite temps |
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29 | #-Q- platine #BSUB -q post # Passage en queue post |
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30 | #-Q- platine #BSUB -L /bin/ksh |
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31 | #-Q- sx8brodie #!/bin/ksh |
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32 | #-Q- sx8brodie ####################### |
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33 | #-Q- sx8brodie ## SX8BRODIE IDRIS ## |
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34 | #-Q- sx8brodie ####################### |
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35 | #-Q- sx8brodie # Temps Elapsed max. d'une requete hh:mm:ss |
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36 | #-Q- sx8brodie # @ wall_clock_limit = 10:00:00 |
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37 | #-Q- sx8brodie # Nom du travail LoadLeveler |
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38 | #-Q- sx8brodie # @ job_name = PACKOUTPUT |
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39 | #-Q- sx8brodie # Fichier de sortie standard du travail |
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40 | #-Q- sx8brodie # @ output = $(job_name).$(jobid) |
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41 | #-Q- sx8brodie # Fichier de sortie d'erreur du travail |
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42 | #-Q- sx8brodie # @ error = $(job_name).$(jobid) |
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43 | #-Q- sx8brodie # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.) |
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44 | #-Q- sx8brodie # @ notification = error |
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45 | #-Q- sx8brodie # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER |
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46 | #-Q- sx8brodie # @ queue |
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47 | #-Q- aix6 #!/bin/ksh |
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48 | #-Q- aix6 ####################### |
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49 | #-Q- aix6 ## VARGAS IDRIS ## |
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50 | #-Q- aix6 ####################### |
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51 | #-Q- aix6 # Temps Elapsed max. d'une requete hh:mm:ss |
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52 | #-Q- aix6 # @ wall_clock_limit = 10:00:00 |
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53 | #-Q- aix6 # Nom du travail LoadLeveler |
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54 | #-Q- aix6 # @ job_name = PACKOUTPUT |
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55 | #-Q- aix6 # Fichier de sortie standard du travail |
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56 | #-Q- aix6 # @ output = $(job_name).$(jobid) |
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57 | #-Q- aix6 # Fichier de sortie d'erreur du travail |
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58 | #-Q- aix6 # @ error = $(job_name).$(jobid) |
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59 | #-Q- aix6 # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.) |
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60 | #-Q- aix6 # @ notification = error |
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61 | #-Q- aix6 # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER |
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62 | #-Q- aix6 # @ queue |
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63 | #-Q- ulam #!/bin/ksh |
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64 | #-Q- ulam ####################### |
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65 | #-Q- ulam ## VARGAS IDRIS ## |
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66 | #-Q- ulam ####################### |
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67 | #-Q- ulam # Temps Elapsed max. d'une requete hh:mm:ss |
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68 | #-Q- ulam # @ wall_clock_limit = 10:00:00 |
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69 | #-Q- ulam # Nom du travail LoadLeveler |
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70 | #-Q- ulam # @ job_name = PACKOUTPUT |
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71 | #-Q- ulam # Fichier de sortie standard du travail |
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72 | #-Q- ulam # @ output = $(job_name).$(jobid) |
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73 | #-Q- ulam # Fichier de sortie d'erreur du travail |
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74 | #-Q- ulam # @ error = $(job_name).$(jobid) |
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75 | #-Q- ulam # pour recevoir un mail en cas de depassement du temps Elapsed (ou autre pb.) |
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76 | #-Q- ulam # @ notification = error |
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77 | #-Q- ulam # @ environment = $DEBUG_debug ; $MODIPSL ; $libIGCM ; $libIGCM_SX ; $SUBMIT_DIR ; $DateBegin ; $DateEnd ; $PeriodPack ; $StandAlone ; $MASTER |
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78 | #-Q- ulam # @ queue |
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79 | #-Q- sx8mercure #!/bin/ksh |
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80 | #-Q- sx8mercure ###################### |
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81 | #-Q- sx8mercure ## SX8MERCURE CEA ## |
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82 | #-Q- sx8mercure ###################### |
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83 | #-Q- sx8mercure #PBS -N PACKOUTPUT # Nom du job |
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84 | #-Q- sx8mercure #PBS -j o # regroupement des stdout et stderr |
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85 | #-Q- sx8mercure #PBS -S /usr/bin/ksh # shell de soumission |
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86 | #-Q- sx8mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go |
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87 | #-Q- sx8mercure #PBS -l cputim_job=48:00:00 # Limite temps a 1 heures |
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88 | #-Q- sx8mercure #PBS -q scalaire |
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89 | #-Q- sx8mercure #PBS -r n |
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90 | #-Q- sx9mercure #!/bin/ksh |
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91 | #-Q- sx9mercure ###################### |
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92 | #-Q- sx9mercure ## SX9MERCURE CCRT ## |
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93 | #-Q- sx9mercure ###################### |
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94 | #-Q- sx9mercure #PBS -N PACKOUTPUT # Nom du job |
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95 | #-Q- sx9mercure #PBS -j o # regroupement des stdout et stderr |
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96 | #-Q- sx9mercure #PBS -S /usr/bin/ksh # shell de soumission |
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97 | #-Q- sx9mercure #PBS -l memsz_job=1gb # Limite memoire a 1 Go |
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98 | #-Q- sx9mercure #PBS -l elapstim_req=48:00:00 # Limite temps a 1 heures |
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99 | #-Q- sx9mercure #PBS -q scalaire |
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100 | #-Q- sx9mercure #PBS -r n |
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101 | #-Q- titane #!/bin/ksh |
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102 | #-Q- titane ###################### |
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103 | #-Q- titane ## TITANE CEA ## |
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104 | #-Q- titane ###################### |
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105 | #-Q- titane #MSUB -r PACKOUTPUT # Nom du job |
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106 | #-Q- titane #MSUB -eo |
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107 | #-Q- titane #MSUB -n 1 # Reservation du processus |
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108 | #-Q- titane #MSUB -T 86400 # Limite de temps elapsed du job |
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109 | #-Q- titane #MSUB -q mono |
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110 | #-Q- titane #MSUB -E '-rn' |
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111 | #-Q- lxiv8 ###################### |
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112 | #-Q- lxiv8 ## OBELIX LSCE ## |
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113 | #-Q- lxiv8 ###################### |
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114 | #-Q- lxiv8 #PBS -N PACKOUTPUT |
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115 | #-Q- lxiv8 #PBS -m a |
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116 | #-Q- lxiv8 #PBS -j oe |
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117 | #-Q- lxiv8 #PBS -q medium |
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118 | #-Q- lxiv8 #PBS -o PACKOUTPUT.$$ |
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119 | #-Q- lxiv8 #PBS -S /bin/ksh |
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120 | #-Q- default #!/bin/ksh |
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121 | #-Q- default ################## |
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122 | #-Q- default ## DEFAULT HOST ## |
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123 | #-Q- default ################## |
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124 | |
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125 | #************************************************************** |
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126 | # Author: Sebastien Denvil |
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127 | # Contact: Sebastien.Denvil__at__ipsl.jussieu.fr |
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128 | # $Revision:: $ Revision of last commit |
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129 | # $Author:: $ Author of last commit |
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130 | # $Date:: $ Date of last commit |
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131 | # IPSL (2006) |
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132 | # This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC |
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133 | # |
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134 | #************************************************************** |
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135 | |
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136 | #set -eu |
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137 | #set -vx |
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138 | |
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139 | date |
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140 | |
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141 | #D- Task type (computing or post-processing) |
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142 | TaskType=post-processing |
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143 | |
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144 | ######################################################################## |
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145 | |
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146 | #D- Flag to determine if this job in a standalone mode |
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147 | #D- Default : value from AA_job if any |
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148 | StandAlone=${StandAlone:=true} |
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149 | |
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150 | #D- Path to libIGCM |
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151 | #D- Default : value from AA_job if any |
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152 | # WARNING For StandAlone use : To run this script on some machine (ulam and cesium) |
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153 | # WARNING you must check MirrorlibIGCM variable in sys library. |
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154 | # WARNING If this variable is true, you must use libIGCM_POST path instead |
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155 | # WARNING of your running libIGCM directory. |
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156 | libIGCM=${libIGCM:=::modipsl::/libIGCM} |
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157 | |
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158 | #-D- $hostname of the MASTER job when SUBMIT_DIR is not visible on postprocessing computer. |
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159 | MASTER=${MASTER:=mercure|titane|brodie|vargas} |
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160 | |
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161 | #D- Flag to determine begin date for restart pack |
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162 | #D- Default : value from AA_job if any |
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163 | DateBegin=${DateBegin:=20000101} |
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164 | |
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165 | #D- Flag to determine end date for restart pack |
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166 | #D- Default : value from AA_job if any |
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167 | DateEnd=${DateEnd:=20691231} |
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168 | |
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169 | #D- Flag to determine pack period |
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170 | #D- Default : value from AA_job if any |
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171 | PeriodPack=${PeriodPack:=10Y} |
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172 | |
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173 | #D- Uncomment to run interactively |
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174 | #D- For testing purpose, will be remove |
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175 | #SUBMIT_DIR=${PWD} |
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176 | #RUN_DIR_PATH=${SCRATCHDIR}/Pack_Test |
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177 | |
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178 | #D- Increased verbosity (1, 2, 3) |
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179 | #D- Default : value from AA_job if any |
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180 | Verbosity=${Verbosity:=3} |
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181 | |
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182 | #D- Low level debug : to bypass lib test checks and stack construction |
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183 | #D- Default : value from AA_job if any |
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184 | DEBUG_debug=${DEBUG_debug:=false} |
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185 | |
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186 | ######################################################################## |
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187 | |
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188 | . ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh |
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189 | ( ${DEBUG_debug} ) && IGCM_debug_Check |
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190 | . ${libIGCM}/libIGCM_card/libIGCM_card.ksh |
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191 | ( ${DEBUG_debug} ) && IGCM_card_Check |
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192 | . ${libIGCM}/libIGCM_date/libIGCM_date.ksh |
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193 | ( ${DEBUG_debug} ) && IGCM_date_Check |
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194 | #------- |
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195 | . ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh |
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196 | . ${libIGCM}/libIGCM_config/libIGCM_config.ksh |
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197 | . ${libIGCM}/libIGCM_post/libIGCM_post.ksh |
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198 | |
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199 | ######################################################################## |
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200 | |
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201 | #set -vx |
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202 | |
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203 | RUN_DIR=${RUN_DIR_PATH} |
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204 | IGCM_sys_MkdirWork ${RUN_DIR} |
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205 | IGCM_sys_Cd ${RUN_DIR} |
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206 | |
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207 | # ------------------------------------------------------------------ |
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208 | # Test if all was right before proceeding further |
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209 | # ------------------------------------------------------------------ |
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210 | IGCM_debug_Verif_Exit_Post |
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211 | |
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212 | if [ ${StandAlone} = true ] ; then |
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213 | CARD_DIR=${SUBMIT_DIR} |
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214 | else |
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215 | CARD_DIR=${RUN_DIR_PATH} |
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216 | IGCM_sys_Get_Master ${SUBMIT_DIR}/config.card ${RUN_DIR_PATH} |
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217 | IGCM_sys_Get_Master ${SUBMIT_DIR}/run.card ${RUN_DIR_PATH} |
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218 | IGCM_sys_Get_Master ${SUBMIT_DIR}/COMP ${RUN_DIR_PATH} |
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219 | IGCM_sys_Get_Master ${SUBMIT_DIR}/POST ${RUN_DIR_PATH} |
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220 | fi |
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221 | |
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222 | #================================== |
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223 | # First of all |
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224 | # |
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225 | # Read libIGCM compatibility version in config.card |
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226 | # Read UserChoices section |
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227 | # Read Ensemble section |
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228 | # Read Post section |
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229 | # Define all netcdf output directories |
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230 | #================================== |
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231 | IGCM_config_CommonConfiguration ${CARD_DIR}/config.card |
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232 | |
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233 | #================================== |
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234 | # Read ListOfComponents section |
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235 | # to drive the loop over find |
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236 | IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card ListOfComponents |
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237 | # |
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238 | IGCM_sys_TestDirArchive ${R_SAVE} |
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239 | [ $? != 0 ] && IGCM_debug_Exit "IGCM_sys_TestDirArchive" |
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240 | |
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241 | # Where to store used file list /!\ TEMPORARY /!\ |
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242 | STORE_DEBUG=${R_SAVE}/DEBUG |
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243 | |
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244 | # Switch to script variables meaning (try to be compatible with ipsl_pack TGCC moving procedure) |
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245 | JobName=${config_UserChoices_JobName} |
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246 | echo $JobName $DateBegin $DateEnd |
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247 | |
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248 | # ------------------------------------------------------------------ |
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249 | # Test if all was right before proceeding further |
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250 | # ------------------------------------------------------------------ |
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251 | IGCM_debug_Verif_Exit_Post |
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252 | |
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253 | IGCM_debug_Print 1 "Check coherence between PackFrequency and PeriodLength" |
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254 | IGCM_post_CheckModuloFrequency PeriodPack config_UserChoices_PeriodLength NbPeriodPerFrequency |
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255 | # ------------------------------------------------------------------ |
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256 | # Test if all was right before proceeding further |
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257 | # ------------------------------------------------------------------ |
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258 | IGCM_debug_Verif_Exit_Post |
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259 | |
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260 | IGCM_debug_Print 1 "We must process ${NbPeriodPerFrequency} files for each pack" |
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261 | |
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262 | # Init loop |
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263 | date_begin_pack=${DateBegin} |
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264 | date_end_simulation=${DateEnd} |
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265 | number_pack=1 |
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266 | |
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267 | IGCM_debug_PrintVariables 3 date_begin_pack |
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268 | IGCM_debug_PrintVariables 3 date_end_simulation |
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269 | |
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270 | while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do |
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271 | |
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272 | IGCM_debug_PrintVariables 3 number_pack |
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273 | DaysTemp=$( IGCM_date_DaysInCurrentPeriod ${date_begin_pack} ${PeriodPack} ) |
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274 | date_end_pack=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} $(( ${DaysTemp} - 1 )) ) |
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275 | |
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276 | for comp in ${config_ListOfComponents[*]} ; do |
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277 | dirList=$( find ${R_BUFR}/${comp}/Output -maxdepth 1 -mindepth 1 -type d ) |
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278 | for dir in ${dirList} ; do |
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279 | # dirID is like ATM.Output.MO |
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280 | dirID=$( echo $dir | sed "s:${R_BUFR}/::" | sed "s:/:.:g" ) |
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281 | # Sort what's in the directory |
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282 | find ${dir} -type f -name "${JobName}*.nc" -ls | sort -k 11 > liste_files.${dirID}.txt |
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283 | # How much file type. Example : 1M_histmthCOSP.nc, 1M_histmth.nc, 1M_histmthNMC.nc, 1M_paramLMDZ_phy.nc |
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284 | # /!\ fileType include the .nc extension /!\ |
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285 | fileType=$( 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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286 | # Loop over the file type and pack them when in between date_begin_pack and date_end_pack |
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287 | for myType in ${fileType} ; do |
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288 | grep ${myType} liste_files.${dirID}.txt > liste_files.${dirID}.${myType}.txt |
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289 | nbfile=0 |
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290 | for file in $( gawk '{print $11}' liste_files.${dirID}.${myType}.txt ); do |
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291 | extract_date_file=$( echo ${file} | sed -e "s/.*${JobName}_[0-9]*_//" ) |
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292 | date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' ) |
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293 | # echo pack n°${number_pack} ${date_file} ${date_begin_pack} ${date_end_pack} |
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294 | if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then |
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295 | echo ${file} >> liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt |
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296 | 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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297 | (( nbfile = nbfile + 1 )) |
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298 | fi |
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299 | done |
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300 | |
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301 | if [ ${nbfile} = 0 ] ; then |
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302 | IGCM_debug_Print 1 "We found no file to process" |
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303 | IGCM_debug_Print 1 "We should have found ${NbPeriodPerFrequency} files" |
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304 | IGCM_debug_Print 1 "As some files can be produced only for some selected period we consider we can move to the next file type" |
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305 | continue |
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306 | fi |
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307 | |
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308 | # Select list of variables to work with |
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309 | list_var=$( cat liste_variables_${myType}_${date_begin_pack}_${date_end_pack}.txt | sort | uniq -c | awk -v nbfile=$nbfile '{if ($1 != nbfile) {print $2}}' | paste -s -d ',' ) |
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310 | liste_file_tmp=$( for i in $( cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ) ; do basename $i ; done ) |
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311 | # Create packed files |
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312 | IGCM_debug_Print 1 "Ncrcat ongoing for ${dir} and ${myType}" |
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313 | if [ ! ${nbfile} = ${NbPeriodPerFrequency} ] ; then |
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314 | IGCM_debug_Print 1 "Number of files to process is not equal to what it should be" |
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315 | IGCM_debug_Print 1 "We found ${nbfile} files and it should have been ${NbPeriodPerFrequency} files" |
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316 | IGCM_debug_Exit "ERROR in number of files to process. STOP HERE INCLUDING THE COMPUTING JOB" |
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317 | IGCM_debug_Verif_Exit |
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318 | fi |
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319 | output=${JobName}_${date_begin_pack}_${date_end_pack}_${myType} |
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320 | #cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs ncrcat -v ${list_var} -o ${output} |
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321 | if [ X${list_var} = X ] ; then |
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322 | IGCM_sys_ncrcat -p ${dir} ${liste_file_tmp} --output ${output} |
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323 | else |
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324 | IGCM_sys_ncrcat -x -v ${list_var} -p ${dir} ${liste_file_tmp} --output ${output} |
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325 | fi |
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326 | # ------------------------------------------------------------------ |
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327 | # Test if all was right before proceeding further |
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328 | # ------------------------------------------------------------------ |
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329 | IGCM_debug_Verif_Exit_Post |
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330 | # Save it |
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331 | IGCM_sys_Put_Out ${output} ${R_SAVE}/$( echo $dir | sed "s:${R_BUFR}/::" )/${output} |
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332 | # Clean file produced by ncrcat |
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333 | IGCM_sys_Rm ${output} |
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334 | # ------------------------------------------------------------------ |
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335 | # Test if all was right before proceeding further |
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336 | # ------------------------------------------------------------------ |
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337 | IGCM_debug_Verif_Exit_Post |
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338 | # Clean files used by ncrcat |
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339 | cat liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt | xargs rm |
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340 | # Save the list of files that has been pack (ncrcat) |
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341 | #mv liste_pack_${myType}_${date_begin_pack}_${date_end_pack}.txt ${STORE_DEBUG} |
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342 | IGCM_debug_Print 1 "Ncrcat and cleaning done for ${dir} and ${myType}" |
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343 | echo |
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344 | done |
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345 | done |
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346 | done |
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347 | (( number_pack = number_pack + 1 )) |
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348 | # Add 1 day to date_end_pack to have the new date_begin_pack |
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349 | date_begin_pack=$( IGCM_date_AddDaysToGregorianDate ${date_end_pack} 1 ) |
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350 | done |
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351 | |
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352 | # Flush post-processing submission |
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353 | if [ -f ${R_BUFR}/FlushPost_${DateEnd}.ksh ] ; then |
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354 | . ${R_BUFR}/FlushPost_${DateEnd}.ksh |
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355 | IGCM_FlushPost |
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356 | #IGCM_sys_Rm -f ${R_BUFR}/FlushPost_${DateEnd}.ksh |
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357 | fi |
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358 | |
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359 | # Clean RUN_DIR_PATH (necessary for cesium and titane only) |
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360 | IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH} |
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361 | |
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362 | date |
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