1 | #!/bin/ksh |
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2 | |
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3 | #************************************************************** |
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4 | # Author: Sébastien Denvil |
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5 | # Contact: Sebastien.Denvil__at__ipsl.jussieu.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 Ada |
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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 and user names |
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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 | # $hostname of the MASTER job |
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70 | typeset MASTER=ada |
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71 | # project name |
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72 | typeset PROJECT=$(echo ${LOADL_STEP_GROUP:=NONE}) |
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73 | # jobWarningDelay in seconds |
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74 | typeset jobWarningDelay=$( TZ=utc date -d '1970-01-01 '${wall_clock_limit} +%s ) |
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75 | |
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76 | #D- |
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77 | #D-#================================================== |
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78 | #D-Program used in libIGCM |
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79 | #D-#================================================== |
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80 | |
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81 | # Submit command |
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82 | typeset SUBMIT=${SUBMIT:=llsubmit} |
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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=ergon |
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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 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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93 | #==================================================== |
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94 | source /smplocal/pub/Modules/default/init/ksh |
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95 | if ( [ "X${LOADL_STEP_TYPE}" = "XPARALLEL" ] || [ "X${LOADL_STEP_TYPE}" = "XSERIAL" ] ) ; then |
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96 | module load python/2.7.10 > /dev/null 2>&1 |
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97 | . /smphome/rech/psl/rpsl035/.atlas_env_ada_intel_2013_0_bash > /dev/null 2>&1 |
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98 | else |
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99 | module load python/2.7.10 > /dev/null 2>&1 |
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100 | module unload intel > /dev/null 2>&1 |
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101 | module load intel/2016.2 > /dev/null 2>&1 |
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102 | . /smphome/rech/psl/rpsl035/.atlas_env_ada_bash > /dev/null 2>&1 |
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103 | export PCMDI_MP=/workgpfs/rech/psl/rpsl035/PCMDI-MP |
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104 | export UVCDAT_ANONYMOUS_LOG=no |
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105 | fi |
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106 | [ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:" |
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107 | [ ! X${TaskType} = Xchecking ] && module list |
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108 | |
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109 | export PATH=${PATH}:/smphome/rech/psl/rpsl035/AddNoise/src_X64_ADA/bin |
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110 | export PATH=${PATH}:/smphome/rech/psl/rpsl035/AddPerturbation/src_X64_ADA/bin |
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111 | export PATH=${PATH}:/smphome/rech/psl/rpsl035/bin/ |
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112 | |
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113 | #==================================================== |
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114 | # Host specific DIRECTORIES |
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115 | #==================================================== |
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116 | |
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117 | #==================================================== |
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118 | #- MirrorlibIGCM for frontend |
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119 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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120 | |
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121 | #==================================================== |
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122 | #- libIGCM_POST for frontend |
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123 | typeset -r libIGCM_POST=${libIGCM} |
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124 | |
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125 | #==================================================== |
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126 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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127 | typeset -r R_EXE="${MODIPSL}/bin" |
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128 | |
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129 | #==================================================== |
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130 | #- SUBMIT_DIR : submission dir |
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131 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${LOADL_STEP_INITDIR}} |
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132 | |
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133 | #==================================================== |
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134 | #- IN |
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135 | typeset -r R_IN=${R_IN:=/workgpfs/rech/psl/rpsl035/IGCM} |
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136 | typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/u/rech/psl/rpsl376} |
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137 | |
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138 | #==================================================== |
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139 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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140 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${TMPDIR}} |
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141 | |
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142 | #==================================================== |
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143 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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144 | typeset -r OUTCOMMAND_PATH=${RUN_DIR_PATH:-/tmp} |
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145 | |
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146 | #==================================================== |
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147 | #- HOST_MPIRUN_COMMAND |
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148 | if ( [ "X${LOADL_STEP_TYPE}" = "XPARALLEL" ] || [ "X${LOADL_STEP_TYPE}" = "XSERIAL" ] ) ; then |
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149 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time poe"} |
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150 | else |
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151 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time mpirun"} |
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152 | fi |
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153 | #==================================================== |
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154 | #- Max number of arguments passed to nco operator or demigration command |
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155 | UNIX_MAX_LIMIT=360 |
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156 | |
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157 | #==================================================== |
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158 | #- set PackDefault to true on ada |
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159 | PackDefault=true |
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160 | |
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161 | #==================================================== |
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162 | #- Number of cores per node |
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163 | core_per_node=32 |
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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 | #D-#================================================== |
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174 | #D-function IGCM_sys_defineArchives |
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175 | #D-* Purpose: |
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176 | #D-* Define ARCHIVE : Dedicated to large files |
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177 | #D-* Define STORAGE : Dedicated to small/medium files |
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178 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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179 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) |
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180 | #D-* Define R_BUF : Output tree located on SCRATCHDIR hosting files waiting for rebuild or pack processes |
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181 | #D-* if SpaceName=TEST everything is stored on WORKDIR |
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182 | #D-* Examples: |
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183 | #D- |
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184 | function IGCM_sys_defineArchives { |
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185 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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186 | |
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187 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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188 | #==================================================== |
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189 | #- ARCHIVE (dedicated to large files) |
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190 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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191 | else |
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192 | #==================================================== |
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193 | #- ARCHIVE (dedicated to large files) |
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194 | ARCHIVE=$(echo ${HOME} | sed -e "s,/.*home/,/arch/home/,") |
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195 | fi |
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196 | |
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197 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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198 | #==================================================== |
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199 | #- STORAGE (dedicated to small/medium files) |
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200 | STORAGE=${config_UserChoices_STORAGE} |
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201 | else |
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202 | #==================================================== |
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203 | #- STORAGE (dedicated to small/medium files) |
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204 | STORAGE=${WORKDIR} |
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205 | fi |
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206 | |
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207 | if [ X${config_UserChoices_SpaceName} = XTEST ]; then |
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208 | #==================================================== |
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209 | #- R_OUT |
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210 | R_OUT=${WORKDIR}/IGCM_OUT |
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211 | |
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212 | #==================================================== |
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213 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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214 | R_FIG=${WORKDIR}/IGCM_OUT |
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215 | |
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216 | IGCM_debug_Print 1 "SpaceName=TEST ==> OVERRULE destination path directories" |
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217 | |
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218 | else |
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219 | #==================================================== |
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220 | #- R_OUT |
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221 | R_OUT=${ARCHIVE}/IGCM_OUT |
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222 | |
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223 | #==================================================== |
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224 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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225 | R_FIG=${ARCHIVE}/IGCM_OUT |
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226 | fi |
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227 | |
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228 | #==================================================== |
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229 | #- R_BUF (ONLY FOR double copy an scratch) |
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230 | R_BUF=${WORKDIR}/IGCM_OUT |
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231 | |
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232 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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233 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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234 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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235 | |
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236 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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237 | } |
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238 | |
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239 | #D-#================================================== |
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240 | #D-function IGCM_sys_RshArchive |
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241 | #D-* Purpose: Archive rsh command |
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242 | #D-* Examples: |
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243 | #D- |
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244 | function IGCM_sys_RshArchive { |
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245 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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246 | DEBUG_sys=false IGCM_sys_IsFileArchived "$@" |
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247 | if [ $? = 0 ] ; then |
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248 | rsh ${STOREHOST} exec /bin/ksh <<-EOF |
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249 | ${@} |
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250 | EOF |
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251 | status=$? |
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252 | else |
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253 | /bin/ksh <<-EOF |
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254 | ${@} |
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255 | EOF |
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256 | status=$? |
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257 | fi |
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258 | if [ ${status} -gt 0 ] ; then |
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259 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : rsh or command failed error code ${status}" |
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260 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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261 | fi |
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262 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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263 | } |
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264 | |
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265 | #D-#================================================== |
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266 | #D-function IGCM_sys_RshArchive_NoError |
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267 | #D-* Purpose: Archive rsh command, without error |
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268 | #D-* used only in monitoring.job |
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269 | #D-* Examples: |
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270 | #D- |
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271 | function IGCM_sys_RshArchive_NoError { |
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272 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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273 | DEBUG_sys=false IGCM_sys_IsFileArchived "$@" |
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274 | if [ $? = 0 ] ; then |
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275 | rsh ${STOREHOST} exec /bin/ksh <<-EOF |
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276 | ${@} 2> /dev/null |
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277 | EOF |
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278 | else |
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279 | /bin/ksh <<-EOF |
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280 | ${@} 2> /dev/null |
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281 | EOF |
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282 | fi |
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283 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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284 | } |
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285 | |
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286 | #D-#================================================== |
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287 | #D-function IGCM_sys_MkdirArchive |
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288 | #D-* Purpose: Mkdir on Archive |
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289 | #D-* Examples: |
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290 | #D- |
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291 | function IGCM_sys_MkdirArchive { |
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292 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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293 | if ( $DEBUG_sys ) ; then |
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294 | echo "IGCM_sys_MkdirArchive :" $@ |
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295 | fi |
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296 | #- creation de repertoire sur le serveur fichier |
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297 | DEBUG_sys=false IGCM_sys_IsFileArchived $1 |
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298 | if [ $? = 0 ] ; then |
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299 | rsh ${STOREHOST} -n mkdir -p $1 |
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300 | status=$? |
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301 | else |
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302 | mkdir -p $1 |
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303 | status=$? |
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304 | fi |
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305 | |
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306 | if [ ${status} -gt 0 ] ; then |
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307 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : rsh or mkdir failed error code ${status}" |
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308 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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309 | fi |
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310 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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311 | } |
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312 | |
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313 | #D-#================================================== |
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314 | #D-function IGCM_sys_TestDirArchive |
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315 | #D-* Purpose: Test Directory that must exists on Archive |
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316 | #D-* Examples: |
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317 | #D- |
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318 | function IGCM_sys_TestDirArchive { |
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319 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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320 | if ( $DEBUG_sys ) ; then |
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321 | echo "IGCM_sys_TestDirArchive :" $@ |
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322 | fi |
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323 | typeset ExistFlag |
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324 | #Command depends on targeted file system |
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325 | DEBUG_sys=false IGCM_sys_IsFileArchived $1 |
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326 | if [ $? = 0 ] ; then |
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327 | ExistFlag=$( IGCM_sys_RshArchive "[ -d $1 ] && echo 0 || echo 1" ) |
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328 | else |
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329 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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330 | fi |
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331 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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332 | return ${ExistFlag} |
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333 | } |
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334 | |
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335 | #D-#================================================== |
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336 | #D-function IGCM_sys_IsFileArchived |
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337 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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338 | #D-* Examples: |
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339 | #D- |
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340 | function IGCM_sys_IsFileArchived { |
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341 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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342 | if ( $DEBUG_sys ) ; then |
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343 | echo "IGCM_sys_IsFileArchived :" $@ |
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344 | fi |
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345 | typeset IsArchivedFlag |
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346 | IsArchivedFlag=$( [ "X$( echo $@ | grep \/arch\/home )" != "X" ] && echo 0 || echo 1 ) |
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347 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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348 | |
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349 | return ${IsArchivedFlag} |
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350 | } |
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351 | |
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352 | #D-#================================================== |
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353 | #D-function IGCM_sys_TestFileArchive |
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354 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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355 | #D-* Examples: |
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356 | #D- |
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357 | function IGCM_sys_TestFileArchive { |
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358 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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359 | typeset ExistFlag |
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360 | ExistFlag=$( IGCM_sys_RshArchive "[ -f $1 ] && echo 0 || echo 1" ) |
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361 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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362 | |
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363 | return ${ExistFlag} |
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364 | } |
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365 | |
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366 | #D-#================================================== |
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367 | #D-function IGCM_sys_CountFileArchive |
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368 | #D-* Purpose: Count files on Archive filesystem |
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369 | #D-* Examples: |
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370 | #D- |
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371 | function IGCM_sys_CountFileArchive { |
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372 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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373 | #Command depends on targeted file system |
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374 | DEBUG_sys=false IGCM_sys_IsFileArchived $1 |
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375 | if [ $? = 0 ] ; then |
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376 | IGCM_sys_RshArchive "ls ${@} 2>/dev/null | wc -l" |
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377 | status=$? |
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378 | else |
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379 | ls ${@} 2>/dev/null | wc -l |
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380 | status=$? |
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381 | fi |
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382 | if [ ${status} -gt 0 ] ; then |
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383 | echo "IGCM_sys_CountFileArchive : erreur." |
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384 | fi |
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385 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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386 | } |
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387 | |
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388 | #D-#================================================== |
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389 | #D-function IGCM_sys_Tree |
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390 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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391 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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392 | #D- |
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393 | function IGCM_sys_Tree { |
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394 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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395 | if ( $DEBUG_sys ) ; then |
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396 | echo "IGCM_sys_Tree :" $@ |
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397 | fi |
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398 | |
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399 | \mfls -R $@ |
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400 | |
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401 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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402 | } |
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403 | |
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404 | #D-#================================================== |
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405 | #D-function IGCM_sys_Qsub |
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406 | #D-* Purpose: Qsub new job |
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407 | #D-* Examples: |
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408 | #D- |
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409 | function IGCM_sys_Qsub { |
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410 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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411 | if ( $DEBUG_sys ) ; then |
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412 | echo "IGCM_sys_Qsub :" $@ |
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413 | fi |
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414 | typeset status |
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415 | |
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416 | # We have to change output/error file |
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417 | [ ${#@} = 1 ] && REP_FOR_JOB=${SUBMIT_DIR} |
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418 | [ ${#@} = 2 ] && REP_FOR_JOB=${2} |
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419 | sed -e "s:\# \@ output *= .*:\# \@ output = ${Script_Output}:" \ |
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420 | -e "s:\# \@ error *= .*:\# \@ error = ${Script_Output}:" \ |
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421 | $1 > ${REP_FOR_JOB}/JOB_FOR_IGCM |
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422 | cd $REP_FOR_JOB ; /usr/bin/llsubmit JOB_FOR_IGCM > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 ; status=$? ; cd - ; |
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423 | |
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424 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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425 | if [ ${status} -gt 0 ] ; then |
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426 | IGCM_debug_Print 2 "IGCM_sys_Qsub $1 : error code ${status}" |
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427 | IGCM_debug_Exit "IGCM_sys_Qsub" |
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428 | else |
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429 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ | tail -1 | sed -e s/\"//g ) |
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430 | IGCM_sys_Rm ${REP_FOR_JOB}/JOB_FOR_IGCM |
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431 | fi |
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432 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
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433 | } |
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434 | |
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435 | #D-#================================================== |
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436 | #D-function IGCM_sys_QsubPost |
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437 | #D-* Purpose: Qsub new job on scalaire |
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438 | #D-* Examples: |
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439 | #D- |
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440 | function IGCM_sys_QsubPost { |
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441 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
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442 | if ( $DEBUG_sys ) ; then |
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443 | echo "IGCM_sys_QsubPost :" $@ |
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444 | fi |
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445 | typeset status |
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446 | |
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447 | # We have to change output/error file |
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448 | [ ${#@} = 1 ] && REP_FOR_JOB=${POST_DIR} |
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449 | [ ${#@} = 2 ] && REP_FOR_JOB=${2} |
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450 | |
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451 | sed -e "s:\# \@ output *= .*:\# \@ output = ${Script_Post_Output}.out:" \ |
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452 | -e "s:\# \@ error *= .*:\# \@ error = ${Script_Post_Output}.out:" \ |
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453 | ${libIGCM_POST}/$1.job > ${REP_FOR_JOB}/JOB_FOR_IGCM_$$ |
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454 | |
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455 | cd $REP_FOR_JOB ; /usr/bin/llsubmit JOB_FOR_IGCM_$$ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 ; status=$? ; cd - ; |
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456 | |
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457 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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458 | if [ ${status} -gt 0 ] ; then |
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459 | IGCM_debug_Print 2 "IGCM_sys_QsubPost $1 : error code ${status}" |
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460 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
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461 | else |
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462 | JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ | tail -1 | sed -e s/\"//g ) |
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463 | IGCM_sys_Rm ${REP_FOR_JOB}/JOB_FOR_IGCM_$$ |
---|
464 | fi |
---|
465 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
---|
466 | } |
---|
467 | |
---|
468 | #D-************************* |
---|
469 | #D- File transfer functions |
---|
470 | #D-************************* |
---|
471 | #D- |
---|
472 | |
---|
473 | #D-#================================================== |
---|
474 | #D-function IGCM_sys_RmRunDir |
---|
475 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
---|
476 | #D- scheduler will do the job) |
---|
477 | #D-* Examples: |
---|
478 | #D- |
---|
479 | function IGCM_sys_RmRunDir { |
---|
480 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
---|
481 | if ( $DEBUG_sys ) ; then |
---|
482 | echo "IGCM_sys_RmRunDir :" $@ |
---|
483 | IGCM_debug_Print 1 "Dummy call, let the scheduler do that." |
---|
484 | fi |
---|
485 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
---|
486 | } |
---|
487 | |
---|
488 | #D-#================================================== |
---|
489 | #D-function IGCM_sys_Put_Dir |
---|
490 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
---|
491 | #D-* Examples: |
---|
492 | #D- |
---|
493 | function IGCM_sys_Put_Dir { |
---|
494 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
---|
495 | if ( $DEBUG_sys ) ; then |
---|
496 | echo "IGCM_sys_Put_Dir :" $@ |
---|
497 | fi |
---|
498 | if [ $DRYRUN = 0 ]; then |
---|
499 | if [ ! -d ${1} ] ; then |
---|
500 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
---|
501 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
502 | return |
---|
503 | fi |
---|
504 | |
---|
505 | typeset status |
---|
506 | |
---|
507 | # Only if we use rsync |
---|
508 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
---|
509 | # |
---|
510 | #Command depends on targeted file system |
---|
511 | DEBUG_sys=false IGCM_sys_IsFileArchived $2 |
---|
512 | if [ $? = 0 ] ; then |
---|
513 | \rcp -r $1 ${STOREHOST}:$2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
514 | status=$? |
---|
515 | else |
---|
516 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
517 | status=$? |
---|
518 | fi |
---|
519 | |
---|
520 | if [ ${status} -gt 0 ] ; then |
---|
521 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : rcp or cp failed error code ${status}" |
---|
522 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
523 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
---|
524 | else |
---|
525 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
526 | fi |
---|
527 | fi |
---|
528 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
529 | } |
---|
530 | |
---|
531 | #D-#================================================== |
---|
532 | #D-function IGCM_sys_Get_Dir |
---|
533 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
534 | #D-* Examples: |
---|
535 | #D- |
---|
536 | function IGCM_sys_Get_Dir { |
---|
537 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
538 | if ( $DEBUG_sys ) ; then |
---|
539 | echo "IGCM_sys_Get_Dir :" $@ |
---|
540 | fi |
---|
541 | if [ $DRYRUN = 0 ]; then |
---|
542 | typeset NB_ESSAI DELAI status i |
---|
543 | # number of tentative |
---|
544 | NB_ESSAI=3 |
---|
545 | # time delay between tentative |
---|
546 | DELAI=2 |
---|
547 | |
---|
548 | # Only if we use rsync |
---|
549 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
---|
550 | # |
---|
551 | # Command depends on targeted filesystem |
---|
552 | DEBUG_sys=false IGCM_sys_IsFileArchived $1 |
---|
553 | if [ $? = 0 ] ; then |
---|
554 | # add dmget (to demigrate all offline files) to reduce time of this command : |
---|
555 | #IGCM_sys_RshArchive "dmfind $1 -state MIG -o -state OFL -o -state PAR | dmget -q -n" |
---|
556 | i=0 |
---|
557 | while [ $i -lt $NB_ESSAI ] ; do |
---|
558 | \rcp -rp ${STOREHOST}:$1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
559 | status=$? |
---|
560 | if [ ${status} -gt 0 ]; then |
---|
561 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : rcp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
562 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
563 | sleep $DELAI |
---|
564 | else |
---|
565 | break |
---|
566 | fi |
---|
567 | (( i = i + 1 )) |
---|
568 | done |
---|
569 | else |
---|
570 | \cp -rp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
571 | status=$? |
---|
572 | if [ ${status} -gt 0 ] ; then |
---|
573 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
574 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
575 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
576 | else |
---|
577 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
578 | fi |
---|
579 | fi |
---|
580 | if [ ${status} -gt 0 ] ; then |
---|
581 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : (r)cp failed error code ${status}" |
---|
582 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
583 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
584 | else |
---|
585 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
586 | fi |
---|
587 | fi |
---|
588 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
589 | } |
---|
590 | |
---|
591 | #D-#================================================== |
---|
592 | #D-function IGCM_sys_Put_Rest |
---|
593 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
594 | #D- File and target directory must exist. |
---|
595 | #D-* Examples: |
---|
596 | #D- |
---|
597 | function IGCM_sys_Put_Rest { |
---|
598 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
599 | if ( $DEBUG_sys ) ; then |
---|
600 | echo "IGCM_sys_Put_Rest :" $@ |
---|
601 | fi |
---|
602 | if [ $DRYRUN = 0 ]; then |
---|
603 | if [ ! -f ${1} ] ; then |
---|
604 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
605 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
606 | fi |
---|
607 | |
---|
608 | typeset status |
---|
609 | # |
---|
610 | if [ X${JobType} = XRUN ] ; then |
---|
611 | IGCM_sys_Chmod 444 ${1} |
---|
612 | fi |
---|
613 | # |
---|
614 | # |
---|
615 | #Command depends on targeted file system |
---|
616 | DEBUG_sys=false IGCM_sys_IsFileArchived $2 |
---|
617 | if [ $? = 0 ] ; then |
---|
618 | mfput $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
619 | status=$? |
---|
620 | else |
---|
621 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
622 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
623 | status=$? |
---|
624 | fi |
---|
625 | |
---|
626 | # #RSYNC WITH NETWORK RSH CALL |
---|
627 | # IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
628 | # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
629 | # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
630 | |
---|
631 | # #RSYNC WITH NFS USE |
---|
632 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
633 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
634 | |
---|
635 | # status=$? |
---|
636 | # IGCM_sys_Rsync_out $status |
---|
637 | |
---|
638 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
639 | # (( status=status+$? )) |
---|
640 | |
---|
641 | if [ ${status} -gt 0 ] ; then |
---|
642 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : mfput or cp failed error code ${status}" |
---|
643 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
644 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
645 | else |
---|
646 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
647 | fi |
---|
648 | fi |
---|
649 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
650 | } |
---|
651 | |
---|
652 | #D-#================================================== |
---|
653 | #D-function IGCM_sys_Put_Out |
---|
654 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
655 | #D-* Examples: |
---|
656 | #D- |
---|
657 | function IGCM_sys_Put_Out { |
---|
658 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
659 | if ( $DEBUG_sys ) ; then |
---|
660 | echo "IGCM_sys_Put_Out :" $@ |
---|
661 | fi |
---|
662 | |
---|
663 | typeset status |
---|
664 | |
---|
665 | if [ $DRYRUN = 0 ]; then |
---|
666 | if [ ! -f ${1} ] ; then |
---|
667 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
668 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
669 | return 1 |
---|
670 | fi |
---|
671 | # |
---|
672 | if [ X${JobType} = XRUN ] ; then |
---|
673 | if [ X${3} = X ] ; then |
---|
674 | IGCM_sys_Chmod 444 ${1} |
---|
675 | fi |
---|
676 | fi |
---|
677 | # |
---|
678 | # |
---|
679 | #Command depends on targeted file system |
---|
680 | DEBUG_sys=false IGCM_sys_IsFileArchived $2 |
---|
681 | if [ $? = 0 ] ; then |
---|
682 | mfput $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
683 | status=$? |
---|
684 | else |
---|
685 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
686 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
687 | status=$? |
---|
688 | fi |
---|
689 | |
---|
690 | # #RSYNC WITH NETWORK RSH CALL |
---|
691 | # IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
692 | # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
693 | # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
694 | |
---|
695 | # #RSYNC WITH NFS USE |
---|
696 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
697 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
698 | |
---|
699 | # status=$? |
---|
700 | # IGCM_sys_Rsync_out $status |
---|
701 | |
---|
702 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
703 | # (( status=status+$? )) |
---|
704 | |
---|
705 | if [ ${status} -gt 0 ] ; then |
---|
706 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : mfput or cp failed error code ${status}" |
---|
707 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
708 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
709 | else |
---|
710 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
711 | fi |
---|
712 | fi |
---|
713 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
714 | return 0 |
---|
715 | } |
---|
716 | |
---|
717 | #D-#================================================== |
---|
718 | #D-function IGCM_sys_Get |
---|
719 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
720 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
721 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
722 | function IGCM_sys_Get { |
---|
723 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
724 | |
---|
725 | typeset DEST status dm_liste |
---|
726 | |
---|
727 | if ( $DEBUG_sys ) ; then |
---|
728 | echo "IGCM_sys_Get :" $@ |
---|
729 | fi |
---|
730 | if [ $DRYRUN -le 2 ]; then |
---|
731 | if [ X${1} = X'/l' ] ; then |
---|
732 | eval set +A dm_liste \${${2}} |
---|
733 | else |
---|
734 | dm_liste=${1} |
---|
735 | fi |
---|
736 | eval DEST=\${${#}} |
---|
737 | |
---|
738 | # test if the (first) file is present in the old computation : |
---|
739 | DEBUG_sys=false IGCM_sys_IsFileArchived ${dm_liste[0]} |
---|
740 | if [ $? = 0 ] ; then |
---|
741 | IGCM_sys_TestFileArchive ${dm_liste[0]} |
---|
742 | status=$? |
---|
743 | else |
---|
744 | IGCM_sys_TestFileBuffer ${dm_liste[0]} |
---|
745 | status=$? |
---|
746 | fi |
---|
747 | |
---|
748 | if [ ${status} -gt 0 ] ; then |
---|
749 | echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." |
---|
750 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
751 | return |
---|
752 | fi |
---|
753 | |
---|
754 | #Command depends on targeted file system |
---|
755 | DEBUG_sys=false IGCM_sys_IsFileArchived ${dm_liste[0]} |
---|
756 | if [ $? = 0 ] ; then |
---|
757 | mfget ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
758 | status=$? |
---|
759 | else |
---|
760 | \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
761 | status=$? |
---|
762 | fi |
---|
763 | |
---|
764 | # #RSYNC WITH NETWORK RSH CALL |
---|
765 | # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
766 | # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
767 | |
---|
768 | # #RSYNC WITH NFS USE |
---|
769 | # echo ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
770 | # ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
771 | |
---|
772 | # status=$? |
---|
773 | # IGCM_sys_Rsync_out $status |
---|
774 | |
---|
775 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
776 | # (( status=status+$? )) |
---|
777 | |
---|
778 | if [ ${status} -gt 0 ] ; then |
---|
779 | IGCM_debug_Print 2 "IGCM_sys_Get : mfget or cp failed error code ${status}" |
---|
780 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
781 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
782 | else |
---|
783 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
784 | fi |
---|
785 | fi |
---|
786 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
787 | } |
---|
788 | |
---|
789 | #D-#================================================== |
---|
790 | #D-function IGCM_sys_GetDate_Monitoring |
---|
791 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
792 | #D-* Examples: |
---|
793 | #D- |
---|
794 | function IGCM_sys_GetDate_Monitoring { |
---|
795 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
796 | if ( $DEBUG_sys ) ; then |
---|
797 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
798 | fi |
---|
799 | |
---|
800 | IGCM_sys_Cd /tmp |
---|
801 | # NASTY HACK. We force /tmp here. This function is called only from the front-end and interactively. |
---|
802 | RUN_DIR_PATH=/tmp IGCM_sys_Get ${1} . |
---|
803 | eval ${2}=$( cdo showyear $( basename ${1} ) 2> /dev/null | gawk '{ print $NF }' ) |
---|
804 | # Need to erase this file to avoid collision (permission denied getting file) between users on the front-end |
---|
805 | IGCM_sys_Rm -f $( basename ${1} ) |
---|
806 | IGCM_sys_Cd - |
---|
807 | |
---|
808 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
809 | } |
---|
810 | |
---|
811 | #D-#================================================== |
---|
812 | #D-function IGCM_sys_Put_Dods |
---|
813 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. |
---|
814 | #D-* Examples: |
---|
815 | #D- |
---|
816 | function IGCM_sys_Put_Dods { |
---|
817 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
818 | if ( $DEBUG_sys ) ; then |
---|
819 | echo "IGCM_sys_Put_Dods :" $@ |
---|
820 | fi |
---|
821 | typeset status |
---|
822 | if [ $DRYRUN = 0 ]; then |
---|
823 | # We take our time on that |
---|
824 | sleep 10 |
---|
825 | IGCM_sys_TestDirArchive ${R_SAVE}/${1} |
---|
826 | if [ $? != 0 ] ; then |
---|
827 | echo "WARNING : IGCM_sys_Put_Dods ${R_SAVE}/${1} DOES NOT EXIST ." |
---|
828 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
829 | return |
---|
830 | fi |
---|
831 | |
---|
832 | rsh ${STOREHOST} exec /bin/ksh <<EOF |
---|
833 | cd ${R_SAVE} |
---|
834 | /arch/local/bin/dods_rm DODS/pub/${LOGIN}/${R_DODS}/${1} > /dev/null 2>&1 |
---|
835 | /bin/chmod -R u+w ${R_SAVE}/${1} |
---|
836 | /arch/local/bin/dods_cp ${1} DODS/pub/${LOGIN}/${R_DODS} > /dev/null 2>&1 |
---|
837 | /bin/chmod -R +rX ${R_SAVE}/${1} |
---|
838 | /bin/chmod -R u+w ${R_SAVE}/${1} |
---|
839 | EOF |
---|
840 | status=$? |
---|
841 | |
---|
842 | if [ ${status} -gt 0 ] ; then |
---|
843 | echo "IGCM_sys_Put_Dods : error." |
---|
844 | IGCM_debug_Exit "IGCM_sys_Put_Dods" |
---|
845 | fi |
---|
846 | fi |
---|
847 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
848 | } |
---|
849 | |
---|
850 | ############################################################## |
---|
851 | # REBUILD OPERATOR |
---|
852 | |
---|
853 | #D-#================================================== |
---|
854 | #D-function IGCM_sys_sync |
---|
855 | #D-* Purpose: flush buffer on disk (dummy function on Ada) |
---|
856 | #D-* Examples: |
---|
857 | #D- |
---|
858 | function IGCM_sys_sync { |
---|
859 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
860 | if ( $DEBUG_sys ) ; then |
---|
861 | echo "IGCM_sys_sync :" $@ |
---|
862 | echo "Dummy call, let the system do that." |
---|
863 | fi |
---|
864 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
865 | } |
---|
866 | |
---|
867 | ############################################################ |
---|
868 | # Activate Running Environnment Variables |
---|
869 | |
---|
870 | #D-#================================================== |
---|
871 | #D-function IGCM_sys_activ_variables |
---|
872 | #D-* Purpose: set environement variables prior to execution |
---|
873 | #D-* Examples: |
---|
874 | #D- |
---|
875 | function IGCM_sys_activ_variables { |
---|
876 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
877 | if ( $DEBUG_sys ) ; then |
---|
878 | echo "IGCM_sys_activ_variables" |
---|
879 | fi |
---|
880 | |
---|
881 | # -------------------------------------------------------------------- |
---|
882 | #D- MPI specifications |
---|
883 | # -------------------------------------------------------------------- |
---|
884 | |
---|
885 | # -------------------------------------------------------------------- |
---|
886 | #D- Other specifications |
---|
887 | # -------------------------------------------------------------------- |
---|
888 | |
---|
889 | ulimit -s unlimited |
---|
890 | ## to be done only one time |
---|
891 | ## export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/smplocal/pub/NetCDF/4.1.3/lib:/smplocal/pub/HDF5/1.8.9/seq/lib |
---|
892 | ## echo ${LD_LIBRARY_PATH} | grep -i netcdf >/dev/null 2>&1 || export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/smplocal/pub/NetCDF/4.1.3/lib:/smplocal/pub/HDF5/1.8.9/seq/lib |
---|
893 | IGCM_debug_Print 1 "set LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" |
---|
894 | |
---|
895 | export MP_STDOUTMODE=combined |
---|
896 | IGCM_debug_Print 1 "set MP_STDOUTMODE=${MP_STDOUTMODE}" |
---|
897 | |
---|
898 | ## fix to reduce memory usage. Required since 2014/22/04. On ada IDRIS. |
---|
899 | #export MP_EUILIBPATH=/smplocal/lib/ibmhpc/pe12012/ppe.pami/gnu/lib64/pami64 |
---|
900 | #IGCM_debug_Print 1 "set MP_EUILIBPATH=${MP_EUILIBPATH}" |
---|
901 | |
---|
902 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
903 | } |
---|
904 | |
---|
905 | ############################################################ |
---|
906 | # Desactivate Running Environnment Variables |
---|
907 | |
---|
908 | #D-#================================================== |
---|
909 | #D-function IGCM_sys_desactiv_variables |
---|
910 | #D-* Purpose: unset environement variables after execution |
---|
911 | #D-* Examples: |
---|
912 | #D- |
---|
913 | function IGCM_sys_desactiv_variables { |
---|
914 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
915 | if ( $DEBUG_sys ) ; then |
---|
916 | echo "IGCM_sys_desactiv_variables" |
---|
917 | fi |
---|
918 | # -------------------------------------------------------------------- |
---|
919 | #D- MPI specifications |
---|
920 | # -------------------------------------------------------------------- |
---|
921 | |
---|
922 | # -------------------------------------------------------------------- |
---|
923 | #D- Other specifications |
---|
924 | # -------------------------------------------------------------------- |
---|
925 | |
---|
926 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
927 | } |
---|
928 | |
---|
929 | ############################################################ |
---|
930 | # Update job headers to be used by the scheduler |
---|
931 | |
---|
932 | #D-#================================================== |
---|
933 | #D-function IGCM_sys_updateHeaders |
---|
934 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
935 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
936 | #D- |
---|
937 | function IGCM_sys_updateHeaders { |
---|
938 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
939 | if ( $DEBUG_sys ) ; then |
---|
940 | echo "IGCM_sys_updateHeaders" |
---|
941 | fi |
---|
942 | typeset file |
---|
943 | file=$1 |
---|
944 | |
---|
945 | if [ ${executionType} -eq 1 ] ; then |
---|
946 | # MPMD + MPI |
---|
947 | if [ X${MPIEnvironment} = XIBM ] ; then |
---|
948 | sed -e "/::openMPthreads::/d" \ |
---|
949 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
950 | ${file} > ${file}.tmp |
---|
951 | else |
---|
952 | sed -e "/::openMPthreads::/d" \ |
---|
953 | -e "s/@ job_type = parallel/@ job_type = mpich/" \ |
---|
954 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
955 | ${file} > ${file}.tmp |
---|
956 | fi |
---|
957 | |
---|
958 | elif [ ${executionType} -eq 2 ] ; then |
---|
959 | # MPMD + MPI + OMP |
---|
960 | if [ X${MPIEnvironment} = XIBM ] ; then |
---|
961 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
962 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
963 | ${file} > ${file}.tmp |
---|
964 | else |
---|
965 | (( nodeNumber = coreNumber / core_per_node )) |
---|
966 | [ $(( ${coreNumber} % ${core_per_node} )) -ne 0 ] && (( nodeNumber = nodeNumber + 1 )) |
---|
967 | sed -e "/::openMPthreads::/d" \ |
---|
968 | -e "s/@ job_type = parallel/@ job_type = mpich/" \ |
---|
969 | -e "s/@ total_tasks = ::JobNumProcTot::/@ node = ${nodeNumber} /" \ |
---|
970 | -e "/@ as_limit = 3.5gb/d" \ |
---|
971 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
972 | ${file} > ${file}.tmp |
---|
973 | fi |
---|
974 | |
---|
975 | elif [ ${executionType} -eq 3 ] ; then |
---|
976 | # SPMD + MPI/OMP |
---|
977 | if [ X${MPIEnvironment} = XIBM ] ; then |
---|
978 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
979 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
980 | ${file} > ${file}.tmp |
---|
981 | else |
---|
982 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
983 | -e "s/@ job_type = parallel/@ job_type = mpich/" \ |
---|
984 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
985 | ${file} > ${file}.tmp |
---|
986 | fi |
---|
987 | |
---|
988 | elif [ ${executionType} -eq 4 ] ; then |
---|
989 | # SPMD + MPI only |
---|
990 | if [ X${MPIEnvironment} = XIBM ] ; then |
---|
991 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
992 | -e "/::openMPthreads::/d" \ |
---|
993 | ${file} > ${file}.tmp |
---|
994 | else |
---|
995 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
996 | -e "s/@ job_type = parallel/@ job_type = mpich/" \ |
---|
997 | -e "/::openMPthreads::/d" \ |
---|
998 | ${file} > ${file}.tmp |
---|
999 | fi |
---|
1000 | |
---|
1001 | elif [ ${executionType} -eq 5 ] ; then |
---|
1002 | # SPMD + OMP only |
---|
1003 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
1004 | -e "s/@ job_type = parallel/@ job_type = serial/" \ |
---|
1005 | -e "/::JobNumProcTot::/d" \ |
---|
1006 | ${file} > ${file}.tmp |
---|
1007 | |
---|
1008 | elif [ ${executionType} -eq 6 ] ; then |
---|
1009 | # SEQUENTIAL THEN |
---|
1010 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
1011 | -e "s/@ job_type = parallel/@ job_type = serial/" \ |
---|
1012 | -e "/::openMPthreads::/d" \ |
---|
1013 | ${file} > ${file}.tmp |
---|
1014 | |
---|
1015 | fi |
---|
1016 | |
---|
1017 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
1018 | |
---|
1019 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
1020 | } |
---|
1021 | |
---|
1022 | ############################################################ |
---|
1023 | # Build MPI/OMP scripts run file (dummy function) |
---|
1024 | |
---|
1025 | #D-#================================================== |
---|
1026 | #D-function IGCM_sys_build_run_file |
---|
1027 | #D-* Purpose: build run file (deprecated) |
---|
1028 | #D-* Examples: |
---|
1029 | #D- |
---|
1030 | function IGCM_sys_build_run_file { |
---|
1031 | |
---|
1032 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
1033 | |
---|
1034 | } |
---|
1035 | |
---|
1036 | ############################################################ |
---|
1037 | # Build MPI/OMP scripts |
---|
1038 | |
---|
1039 | #D-#================================================== |
---|
1040 | #D-function IGCM_sys_build_execution_scripts |
---|
1041 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
1042 | #D-* Examples: |
---|
1043 | #D- |
---|
1044 | function IGCM_sys_build_execution_scripts |
---|
1045 | { |
---|
1046 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
1047 | if ( $DEBUG_sys ) ; then |
---|
1048 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
1049 | fi |
---|
1050 | |
---|
1051 | EXECUTION=${HOST_MPIRUN_COMMAND} |
---|
1052 | |
---|
1053 | # MPMD mode |
---|
1054 | if ( ${OK_PARA_MPMD} ) ; then |
---|
1055 | |
---|
1056 | # MPI IBM Environment |
---|
1057 | if ( [ "X${LOADL_STEP_TYPE}" = "XPARALLEL" ] || [ "X${LOADL_STEP_TYPE}" = "XSERIAL" ] ) ; then |
---|
1058 | IGCM_debug_Print 1 "You use IBM MPI environment" |
---|
1059 | if [ -f run_file ] ; then |
---|
1060 | IGCM_sys_Rm -f run_file |
---|
1061 | fi |
---|
1062 | touch run_file |
---|
1063 | |
---|
1064 | # Build run_file |
---|
1065 | |
---|
1066 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
1067 | # the coupler ie oasis3 must be the first one |
---|
1068 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1069 | |
---|
1070 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
1071 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1072 | |
---|
1073 | # for CPL component only |
---|
1074 | if [ "X${comp}" = "XCPL" ] ; then |
---|
1075 | |
---|
1076 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1077 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1078 | |
---|
1079 | if ( ${OK_PARA_MPI} ) ; then |
---|
1080 | (( mpi_count = 1 )) |
---|
1081 | until [ ${mpi_count} -gt ${comp_proc_mpi_loc} ] ; do |
---|
1082 | echo "./${ExeNameOut}" >> run_file |
---|
1083 | (( mpi_count = mpi_count + 1 )) |
---|
1084 | done |
---|
1085 | else |
---|
1086 | echo "./${ExeNameOut} " >> run_file |
---|
1087 | fi |
---|
1088 | fi |
---|
1089 | |
---|
1090 | done |
---|
1091 | |
---|
1092 | # Then second loop on the components |
---|
1093 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1094 | |
---|
1095 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
1096 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1097 | |
---|
1098 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
1099 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
1100 | |
---|
1101 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1102 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1103 | |
---|
1104 | if ( ${OK_PARA_OMP} ) ; then |
---|
1105 | # Check if the number of threads is correct |
---|
1106 | case ${comp_proc_omp_loc} in |
---|
1107 | 1|2|4) |
---|
1108 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads on IBM MPI Environment" |
---|
1109 | IGCM_debug_Print 1 "Beware : it may you use more CPU than needed." |
---|
1110 | ;; |
---|
1111 | 8) |
---|
1112 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads on IBM MPI Environment" |
---|
1113 | IGCM_debug_Print 1 "Beware : it may you use more CPU than needed." |
---|
1114 | IGCM_debug_Print 1 "Beware : these settings should not be used for IPSLCM coupled model!" |
---|
1115 | ;; |
---|
1116 | 16) |
---|
1117 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
1118 | IGCM_debug_Print 2 "Beware : ${comp_proc_omp_loc} is too much for MPMD mode" |
---|
1119 | IGCM_debug_Print 2 "You will use more CPU than needed : try to use Intel-MPI environment to do such a thing !" |
---|
1120 | IGCM_debug_Verif_Exit |
---|
1121 | ;; |
---|
1122 | *) |
---|
1123 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
1124 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
1125 | IGCM_debug_Print 2 "Only 1,2,4,8,16 as number of OMP threads are possible " |
---|
1126 | IGCM_debug_Verif_Exit |
---|
1127 | ;; |
---|
1128 | esac |
---|
1129 | |
---|
1130 | fi |
---|
1131 | |
---|
1132 | if ( ${OK_PARA_MPI} ) ; then |
---|
1133 | (( mpi_count = 1 )) |
---|
1134 | until [ ${mpi_count} -gt ${comp_proc_mpi_loc} ] ; do |
---|
1135 | if ( ${OK_PARA_OMP} ) ; then |
---|
1136 | echo "env OMP_NUM_THREADS=$comp_proc_omp_loc ./${ExeNameOut}" >> run_file |
---|
1137 | else |
---|
1138 | echo "./${ExeNameOut}" >> run_file |
---|
1139 | fi |
---|
1140 | (( mpi_count = mpi_count + 1 )) |
---|
1141 | done |
---|
1142 | else |
---|
1143 | echo "./${ExeNameOut} " >> run_file |
---|
1144 | fi |
---|
1145 | fi |
---|
1146 | done |
---|
1147 | if ( ${OK_PARA_OMP} ) ; then |
---|
1148 | export KMP_STACKSIZE=200m |
---|
1149 | fi |
---|
1150 | |
---|
1151 | EXECUTION="${HOST_MPIRUN_COMMAND} -pgmmodel mpmd -cmdfile ./run_file" |
---|
1152 | |
---|
1153 | IGCM_sys_Chmod u+x run_file |
---|
1154 | if ( $DEBUG_sys ) ; then |
---|
1155 | echo "run_file contains : " |
---|
1156 | cat run_file |
---|
1157 | fi |
---|
1158 | |
---|
1159 | |
---|
1160 | # MPI Intel Environment |
---|
1161 | else |
---|
1162 | IGCM_debug_Print 1 "You use Intel MPI environment" |
---|
1163 | |
---|
1164 | # Only MPI (MPMD) |
---|
1165 | if ( ! ${OK_PARA_OMP} ) ; then |
---|
1166 | init_exec=n |
---|
1167 | |
---|
1168 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
1169 | # the coupler ie oasis3 must be the first one |
---|
1170 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1171 | |
---|
1172 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
1173 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1174 | |
---|
1175 | # for CPL component only |
---|
1176 | if [ "X${comp}" = "XCPL" ] && [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
1177 | |
---|
1178 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1179 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1180 | |
---|
1181 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
1182 | echo "" >> script_${ExeNameOut}.ksh |
---|
1183 | echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
1184 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
1185 | EXECUTION="${EXECUTION} -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
1186 | init_exec=y |
---|
1187 | fi |
---|
1188 | done |
---|
1189 | # Then second loop on the components |
---|
1190 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1191 | |
---|
1192 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
1193 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1194 | |
---|
1195 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
1196 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
1197 | |
---|
1198 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1199 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1200 | |
---|
1201 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
1202 | echo "" >> script_${ExeNameOut}.ksh |
---|
1203 | echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
1204 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
1205 | |
---|
1206 | if [ ${init_exec} = y ] ; then |
---|
1207 | EXECUTION="${EXECUTION} : -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
1208 | else |
---|
1209 | EXECUTION="${EXECUTION} -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
1210 | init_exec=y |
---|
1211 | fi |
---|
1212 | fi |
---|
1213 | done |
---|
1214 | # MPI-OpenMP (MPMD) |
---|
1215 | else |
---|
1216 | |
---|
1217 | # Execution specifications |
---|
1218 | EXECUTION="${EXECUTION} -configfile run_file" |
---|
1219 | export KMP_STACKSIZE=200m |
---|
1220 | if [ -f run_file ] ; then |
---|
1221 | IGCM_sys_Rm -f run_file |
---|
1222 | fi |
---|
1223 | touch run_file |
---|
1224 | |
---|
1225 | # Initialisation of variables |
---|
1226 | string_final="" |
---|
1227 | string_final_hexa="" |
---|
1228 | current_core=0 |
---|
1229 | executable_nb=1 |
---|
1230 | |
---|
1231 | # Hosts treatment |
---|
1232 | for nodes in `echo $LOADL_PROCESSOR_LIST` |
---|
1233 | do |
---|
1234 | host[$i]=$nodes |
---|
1235 | i=$((i+1)) |
---|
1236 | done |
---|
1237 | |
---|
1238 | # Loop on the components |
---|
1239 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1240 | |
---|
1241 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
1242 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1243 | |
---|
1244 | # Not possible if oasis has an executable (i.e old version of oasis3) |
---|
1245 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
---|
1246 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
---|
1247 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
---|
1248 | IGCM_debug_Verif_Exit |
---|
1249 | fi |
---|
1250 | |
---|
1251 | # Only if we really have an executable for the component : |
---|
1252 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
1253 | |
---|
1254 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1255 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1256 | |
---|
1257 | # Check if the number of threads is correct |
---|
1258 | case ${comp_proc_omp_loc} in |
---|
1259 | 1|2|4|8|16) |
---|
1260 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
---|
1261 | ;; |
---|
1262 | *) |
---|
1263 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
1264 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
1265 | IGCM_debug_Print 2 "Only 1,2,4,8,16 as number of OMP threads are possible " |
---|
1266 | IGCM_debug_Verif_Exit |
---|
1267 | ;; |
---|
1268 | esac |
---|
1269 | |
---|
1270 | |
---|
1271 | # Build run_file for Ada Intel-MPI environment : method used to assign cores and nodes for the MPI process by using hexadecimal mask |
---|
1272 | # Example of run_file : |
---|
1273 | #-host host0 -n 4 -env I_MPI_PIN_DOMAIN=[ff,ff00,ff0000,ff000000] ./a.out |
---|
1274 | #-host host1 -n 4 -env I_MPI_PIN_DOMAIN=[ff,ff00,ff0000,ff000000] ./a.out |
---|
1275 | #-host host2 -n 10 -env I_MPI_PIN_DOMAIN=[3,c,30,c0,300,c00,3000,c000,30000,c0000,100000,200000,400000,800000,1000000,2000000,4000000,8000000,10000000,20000000] ./b.out |
---|
1276 | #-host host2 -n 10 ./c.out |
---|
1277 | # Example of final command : |
---|
1278 | # mpirun -configfile run_file |
---|
1279 | |
---|
1280 | rank=0 |
---|
1281 | # For one specific executable, loop on mpi process |
---|
1282 | for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do |
---|
1283 | (( index_host = current_core / core_per_node )) |
---|
1284 | host_value=${host[${index_host}]} |
---|
1285 | (( slot = current_core % core_per_node )) |
---|
1286 | # loop on omp threads for each mpi process (set the appropriate bit to 1 and append it to previous one) |
---|
1287 | for index in `seq $slot $(($slot+$comp_proc_omp_loc-1))`; do |
---|
1288 | string_final="1"$string_final |
---|
1289 | done |
---|
1290 | # convert binary mask to hexadecimal mask |
---|
1291 | if [ $rank -ne 0 ] ; then |
---|
1292 | string_final_hexa=$string_final_hexa","$( printf '%x\n' "$((2#$string_final))" ) |
---|
1293 | else |
---|
1294 | string_final_hexa=$( printf '%x\n' "$((2#$string_final))" ) |
---|
1295 | fi |
---|
1296 | # replace bit 1 by bit 0 in order to append next one (next one wil be 1) |
---|
1297 | string_final=$( echo $string_final | sed "s/1/0/g" ) |
---|
1298 | # mpi rank = mpi_rank + 1 |
---|
1299 | (( rank = rank + 1 )) |
---|
1300 | # current core takes into account the number of omp threads which was previously append |
---|
1301 | (( current_core = current_core + comp_proc_omp_loc )) |
---|
1302 | # We write to the configuration file either we switch to the next node or we switch to the next executable |
---|
1303 | if ( [ $(( current_core / core_per_node )) -ne $index_host ] || [ $nb_proc_mpi -eq $(($comp_proc_mpi_loc-1)) ] ) ; then |
---|
1304 | # I_MPI_PIN_DOMAIN variable must be given once per node |
---|
1305 | if [ $executable_nb -eq 1 ] ; then |
---|
1306 | echo "-host $host_value -n $rank -env I_MPI_PIN_DOMAIN=[$string_final_hexa] ./$ExeNameOut" >> run_file |
---|
1307 | else |
---|
1308 | sed -i "/$host_value/s/\]/\,$string_final_hexa\]/g" run_file |
---|
1309 | echo "-host $host_value -n $rank ./$ExeNameOut" >> run_file |
---|
1310 | fi |
---|
1311 | # +1 for the number of executbale on the same node |
---|
1312 | if [ $nb_proc_mpi -eq $(($comp_proc_mpi_loc-1)) ] ; then |
---|
1313 | (( executable_nb = executable_nb + 1 )) |
---|
1314 | fi |
---|
1315 | # Some initializations if we switch to the next node |
---|
1316 | if [ $(( current_core / core_per_node )) -ne $index_host ] ; then |
---|
1317 | string_final="" |
---|
1318 | string_final_hexa="" |
---|
1319 | rank=0 |
---|
1320 | executable_nb=1 |
---|
1321 | fi |
---|
1322 | fi |
---|
1323 | done |
---|
1324 | |
---|
1325 | fi |
---|
1326 | done |
---|
1327 | IGCM_sys_Chmod u+x run_file |
---|
1328 | if ( $DEBUG_sys ) ; then |
---|
1329 | echo "run_file contains : " |
---|
1330 | cat run_file |
---|
1331 | fi |
---|
1332 | fi |
---|
1333 | fi |
---|
1334 | |
---|
1335 | # Only one executable (SPMD mode). |
---|
1336 | else |
---|
1337 | |
---|
1338 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1339 | |
---|
1340 | # Only if we really have an executable for the component : |
---|
1341 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1342 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
1343 | |
---|
1344 | if ( ${OK_PARA_OMP} ) ; then |
---|
1345 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1346 | export KMP_STACKSIZE=200m |
---|
1347 | #export KMP_LIBRARY=turnaround |
---|
1348 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
1349 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
1350 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
1351 | fi |
---|
1352 | if ( ${OK_PARA_MPI} ) ; then |
---|
1353 | if ( [ "X${LOADL_STEP_TYPE}" = "XPARALLEL" ] || [ "X${LOADL_STEP_TYPE}" = "XSERIAL" ] ) ; then |
---|
1354 | EXECUTION="${HOST_MPIRUN_COMMAND} ./${ExeNameOut}" |
---|
1355 | else |
---|
1356 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
1357 | EXECUTION="${HOST_MPIRUN_COMMAND} -np ${comp_proc_mpi_loc} ./${ExeNameOut}" |
---|
1358 | fi |
---|
1359 | else |
---|
1360 | EXECUTION="/usr/bin/time ./${ExeNameOut}" |
---|
1361 | fi |
---|
1362 | fi |
---|
1363 | |
---|
1364 | done |
---|
1365 | |
---|
1366 | fi |
---|
1367 | |
---|
1368 | IGCM_debug_Print 1 "sys ada : execution command is " |
---|
1369 | IGCM_debug_Print 1 "$EXECUTION" |
---|
1370 | |
---|
1371 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
1372 | } |
---|
1373 | |
---|
1374 | #D-#================================================== |
---|
1375 | #D-function IGCM_sys_check_path |
---|
1376 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
1377 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
1378 | #D-* Examples: |
---|
1379 | #D- |
---|
1380 | function IGCM_sys_check_path { |
---|
1381 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
1382 | if ( $DEBUG_sys ) ; then |
---|
1383 | echo "IGCM_sys_check_path" |
---|
1384 | fi |
---|
1385 | |
---|
1386 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${WORKDIR} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then |
---|
1387 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
1388 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
1389 | IGCM_debug_Exit "This will stop the job" |
---|
1390 | fi |
---|
1391 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
1392 | } |
---|
1393 | |
---|
1394 | #D-#================================================== |
---|
1395 | #D-function IGCM_sys_check_quota |
---|
1396 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
1397 | #D-* Examples: |
---|
1398 | #D- |
---|
1399 | function IGCM_sys_check_quota { |
---|
1400 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
1401 | if ( $DEBUG_sys ) ; then |
---|
1402 | echo "IGCM_sys_check_quota" |
---|
1403 | fi |
---|
1404 | # Limit of quota (in %) |
---|
1405 | limit_quota=90 |
---|
1406 | |
---|
1407 | # Check of the volume |
---|
1408 | volume_quota=$(quota_u -w 2>/dev/null| grep 'Quota soft' | gawk '{print $5}') |
---|
1409 | if [ ! X${volume_quota} = X ] ; then |
---|
1410 | quota_volume=${volume_quota%%\%} |
---|
1411 | # echo $quota_volume |
---|
1412 | if [ $(echo "${quota_volume} > ${limit_quota}" | bc) -eq 1 ] ; then |
---|
1413 | IGCM_debug_Print 1 "Please, check your quota of volume on workgpfs" |
---|
1414 | IGCM_debug_Print 1 "${quota_volume}% of your quota is used" |
---|
1415 | IGCM_debug_Print 1 "Use the quota_u -w command to check" |
---|
1416 | IGCM_debug_Print 1 "You must have more than 10% available to run" |
---|
1417 | IGCM_debug_Exit "Not enough space to run ! STOP HERE" |
---|
1418 | IGCM_debug_Verif_Exit |
---|
1419 | fi |
---|
1420 | |
---|
1421 | fi |
---|
1422 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
1423 | } |
---|
1424 | |
---|
1425 | #D-#================================================== |
---|
1426 | #D-function IGCM_sys_projectAccounting |
---|
1427 | #D-* Purpose: store project accounting information in a file |
---|
1428 | #D-* Examples: |
---|
1429 | #D- |
---|
1430 | function IGCM_sys_projectAccounting { |
---|
1431 | IGCM_debug_PushStack "IGCM_sys_projectAccounting" |
---|
1432 | if ( $DEBUG_sys ) ; then |
---|
1433 | echo "IGCM_sys_check_quota" |
---|
1434 | fi |
---|
1435 | |
---|
1436 | cpt > $1 |
---|
1437 | |
---|
1438 | IGCM_debug_PopStack "IGCM_sys_projectAccounting" |
---|
1439 | } |
---|
1440 | |
---|
1441 | #D-#================================================== |
---|
1442 | #D-function IGCM_sys_getJobSchedulerID |
---|
1443 | #D-* Purpose: Get the job ID during execution |
---|
1444 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
1445 | #D- |
---|
1446 | function IGCM_sys_getJobSchedulerID { |
---|
1447 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
1448 | if ( $DEBUG_sys ) ; then |
---|
1449 | echo "IGCM_sys_getJobSchedulerID" |
---|
1450 | fi |
---|
1451 | |
---|
1452 | eval ${1}=$( echo $LOADL_STEP_ID | awk -F. '{print $4}' ) |
---|
1453 | |
---|
1454 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
1455 | } |
---|
1456 | |
---|
1457 | #D-#================================================== |
---|
1458 | #D-function IGCM_sys_GetJobID |
---|
1459 | #D-* Purpose: Get the job ID from the JobName |
---|
1460 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
1461 | #D- |
---|
1462 | function IGCM_sys_GetJobID { |
---|
1463 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
1464 | if ( $DEBUG_sys ) ; then |
---|
1465 | echo "IGCM_sys_GetJobID" |
---|
1466 | fi |
---|
1467 | |
---|
1468 | # Print only the full (-W) JobID (%id) and JobName (%jn) |
---|
1469 | ID=$( llq -u $2 -W -f %id %jn | \ |
---|
1470 | gawk -v JobName=$1 '( $NF ~ JobName ) { print $1 }' ) |
---|
1471 | |
---|
1472 | eval ${3}=${ID} |
---|
1473 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
1474 | } |
---|
1475 | |
---|
1476 | #D-#================================================== |
---|
1477 | #D-function IGCM_sys_CountJobInQueue |
---|
1478 | #D-* Purpose: Count number of users job |
---|
1479 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
1480 | #D- |
---|
1481 | function IGCM_sys_CountJobInQueue { |
---|
1482 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
1483 | if ( $DEBUG_sys ) ; then |
---|
1484 | echo "IGCM_sys_CountJobInQueue" |
---|
1485 | fi |
---|
1486 | |
---|
1487 | # Print only the full (-W) JobName (%jn) |
---|
1488 | NbRun=$( llq -W -f %jn | grep -c "$1" ) |
---|
1489 | |
---|
1490 | eval ${2}=${NbRun} |
---|
1491 | |
---|
1492 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
1493 | } |
---|
1494 | |
---|
1495 | #D-#================================================== |
---|
1496 | #D-function IGCM_sys_ListJobInQueue |
---|
1497 | #D-* Purpose: Produce a list of users jobs |
---|
1498 | #D-* Examples: IGCM_sys_ListJobInQueue ${User} JobNameList |
---|
1499 | #D- |
---|
1500 | function IGCM_sys_ListJobInQueue { |
---|
1501 | IGCM_debug_PushStack "IGCM_sys_ListJobInQueue" |
---|
1502 | if ( $DEBUG_sys ) ; then |
---|
1503 | echo "IGCM_sys_ListJobInQueue" |
---|
1504 | fi |
---|
1505 | |
---|
1506 | # With -W option, column width is as large as necessary |
---|
1507 | set -A JobList $( llq -u $1 -W -f %jn | head -n -2 | tail -n +3 | \ |
---|
1508 | gawk '( $1 != /TS/ && \ |
---|
1509 | $1 !~ /PACK/ && \ |
---|
1510 | $1 !~ /REBUILD/ && \ |
---|
1511 | $1 !~ /pack/ ) \ |
---|
1512 | { print $1 }' | sed -e "s/\(.*\)\.[0-9]*/\1/" ) |
---|
1513 | |
---|
1514 | eval set -A ${2} ${JobList[*]} |
---|
1515 | |
---|
1516 | IGCM_debug_PopStack "IGCM_sys_ListJobInQueue" |
---|
1517 | } |
---|
1518 | |
---|
1519 | #D-#================================================== |
---|
1520 | #D-function IGCM_sys_atlas |
---|
1521 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
---|
1522 | #D-* Examples: |
---|
1523 | #D- |
---|
1524 | function IGCM_sys_atlas { |
---|
1525 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
---|
1526 | if ( $DEBUG_sys ) ; then |
---|
1527 | echo "IGCM_sys_atlas :" $@ |
---|
1528 | fi |
---|
1529 | |
---|
1530 | typeset status |
---|
1531 | |
---|
1532 | \atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
1533 | status=$? |
---|
1534 | if [ ${status} -gt 0 ] ; then |
---|
1535 | echo "IGCM_sys_atlas : error code ${status}" |
---|
1536 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
1537 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
1538 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1539 | return 1 |
---|
1540 | else |
---|
1541 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1542 | return 0 |
---|
1543 | fi |
---|
1544 | |
---|
1545 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1546 | } |
---|
1547 | |
---|