1 | #!/bin/ksh |
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2 | |
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3 | #************************************************************** |
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4 | # Author: Sebastien Denvil, Martial Mancip, Arnaud Caubel |
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5 | # Contact: Arnaud.Caubel__at__lsce.ipsl.fr |
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6 | # $Revision:: $ Revision of last commit |
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7 | # $Author:: $ Author of last commit |
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8 | # $Date:: $ Date of last commit |
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9 | # IPSL (2006) |
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10 | # This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC |
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11 | # |
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12 | #************************************************************** |
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13 | |
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14 | #========================================================= |
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15 | # The documentation of this file can be automatically generated |
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16 | # if you use the prefix #D- for comments to be extracted. |
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17 | # Extract with command: cat lib* | grep "^#D-" | cut -c "4-" |
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18 | #========================================================= |
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19 | |
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20 | #D-#================================================== |
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21 | #D-LibIGCM_sys for Jean-Zay |
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22 | #D-#================================================== |
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23 | #D- |
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24 | #D- This ksh library if a layer under some usefull |
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25 | #D-environment variables and shell commands. |
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26 | #D-All those definitions depend on host particularities. |
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27 | #D-It manages a stack mechanism and test validity of operations. |
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28 | #D-All function described bellow must be prefixed by IGCM_sys. |
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29 | |
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30 | #==================================================== |
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31 | # libIGCM_sys PARAMETERS |
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32 | #==================================================== |
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33 | |
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34 | #==================================================== |
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35 | # set DEBUG_sys to true to output calls of function |
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36 | typeset -r DEBUG_sys=${DEBUG_sys:=true} |
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37 | |
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38 | #==================================================== |
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39 | # Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get) |
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40 | typeset -r DRYRUN=${DRYRUN:=0} |
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41 | |
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42 | # YOU MUST COMPILE YOUR EXE FILES FOR DRYRUN MODE ! |
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43 | # ------------------------------------------------------------------------------------- |
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44 | # | DRYRUN= | Date computations, | sys_Get | Exe | sys_Put_Out; sys_Put_Rest | |
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45 | # | | Cp/Exe/param/files | | | | |
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46 | # | | Chmod Qsub | | | | |
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47 | # ------------------------------------------------------------------------------------- |
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48 | # | 0 | yes | yes | yes | yes | |
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49 | # ------------------------------------------------------------------------------------- |
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50 | # | 1 | yes | yes | yes | no | |
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51 | # ------------------------------------------------------------------------------------- |
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52 | # | 2 | yes | yes | no | no | |
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53 | # ------------------------------------------------------------------------------------- |
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54 | # | 3 | yes | no | no | no | |
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55 | # ------------------------------------------------------------------------------------- |
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56 | |
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57 | #===================================================== |
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58 | # Global Variables : |
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59 | #===================================================== |
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60 | # Language : "fr" or "en" |
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61 | typeset -r MYLANG="fr" |
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62 | |
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63 | #===================================================== |
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64 | # Host user names project maxCpuTime |
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65 | # $hostname ou hostname |
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66 | typeset HOST=${HOST:=$( hostname )} |
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67 | # $username ou whoami |
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68 | typeset LOGIN=${LOGIN:=$( whoami )} |
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69 | # $hostname of the MASTER job |
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70 | typeset MASTER=jeanzay |
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71 | # add default project set by ins_job |
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72 | typeset PROJECT=$( echo ${SLURM_JOB_ACCOUNT:=::default_project::} | cut -c "1-3" ) |
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73 | ### jobWarningDelay in seconds |
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74 | ##typeset jobWarningDelay=${BRIDGE_MSUB_MAXTIME} |
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75 | |
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76 | #D- |
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77 | #D-#================================================== |
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78 | #D-Program used in libIGCM |
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79 | #D-#================================================== |
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80 | |
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81 | # Submit command |
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82 | typeset SUBMIT=${SUBMIT:=sbatch} |
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83 | # rsync with path |
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84 | typeset -r RSYNC=/usr/bin/rsync |
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85 | # RSYNC_opt args to rsync |
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86 | typeset -r RSYNC_opt="-va" |
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87 | # ie storage filesystem |
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88 | typeset -r STOREHOST=${MASTER} |
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89 | typeset -r REMOTE_RSYNC=/usr/bin/rsync |
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90 | |
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91 | #==================================================== |
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92 | # Access to module command |
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93 | #==================================================== |
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94 | . /usr/share/Modules/init/ksh |
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95 | |
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96 | #==================================================== |
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97 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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98 | #==================================================== |
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99 | if [ X${TaskType} = Xcomputing ] ; then |
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100 | IGCM_debug_Print 1 "Modules will be loaded later in IGCM_sys_activ_variables." |
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101 | else |
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102 | module purge > /dev/null 2>&1 |
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103 | . /gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_jeanzay > /dev/null 2>&1 |
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104 | |
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105 | . /gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_atlas_jeanzay > /dev/null 2>&1 |
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106 | |
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107 | # export PCMDI_MP=/ccc/work/cont003/igcmg/igcmg/PCMDI-MP |
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108 | export UVCDAT_ANONYMOUS_LOG=FALSE |
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109 | fi |
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110 | |
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111 | # FYI |
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112 | [ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:" |
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113 | [ ! X${TaskType} = Xchecking ] && module list |
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114 | |
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115 | # For AddNoise (not yet AddPertu3DOCE) |
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116 | export PATH=${PATH}:/gpfswork/rech/psl/commun/Tools/AddNoise/bin |
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117 | |
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118 | # For rebuild |
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119 | export PATH=${PATH}:/gpfswork/rech/psl/commun/Tools/rebuild/modipsl_IOIPSL_PLUS_v2_2_4/bin |
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120 | |
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121 | #==================================================== |
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122 | # Host specific DIRECTORIES |
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123 | #==================================================== |
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124 | |
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125 | #==================================================== |
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126 | #- MirrorlibIGCM for frontend |
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127 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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128 | |
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129 | #==================================================== |
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130 | #- libIGCM_POST for frontend |
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131 | typeset -r libIGCM_POST=${libIGCM} |
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132 | |
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133 | #==================================================== |
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134 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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135 | typeset -r R_EXE="${MODIPSL}/bin" |
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136 | |
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137 | #==================================================== |
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138 | #- SUBMIT_DIR : submission dir |
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139 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${SLURM_SUBMIT_DIR}} |
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140 | |
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141 | #==================================================== |
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142 | #- IN |
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143 | typeset -r R_IN=${R_IN:=/gpfswork/rech/psl/commun/IGCM} |
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144 | |
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145 | #==================================================== |
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146 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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147 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${SCRATCH}/RUN_DIR/${SLURM_JOBID}_${$}} |
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148 | |
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149 | #==================================================== |
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150 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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151 | typeset -r OUTCOMMAND_PATH=/tmp |
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152 | |
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153 | #==================================================== |
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154 | #- HOST_MPIRUN_COMMAND |
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155 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time srun "} |
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156 | |
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157 | #==================================================== |
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158 | #- Max number of arguments passed to nco operator or demigration command |
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159 | UNIX_MAX_LIMIT=360 |
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160 | |
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161 | #==================================================== |
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162 | #- set PackDefault to true |
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163 | PackDefault=true |
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164 | |
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165 | #==================================================== |
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166 | #- Default number of MPI task for IPSL coupled model |
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167 | #- required for backward compatibility |
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168 | #- |
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169 | DEFAULT_NUM_PROC_OCE=5 |
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170 | DEFAULT_NUM_PROC_CPL=1 |
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171 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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172 | |
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173 | #==================================================== |
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174 | #- Number of computing cores per node |
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175 | #- |
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176 | NB_CORE_PER_NODE=40 |
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177 | |
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178 | #D-#================================================== |
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179 | #D-function IGCM_sys_defineArchives |
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180 | #D-* Purpose: |
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181 | #D-* Load dfldatadir module : According to project used for submission (default) or set in config.card (optional) |
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182 | #D-* Define ARCHIVE : Dedicated to large files |
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183 | #D-* Define STORAGE : Dedicated to small/medium files |
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184 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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185 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monsitoring and atlas, and/or small files) |
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186 | #D-* Define R_BUF : Output tree located on SCRATCH hosting files waiting for rebuild or pack processes |
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187 | #D-* if SpaceName=TEST everything is stored on SCRATCH |
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188 | #D-* Examples: |
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189 | #D- |
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190 | function IGCM_sys_defineArchives { |
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191 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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192 | |
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193 | # Load dfldatadir depending on the project used for submission (default) or set in config.card (optional) |
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194 | if [ X${config_UserChoices_DataProject} = X ] || [ X${config_UserChoices_DataProject} = DEFAULT ]; then |
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195 | # The variable DataProject is not set in in section UserChoices in config.card or it is set to DEFAULT |
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196 | # Default option: Change IDRPROJ according to the project used for submission |
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197 | |
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198 | # jg following line does not work in a submitted job: |
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199 | eval $(idrenv -d ${PROJECT}) |
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200 | else |
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201 | # Use the project set by the variable DataProject in section UserChoices in config.card |
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202 | eval $(idrenv -d ${config_UserChoices_DataProject}) |
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203 | IGCM_debug_Print 1 "Change DataProject red in config.card : ${config_UserChoices_DataProject}" |
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204 | fi |
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205 | IGCM_debug_Print 1 "Data project for output to be used: ${IDRPROJ}" |
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206 | |
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207 | #==================================================== |
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208 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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209 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${SCRATCH}/RUN_DIR/${SLURM_JOBID}_${$}} |
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210 | |
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211 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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212 | #==================================================== |
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213 | #- ARCHIVE (dedicated to large files) |
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214 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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215 | else |
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216 | #==================================================== |
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217 | #- ARCHIVE (dedicated to large files) |
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218 | ARCHIVE=${STORE} |
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219 | fi |
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220 | |
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221 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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222 | #==================================================== |
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223 | #- STORAGE (dedicated to small/medium files) |
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224 | STORAGE=${config_UserChoices_STORAGE} |
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225 | else |
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226 | #==================================================== |
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227 | #- STORAGE (dedicated to small/medium files) |
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228 | STORAGE=${WORK} |
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229 | fi |
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230 | |
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231 | if [ X${config_UserChoices_SpaceName} = XTEST ]; then |
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232 | #==================================================== |
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233 | #- R_OUT |
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234 | R_OUT=${SCRATCH}/IGCM_OUT |
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235 | |
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236 | #==================================================== |
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237 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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238 | R_FIG=${SCRATCH}/IGCM_OUT |
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239 | |
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240 | IGCM_debug_Print 1 "SpaceName=TEST ==> OVERRULE destination path directories" |
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241 | |
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242 | else |
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243 | #==================================================== |
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244 | #- R_OUT |
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245 | R_OUT=${ARCHIVE}/IGCM_OUT |
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246 | |
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247 | #==================================================== |
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248 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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249 | R_FIG=${STORAGE}/IGCM_OUT |
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250 | fi |
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251 | |
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252 | #==================================================== |
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253 | #- CMIP6 (hosting CMIP6 files produced by XIOS2 and configured by dr2xml) |
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254 | CMIP6_BUF=${STORAGE}/IGCM_OUT |
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255 | |
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256 | #==================================================== |
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257 | #- R_BUF (ONLY FOR double copy an scratch) |
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258 | R_BUF=${SCRATCH}/IGCM_OUT |
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259 | |
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260 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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261 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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262 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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263 | |
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264 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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265 | } |
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266 | |
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267 | #D-#================================================== |
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268 | #D-function IGCM_sys_RshArchive |
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269 | #D-* Purpose: Archive rsh command |
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270 | #D-* Examples: |
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271 | #D- |
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272 | function IGCM_sys_RshArchive { |
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273 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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274 | /bin/ksh <<-EOF |
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275 | ${@} |
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276 | EOF |
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277 | status=$? |
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278 | if [ ${status} -gt 0 ] ; then |
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279 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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280 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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281 | fi |
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282 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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283 | } |
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284 | |
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285 | #D-#================================================== |
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286 | #D-function IGCM_sys_RshArchive_NoError |
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287 | #D-* Purpose: Archive rsh command, without error |
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288 | #D-* used only in monitoring.job |
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289 | #D-* Examples: |
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290 | #D- |
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291 | function IGCM_sys_RshArchive_NoError { |
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292 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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293 | /bin/ksh <<-EOF |
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294 | ${@} 2> /dev/null |
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295 | EOF |
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296 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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297 | } |
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298 | |
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299 | #D-#================================================== |
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300 | #D-function IGCM_sys_MkdirArchive |
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301 | #D-* Purpose: Mkdir on Archive |
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302 | #D-* Examples: |
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303 | #D- |
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304 | function IGCM_sys_MkdirArchive { |
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305 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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306 | if ( $DEBUG_sys ) ; then |
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307 | echo "IGCM_sys_MkdirArchive :" $@ |
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308 | fi |
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309 | #- creation de repertoire sur le serveur fichier |
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310 | if [ ! -d ${1} ]; then |
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311 | \mkdir -p $1 |
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312 | status=$? |
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313 | |
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314 | if [ ${status} -gt 0 ] ; then |
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315 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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316 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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317 | fi |
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318 | fi |
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319 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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320 | } |
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321 | |
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322 | #D-#================================================== |
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323 | #D-function IGCM_sys_TestDirArchive |
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324 | #D-* Purpose: Test Directory that must exists on Archive |
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325 | #D-* Examples: |
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326 | #D- |
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327 | function IGCM_sys_TestDirArchive { |
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328 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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329 | if ( $DEBUG_sys ) ; then |
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330 | echo "IGCM_sys_TestDirArchive :" $@ |
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331 | fi |
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332 | typeset ExistFlag |
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333 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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334 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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335 | return ${ExistFlag} |
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336 | } |
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337 | |
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338 | #D-#================================================== |
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339 | #D-function IGCM_sys_IsFileArchived |
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340 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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341 | #D-* Examples: |
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342 | #D- |
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343 | function IGCM_sys_IsFileArchived { |
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344 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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345 | if ( $DEBUG_sys ) ; then |
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346 | echo "IGCM_sys_IsFileArchived :" $@ |
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347 | fi |
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348 | typeset IsArchivedFlag |
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349 | # To be implemented on Jean Zay |
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350 | # IsArchivedFlag=$( [ X$( echo $@ | grep ^\/ccc\/store ) != X ] && echo 0 || echo 1 ) |
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351 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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352 | |
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353 | return ${IsArchivedFlag} |
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354 | } |
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355 | |
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356 | #D-#================================================== |
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357 | #D-function IGCM_sys_TestFileArchive |
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358 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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359 | #D-* Examples: |
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360 | #D- |
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361 | function IGCM_sys_TestFileArchive { |
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362 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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363 | typeset ExistFlag |
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364 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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365 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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366 | |
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367 | return ${ExistFlag} |
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368 | } |
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369 | |
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370 | #D-#================================================== |
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371 | #D-function IGCM_sys_CountFileArchive |
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372 | #D-* Purpose: Count files on Archive filesystem |
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373 | #D-* Examples: |
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374 | #D- |
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375 | function IGCM_sys_CountFileArchive { |
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376 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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377 | ls ${@} 2>/dev/null | wc -l |
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378 | if [ $? -gt 0 ] ; then |
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379 | echo "IGCM_sys_CountFileArchive : erreur." |
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380 | fi |
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381 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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382 | } |
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383 | |
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384 | #D-#================================================== |
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385 | #D-function IGCM_sys_Tree |
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386 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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387 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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388 | #D- |
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389 | function IGCM_sys_Tree { |
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390 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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391 | if ( $DEBUG_sys ) ; then |
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392 | echo "IGCM_sys_Tree :" $@ |
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393 | fi |
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394 | |
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395 | \ls -lR ${@} |
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396 | |
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397 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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398 | } |
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399 | |
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400 | #D-#================================================== |
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401 | #D-function IGCM_sys_Qsub |
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402 | #D-* Purpose: Qsub new job |
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403 | #D-* Examples: |
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404 | #D- |
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405 | function IGCM_sys_Qsub { |
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406 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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407 | if ( $DEBUG_sys ) ; then |
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408 | echo "IGCM_sys_Qsub :" $@ |
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409 | fi |
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410 | typeset options status |
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411 | options="-o ${SUBMIT_DIR}/${Script_Output} -e ${SUBMIT_DIR}/${Script_Output}" |
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412 | |
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413 | /usr/bin/time sbatch ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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414 | status=$? |
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415 | |
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416 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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417 | if [ ${status} -gt 0 ] ; then |
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418 | IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}" |
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419 | IGCM_debug_Exit "IGCM_sys_Qsub" |
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420 | else |
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421 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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422 | fi |
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423 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
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424 | } |
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425 | |
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426 | #D-#================================================== |
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427 | #D-function IGCM_sys_QsubPost |
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428 | #D-* Purpose: Qsub new job on scalaire |
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429 | #D-* Examples: |
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430 | #D- |
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431 | function IGCM_sys_QsubPost { |
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432 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
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433 | if ( $DEBUG_sys ) ; then |
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434 | echo "IGCM_sys_QsubPost :" $@ |
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435 | fi |
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436 | typeset options status |
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437 | options="-o ${POST_DIR}/${Script_Post_Output}.out -e ${POST_DIR}/${Script_Post_Output}.out" |
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438 | |
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439 | sbatch ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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440 | status=$? |
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441 | |
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442 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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443 | if [ ${status} -gt 0 ] ; then |
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444 | IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}" |
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445 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
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446 | else |
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447 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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448 | fi |
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449 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
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450 | } |
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451 | |
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452 | #D-************************* |
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453 | #D- File transfer functions |
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454 | #D-************************* |
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455 | #D- |
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456 | |
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457 | #D-#================================================== |
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458 | #D-function IGCM_sys_RmRunDir |
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459 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
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460 | #D- scheduler will do the job) |
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461 | #D-* Examples: |
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462 | #D- |
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463 | function IGCM_sys_RmRunDir { |
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464 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
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465 | if ( $DEBUG_sys ) ; then |
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466 | echo "IGCM_sys_RmRunDir :" $@ |
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467 | fi |
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468 | |
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469 | typeset status |
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470 | |
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471 | echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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472 | \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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473 | status=$? |
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474 | |
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475 | if [ ${status} -gt 0 ] ; then |
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476 | IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}." |
---|
477 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
478 | IGCM_debug_Exit "IGCM_sys_RmRunDir" |
---|
479 | else |
---|
480 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
481 | fi |
---|
482 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
---|
483 | } |
---|
484 | |
---|
485 | #D-#================================================== |
---|
486 | #D-function IGCM_sys_Put_Dir |
---|
487 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
---|
488 | #D-* Examples: |
---|
489 | #D- |
---|
490 | function IGCM_sys_Put_Dir { |
---|
491 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
---|
492 | if ( $DEBUG_sys ) ; then |
---|
493 | echo "IGCM_sys_Put_Dir :" $@ |
---|
494 | fi |
---|
495 | if [ $DRYRUN = 0 ]; then |
---|
496 | if [ ! -d ${1} ] ; then |
---|
497 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
---|
498 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
499 | return |
---|
500 | fi |
---|
501 | |
---|
502 | typeset status |
---|
503 | |
---|
504 | # Only if we use rsync |
---|
505 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
---|
506 | # |
---|
507 | #USUAL WAY |
---|
508 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
509 | status=$? |
---|
510 | |
---|
511 | if [ ${status} -gt 0 ] ; then |
---|
512 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
---|
513 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
514 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
---|
515 | else |
---|
516 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
517 | fi |
---|
518 | fi |
---|
519 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
520 | } |
---|
521 | |
---|
522 | #D-#================================================== |
---|
523 | #D-function IGCM_sys_Get_Dir |
---|
524 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
525 | #D-* Examples: |
---|
526 | #D- |
---|
527 | function IGCM_sys_Get_Dir { |
---|
528 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
529 | if ( $DEBUG_sys ) ; then |
---|
530 | echo "IGCM_sys_Get_Dir :" $@ |
---|
531 | fi |
---|
532 | if [ $DRYRUN = 0 ]; then |
---|
533 | typeset NB_ESSAI DELAI status i |
---|
534 | # number of tentative |
---|
535 | NB_ESSAI=3 |
---|
536 | # time delay between tentative |
---|
537 | DELAI=2 |
---|
538 | |
---|
539 | # |
---|
540 | # USUAL WAY |
---|
541 | # add here command to demigrate all offline files to reduce time of this command |
---|
542 | # actually on Jean Zay files are not archive on bands |
---|
543 | |
---|
544 | i=0 |
---|
545 | while [ $i -lt $NB_ESSAI ] ; do |
---|
546 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
547 | status=$? |
---|
548 | if [ ${status} -gt 0 ] ; then |
---|
549 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
550 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
551 | sleep $DELAI |
---|
552 | else |
---|
553 | break |
---|
554 | fi |
---|
555 | (( i = i + 1 )) |
---|
556 | done |
---|
557 | |
---|
558 | if [ ${status} -gt 0 ] ; then |
---|
559 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
560 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
561 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
562 | else |
---|
563 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
564 | fi |
---|
565 | fi |
---|
566 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
567 | } |
---|
568 | |
---|
569 | #D-#================================================== |
---|
570 | #D-function IGCM_sys_Put_Rest |
---|
571 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
572 | #D- File and target directory must exist. |
---|
573 | #D-* Examples: |
---|
574 | #D- |
---|
575 | function IGCM_sys_Put_Rest { |
---|
576 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
577 | if ( $DEBUG_sys ) ; then |
---|
578 | echo "IGCM_sys_Put_Rest :" $@ |
---|
579 | fi |
---|
580 | if [ $DRYRUN = 0 ]; then |
---|
581 | if [ ! -f ${1} ] ; then |
---|
582 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
583 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
584 | fi |
---|
585 | |
---|
586 | typeset status |
---|
587 | # |
---|
588 | # USUAL WAY |
---|
589 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
590 | status=$? |
---|
591 | |
---|
592 | # #RSYNC WITH NETWORK SSH CALL |
---|
593 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
594 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
595 | |
---|
596 | # #RSYNC WITH NFS USE |
---|
597 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
598 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
599 | |
---|
600 | # status=$? |
---|
601 | # IGCM_sys_Rsync_out $status |
---|
602 | |
---|
603 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
604 | # (( status=status+$? )) |
---|
605 | |
---|
606 | if [ ${status} -gt 0 ] ; then |
---|
607 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
608 | [ -f ${1} ] && ls -l ${1} |
---|
609 | [ -f ${2} ] && ls -l ${2} |
---|
610 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
611 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
612 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
613 | else |
---|
614 | |
---|
615 | if [ X${JobType} = XRUN ] ; then |
---|
616 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
617 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
618 | fi |
---|
619 | |
---|
620 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
621 | fi |
---|
622 | fi |
---|
623 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
624 | } |
---|
625 | |
---|
626 | #D-#================================================== |
---|
627 | #D-function IGCM_sys_Put_Out |
---|
628 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
629 | #D-* Examples: |
---|
630 | #D- |
---|
631 | function IGCM_sys_Put_Out { |
---|
632 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
633 | if ( $DEBUG_sys ) ; then |
---|
634 | echo "IGCM_sys_Put_Out :" $@ |
---|
635 | fi |
---|
636 | |
---|
637 | typeset NB_ESSAI DELAI status i exist skip |
---|
638 | typeset fileDeviceNumberInHex directoryDeviceNumberInHex |
---|
639 | |
---|
640 | # number of tentative |
---|
641 | NB_ESSAI=3 |
---|
642 | # time delay between tentative |
---|
643 | DELAI=2 |
---|
644 | |
---|
645 | if [ $DRYRUN = 0 ]; then |
---|
646 | if [ ! -f ${1} ] ; then |
---|
647 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
648 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
649 | return 1 |
---|
650 | fi |
---|
651 | # |
---|
652 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
653 | # |
---|
654 | exist=false |
---|
655 | skip=false |
---|
656 | if [ -f $2 ] ; then |
---|
657 | IGCM_debug_Print 1 "$2 already exist" |
---|
658 | # add here command to demigrate all offline files to reduce time of this command |
---|
659 | # actually on Jean Zay files are not archive on bands |
---|
660 | |
---|
661 | exist=true |
---|
662 | if [ "X$( diff $1 $2 )" = X ] ; then |
---|
663 | IGCM_debug_Print 2 "$1 and $2 are the same file, we skip the copy" |
---|
664 | skip=true |
---|
665 | else |
---|
666 | IGCM_debug_Print 2 "$1 and $2 are not the same file, we force the copy" |
---|
667 | skip=false |
---|
668 | fi |
---|
669 | fi |
---|
670 | # |
---|
671 | if ( [ X${exist} = Xtrue ] && [ X${skip} = Xfalse ] ) ; then |
---|
672 | IGCM_sys_Chmod u+w $2 |
---|
673 | fi |
---|
674 | |
---|
675 | if [ X${skip} = Xfalse ] ; then |
---|
676 | i=0 |
---|
677 | while [ $i -lt $NB_ESSAI ] ; do |
---|
678 | # Identify file system |
---|
679 | fileDeviceNumberInHex=$( stat -c %d $1 ) |
---|
680 | status=$? |
---|
681 | if [ ${status} -gt 0 ] ; then |
---|
682 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
683 | fi |
---|
684 | # Identify file system |
---|
685 | directoryDeviceNumberInHex=$( stat -c %d $( dirname $2 ) ) |
---|
686 | status=$? |
---|
687 | if [ ${status} -gt 0 ] ; then |
---|
688 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
689 | fi |
---|
690 | |
---|
691 | if ( [ ${fileDeviceNumberInHex} -ne ${directoryDeviceNumberInHex} ] || [ X$3 = XNOMOVE ] ) ; then |
---|
692 | # They are not on the same device. USUAL WAY |
---|
693 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
694 | status=$? |
---|
695 | else |
---|
696 | # They are on the same device. NOT SO USUAL WAY |
---|
697 | \mv $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
698 | status=$? |
---|
699 | fi |
---|
700 | if [ ${status} -gt 0 ]; then |
---|
701 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
702 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : sleep ${DELAI} seconds and try again." |
---|
703 | [ -f ${1} ] && ls -l ${1} |
---|
704 | [ -f ${2} ] && ls -l ${2} |
---|
705 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
706 | sleep $DELAI |
---|
707 | else |
---|
708 | break |
---|
709 | fi |
---|
710 | (( i = i + 1 )) |
---|
711 | done |
---|
712 | fi |
---|
713 | |
---|
714 | # #RSYNC WITH NETWORK SSH CALL |
---|
715 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
716 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
717 | |
---|
718 | # #RSYNC WITH NFS USE |
---|
719 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
720 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
721 | |
---|
722 | # status=$? |
---|
723 | # IGCM_sys_Rsync_out $status |
---|
724 | |
---|
725 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
726 | # (( status=status+$? )) |
---|
727 | |
---|
728 | if [ ${status} -gt 0 ] ; then |
---|
729 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status}" |
---|
730 | [ -f ${1} ] && ls -l ${1} |
---|
731 | [ -f ${2} ] && ls -l ${2} |
---|
732 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
733 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
734 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
735 | else |
---|
736 | |
---|
737 | if [ X${JobType} = XRUN ] ; then |
---|
738 | if [ X${3} = X ] ; then |
---|
739 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
740 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
741 | fi |
---|
742 | fi |
---|
743 | |
---|
744 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
745 | fi |
---|
746 | fi |
---|
747 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
748 | return 0 |
---|
749 | } |
---|
750 | |
---|
751 | #D-#================================================== |
---|
752 | #D-function IGCM_sys_Get |
---|
753 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
754 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
755 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
756 | function IGCM_sys_Get { |
---|
757 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
758 | |
---|
759 | typeset DEST dm_liste target file_work |
---|
760 | typeset NB_ESSAI DELAI status i |
---|
761 | |
---|
762 | if ( $DEBUG_sys ) ; then |
---|
763 | echo "IGCM_sys_Get :" $@ |
---|
764 | fi |
---|
765 | |
---|
766 | # number of tentative |
---|
767 | NB_ESSAI=3 |
---|
768 | # time delay between tentative |
---|
769 | DELAI=2 |
---|
770 | |
---|
771 | if [ $DRYRUN -le 2 ]; then |
---|
772 | if [ X${1} = X'/l' ] ; then |
---|
773 | eval set +A dm_liste \${${2}} |
---|
774 | else |
---|
775 | eval set +A dm_liste ${1} |
---|
776 | fi |
---|
777 | eval DEST=\${${#}} |
---|
778 | # add here command to demigrate all offline files to reduce time of this command |
---|
779 | # actually on Jean Zay files are not archive on bands |
---|
780 | |
---|
781 | status=$? |
---|
782 | if [ ${status} -gt 0 ] ; then |
---|
783 | echo "WARNING IGCM_sys_Get : error code ${status}" |
---|
784 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
785 | echo "WARNING IGCM_sys_Get : will stop later if the cp fails." |
---|
786 | fi |
---|
787 | |
---|
788 | #if [ ${status} -gt 0 ] ; then |
---|
789 | # if [ ! "X$( grep "Lost dmusrcmd connection" ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )" = "X" ] ; then |
---|
790 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
791 | # echo "WARNING IGCM_sys_Get : Lost dmusrcmd connection : " |
---|
792 | # sleep 30 |
---|
793 | # echo "We try another time" |
---|
794 | ## dmget ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
795 | # ccc_hsm get ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
796 | # status=$? |
---|
797 | # if [ ${status} -gt 0 ] ; then |
---|
798 | # echo "ERROR IGCM_sys_Get : again demigration error :" |
---|
799 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
800 | # IGCM_debug_Exit "IGCM_sys_Get" |
---|
801 | # fi |
---|
802 | # else |
---|
803 | # echo "ERROR IGCM_sys_Get : demigration error :" |
---|
804 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
805 | # IGCM_debug_Exit "IGCM_sys_Get" |
---|
806 | # fi |
---|
807 | #fi |
---|
808 | |
---|
809 | # #RSYNC WITH NETWORK SSH CALL |
---|
810 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
811 | # ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
812 | |
---|
813 | # #RSYNC WITH NFS USE |
---|
814 | # echo ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
815 | # ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
816 | |
---|
817 | # status=$? |
---|
818 | # IGCM_sys_Rsync_out $status |
---|
819 | |
---|
820 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
821 | # (( status=status+$? )) |
---|
822 | |
---|
823 | #USUAL WAY |
---|
824 | if [ X${1} = X'/l' ] ; then |
---|
825 | for target in ${dm_liste[*]} ; do |
---|
826 | local_file=$( basename ${target} ) |
---|
827 | # test if the target file is present before the loop |
---|
828 | IGCM_sys_TestFileArchive ${target} |
---|
829 | status=$? |
---|
830 | if [ ${status} -gt 0 ] ; then |
---|
831 | echo "IGCM_sys_Get, ERROR : regular file ${target} DOES NOT EXIST ." |
---|
832 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
833 | else |
---|
834 | i=0 |
---|
835 | while [ $i -lt $NB_ESSAI ] ; do |
---|
836 | #if [ X${DoLink} = Xtrue ] ; then |
---|
837 | # \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
838 | # status=$? |
---|
839 | # else |
---|
840 | # \cp ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
841 | # status=$? |
---|
842 | #fi |
---|
843 | \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
844 | status=$? |
---|
845 | if [ ${status} -gt 0 ]; then |
---|
846 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
847 | IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again." |
---|
848 | sleep $DELAI |
---|
849 | else |
---|
850 | break |
---|
851 | fi |
---|
852 | (( i = i + 1 )) |
---|
853 | done |
---|
854 | if [ ${status} -gt 0 ] ; then |
---|
855 | echo "IGCM_sys_Get : error" |
---|
856 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
857 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
858 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
859 | else |
---|
860 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
861 | fi |
---|
862 | fi |
---|
863 | done |
---|
864 | else |
---|
865 | i=0 |
---|
866 | while [ $i -lt $NB_ESSAI ] ; do |
---|
867 | \cp ${dm_liste} ${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
868 | status=$? |
---|
869 | if [ ${status} -gt 0 ]; then |
---|
870 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
871 | IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again." |
---|
872 | sleep $DELAI |
---|
873 | else |
---|
874 | break |
---|
875 | fi |
---|
876 | (( i = i + 1 )) |
---|
877 | done |
---|
878 | if [ ${status} -gt 0 ] ; then |
---|
879 | echo "IGCM_sys_Get : error" |
---|
880 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
881 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
882 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
883 | else |
---|
884 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
885 | fi |
---|
886 | fi |
---|
887 | fi |
---|
888 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
889 | } |
---|
890 | |
---|
891 | #D-#================================================== |
---|
892 | #D-function IGCM_sys_GetDate_Monitoring |
---|
893 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
894 | #D-* Examples: |
---|
895 | #D- |
---|
896 | function IGCM_sys_GetDate_Monitoring { |
---|
897 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
898 | if ( $DEBUG_sys ) ; then |
---|
899 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
900 | fi |
---|
901 | |
---|
902 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
903 | |
---|
904 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
905 | } |
---|
906 | |
---|
907 | #D-#================================================== |
---|
908 | #D-function IGCM_sys_Dods_Rm |
---|
909 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
910 | #D-* Examples: |
---|
911 | #D- |
---|
912 | function IGCM_sys_Dods_Rm { |
---|
913 | if ( $DEBUG_sys ) ; then |
---|
914 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
915 | fi |
---|
916 | typeset status |
---|
917 | if [ $DRYRUN = 0 ]; then |
---|
918 | |
---|
919 | # if [ ! -d /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} ] ; then |
---|
920 | # echo "WARNING : IGCM_sys_Dods_Rm /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} DOES NOT EXIST ." |
---|
921 | # echo "Nothing has been done." |
---|
922 | # return |
---|
923 | # fi |
---|
924 | |
---|
925 | if [ "$#" -eq 1 ]; then |
---|
926 | # $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS}/${1} # > out_dods_rm 2>&1 |
---|
927 | status=$? |
---|
928 | else |
---|
929 | # $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS} # > out_dods_rm 2>&1 |
---|
930 | status=$? |
---|
931 | fi |
---|
932 | |
---|
933 | # if [ ${status} -gt 0 ] ; then |
---|
934 | # echo "IGCM_sys_Dods_Rm : error." |
---|
935 | # cat out_dods_rm |
---|
936 | # IGCM_debug_Exit "IGCM_sys_Dods_Rm" |
---|
937 | # else |
---|
938 | # rm out_dods_rm |
---|
939 | # fi |
---|
940 | |
---|
941 | fi |
---|
942 | return $status |
---|
943 | } |
---|
944 | |
---|
945 | #D-#================================================== |
---|
946 | #D-function IGCM_sys_Dods_Cp |
---|
947 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
948 | #D-* Examples: |
---|
949 | #D- |
---|
950 | function IGCM_sys_Dods_Cp { |
---|
951 | if ( $DEBUG_sys ) ; then |
---|
952 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
953 | fi |
---|
954 | typeset status |
---|
955 | if [ $DRYRUN = 0 ]; then |
---|
956 | |
---|
957 | # if [ ! -d ${R_SAVE}/${1} ] ; then |
---|
958 | # echo "WARNING : IGCM_sys_Dods_Cp ${R_SAVE}/${1} DOES NOT EXIST ." |
---|
959 | # echo "Nothing has been done." |
---|
960 | # return |
---|
961 | # fi |
---|
962 | |
---|
963 | # $(ccc_home -u igcmg)/Tools/irene/thredds_cp ${1} public/${LOGIN}/${R_DODS} # > out_dods_cp 2>&1 |
---|
964 | |
---|
965 | status=$? |
---|
966 | |
---|
967 | # if [ ${status} -gt 0 ] ; then |
---|
968 | # echo "IGCM_sys_Dods_Cp : error." |
---|
969 | # cat out_dods_cp |
---|
970 | # IGCM_debug_Exit "IGCM_sys_Dods_Cp" |
---|
971 | # else |
---|
972 | # rm out_dods_cp |
---|
973 | # fi |
---|
974 | |
---|
975 | fi |
---|
976 | return $status |
---|
977 | } |
---|
978 | |
---|
979 | #D-#================================================== |
---|
980 | #D-function IGCM_sys_Put_Dods |
---|
981 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. |
---|
982 | #D-* Examples: |
---|
983 | #D- |
---|
984 | function IGCM_sys_Put_Dods { |
---|
985 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
986 | if ( $DEBUG_sys ) ; then |
---|
987 | echo "IGCM_sys_Put_Dods :" $@ |
---|
988 | fi |
---|
989 | typeset status |
---|
990 | if [ $DRYRUN = 0 ]; then |
---|
991 | if ( [ ! -d ${R_SAVE}/${1} ] && [ ! -d ${R_FIGR}/${1} ] ) ; then |
---|
992 | echo "WARNING IGCM_sys_Put_Dods : None of the following directories exist. Exactly one should." |
---|
993 | echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} DOES NOT EXIST." |
---|
994 | echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} DOES NOT EXIST." |
---|
995 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
996 | return |
---|
997 | fi |
---|
998 | |
---|
999 | if ( [ -d ${R_SAVE}/${1} ] && [ -d ${R_FIGR}/${1} ] ) ; then |
---|
1000 | echo "WARNING IGCM_sys_Put_Dods : Both of the following directories exist. Exactly one should." |
---|
1001 | echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} EXISTS." |
---|
1002 | echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} EXISTS." |
---|
1003 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
1004 | return |
---|
1005 | fi |
---|
1006 | # |
---|
1007 | if [ -d ${R_SAVE}/${1} ] ; then |
---|
1008 | cd ${R_SAVE} |
---|
1009 | elif [ -d ${R_FIGR}/${1} ] ; then |
---|
1010 | cd ${R_FIGR} |
---|
1011 | fi |
---|
1012 | |
---|
1013 | IGCM_sys_Dods_Rm ${1} |
---|
1014 | IGCM_sys_Dods_Cp ${1} |
---|
1015 | status=0 |
---|
1016 | |
---|
1017 | if [ ${status} -gt 0 ] ; then |
---|
1018 | echo "IGCM_sys_Put_Dods : error." |
---|
1019 | IGCM_debug_Exit "IGCM_sys_Put_Dods" |
---|
1020 | fi |
---|
1021 | fi |
---|
1022 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
1023 | } |
---|
1024 | |
---|
1025 | ############################################################## |
---|
1026 | # REBUILD OPERATOR |
---|
1027 | |
---|
1028 | #D-#================================================== |
---|
1029 | #D-function IGCM_sys_sync |
---|
1030 | #D-* Purpose: flush buffer on disk |
---|
1031 | #D-* Examples: |
---|
1032 | #D- |
---|
1033 | function IGCM_sys_sync { |
---|
1034 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
1035 | if ( $DEBUG_sys ) ; then |
---|
1036 | echo "IGCM_sys_sync :" $@ |
---|
1037 | fi |
---|
1038 | |
---|
1039 | /bin/sync |
---|
1040 | |
---|
1041 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
1042 | } |
---|
1043 | |
---|
1044 | ############################################################ |
---|
1045 | # Activate Running Environnment Variables |
---|
1046 | |
---|
1047 | #D-#================================================== |
---|
1048 | #D-function IGCM_sys_activ_variables |
---|
1049 | #D-* Purpose: set environement variables prior to execution |
---|
1050 | #D-* Examples: |
---|
1051 | #D- |
---|
1052 | function IGCM_sys_activ_variables { |
---|
1053 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
1054 | if ( $DEBUG_sys ) ; then |
---|
1055 | echo "IGCM_sys_activ_variables" |
---|
1056 | fi |
---|
1057 | |
---|
1058 | # -------------------------------------------------------------------- |
---|
1059 | #D- MODULE specifications |
---|
1060 | # -------------------------------------------------------------------- |
---|
1061 | # Source the file EnvFile containing all module load needed to run the model. |
---|
1062 | # EnvFile can be specified in config.card. If this is the case and if the file exists, |
---|
1063 | # it will be used. Otherwise a default file will be used. |
---|
1064 | if [ ! X${config_UserChoices_EnvFile} = X ] && [ -f ${config_UserChoices_EnvFile} ] ; then |
---|
1065 | # EnvFile is set in config.card and the file exists |
---|
1066 | IGCM_debug_Print 1 "EnvFile set in config.card will be used" |
---|
1067 | EnvFile=${config_UserChoices_EnvFile} |
---|
1068 | else |
---|
1069 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Default modules will be used" |
---|
1070 | module purge > /dev/null 2>&1 |
---|
1071 | EnvFile=/gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_jeanzay |
---|
1072 | fi |
---|
1073 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Following EnvFile will be used :" |
---|
1074 | IGCM_debug_Print 1 ${EnvFile} |
---|
1075 | . ${EnvFile} |
---|
1076 | |
---|
1077 | IGCM_debug_Print 1 "IGCM_sys_active_variables : Now loaded modules for Jean-Zay. " |
---|
1078 | module list |
---|
1079 | |
---|
1080 | # -------------------------------------------------------------------- |
---|
1081 | #D- MPI specifications |
---|
1082 | # -------------------------------------------------------------------- |
---|
1083 | |
---|
1084 | # -------------------------------------------------------------------- |
---|
1085 | #D- Other specifications |
---|
1086 | # -------------------------------------------------------------------- |
---|
1087 | |
---|
1088 | ulimit -s unlimited |
---|
1089 | |
---|
1090 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
1091 | } |
---|
1092 | |
---|
1093 | ############################################################ |
---|
1094 | # Desactivate Running Environnment Variables |
---|
1095 | |
---|
1096 | #D-#================================================== |
---|
1097 | #D-function IGCM_sys_desactiv_variables |
---|
1098 | #D-* Purpose: unset environement variables after execution |
---|
1099 | #D-* Examples: |
---|
1100 | #D- |
---|
1101 | function IGCM_sys_desactiv_variables { |
---|
1102 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
1103 | if ( $DEBUG_sys ) ; then |
---|
1104 | echo "IGCM_sys_desactiv_variables" |
---|
1105 | fi |
---|
1106 | # -------------------------------------------------------------------- |
---|
1107 | #D- MPI specifications |
---|
1108 | # -------------------------------------------------------------------- |
---|
1109 | |
---|
1110 | # -------------------------------------------------------------------- |
---|
1111 | #D- Other specifications |
---|
1112 | # -------------------------------------------------------------------- |
---|
1113 | |
---|
1114 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
1115 | } |
---|
1116 | |
---|
1117 | ############################################################ |
---|
1118 | # Update job headers to be used by the scheduler |
---|
1119 | |
---|
1120 | #D-#================================================== |
---|
1121 | #D-function IGCM_sys_updateHeaders |
---|
1122 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
1123 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
1124 | #D- |
---|
1125 | function IGCM_sys_updateHeaders { |
---|
1126 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
1127 | if ( $DEBUG_sys ) ; then |
---|
1128 | echo "IGCM_sys_updateHeaders" |
---|
1129 | fi |
---|
1130 | typeset file |
---|
1131 | file=$1 |
---|
1132 | |
---|
1133 | if [ ${executionType} -eq 1 ] ; then |
---|
1134 | # MPMD + MPI |
---|
1135 | sed -e "/::openMPthreads::/d" \ |
---|
1136 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
1137 | ${file} > ${file}.tmp |
---|
1138 | |
---|
1139 | elif [ ${executionType} -eq 2 ] ; then |
---|
1140 | # MPMD + MPI + OMP |
---|
1141 | (( nodeNumber = coreNumber / NB_CORE_PER_NODE )) |
---|
1142 | [ $(( ${coreNumber} % ${NB_CORE_PER_NODE} )) -ne 0 ] && (( nodeNumber = nodeNumber + 1 )) |
---|
1143 | sed -e "/::openMPthreads::/d" \ |
---|
1144 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
1145 | -e "/ntasks/i\#SBATCH --nodes=${nodeNumber}"\ |
---|
1146 | -e "/ntasks/i\#SBATCH --exclusive" \ |
---|
1147 | ${file} > ${file}.tmp |
---|
1148 | elif [ ${executionType} -eq 3 ] ; then |
---|
1149 | # SPMD + MPI/OMP |
---|
1150 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
1151 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
1152 | ${file} > ${file}.tmp |
---|
1153 | |
---|
1154 | elif [ ${executionType} -eq 4 ] ; then |
---|
1155 | # SPMD + MPI only |
---|
1156 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
1157 | -e "/::openMPthreads::/d" \ |
---|
1158 | ${file} > ${file}.tmp |
---|
1159 | |
---|
1160 | elif [ ${executionType} -eq 5 ] ; then |
---|
1161 | # SPMD + OMP only |
---|
1162 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
1163 | -e "/::JobNumProcTot::/d" \ |
---|
1164 | ${file} > ${file}.tmp |
---|
1165 | |
---|
1166 | elif [ ${executionType} -eq 6 ] ; then |
---|
1167 | # SEQUENTIAL THEN |
---|
1168 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
1169 | -e "/::openMPthreads::/d" \ |
---|
1170 | ${file} > ${file}.tmp |
---|
1171 | |
---|
1172 | fi |
---|
1173 | |
---|
1174 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
1175 | |
---|
1176 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
1177 | } |
---|
1178 | |
---|
1179 | ############################################################ |
---|
1180 | # Build MPI/OMP scripts run file (dummy function) |
---|
1181 | |
---|
1182 | #D-#================================================== |
---|
1183 | #D-function IGCM_sys_build_run_file |
---|
1184 | #D-* Purpose: build run file (deprecated) |
---|
1185 | #D-* Examples: |
---|
1186 | #D- |
---|
1187 | function IGCM_sys_build_run_file { |
---|
1188 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
1189 | } |
---|
1190 | |
---|
1191 | ############################################################ |
---|
1192 | # Build MPI/OMP scripts |
---|
1193 | |
---|
1194 | #D-#================================================== |
---|
1195 | #D-function IGCM_sys_build_execution_scripts |
---|
1196 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
1197 | #D-* Examples: |
---|
1198 | #D- |
---|
1199 | function IGCM_sys_build_execution_scripts |
---|
1200 | { |
---|
1201 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
1202 | if ( $DEBUG_sys ) ; then |
---|
1203 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
1204 | fi |
---|
1205 | IGCM_debug_Print 1 "executionType= ${executionType}" |
---|
1206 | EXECUTION=${HOST_MPIRUN_COMMAND} |
---|
1207 | |
---|
1208 | if ( ${OK_PARA_MPMD} ) ; then |
---|
1209 | |
---|
1210 | # MPMD mode |
---|
1211 | # 1 MPI only : executionType=1 |
---|
1212 | # 2 MPI/OpenMP : executionType=2 |
---|
1213 | |
---|
1214 | if [ -f run_file ] ; then |
---|
1215 | IGCM_sys_Rm -f run_file |
---|
1216 | fi |
---|
1217 | touch run_file |
---|
1218 | |
---|
1219 | # case 1 : Only MPI (MPMD) |
---|
1220 | if ( ! ${OK_PARA_OMP} ) ; then |
---|
1221 | # Build run_file |
---|
1222 | current_core=0 |
---|
1223 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
1224 | # the coupler ie oasis3 must be the first one |
---|
1225 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1226 | |
---|
1227 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
1228 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1229 | |
---|
1230 | # Only if the component has an executable |
---|
1231 | if ( [ "X${ExeNameOut}" != X\"\" ] ) ; then |
---|
1232 | |
---|
1233 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1234 | (( end_core = ${current_core} + ${comp_proc_mpi_loc} - 1 )) |
---|
1235 | echo "${current_core}-${end_core} ./${ExeNameOut}" >> run_file |
---|
1236 | (( current_core = ${end_core} + 1 )) |
---|
1237 | fi |
---|
1238 | done |
---|
1239 | |
---|
1240 | EXECUTION="${HOST_MPIRUN_COMMAND} --multi-prog ./run_file" |
---|
1241 | |
---|
1242 | IGCM_sys_Chmod u+x run_file |
---|
1243 | if ( $DEBUG_sys ) ; then |
---|
1244 | echo "run_file contains : " |
---|
1245 | cat run_file |
---|
1246 | fi |
---|
1247 | |
---|
1248 | else |
---|
1249 | |
---|
1250 | # 2 MPI/OpenMP : executionType=2 |
---|
1251 | |
---|
1252 | # MPI-OpenMP (MPMD) |
---|
1253 | # export SLURM_HOSTFILE=./hostlist |
---|
1254 | # srun --cpu-bind=none --distribution=arbitrary --multi-prog ./run_file |
---|
1255 | # example of hostlist file : |
---|
1256 | # r3i3n33 |
---|
1257 | # r3i3n33 |
---|
1258 | # ... |
---|
1259 | # example of run_file : |
---|
1260 | # 0 taskset -c 0-4 ./script_lmdz.x.ksh |
---|
1261 | # 1 taskset -c 5-9 ./script_lmdz.x.ksh |
---|
1262 | #... |
---|
1263 | # 32 taskset -c 0 ./script_opa.xx.ksh |
---|
1264 | # 33 taskset -c 1 ./script_opa.xx.ksh |
---|
1265 | #... |
---|
1266 | # 62 taskset -c 30 ./script_xios.x.ksh |
---|
1267 | |
---|
1268 | # Hosts treatment |
---|
1269 | IFS=$'\n'; set -f |
---|
1270 | listnodes=($(< <( scontrol show hostnames $SLURM_JOB_NODELIST ))) |
---|
1271 | unset IFS; set +f |
---|
1272 | rm -f hostlist |
---|
1273 | |
---|
1274 | # Loop on the components to build run_file and script_exec files |
---|
1275 | rank=0 |
---|
1276 | current_core=0 |
---|
1277 | |
---|
1278 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1279 | |
---|
1280 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
1281 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1282 | |
---|
1283 | # Not possible if oasis has an executable (i.e old version of oasis3) |
---|
1284 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
---|
1285 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
---|
1286 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
---|
1287 | IGCM_debug_Verif_Exit |
---|
1288 | fi |
---|
1289 | |
---|
1290 | # Only if we really have an executable for the component : |
---|
1291 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
1292 | |
---|
1293 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1294 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1295 | eval comp_proc_nod_loc=\${${comp}_PROC_NOD} |
---|
1296 | |
---|
1297 | |
---|
1298 | # Build script files |
---|
1299 | |
---|
1300 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
1301 | echo "" >> script_${ExeNameOut}.ksh |
---|
1302 | if [ ${comp_proc_omp_loc} -gt 1 ] ; then |
---|
1303 | # Check if the number of threads is correct |
---|
1304 | case ${comp_proc_omp_loc} in |
---|
1305 | 2|4|5|10|20) |
---|
1306 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
---|
1307 | ;; |
---|
1308 | *) |
---|
1309 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
1310 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
1311 | IGCM_debug_Print 2 "Only 2,4,5,10,20 as number of OMP threads are possible " |
---|
1312 | IGCM_debug_Verif_Exit |
---|
1313 | ;; |
---|
1314 | esac |
---|
1315 | echo "export OMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
1316 | echo "export OMP_PLACES=cores" >> script_${ExeNameOut}.ksh |
---|
1317 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
1318 | |
---|
1319 | fi |
---|
1320 | |
---|
1321 | # to have out/err per process on different files |
---|
1322 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh |
---|
1323 | |
---|
1324 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
1325 | |
---|
1326 | # Complete run_file |
---|
1327 | if [ ${comp_proc_nod_loc} -gt 1 ] ; then |
---|
1328 | (( offset_comp_proc_loc = NB_CORE_PER_NODE / (comp_proc_mpi_loc / comp_proc_nod_loc) )) |
---|
1329 | else |
---|
1330 | (( offset_comp_proc_loc = comp_proc_omp_loc )) |
---|
1331 | fi |
---|
1332 | |
---|
1333 | for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do |
---|
1334 | (( index_host = current_core / NB_CORE_PER_NODE )) |
---|
1335 | host_value=${listnodes[${index_host}]} |
---|
1336 | (( slot = current_core % NB_CORE_PER_NODE )) |
---|
1337 | echo "$host_value" >> hostlist |
---|
1338 | echo "$rank taskset -c $slot-$((slot+comp_proc_omp_loc-1)) ./script_${ExeNameOut}.ksh" >> run_file |
---|
1339 | (( rank = rank + 1 )) |
---|
1340 | (( current_core = current_core + offset_comp_proc_loc )) |
---|
1341 | done |
---|
1342 | fi |
---|
1343 | done |
---|
1344 | |
---|
1345 | ## variable added to stop after 60s instead of 600s by default. |
---|
1346 | ## This is used when no error comes from executables and when something stopped an executable without notice. |
---|
1347 | export SLURM_WAIT=60 |
---|
1348 | export SLURM_HOSTFILE=./hostlist |
---|
1349 | |
---|
1350 | EXECUTION="${HOST_MPIRUN_COMMAND} --cpu-bind=none --distribution=arbitrary --multi-prog ./run_file" |
---|
1351 | |
---|
1352 | IGCM_sys_Chmod u+x run_file |
---|
1353 | if ( $DEBUG_sys ) ; then |
---|
1354 | echo "run_file contains : " |
---|
1355 | cat run_file |
---|
1356 | fi |
---|
1357 | |
---|
1358 | fi # if ${OK_PARA_MPMD} |
---|
1359 | |
---|
1360 | else |
---|
1361 | # Only one executable (SPMD mode): executionType=3, 4, 5 and 6 |
---|
1362 | |
---|
1363 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1364 | |
---|
1365 | # Only if we really have an executable for the component : |
---|
1366 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1367 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
1368 | |
---|
1369 | # Build script files |
---|
1370 | |
---|
1371 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
1372 | echo "" >> script_${ExeNameOut}.ksh |
---|
1373 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
1374 | |
---|
1375 | if ( ${OK_PARA_OMP} ) ; then |
---|
1376 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1377 | echo "" >> script_${ExeNameOut}.ksh |
---|
1378 | echo "export OMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
1379 | echo "export OMP_PLACES=cores" >> script_${ExeNameOut}.ksh |
---|
1380 | echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
1381 | fi |
---|
1382 | |
---|
1383 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1384 | |
---|
1385 | # To have out/err per process on different files |
---|
1386 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh |
---|
1387 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
---|
1388 | |
---|
1389 | IGCM_debug_Print 1 "sys Irene : script_${ExeNameOut}.ksh contains" |
---|
1390 | cat script_${ExeNameOut}.ksh |
---|
1391 | |
---|
1392 | fi |
---|
1393 | |
---|
1394 | done |
---|
1395 | |
---|
1396 | fi # ${OK_PARA_MPMD} |
---|
1397 | |
---|
1398 | IGCM_debug_Print 1 "sys Irene : execution command is " |
---|
1399 | IGCM_debug_Print 1 "$EXECUTION" |
---|
1400 | |
---|
1401 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
1402 | } |
---|
1403 | |
---|
1404 | #D-#================================================== |
---|
1405 | #D-function IGCM_sys_check_path |
---|
1406 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
1407 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
1408 | #D-* Examples: |
---|
1409 | #D- |
---|
1410 | function IGCM_sys_check_path { |
---|
1411 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
1412 | if ( $DEBUG_sys ) ; then |
---|
1413 | echo "IGCM_sys_check_path" |
---|
1414 | fi |
---|
1415 | |
---|
1416 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${WORK} ] || [ X${RUN_DIR_PATH} = X${SCRATCH} ] || [ X${RUN_DIR_PATH} = X${STORE} ] ) ; then |
---|
1417 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
1418 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
1419 | IGCM_debug_Exit "This will stop the job" |
---|
1420 | fi |
---|
1421 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
1422 | } |
---|
1423 | |
---|
1424 | #D-#================================================== |
---|
1425 | #D-function IGCM_sys_check_quota |
---|
1426 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
1427 | #D-* Examples: |
---|
1428 | #D- |
---|
1429 | function IGCM_sys_check_quota { |
---|
1430 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
1431 | echo "IGCM_sys_check_quota is desactivated on JeanZay because there is actually no way to check scratch quota on this computing center (2019.11.19)" |
---|
1432 | # if ( $DEBUG_sys ) ; then |
---|
1433 | # echo "IGCM_sys_check_quota" |
---|
1434 | # fi |
---|
1435 | # # Limit of quota (in %) |
---|
1436 | # limit_quota=90 |
---|
1437 | # |
---|
1438 | # # Check of the volume |
---|
1439 | # volume_quota=$(ccc_quota | grep ' scratch' | gawk '{print $2}') |
---|
1440 | # volume_avail=$(ccc_quota | grep ' scratch' | gawk '{print $3}') |
---|
1441 | # |
---|
1442 | # if ( [ ! X${volume_quota} = X ] && [ ! ${volume_quota} = "-" ] ) ; then |
---|
1443 | # |
---|
1444 | # unit_avail=${volume_avail: -1} |
---|
1445 | # unit_quota=${volume_quota: -1} |
---|
1446 | # |
---|
1447 | # if [ "${unit_quota}" = "*" ] ; then |
---|
1448 | # IGCM_debug_Print 1 "Please, check your quota of volume on scratch" |
---|
1449 | # IGCM_debug_Print 1 "More than 100% of your quota is used" |
---|
1450 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
1451 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
1452 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
1453 | # IGCM_debug_Verif_Exit |
---|
1454 | # fi |
---|
1455 | # |
---|
1456 | # temp_avail=${volume_avail%%${volume_avail: -1}*} |
---|
1457 | # temp_quota=${volume_quota%%${volume_quota: -1}*} |
---|
1458 | # |
---|
1459 | # if [ ! ${unit_avail} = ${unit_quota} ] ; then |
---|
1460 | # |
---|
1461 | # # Convertion |
---|
1462 | # if [ ${volume_avail: -1} = "T" ] ; then |
---|
1463 | # (( temp_avail = temp_avail * 1000000000000 )) |
---|
1464 | # elif [ ${volume_avail: -1} = "G" ] ; then |
---|
1465 | # (( temp_avail = temp_avail * 1000000000 )) |
---|
1466 | # elif [ ${volume_avail: -1} = "M" ] ; then |
---|
1467 | # (( temp_avail = temp_avail * 1000000 )) |
---|
1468 | # elif [ ${volume_avail: -1} = "k" ] ; then |
---|
1469 | # (( temp_avail = temp_avail * 1000 )) |
---|
1470 | # else |
---|
1471 | # (( temp_avail = volume_avail )) |
---|
1472 | # fi |
---|
1473 | # if [ ${volume_quota: -1} = "T" ] ; then |
---|
1474 | # (( temp_quota = temp_quota * 1000000000000 )) |
---|
1475 | # elif [ ${volume_quota: -1} = "G" ] ; then |
---|
1476 | # (( temp_quota = temp_quota * 1000000000 )) |
---|
1477 | # elif [ ${volume_quota: -1} = "M" ] ; then |
---|
1478 | # (( temp_quota = temp_quota * 1000000 )) |
---|
1479 | # elif [ ${volume_quota: -1} = "k" ] ; then |
---|
1480 | # (( temp_quota = temp_quota * 1000 )) |
---|
1481 | # else |
---|
1482 | # (( temp_quota = volume_quota )) |
---|
1483 | # fi |
---|
1484 | # fi |
---|
1485 | # |
---|
1486 | # quota_volume=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc) |
---|
1487 | ## echo "volume ratio is " $quota_volume |
---|
1488 | # |
---|
1489 | # if [ ${quota_volume} -ge ${limit_quota} ] ; then |
---|
1490 | # IGCM_debug_Print 1 "Please, check your quota of volume on scratch" |
---|
1491 | # IGCM_debug_Print 1 "${quota_volume}% of your quota is used" |
---|
1492 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
1493 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
1494 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
1495 | # IGCM_debug_Verif_Exit |
---|
1496 | # fi |
---|
1497 | # |
---|
1498 | # fi |
---|
1499 | # |
---|
1500 | ## Check of the number of inodes |
---|
1501 | # |
---|
1502 | # inode_quota=$(ccc_quota | grep ' scratch' | gawk '{print $6}') |
---|
1503 | # inode_avail=$(ccc_quota | grep ' scratch' | gawk '{print $7}') |
---|
1504 | # |
---|
1505 | # if ( [ ! X${inode_quota} = X ] && [ ! ${inode_quota} = "-" ] ) ; then |
---|
1506 | # |
---|
1507 | # unit_avail=${inode_avail: -1} |
---|
1508 | # unit_quota=${inode_quota: -1} |
---|
1509 | # |
---|
1510 | # if [ "${unit_quota}" = "*" ] ; then |
---|
1511 | # IGCM_debug_Print 1 "Please, check your quota of inode on scratch" |
---|
1512 | # IGCM_debug_Print 1 "More than 100% of your quota is used" |
---|
1513 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
1514 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
1515 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
1516 | # IGCM_debug_Verif_Exit |
---|
1517 | # fi |
---|
1518 | # |
---|
1519 | # temp_avail=${inode_avail%%${inode_avail: -1}*} |
---|
1520 | # temp_quota=${inode_quota%%${inode_quota: -1}*} |
---|
1521 | # |
---|
1522 | # if [ ! ${unit_avail} = ${unit_quota} ] ; then |
---|
1523 | # |
---|
1524 | # # Convertion |
---|
1525 | # if [ ${inode_avail: -1} = "T" ] ; then |
---|
1526 | # (( temp_avail = temp_avail * 1000000000000 )) |
---|
1527 | # elif [ ${inode_avail: -1} = "G" ] ; then |
---|
1528 | # (( temp_avail = temp_avail * 1000000000 )) |
---|
1529 | # elif [ ${inode_avail: -1} = "M" ] ; then |
---|
1530 | # (( temp_avail = temp_avail * 1000000 )) |
---|
1531 | # elif [ ${inode_avail: -1} = "k" ] ; then |
---|
1532 | # (( temp_avail = temp_avail * 1000 )) |
---|
1533 | # else |
---|
1534 | # (( temp_avail = inode_avail )) |
---|
1535 | # fi |
---|
1536 | # |
---|
1537 | # if [ ${inode_quota: -1} = "T" ] ; then |
---|
1538 | # (( temp_quota = temp_quota * 1000000000000 )) |
---|
1539 | # elif [ ${inode_quota: -1} = "G" ] ; then |
---|
1540 | # (( temp_quota = temp_quota * 1000000000 )) |
---|
1541 | # elif [ ${inode_quota: -1} = "M" ] ; then |
---|
1542 | # (( temp_quota = temp_quota * 1000000 )) |
---|
1543 | # elif [ ${inode_quota: -1} = "k" ] ; then |
---|
1544 | # (( temp_quota = temp_quota * 1000 )) |
---|
1545 | # else |
---|
1546 | # (( temp_quota = inode_quota )) |
---|
1547 | # fi |
---|
1548 | # fi |
---|
1549 | # quota_inode=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc) |
---|
1550 | ## echo "inode ratio is " $quota_inode |
---|
1551 | # |
---|
1552 | # if [ ${quota_inode} -ge ${limit_quota} ] ; then |
---|
1553 | # IGCM_debug_Print 1 "Please, check your quota of inode on scratch" |
---|
1554 | # IGCM_debug_Print 1 "${quota_inode}% of your quota is used" |
---|
1555 | # IGCM_debug_Print 1 "Use the ccc_quota command to check" |
---|
1556 | # IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
1557 | # IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
1558 | # IGCM_debug_Verif_Exit |
---|
1559 | # fi |
---|
1560 | # fi |
---|
1561 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
1562 | } |
---|
1563 | |
---|
1564 | #D-#================================================== |
---|
1565 | #D-function IGCM_sys_projectAccounting |
---|
1566 | #D-* Purpose: store project accounting information in a file |
---|
1567 | #D-* Examples: |
---|
1568 | #D- |
---|
1569 | function IGCM_sys_projectAccounting { |
---|
1570 | IGCM_debug_PushStack "IGCM_sys_projectAccounting" |
---|
1571 | if ( $DEBUG_sys ) ; then |
---|
1572 | echo "IGCM_sys_check_quota" |
---|
1573 | fi |
---|
1574 | #need to implemented on Jean Zay |
---|
1575 | touch $1 |
---|
1576 | # ssh irene191 /usr/bin/ccc_myproject > $1 |
---|
1577 | |
---|
1578 | IGCM_debug_PopStack "IGCM_sys_projectAccounting" |
---|
1579 | } |
---|
1580 | |
---|
1581 | #D-#================================================== |
---|
1582 | #D-function IGCM_sys_getJobSchedulerID |
---|
1583 | #D-* Purpose: Get the job ID during execution |
---|
1584 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
1585 | #D- |
---|
1586 | function IGCM_sys_getJobSchedulerID { |
---|
1587 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
1588 | if ( $DEBUG_sys ) ; then |
---|
1589 | echo "IGCM_sys_getJobSchedulerID" |
---|
1590 | fi |
---|
1591 | |
---|
1592 | eval ${1}=${SLURM_JOBID} |
---|
1593 | |
---|
1594 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
1595 | } |
---|
1596 | |
---|
1597 | #D-#================================================== |
---|
1598 | #D-function IGCM_sys_GetJobID |
---|
1599 | #D-* Purpose: Get the job ID from the JobName |
---|
1600 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
1601 | #D- |
---|
1602 | function IGCM_sys_GetJobID { |
---|
1603 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
1604 | if ( $DEBUG_sys ) ; then |
---|
1605 | echo "IGCM_sys_GetJobID" |
---|
1606 | fi |
---|
1607 | |
---|
1608 | ID=$( squeue -u $user | grep Job_${config_UserChoices_JobName} | gawk ' { print $1}' ) |
---|
1609 | |
---|
1610 | |
---|
1611 | eval ${3}=${ID} |
---|
1612 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
1613 | } |
---|
1614 | |
---|
1615 | #D-#================================================== |
---|
1616 | #D-function IGCM_sys_CountJobInQueue |
---|
1617 | #D-* Purpose: Count number of users job |
---|
1618 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
1619 | #D- |
---|
1620 | function IGCM_sys_CountJobInQueue { |
---|
1621 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
1622 | if ( $DEBUG_sys ) ; then |
---|
1623 | echo "IGCM_sys_CountJobInQueue" |
---|
1624 | fi |
---|
1625 | |
---|
1626 | # With -f option, the full job name is given in the last column |
---|
1627 | NbRun=$(squeue -u $user | \ |
---|
1628 | grep -v JOBID | gawk 'BEGIN { x=0 } ( $NF ~ JobName ) { x=x+1 } END { print x }' ) |
---|
1629 | |
---|
1630 | eval ${2}=${NbRun} |
---|
1631 | |
---|
1632 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
1633 | } |
---|
1634 | |
---|
1635 | #D-#================================================== |
---|
1636 | #D-function IGCM_sys_ListJobInQueue |
---|
1637 | #D-* Purpose: Produce a list of users computing jobs (excluding post-processing) |
---|
1638 | #D-* Examples: IGCM_sys_ListJobInQueue ${User} JobNameList |
---|
1639 | #D- |
---|
1640 | function IGCM_sys_ListJobInQueue { |
---|
1641 | IGCM_debug_PushStack "IGCM_sys_ListJobInQueue" |
---|
1642 | if ( $DEBUG_sys ) ; then |
---|
1643 | echo "IGCM_sys_ListJobInQueue" |
---|
1644 | fi |
---|
1645 | |
---|
1646 | # to be implemented on Jean Zay |
---|
1647 | set -A JobList $( squeue -u $user | gawk '{print $3}' | grep -v NAME) |
---|
1648 | # # With -f option, the full job name is given in the last column |
---|
1649 | # set -A JobList $( ccc_mstat -f | gawk -v User=$1 \ |
---|
1650 | # '( $2 == User && \ |
---|
1651 | # $NF != /TS/ && \ |
---|
1652 | # $NF !~ /PACK/ && \ |
---|
1653 | # $NF !~ /REBUILD/ && \ |
---|
1654 | # $NF !~ /pack/ ) \ |
---|
1655 | # { print $NF }' | sed -e "s/\(.*\)\.[0-9]*/\1/" ) |
---|
1656 | # |
---|
1657 | eval set -A ${2} ${JobList[*]} |
---|
1658 | |
---|
1659 | IGCM_debug_PopStack "IGCM_sys_ListJobInQueue" |
---|
1660 | } |
---|
1661 | |
---|
1662 | #D-#================================================== |
---|
1663 | #D-function IGCM_sys_atlas |
---|
1664 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
---|
1665 | #D-* Examples: |
---|
1666 | #D- |
---|
1667 | function IGCM_sys_atlas { |
---|
1668 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
---|
1669 | if ( $DEBUG_sys ) ; then |
---|
1670 | echo "IGCM_sys_atlas :" $@ |
---|
1671 | fi |
---|
1672 | |
---|
1673 | typeset status |
---|
1674 | # To be implemented on Jean Zay |
---|
1675 | # |
---|
1676 | # \ccc_mprun atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
1677 | # status=$? |
---|
1678 | # if [ ${status} -gt 0 ] ; then |
---|
1679 | # echo "IGCM_sys_atlas : error code ${status}" |
---|
1680 | # cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
1681 | # \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
1682 | # IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1683 | # return 1 |
---|
1684 | # else |
---|
1685 | # IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1686 | # return 0 |
---|
1687 | # fi |
---|
1688 | # |
---|
1689 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1690 | } |
---|
1691 | |
---|
1692 | #D-#================================================== |
---|
1693 | #D-function IGCM_sys_rebuild_nemo |
---|
1694 | #D-* Purpose: rebuild nemo parallel files with nemo specific rebuild on curie |
---|
1695 | #D-* Examples: |
---|
1696 | #D- |
---|
1697 | |
---|
1698 | function IGCM_sys_rebuild_nemo { |
---|
1699 | IGCM_debug_PushStack "IGCM_sys_rebuild_nemo" $@ |
---|
1700 | if ( $DEBUG_sys ) ; then |
---|
1701 | echo "IGCM_sys_rebuild_nemo :" $@ |
---|
1702 | fi |
---|
1703 | |
---|
1704 | /gpfswork/rech/psl/commun/Tools/rebuild_nemo/bin/rebuild_nemo ${1} ${2} |
---|
1705 | |
---|
1706 | IGCM_debug_PopStack "IGCM_sys_rebuild_nemo" |
---|
1707 | } |
---|
1708 | |
---|