Changeset 616


Ignore:
Timestamp:
03/29/12 10:56:09 (12 years ago)
Author:
sdipsl
Message:
  • Merge libIGCM_MPI_OpenMP branch within the trunk
  • trunk will shortly be tagged libIGCM_2.0_beta
Location:
trunk/libIGCM
Files:
21 edited

Legend:

Unmodified
Added
Removed

  • trunk/libIGCM/AA_SE_Checker

    r554 r616  
    5757#set -vx 
    5858 
     59#================================== 
    5960# First of all 
     61# 
     62typeset option 
     63 
     64#================================== 
     65# Read UserChoices section:  
    6066IGCM_card_DefineArrayFromSection       ${CARD_DIR}/config.card UserChoices 
    61 typeset option 
     67echo 
     68IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices" 
    6269for option in ${config_UserChoices[*]} ; do 
    6370    IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option} 
     71    eval auxprint=\${config_UserChoices_${option}} 
     72    IGCM_debug_Print 3 "${option} : ${auxprint}" 
    6473done 
    65  
    66 echo 
    67 IGCM_debug_Print 1 "DefineVariableFromOption  : config_UserChoices" 
    68 IGCM_debug_PrintVariables 3 config_UserChoices_JobName 
    69 #IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName 
    70 #IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName 
    71 IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType 
    72 IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin 
    73 IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd 
     74# 
     75echo 
     76 
     77#================================== 
     78# Read Post section:  
     79IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card Post 
     80echo 
     81IGCM_debug_Print 1 "DefineArrayFromOption : config_Post" 
     82 
     83for option in ${config_Post[*]} ; do 
     84  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post ${option} 
     85  eval auxprint=\${config_Post_${option}} 
     86  IGCM_debug_Print 3 "${option} : ${auxprint}" 
     87done 
     88# 
     89echo 
    7490 
    7591DateEnd=$( IGCM_date_ConvertFormatToGregorian ${config_UserChoices_DateEnd} ) 
    … …  
    7995IGCM_date_GetYearMonth ${DateEnd}   YearEnd   MonthEnd 
    8096 
    81 echo 
    8297IGCM_debug_Print 1 "DateBegin for SE_Checker : "${DateBegin} 
    8398IGCM_debug_Print 1 "DateEnd   for SE_Checker : "${DateEnd} 

  • trunk/libIGCM/AA_SaveSourceModifications

    r590 r616  
    3535#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
    3636#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
    37 #-Q- sx9mercure #PBS -l cputim_job=0:10:00   # Limite temps a 1 heures 
     37#-Q- sx9mercure #PBS -l elapstim_req=0:10:00   # Limite temps a 1 heures 
    3838#-Q- sx9mercure #PBS -q scalaire 
    3939#-Q- titane #!/bin/ksh 

  • trunk/libIGCM/AA_additionnal

    r544 r616  
    7979#-Q- sx8mercure #PBS -q scalaire 
    8080#-Q- sx9mercure #!/bin/ksh 
    81 #-Q- sx9mercure ######################### 
    82 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    83 #-Q- sx9mercure ######################### 
    84 #-Q- sx9mercure #MSUB -r ATL_ADD        # Nom du job 
    85 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    86 #-Q- sx9mercure #MSUB -n 2              # Reservation du processus 
    87 #-Q- sx9mercure #MSUB -c 4              # Reservation du core 
    88 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    89 #-Q- sx9mercure #MSUB -E "-j o" 
    90 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     81#-Q- sx9mercure ###################### 
     82#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     83#-Q- sx9mercure ###################### 
     84#-Q- sx9mercure #PBS -N  ATL_ADD            # Nom du job 
     85#-Q- sx9mercure #PBS -j o                   # regroupement des stdout et stderr 
     86#-Q- sx9mercure #PBS -S /usr/bin/ksh        # shell de soumission 
     87#-Q- sx9mercure #PBS -l memsz_job=1gb       # Limite memoire a 1 Go 
     88#-Q- sx9mercure #PBS -l elapstim_req=2:00:00  # Limite temps a 2 heures 
     89#-Q- sx9mercure #PBS -q scalaire 
    9190#-Q- titane #!/bin/ksh 
    9291#-Q- titane ###################### 

  • trunk/libIGCM/AA_atlas_LMDZ

    r591 r616  
    7878#-Q- sx8mercure #PBS -q scalaire 
    7979#-Q- sx9mercure #!/bin/ksh 
    80 #-Q- sx9mercure ######################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    82 #-Q- sx9mercure ######################### 
    83 #-Q- sx9mercure #MSUB -r ATL_LMDZ       # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     80#-Q- sx9mercure ###################### 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     82#-Q- sx9mercure ###################### 
     83#-Q- sx9mercure #PBS -N  ATL_LMDZ           # Nom du job 
     84#-Q- sx9mercure #PBS -j o                   # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh        # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb       # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=2:00:00  # Limite temps a 2 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/AA_atlas_ORCA_LIM

    r591 r616  
    7878#-Q- sx8mercure #PBS -q scalaire 
    7979#-Q- sx9mercure #!/bin/ksh 
    80 #-Q- sx9mercure ######################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    82 #-Q- sx9mercure ######################### 
    83 #-Q- sx9mercure #MSUB -r ATL_OPA        # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     80#-Q- sx9mercure ###################### 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     82#-Q- sx9mercure ###################### 
     83#-Q- sx9mercure #PBS -N  ATL_OPA             # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=2:00:00   # Limite temps a 2 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/AA_atlas_ORCHIDEE

    r591 r616  
    7878#-Q- sx8mercure #PBS -q scalaire 
    7979#-Q- sx9mercure #!/bin/ksh 
    80 #-Q- sx9mercure ######################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    82 #-Q- sx9mercure ######################### 
    83 #-Q- sx9mercure #MSUB -r ATL_ORCH       # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     80#-Q- sx9mercure ###################### 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     82#-Q- sx9mercure ###################### 
     83#-Q- sx9mercure #PBS -N  ATL_ORCH            # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=1:00:00   # Limite temps a 2 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/AA_atlas_PISCES

    r591 r616  
    7878#-Q- sx8mercure #PBS -q scalaire 
    7979#-Q- sx9mercure #!/bin/ksh 
    80 #-Q- sx9mercure ######################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    82 #-Q- sx9mercure ######################### 
    83 #-Q- sx9mercure #MSUB -r ATL_PIS        # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     80#-Q- sx9mercure ###################### 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     82#-Q- sx9mercure ###################### 
     83#-Q- sx9mercure #PBS -N  ATL_PIS             # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=2:00:00   # Limite temps a 2 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/AA_create_multi_se

    r590 r616  
    7878#-Q- sx8mercure #PBS -q scalaire 
    7979#-Q- sx9mercure #!/bin/ksh 
    80 #-Q- sx9mercure ######################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    82 #-Q- sx9mercure ######################### 
    83 #-Q- sx9mercure #MSUB -r MULTISE             # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     80#-Q- sx9mercure ###################### 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     82#-Q- sx9mercure ###################### 
     83#-Q- sx9mercure #PBS -N MULTISE                   # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=1:00:00   # Limite temps a 1 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/AA_create_se

    r590 r616  
    7878#-Q- sx8mercure #PBS -q scalaire 
    7979#-Q- sx9mercure #!/bin/ksh 
    80 #-Q- sx9mercure ######################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    82 #-Q- sx9mercure ######################### 
    83 #-Q- sx9mercure #MSUB -r SE             # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     80#-Q- sx9mercure ###################### 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     82#-Q- sx9mercure ###################### 
     83#-Q- sx9mercure #PBS -N SE                   # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=1:00:00   # Limite temps a 1 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 
    … …  
    217217fi 
    218218 
    219 # 
     219#================================== 
    220220# First of all 
    221221# 
    222 IGCM_card_DefineArrayFromSection   ${CARD_DIR}/config.card UserChoices 
    223222typeset option 
     223 
     224#================================== 
     225# Read UserChoices section:  
     226IGCM_card_DefineArrayFromSection       ${CARD_DIR}/config.card UserChoices 
     227echo 
     228IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices" 
    224229for option in ${config_UserChoices[*]} ; do 
    225230    IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option} 
     231    eval auxprint=\${config_UserChoices_${option}} 
     232    IGCM_debug_Print 3 "${option} : ${auxprint}" 
    226233done 
    227234# 
    228235echo 
    229 IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices" 
    230 IGCM_debug_PrintVariables 3 config_UserChoices_JobName 
    231 IGCM_debug_PrintVariables 3 config_UserChoices_LongName 
    232 IGCM_debug_PrintVariables 3 config_UserChoices_TagName 
    233 IGCM_debug_PrintVariables 3 config_UserChoices_SpaceName 
    234 IGCM_debug_PrintVariables 3 config_UserChoices_ExperimentName 
    235 IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType 
    236 IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin 
    237 IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd 
    238 IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength 
     236 
     237#================================== 
     238# Read Post section:  
     239IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card Post 
    239240echo 
     241IGCM_debug_Print 1 "DefineArrayFromOption : config_Post" 
     242for option in ${config_Post[*]} ; do 
     243  IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card Post ${option} 
     244  eval auxprint=\${config_Post_${option}} 
     245  IGCM_debug_Print 3 "${option} : ${auxprint}" 
     246done 
     247# 
     248echo 
     249 
     250#================================== 
     251# Define default value to keep compatibility with previous card: means before changes due to TGCC  
     252[ X${config_Post_PackFrequency} = X ] && config_Post_PackFrequency=${config_Post_RebuildFrequency} 
     253 
     254#================================== 
     255# If pack is active then PackFrequency overule the config_UserChoices_PeriodLength 
     256if ( [ ! X${config_Post_PackFrequency} = X${NULL_STR} ] && [ ! X${config_Post_PackFrequency} = XNONE ] ) ; then 
     257  config_UserChoices_PeriodLength=${config_Post_PackFrequency} 
     258fi 
    240259 
    241260#================================== 

  • trunk/libIGCM/AA_create_ts

    r591 r616  
    7878#-Q- sx8mercure #PBS -q scalaire 
    7979#-Q- sx9mercure #!/bin/ksh 
    80 #-Q- sx9mercure ######################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    82 #-Q- sx9mercure ######################### 
    83 #-Q- sx9mercure #MSUB -r TS             # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     80#-Q- sx9mercure ###################### 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     82#-Q- sx9mercure ###################### 
     83#-Q- sx9mercure #PBS -N TS                   # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=24:00:00   # Limite temps a 2 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 
    … …  
    815815                        IGCM_sys_ncks -Oh -x -v ${var} ${file_out} ${file_out_YE%%.nc}_tmp1.nc 
    816816                        # This will remove the time axis because cdo rewrites severely with only considered useful variables 
    817                         IGCM_sys_cdo -mulc,1 ${file_out_YE%%.nc}_tmp1.nc ${file_out_YE%%.nc}_tmp2.nc 
     817                        IGCM_sys_cdo -mulc,1 ${file_out_YE%%.nc}_tmp1.nc ${file_out_YE%%.nc}_tmp2.nc 2>/dev/null 
    818818                        if [ $? -eq 0 ] ; then 
    819819                                # Now append all ancillary variables if previous cdo operator ok 

  • trunk/libIGCM/AA_monitoring

    r591 r616  
    7878#-Q- sx8mercure #PBS -q scalaire 
    7979#-Q- sx9mercure #!/bin/ksh 
    80 #-Q- sx9mercure ######################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
    82 #-Q- sx9mercure ######################### 
    83 #-Q- sx9mercure #MSUB -r MONITORING     # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     80#-Q- sx9mercure ###################### 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
     82#-Q- sx9mercure ###################### 
     83#-Q- sx9mercure #PBS -N  MONITORING          # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=1:00:00   # Limite temps a 2 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/AA_pack_debug

    r590 r616  
    7979#-Q- sx9mercure #!/bin/ksh 
    8080#-Q- sx9mercure ###################### 
    81 #-Q- sx9mercure ## CESIUM   CEA ## 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
    8282#-Q- sx9mercure ###################### 
    83 #-Q- sx9mercure #MSUB -r PACKDEBUG    # Nom du job 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     83#-Q- sx9mercure #PBS -N PACKDEBUG          # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 
    … …  
    220220else 
    221221    CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} ) 
     222    # warning! we copy useless files : Job_xxx, Script_output_xxx, .... 
    222223    IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH} 
    223224fi 
    … …  
    276277# Clear txt file lists 
    277278rm -f ${RUN_DIR}/liste_debug_files.txt 
     279rm -f ${RUN_DIR}/liste_out_files.txt 
    278280rm -f ${RUN_DIR}/new_liste_debug_files.txt 
    279281rm -f ${RUN_DIR}/liste_pack_*.txt 
    … …  
    282284find ${R_BUFR}/*/Debug -type f | sort >> ${RUN_DIR}/liste_debug_files.txt 
    283285 
    284 # Rename debug files we will work with using symlinks 
     286# Rename debug files we will work with using symlinks. use ???_ prefix ie NF-2 
    285287#gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("cp --preserve " $0 " "dest_name)}' ${RUN_DIR}/liste_debug_files.txt 
    286288gawk -F/ '{dest_name=$(NF-2)("_") $(NF); system("ln -s " $0 " "dest_name)}' ${RUN_DIR}/liste_debug_files.txt 
    287289 
    288 # List renamed debug files 
    289 find ${RUN_DIR} -name "???_*${JobName}*" -ls | sort -k 11 > ${RUN_DIR}/new_liste_debug_files.txt 
     290# Add out_ : output of execution files 
     291find ${R_BUFR}/Out -type f -name '*out_*' | sort >> ${RUN_DIR}/liste_out_files.txt 
     292 
     293# Rename out files we will work with using symlinks. use Out_ prefix ie NF-1 
     294gawk -F/ '{dest_name=$(NF-1)("_") $(NF); system("ln -s " $0 " "dest_name)}' ${RUN_DIR}/liste_out_files.txt 
     295 
     296# List renamed debug files. Exclude Job_xxx files. 
     297find ${RUN_DIR} -name "???_*${JobName}*" -ls | grep -v Job_ | sort -k 11 > ${RUN_DIR}/new_liste_debug_files.txt 
    290298 
    291299# ------------------------------------------------------------------ 

  • trunk/libIGCM/AA_pack_output

    r590 r616  
    7979#-Q- sx9mercure #!/bin/ksh 
    8080#-Q- sx9mercure ###################### 
    81 #-Q- sx9mercure ## CESIUM   CEA ## 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
    8282#-Q- sx9mercure ###################### 
    83 #-Q- sx9mercure #MSUB -r PACKOUTPUT    # Nom du job 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     83#-Q- sx9mercure #PBS -N PACKOUTPUT          # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/AA_pack_restart

    r590 r616  
    7979#-Q- sx9mercure #!/bin/ksh 
    8080#-Q- sx9mercure ###################### 
    81 #-Q- sx9mercure ## CESIUM   CEA ## 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
    8282#-Q- sx9mercure ###################### 
    83 #-Q- sx9mercure #MSUB -r PACKRESTART    # Nom du job 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     83#-Q- sx9mercure #PBS -N PACKRESTART          # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 
    … …  
    303303IGCM_debug_PrintVariables 3 date_end_simulation 
    304304 
     305# last restart of the previous period : to be deleted 
     306typeset date_end_previous 
     307date_end_previous=$( IGCM_date_AddDaysToGregorianDate ${date_begin_pack} -1 ) 
     308 
    305309while [ ${date_begin_pack} -le ${date_end_simulation} ] ; do 
    306310 
    … …  
    313317    extract_date_file=$( echo ${file}  | sed -e "s/.*${JobName}_//" ) 
    314318    date_file=$( echo ${extract_date_file} | sed 's/\([0-9]\{8\}\)_.*$/\1/g' ) 
    315 #   echo pack n°${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack} 
     319#   warning demenagement. delete last restart of the previous pack 
     320    [  ${date_file} -eq ${date_end_previous} ] && echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${number_pack}.txt 
     321#   echo pack number ${number_pack}  ${date_file} ${date_begin_pack} ${date_end_pack} 
    316322    if [ ${date_file} -le ${date_end_pack} ] && [ ${date_file} -ge ${date_begin_pack} ] ; then 
    317323      echo $( basename ${file} ) >> ${RUN_DIR}/liste_pack_${number_pack}.txt 
    318       echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${number_pack}.txt 
     324#   warning demenagement. do not delete last restart of this pack 
     325      [ ${date_file} -eq ${date_end_pack} ] || echo $( readlink ${file} ) >> ${RUN_DIR}/liste_remove_pack_${number_pack}.txt 
    319326#   Will not work. Need to find a better ordering. 
    320327#   elif [ ${date_file} -ge ${date_end_pack} ] ; then 

  • trunk/libIGCM/AA_rebuild_fromArchive

    r590 r616  
    7979#-Q- sx9mercure #!/bin/ksh 
    8080#-Q- sx9mercure ###################### 
    81 #-Q- sx9mercure ## CESIUM FOR SX9  CEA ## 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
    8282#-Q- sx9mercure ###################### 
    83 #-Q- sx9mercure #MSUB -r REBUILDARCH    # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     83#-Q- sx9mercure #PBS -N REBUILDARCH          # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/AA_rebuild_fromWorkdir

    r590 r616  
    7979#-Q- sx9mercure #!/bin/ksh 
    8080#-Q- sx9mercure ###################### 
    81 #-Q- sx9mercure ## CESIUM   CEA ## 
     81#-Q- sx9mercure ## SX9MERCURE  CCRT ## 
    8282#-Q- sx9mercure ###################### 
    83 #-Q- sx9mercure #MSUB -r REBUILDWRK     # Nom du job                 
    84 #-Q- sx9mercure #MSUB -N 1              # Reservation du noeud 
    85 #-Q- sx9mercure #MSUB -n 1              # Reservation du processus 
    86 #-Q- sx9mercure #MSUB -T 86400          # Limite de temps elapsed du job 
    87 #-Q- sx9mercure #MSUB -E "-j o" 
    88 #-Q- sx9mercure #MSUB -E "-S /bin/ksh" 
     83#-Q- sx9mercure #PBS -N REBUILDWRK           # Nom du job 
     84#-Q- sx9mercure #PBS -j o                    # regroupement des stdout et stderr 
     85#-Q- sx9mercure #PBS -S /usr/bin/ksh         # shell de soumission 
     86#-Q- sx9mercure #PBS -l memsz_job=1gb        # Limite memoire a 1 Go 
     87#-Q- sx9mercure #PBS -l elapstim_req=24:00:00  # Limite temps a 1 heures 
     88#-Q- sx9mercure #PBS -q scalaire 
    8989#-Q- titane #!/bin/ksh 
    9090#-Q- titane ###################### 

  • trunk/libIGCM/libIGCM_config/libIGCM_config.ksh

    r591 r616  
    603603  fi 
    604604 
     605  typeset ExeNameIn ExeNameFirst CompNameFirst 
     606  typeset comp i 
     607  typeset tempvar tempvarMPI tempvarNOD NbElts j NbExec 
     608 
     609  (( PROCESSUS_NUMBER = 0 )) 
     610  (( i=0 )) 
     611  (( NbExec=0 )) 
     612 
     613  OK_PARA_MPI=false 
     614  OK_PARA_OMP=false 
     615  OK_PARA_NOD=false 
     616  OK_PARA_MPMD=false 
     617 
     618  for comp in ${config_ListOfComponents[*]} ; do 
     619 
     620    IGCM_debug_Print 1 ${comp} 
     621 
     622    eval ExeNameIn=\${config_Executable_${comp}[0]} 
     623 
     624    # NO order in config.card for parallelized values !  
     625    # just use suffix : MPI , OMP and NOD (for number of NODes.) 
     626 
     627    # NOD is the number of NODes allocated 
     628    eval ${comp}_PROC_NOD=0 
     629 
     630    # MPI is the number of MPI processus per nodes 
     631    eval ${comp}_PROC_MPI=0 
     632 
     633    # OMP is the number of OpenMP threads per MPI processus 
     634    eval ${comp}_PROC_OMP=0 
     635         
     636    # Only if we really have an executable for the component : 
     637    if [ X${ExeNameIn} != X\"\" ] ; then 
     638 
     639      # Keep the first executable found and the first CompName 
     640      ExeNameFirst=${ExeNameIn} 
     641      CompNameFirst=${comp} 
     642 
     643      # Are we a second executable? 
     644      (( NbExec = NbExec + 1 )) 
     645 
     646      # set 1 MPI task, 1 OpenMP thread and 1 node as default 
     647      eval ${comp}_PROC_MPI=1 
     648      eval ${comp}_PROC_OMP=1 
     649      eval ${comp}_PROC_NOD=1 
     650 
     651      eval NbElts=\${#config_Executable_${comp}[@]} 
     652 
     653      if [ ${NbElts} -ge 2 ] ; then 
     654        (( j = 2 )) 
     655 
     656        while [ $j -lt ${NbElts} ] ; do  
     657          eval tempvar=\${config_Executable_${comp}[${j}]} 
     658 
     659          if [ X${tempvar} = X ] ; then 
     660            echo "Error reading MPI/OMP parameters !!!"  
     661            echo "Check your config.card."  
     662            exit 1 
     663          fi 
     664 
     665          eval IGCM_debug_Print 2 ${tempvar} 
     666 
     667          case ${tempvar} in 
     668            *[mM][pP][iI]*) 
     669               # Read MPI parameter for composante 
     670               eval ${comp}_PROC_MPI=$( echo ${tempvar} | tr '[a-z]' '[A-Z]' | sed -e "s/MPI//" ) 
     671               OK_PARA_MPI=true;; 
     672            *[oO][mM][pP]*) 
     673               # Read OMP parameter for composante 
     674               eval ${comp}_PROC_OMP=$( echo ${tempvar} | tr '[a-z]' '[A-Z]' | sed -e "s/OMP//" ) 
     675               OK_PARA_OMP=true;; 
     676            *[nN][oO][dD]*) 
     677               # Read NOD (NumBer of Nodes) parameter for composante 
     678               eval ${comp}_PROC_NOD=$( echo ${tempvar} | tr '[a-z]' '[A-Z]' | sed -e "s/NOD//" ) 
     679               OK_PARA_NOD=true 
     680               OK_PARA_MPI=true;; 
     681          esac 
     682 
     683          (( j = j + 1 )) 
     684        done 
     685 
     686      fi 
     687 
     688      eval tempvarMPI=\${${comp}_PROC_MPI} 
     689      eval tempvarNOD=\${${comp}_PROC_NOD} 
     690      eval tempvarOMP=\${${comp}_PROC_OMP} 
     691 
     692      (( PROCESSUS_NUMBER = PROCESSUS_NUMBER + tempvarMPI * tempvarNOD * tempvarOMP )) 
     693 
     694    fi 
     695 
     696    (( i=i+1 )) 
     697  done 
     698 
     699  # set MPMD mode if more than 2 executable names. 
     700  [ ${NbExec} -ge 2 ] && OK_PARA_MPMD=true 
     701 
     702  # Verification of BATCH_NUM_PROC_TOT total number of processors set in job header. 
     703  if [ X${BATCH_NUM_PROC_TOT} != X ] ; then 
     704    # BATCH_NUM_PROC_TOT is set 
     705    if ( ${OK_PARA_MPI} ) ; then 
     706      IGCM_debug_Print 1 "MPI/OMP/NOD found into config.card and BATCH_NUM_PROC_TOT = ${BATCH_NUM_PROC_TOT} " 
     707    else 
     708      # with previous method. 
     709      if [ ${BATCH_NUM_PROC_TOT} -gt 1 ] ; then 
     710        # with more than 1 proc 
     711        if ( ${OK_PARA_MPMD} ) ; then 
     712          # with MPMD ie CPL/oasis method 
     713          echo "We will use default number of MPI tasks for this machine : " 
     714          echo "${DEFAULT_NUM_PROC_OCE} for OCE; " 
     715          echo "${DEFAULT_NUM_PROC_CPL} for CPL; " 
     716          echo "${DEFAULT_NUM_PROC_ATM} for ATM; " 
     717          echo "${DEFAULT_NUM_PROC_TOTAL} for the total number of processors; " 
     718          OK_PARA_MPI=true 
     719          CPL_PROC_MPI=${DEFAULT_NUM_PROC_CPL} 
     720          OCE_PROC_MPI=${DEFAULT_NUM_PROC_OCE} 
     721          ATM_PROC_MPI=${DEFAULT_NUM_PROC_ATM} 
     722          NUM_PROC_CPL=${DEFAULT_NUM_PROC_CPL} # for backward compatibility 
     723          NUM_PROC_OCE=${DEFAULT_NUM_PROC_OCE} # for backward compatibility 
     724          NUM_PROC_ATM=${DEFAULT_NUM_PROC_ATM} # for backward compatibility 
     725          PROCESSUS_NUMBER=${DEFAULT_NUM_PROC_TOTAL} 
     726        else 
     727          # with have only one executable 
     728          echo "We will use ${BATCH_NUM_PROC_TOT} MPI tasks for ${CompNameFirst} : ${config_Executable_Name} " 
     729          OK_PARA_MPI=true 
     730          eval ${CompNameFirst}_PROC_MPI=${BATCH_NUM_PROC_TOT} 
     731          PROCESSUS_NUMBER=${BATCH_NUM_PROC_TOT} 
     732        fi 
     733      else  
     734        PROCESSUS_NUMBER=1 
     735      fi 
     736    fi 
     737    # Verification with PBS parameter 
     738    if [ ${BATCH_NUM_PROC_TOT} -ne ${PROCESSUS_NUMBER} ] ; then 
     739      echo "Warning with parallelization parameters !" 
     740      echo "Job header variable BATCH_NUM_PROC_TOT = ${BATCH_NUM_PROC_TOT} " 
     741      echo "is the total number of _processors_ reserved." 
     742      echo "It is not equal to the sum of _processus_  = ${PROCESSUS_NUMBER}." 
     743      echo "We stop now." 
     744      exit 1 
     745    fi 
     746  else # BATCH_NUM_PROC_TOT="" 
     747    if ( ${OK_PARA_MPI} ) ; then 
     748      echo "You have not given a value of ${BATCH_NUM_PROC_TOT} processors," 
     749      echo "but you have filled the parallel parameter in config->Executable->list." 
     750      echo "Please add BATCH_NUM_PROC_TOT variable in job header." 
     751      echo "We stop now." 
     752      exit 1 
     753    else 
     754      # sequential case ! 
     755      if [ ${PROCESSUS_NUMBER} -eq 0 ] ; then 
     756        (( PROCESSUS_NUMBER = 1 )) 
     757        echo "PROCESSUS_NUMBER is all 0 (sequential use of old definition in config->Executable->list)." 
     758        echo "We set it to 1." 
     759      fi 
     760    fi 
     761  fi 
     762 
     763  IGCM_debug_Print 1 "MPI/OMP treatment PROCESSUS_NUMBER = ${PROCESSUS_NUMBER}" 
     764 
     765  IGCM_sys_build_execution_scripts 
     766 
    605767  ExecutionFail=false 
    606768 

  • trunk/libIGCM/libIGCM_sys/libIGCM_sys.ksh

    r449 r616  
    3434    echo "====================================================" 
    3535fi 
     36 
     37#==================================================== 
     38#- set PackDefault false by default 
     39PackDefault=false  
    3640 
    3741case $( hostname -s ) in 

  • trunk/libIGCM/libIGCM_sys/libIGCM_sys_mercure.ksh

    r615 r616  
    135135#==================================================== 
    136136#- RUN_DIR_PATH : Temporary working directory (=> TMP) 
    137 #typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${CSCRATCHDIR}/TMPDIR_IGCM/${JOBID}} 
    138137typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${TMPDIR}} 
    139138 
    … …  
    721720#D-* Purpose: rm tmpdir (dummy function most of the time batch 
    722721#D-                      scheduler will do the job) 
     722#D-           Dummy function on mercure front-end 
    723723#D-* Examples: 
    724724#D- 
    725725function IGCM_sys_RmRunDir { 
    726   IGCM_debug_PushStack "IGCM_sys_RmRunDir" -- $@ 
    727   if ( $DEBUG_sys ) ; then 
    728     echo "IGCM_sys_RmRunDir :" $@ 
    729   fi 
    730  
    731   typeset RET 
    732  
    733   echo rm $@ > out_rsync 2>&1 
    734   \rm $@ >> out_rsync 2>&1 
    735   RET=$? 
    736  
    737   if [ ${RET} -gt 0 ] ; then 
    738     echo "IGCM_sys_RmRunDir : error." 
    739     cat out_rsync 
    740     IGCM_debug_Exit "IGCM_sys_RmRunDir" 
    741   else 
    742     \rm out_rsync 
    743   fi 
    744   IGCM_debug_PopStack "IGCM_sys_RmRunDir" 
     726    IGCM_debug_PushStack "IGCM_sys_RmRunDir" -- $@ 
     727    if ( $DEBUG_sys ) ; then 
     728        echo "IGCM_sys_RmRunDir :" $@ 
     729        echo "Dummy call, let the scheduler do that." 
     730    fi 
     731    IGCM_debug_PopStack "IGCM_sys_RmRunDir" 
    745732} 
    746733 

  • trunk/libIGCM/libIGCM_sys/libIGCM_sys_mercurex9.ksh

    r587 r616  
    170170#- Max number of arguments passed to nco operator or demigration command 
    171171UNIX_MAX_LIMIT=360 
     172 
     173#==================================================== 
     174#- set PackDefault true on NEC SX9 
     175PackDefault=true 
     176 
     177#==================================================== 
     178#- Default number of MPI task for IPSL coupled model 
     179#- required for backward compatibility 
     180#- 
     181DEFAULT_NUM_PROC_OCE=1 
     182DEFAULT_NUM_PROC_CPL=1 
     183(( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - 1 )) 
     184DEFAULT_NUM_PROC_TOTAL=${BATCH_NUM_PROC_TOT} 
    172185 
    173186#D-#================================================== 
    … …  
    285298  Job ended   : ${DateEnd} 
    286299  Output files are available in ${R_SAVE} 
     300  Files to be rebuild are temporarily available in ${REBUILD_DIR} 
     301  Pre-packed files are temporarily available in ${R_BUFR} 
    287302  Script files, Script Outputs and Debug files (if necessary) are available in ${SUBMIT_DIR} 
    288303END_MAIL 

  • trunk/libIGCM/libIGCM_sys/libIGCM_sys_titane.ksh

    r591 r616  
    188188#- Max number of arguments passed to nco operator or demigration command 
    189189UNIX_MAX_LIMIT=360 
     190 
     191#==================================================== 
     192#- set PackDefault true on titane 
     193PackDefault=true 
     194 
     195NUM_COREPERNODE=8 
     196         
     197#==================================================== 
     198#- Default number of MPI task for IPSL coupled model 
     199#- required for backward compatibility 
     200#- 
     201DEFAULT_NUM_PROC_OCE=5 
     202DEFAULT_NUM_PROC_CPL=1 
     203DEFAULT_NUM_PROC_ATM=26 
     204DEFAULT_NUM_PROC_TOTAL=32 
    190205 
    191206#D-#================================================== 
    … …  
    334349  Job ended   : ${DateEnd} 
    335350  Output files are available in ${R_SAVE} 
     351  Files to be rebuild are temporarily available in ${REBUILD_DIR} 
     352  Pre-packed files are temporarily available in ${R_BUFR} 
    336353  Script files, Script Outputs and Debug files (if necessary) are available in ${SUBMIT_DIR} 
    337354END_MAIL 
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