1 | #!/bin/ksh |
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2 | |
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3 | #************************************************************** |
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4 | # Author: Sebastien 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 ciclad |
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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 | # $hostname of the MASTER job |
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70 | typeset MASTER=${MASTER:=$( hostname )} |
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71 | # project name |
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72 | typeset PROJECT=NONE |
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73 | # jobWarningDelay in seconds |
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74 | typeset jobWarningDelay=${PBS_WALLTIME} |
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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=${SUBMIT:=qsub} |
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83 | # rsync with path |
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84 | typeset -r RSYNC=/usr/bin/rsync |
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85 | # RSYNC_opt args to rsync |
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86 | typeset -r RSYNC_opt="-va" |
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87 | # ie storage filesystem |
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88 | typeset -r STOREHOST=${MASTER} |
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89 | |
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90 | #==================================================== |
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91 | # Access to module command |
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92 | #==================================================== |
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93 | . /usr/share/Modules/init/ksh |
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94 | |
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95 | #==================================================== |
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96 | # Set environment tools (ferret, nco, cdo, rebuild, ...) |
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97 | #==================================================== |
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98 | if [ $CENTER == IPSL-ciclad ] ; then |
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99 | # At ciclad |
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100 | export PATH=${PATH}:/home/igcmg/rebuild/src_X64_CICLAD/modipsl_v2_2_3_netcdf4.2/bin/ |
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101 | . /home/igcmg/.atlas_env_ciclad_ksh |
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102 | else |
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103 | # At climserv use the same files stored at ciclad but adapt the path |
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104 | export PATH=${PATH}:/ciclad-home/igcmg/rebuild/src_X64_CICLAD/modipsl_v2_2_3_netcdf4.2/bin/ |
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105 | . /ciclad-home/igcmg/.atlas_env_ciclad_ksh |
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106 | fi |
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107 | |
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108 | [ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:" |
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109 | [ ! X${TaskType} = Xchecking ] && module list |
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110 | |
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111 | #==================================================== |
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112 | # Host specific DIRECTORIES |
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113 | #==================================================== |
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114 | |
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115 | #==================================================== |
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116 | #- MirrorlibIGCM for frontend |
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117 | typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} |
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118 | |
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119 | #==================================================== |
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120 | #- libIGCM_POST for frontend |
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121 | typeset -r libIGCM_POST=${libIGCM} |
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122 | |
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123 | #==================================================== |
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124 | #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) |
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125 | typeset -r R_EXE="${MODIPSL}/bin" |
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126 | |
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127 | #==================================================== |
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128 | #- SUBMIT_DIR : submission dir |
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129 | if [ X${PBS_O_WORKDIR} != X ] ; then |
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130 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PBS_O_WORKDIR}} |
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131 | else |
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132 | typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PWD}} |
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133 | fi |
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134 | |
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135 | #==================================================== |
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136 | #- IN |
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137 | typeset -r R_IN=${R_IN:=/prodigfs/ipslfs/igcmg/IGCM} |
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138 | typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/prodigfs/ipslfs/igcmg/IGCM} |
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139 | |
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140 | #==================================================== |
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141 | #- RUN_DIR_PATH : Temporary working directory (=> TMP) |
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142 | if [ X${PBS_JOBID} != X ] ; then |
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143 | if [ $CENTER == IPSL-ciclad ] ; then |
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144 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/data/${LOGIN}/RUN_DIR/${PBS_JOBID}_${$}} |
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145 | else |
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146 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/homedata/${LOGIN}/RUN_DIR/${PBS_JOBID}_${$}} |
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147 | fi |
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148 | else |
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149 | typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/tmp/tmp$$} |
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150 | fi |
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151 | |
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152 | #==================================================== |
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153 | #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs |
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154 | typeset -r OUTCOMMAND_PATH=/tmp |
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155 | |
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156 | #==================================================== |
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157 | #- HOST_MPIRUN_COMMAND |
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158 | typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="time mpirun"} |
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159 | |
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160 | #==================================================== |
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161 | #- Max number of arguments passed to nco operator or demigration command |
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162 | UNIX_MAX_LIMIT=360 |
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163 | |
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164 | #==================================================== |
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165 | #- set PackDefault to false on ciclad |
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166 | PackDefault=false |
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167 | |
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168 | #==================================================== |
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169 | #- Default number of MPI task for IPSL coupled model |
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170 | #- required for backward compatibility |
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171 | #- |
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172 | DEFAULT_NUM_PROC_OCE=5 |
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173 | DEFAULT_NUM_PROC_CPL=1 |
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174 | (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) |
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175 | |
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176 | #D-#================================================== |
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177 | #D-function IGCM_sys_defineArchives |
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178 | #D-* Purpose: |
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179 | #D-* Define ARCHIVE : Dedicated to large files |
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180 | #D-* Define STORAGE : Dedicated to small/medium files |
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181 | #D-* Define R_OUT : Output tree located on ARCHIVE |
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182 | #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) |
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183 | #D-* Define R_BUF : Output tree located on STORAGE hosting files waiting for rebuild or pack processes |
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184 | #D-* if SpaceName=TEST nothing special will hapen |
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185 | #D-* Examples: |
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186 | #D- |
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187 | function IGCM_sys_defineArchives { |
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188 | IGCM_debug_PushStack "IGCM_sys_defineArchives" |
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189 | |
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190 | if [ ! X${config_UserChoices_ARCHIVE} = X ]; then |
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191 | #==================================================== |
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192 | #- ARCHIVE (dedicated to large files) |
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193 | ARCHIVE=${config_UserChoices_ARCHIVE} |
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194 | else |
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195 | #==================================================== |
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196 | #- ARCHIVE (dedicated to large files) |
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197 | if [ $CENTER == IPSL-ciclad ] ; then |
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198 | # At ciclad |
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199 | ARCHIVE=${ARCHIVE:=/data/${LOGIN}} |
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200 | else |
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201 | # At climserv |
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202 | ARCHIVE=${ARCHIVE:=/homedata/${LOGIN}} |
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203 | fi |
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204 | fi |
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205 | |
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206 | if [ ! X${config_UserChoices_STORAGE} = X ]; then |
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207 | #==================================================== |
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208 | #- STORAGE (dedicated to small/medium files) |
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209 | STORAGE=${config_UserChoices_STORAGE} |
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210 | else |
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211 | #==================================================== |
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212 | #- STORAGE (dedicated to small/medium files) |
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213 | STORAGE=${ARCHIVE} |
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214 | fi |
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215 | |
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216 | # ON CICLAD NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST |
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217 | |
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218 | #==================================================== |
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219 | #- R_OUT |
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220 | R_OUT=${ARCHIVE}/IGCM_OUT |
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221 | |
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222 | #==================================================== |
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223 | #- R_FIG (hosting figures : monitoring and atlas, and/or small files) |
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224 | R_FIG=${STORAGE}/IGCM_OUT |
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225 | |
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226 | #==================================================== |
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227 | #- R_BUF (ONLY FOR double copy an scratch) |
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228 | R_BUF=${STORAGE}/IGCM_OUT |
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229 | |
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230 | IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" |
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231 | IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" |
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232 | IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" |
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233 | |
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234 | IGCM_debug_PopStack "IGCM_sys_defineArchives" |
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235 | } |
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236 | |
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237 | #D-#================================================== |
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238 | #D-function IGCM_sys_RshArchive |
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239 | #D-* Purpose: Archive rsh command |
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240 | #D-* Examples: |
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241 | #D- |
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242 | function IGCM_sys_RshArchive { |
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243 | IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ |
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244 | /bin/ksh <<-EOF |
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245 | ${@} |
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246 | EOF |
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247 | status=$? |
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248 | if [ ${status} -gt 0 ] ; then |
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249 | IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" |
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250 | IGCM_debug_Exit "IGCM_sys_RshArchive" |
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251 | fi |
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252 | IGCM_debug_PopStack "IGCM_sys_RshArchive" |
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253 | } |
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254 | |
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255 | #D-#================================================== |
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256 | #D-function IGCM_sys_RshArchive_NoError |
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257 | #D-* Purpose: Archive rsh command, without error |
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258 | #D-* used only in monitoring.job |
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259 | #D-* Examples: |
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260 | #D- |
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261 | function IGCM_sys_RshArchive_NoError { |
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262 | IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ |
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263 | /bin/ksh <<-EOF |
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264 | ${@} 2> /dev/null |
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265 | EOF |
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266 | IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" |
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267 | } |
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268 | |
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269 | #D-#================================================== |
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270 | #D-function IGCM_sys_MkdirArchive |
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271 | #D-* Purpose: Mkdir on Archive |
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272 | #D-* Examples: |
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273 | #D- |
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274 | function IGCM_sys_MkdirArchive { |
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275 | IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ |
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276 | if ( $DEBUG_sys ) ; then |
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277 | echo "IGCM_sys_MkdirArchive :" $@ |
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278 | fi |
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279 | #- creation de repertoire sur le serveur fichier |
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280 | if [ ! -d ${1} ]; then |
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281 | \mkdir -p $1 |
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282 | status=$? |
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283 | |
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284 | if [ ${status} -gt 0 ] ; then |
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285 | IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" |
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286 | IGCM_debug_Exit "IGCM_sys_MkdirArchive" |
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287 | fi |
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288 | fi |
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289 | IGCM_debug_PopStack "IGCM_sys_MkdirArchive" |
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290 | } |
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291 | |
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292 | #D-#================================================== |
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293 | #D-function IGCM_sys_TestDirArchive |
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294 | #D-* Purpose: Test Directory that must exists on Archive |
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295 | #D-* Examples: |
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296 | #D- |
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297 | function IGCM_sys_TestDirArchive { |
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298 | IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ |
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299 | if ( $DEBUG_sys ) ; then |
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300 | echo "IGCM_sys_TestDirArchive :" $@ |
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301 | fi |
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302 | typeset ExistFlag |
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303 | ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) |
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304 | IGCM_debug_PopStack "IGCM_sys_TestDirArchive" |
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305 | return ${ExistFlag} |
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306 | } |
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307 | |
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308 | #D-#================================================== |
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309 | #D-function IGCM_sys_IsFileArchived |
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310 | #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only |
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311 | #D-* Examples: |
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312 | #D- |
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313 | function IGCM_sys_IsFileArchived { |
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314 | IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ |
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315 | if ( $DEBUG_sys ) ; then |
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316 | echo "IGCM_sys_IsFileArchived :" $@ |
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317 | fi |
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318 | typeset IsArchivedFlag |
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319 | # Never archived for this system |
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320 | IsArchivedFlag=1 |
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321 | IGCM_debug_PopStack "IGCM_sys_IsFileArchived" |
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322 | |
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323 | return ${IsArchivedFlag} |
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324 | } |
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325 | |
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326 | #D-#================================================== |
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327 | #D-function IGCM_sys_TestFileArchive |
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328 | #D-* Purpose: Test file that must NOT EXISTS on Archive |
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329 | #D-* Examples: |
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330 | #D- |
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331 | function IGCM_sys_TestFileArchive { |
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332 | IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ |
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333 | typeset ExistFlag |
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334 | ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) |
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335 | IGCM_debug_PopStack "IGCM_sys_TestFileArchive" |
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336 | |
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337 | return ${ExistFlag} |
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338 | } |
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339 | |
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340 | #D-#================================================== |
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341 | #D-function IGCM_sys_CountFileArchive |
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342 | #D-* Purpose: Count files on Archive filesystem |
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343 | #D-* Examples: |
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344 | #D- |
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345 | function IGCM_sys_CountFileArchive { |
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346 | IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ |
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347 | ls ${@} 2>/dev/null | wc -l |
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348 | if [ $? -gt 0 ] ; then |
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349 | echo "IGCM_sys_CountFileArchive : erreur." |
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350 | fi |
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351 | IGCM_debug_PopStack "IGCM_sys_CountFileArchive" |
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352 | } |
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353 | |
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354 | #D-#================================================== |
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355 | #D-function IGCM_sys_Tree |
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356 | #D-* Purpose: Tree directories with files on ${ARCHIVE} |
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357 | #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} |
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358 | #D- |
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359 | function IGCM_sys_Tree { |
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360 | IGCM_debug_PushStack "IGCM_sys_Tree" $@ |
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361 | if ( $DEBUG_sys ) ; then |
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362 | echo "IGCM_sys_Tree :" $@ |
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363 | fi |
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364 | |
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365 | \ls -lR ${@} |
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366 | |
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367 | IGCM_debug_PopStack "IGCM_sys_Tree" |
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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_Qsub |
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372 | #D-* Purpose: Qsub new job |
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373 | #D-* Examples: |
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374 | #D- |
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375 | function IGCM_sys_Qsub { |
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376 | IGCM_debug_PushStack "IGCM_sys_Qsub" $@ |
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377 | if ( $DEBUG_sys ) ; then |
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378 | echo "IGCM_sys_Qsub :" $@ |
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379 | fi |
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380 | typeset options status |
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381 | options="-o ${SUBMIT_DIR}/${Script_Output}" |
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382 | /usr/bin/qsub ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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383 | status=$? |
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384 | |
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385 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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386 | if [ ${status} -gt 0 ] ; then |
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387 | IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}" |
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388 | IGCM_debug_Exit "IGCM_sys_Qsub" |
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389 | else |
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390 | JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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391 | fi |
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392 | IGCM_debug_PopStack "IGCM_sys_Qsub" |
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393 | } |
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394 | |
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395 | #D-#================================================== |
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396 | #D-function IGCM_sys_QsubPost |
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397 | #D-* Purpose: Qsub new job on scalaire |
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398 | #D-* Examples: |
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399 | #D- |
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400 | function IGCM_sys_QsubPost { |
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401 | IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ |
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402 | if ( $DEBUG_sys ) ; then |
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403 | echo "IGCM_sys_QsubPost :" $@ |
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404 | fi |
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405 | typeset options status |
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406 | options="-o ${POST_DIR}/${Script_Post_Output}.out -v ${listVarEnv}" |
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407 | /usr/bin/qsub ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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408 | status=$? |
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409 | |
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410 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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411 | if [ ${status} -gt 0 ] ; then |
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412 | IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}" |
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413 | IGCM_debug_Exit "IGCM_sys_QsubPost" |
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414 | else |
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415 | JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ ) |
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416 | fi |
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417 | IGCM_debug_PopStack "IGCM_sys_QsubPost" |
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418 | } |
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419 | |
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420 | #D-************************* |
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421 | #D- File transfer functions |
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422 | #D-************************* |
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423 | #D- |
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424 | |
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425 | #D-#================================================== |
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426 | #D-function IGCM_sys_RmRunDir |
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427 | #D-* Purpose: rm tmpdir (dummy function most of the time batch |
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428 | #D- scheduler will do the job) |
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429 | #D-* Examples: |
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430 | #D- |
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431 | function IGCM_sys_RmRunDir { |
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432 | IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ |
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433 | if ( $DEBUG_sys ) ; then |
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434 | echo "IGCM_sys_RmRunDir :" $@ |
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435 | fi |
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436 | |
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437 | typeset status |
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438 | |
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439 | echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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440 | \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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441 | status=$? |
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442 | |
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443 | if [ ${status} -gt 0 ] ; then |
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444 | IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}." |
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445 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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446 | IGCM_debug_Exit "IGCM_sys_RmRunDir" |
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447 | else |
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448 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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449 | fi |
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450 | IGCM_debug_PopStack "IGCM_sys_RmRunDir" |
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451 | } |
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452 | |
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453 | #D-#================================================== |
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454 | #D-function IGCM_sys_Put_Dir |
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455 | #D-* Purpose: Copy a complete directory on $(ARCHIVE) |
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456 | #D-* Examples: |
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457 | #D- |
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458 | function IGCM_sys_Put_Dir { |
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459 | IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ |
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460 | if ( $DEBUG_sys ) ; then |
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461 | echo "IGCM_sys_Put_Dir :" $@ |
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462 | fi |
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463 | if [ $DRYRUN = 0 ]; then |
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464 | if [ ! -d ${1} ] ; then |
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465 | echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." |
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466 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
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467 | return |
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468 | fi |
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469 | |
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470 | typeset status |
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471 | |
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472 | # Only if we use rsync |
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473 | #IGCM_sys_TestDirArchive $( dirname $2 ) |
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474 | # |
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475 | #USUAL WAY |
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476 | \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
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477 | status=$? |
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478 | |
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479 | if [ ${status} -gt 0 ] ; then |
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480 | IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" |
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481 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
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482 | IGCM_debug_Exit "IGCM_sys_Put_Dir" |
---|
483 | else |
---|
484 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
485 | fi |
---|
486 | fi |
---|
487 | IGCM_debug_PopStack "IGCM_sys_Put_Dir" |
---|
488 | } |
---|
489 | |
---|
490 | #D-#================================================== |
---|
491 | #D-function IGCM_sys_Get_Dir |
---|
492 | #D-* Purpose: Copy a complete directory from ${ARCHIVE} |
---|
493 | #D-* Examples: |
---|
494 | #D- |
---|
495 | function IGCM_sys_Get_Dir { |
---|
496 | IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ |
---|
497 | if ( $DEBUG_sys ) ; then |
---|
498 | echo "IGCM_sys_Get_Dir :" $@ |
---|
499 | fi |
---|
500 | if [ $DRYRUN = 0 ]; then |
---|
501 | typeset NB_ESSAI DELAI status i |
---|
502 | # number of tentative |
---|
503 | NB_ESSAI=3 |
---|
504 | # time delay between tentative |
---|
505 | DELAI=2 |
---|
506 | |
---|
507 | # |
---|
508 | # USUAL WAY |
---|
509 | i=0 |
---|
510 | while [ $i -lt $NB_ESSAI ] ; do |
---|
511 | \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
512 | status=$? |
---|
513 | if [ ${status} -gt 0 ] ; then |
---|
514 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}" |
---|
515 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." |
---|
516 | sleep $DELAI |
---|
517 | else |
---|
518 | break |
---|
519 | fi |
---|
520 | (( i = i + 1 )) |
---|
521 | done |
---|
522 | |
---|
523 | if [ ${status} -gt 0 ] ; then |
---|
524 | IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" |
---|
525 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
526 | IGCM_debug_Exit "IGCM_sys_Get_Dir" |
---|
527 | else |
---|
528 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
529 | fi |
---|
530 | fi |
---|
531 | IGCM_debug_PopStack "IGCM_sys_Get_Dir" |
---|
532 | } |
---|
533 | |
---|
534 | #D-#================================================== |
---|
535 | #D-function IGCM_sys_Put_Rest |
---|
536 | #D-* Purpose: Put computied restarts on ${ARCHIVE}. |
---|
537 | #D- File and target directory must exist. |
---|
538 | #D-* Examples: |
---|
539 | #D- |
---|
540 | function IGCM_sys_Put_Rest { |
---|
541 | IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ |
---|
542 | if ( $DEBUG_sys ) ; then |
---|
543 | echo "IGCM_sys_Put_Rest :" $@ |
---|
544 | fi |
---|
545 | if [ $DRYRUN = 0 ]; then |
---|
546 | if [ ! -f ${1} ] ; then |
---|
547 | echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." |
---|
548 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
549 | fi |
---|
550 | |
---|
551 | typeset status |
---|
552 | # |
---|
553 | # USUAL WAY |
---|
554 | \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
555 | status=$? |
---|
556 | |
---|
557 | # #RSYNC WITH NETWORK SSH CALL |
---|
558 | # echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
559 | # ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
560 | |
---|
561 | # #RSYNC WITH NFS USE |
---|
562 | # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
563 | # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
564 | |
---|
565 | # status=$? |
---|
566 | # IGCM_sys_Rsync_out $status |
---|
567 | |
---|
568 | # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
569 | # (( status=status+$? )) |
---|
570 | |
---|
571 | if [ ${status} -gt 0 ] ; then |
---|
572 | IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" |
---|
573 | [ -f ${1} ] && ls -l ${1} |
---|
574 | [ -f ${2} ] && ls -l ${2} |
---|
575 | [ -f ${2}/${1} ] && ls -l ${2}/${1} |
---|
576 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
577 | IGCM_debug_Exit "IGCM_sys_Put_Rest" |
---|
578 | else |
---|
579 | |
---|
580 | if [ X${JobType} = XRUN ] ; then |
---|
581 | [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} |
---|
582 | [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} |
---|
583 | fi |
---|
584 | |
---|
585 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
586 | fi |
---|
587 | fi |
---|
588 | IGCM_debug_PopStack "IGCM_sys_Put_Rest" |
---|
589 | } |
---|
590 | |
---|
591 | #D-#================================================== |
---|
592 | #D-function IGCM_sys_Put_Out |
---|
593 | #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly |
---|
594 | #D-* Examples: |
---|
595 | #D- |
---|
596 | function IGCM_sys_Put_Out { |
---|
597 | IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ |
---|
598 | if ( $DEBUG_sys ) ; then |
---|
599 | echo "IGCM_sys_Put_Out :" $@ |
---|
600 | fi |
---|
601 | |
---|
602 | typeset status |
---|
603 | |
---|
604 | if [ $DRYRUN = 0 ]; then |
---|
605 | if [ ! -f ${1} ] ; then |
---|
606 | echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." |
---|
607 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
608 | return 1 |
---|
609 | fi |
---|
610 | # |
---|
611 | IGCM_sys_MkdirArchive $( dirname $2 ) |
---|
612 | # |
---|
613 | if [ X${JobType} = XRUN ] ; then |
---|
614 | if [ X${3} = X ] ; then |
---|
615 | IGCM_sys_Chmod 444 ${1} |
---|
616 | fi |
---|
617 | fi |
---|
618 | # |
---|
619 | |
---|
620 | echo ${RSYNC} ${RSYNC_opt} $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
621 | ${RSYNC} ${RSYNC_opt} $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
622 | status=$? |
---|
623 | IGCM_sys_Rsync_out $status |
---|
624 | |
---|
625 | ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
626 | (( status=status+$? )) |
---|
627 | |
---|
628 | if [ ${status} -gt 0 ] ; then |
---|
629 | IGCM_debug_Print 2 "IGCM_sys_Put_Out : rsync failed error code ${status}" |
---|
630 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
631 | IGCM_debug_Exit "IGCM_sys_Put_Out" |
---|
632 | else |
---|
633 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
634 | fi |
---|
635 | fi |
---|
636 | IGCM_debug_PopStack "IGCM_sys_Put_Out" |
---|
637 | return 0 |
---|
638 | } |
---|
639 | |
---|
640 | #D-#================================================== |
---|
641 | #D-function IGCM_sys_Get |
---|
642 | #D-* Purpose: Get a file from ${ARCHIVE} |
---|
643 | #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX |
---|
644 | #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ |
---|
645 | function IGCM_sys_Get { |
---|
646 | IGCM_debug_PushStack "IGCM_sys_Get" $@ |
---|
647 | |
---|
648 | typeset DEST status dm_liste |
---|
649 | |
---|
650 | if ( $DEBUG_sys ) ; then |
---|
651 | echo "IGCM_sys_Get :" $@ |
---|
652 | fi |
---|
653 | if [ $DRYRUN -le 2 ]; then |
---|
654 | if [ X${1} = X'/l' ] ; then |
---|
655 | eval set +A dm_liste \${${2}} |
---|
656 | else |
---|
657 | dm_liste=${1} |
---|
658 | fi |
---|
659 | eval DEST=\${${#}} |
---|
660 | |
---|
661 | # test if the (first) file is present in the old computation : |
---|
662 | IGCM_sys_TestFileArchive ${dm_liste[0]} |
---|
663 | status=$? |
---|
664 | if [ ${status} -gt 0 ] ; then |
---|
665 | echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." |
---|
666 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
667 | return |
---|
668 | fi |
---|
669 | |
---|
670 | #USUAL WAY |
---|
671 | \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
672 | status=$? |
---|
673 | |
---|
674 | if [ ${status} -gt 0 ] ; then |
---|
675 | IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}" |
---|
676 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
677 | IGCM_debug_Exit "IGCM_sys_Get" |
---|
678 | else |
---|
679 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
680 | fi |
---|
681 | fi |
---|
682 | IGCM_debug_PopStack "IGCM_sys_Get" |
---|
683 | } |
---|
684 | |
---|
685 | #D-#================================================== |
---|
686 | #D-function IGCM_sys_GetDate_Monitoring |
---|
687 | #D-* Purpose: get the last year for which the monitoring has been computed |
---|
688 | #D-* Examples: |
---|
689 | #D- |
---|
690 | function IGCM_sys_GetDate_Monitoring { |
---|
691 | IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ |
---|
692 | if ( $DEBUG_sys ) ; then |
---|
693 | echo "IGCM_sys_GetDate_Monitoring :" $@ |
---|
694 | fi |
---|
695 | |
---|
696 | eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' ) |
---|
697 | |
---|
698 | IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" |
---|
699 | } |
---|
700 | |
---|
701 | #D-#================================================== |
---|
702 | #D-function IGCM_sys_Dods_Rm |
---|
703 | #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. |
---|
704 | #D-* Examples: |
---|
705 | #D- |
---|
706 | function IGCM_sys_Dods_Rm { |
---|
707 | if ( $DEBUG_sys ) ; then |
---|
708 | echo "IGCM_sys_Dods_Rm :" $@ |
---|
709 | fi |
---|
710 | return 0 |
---|
711 | } |
---|
712 | |
---|
713 | #D-#================================================== |
---|
714 | #D-function IGCM_sys_Dods_Cp |
---|
715 | #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. |
---|
716 | #D-* Examples: |
---|
717 | #D- |
---|
718 | function IGCM_sys_Dods_Cp { |
---|
719 | if ( $DEBUG_sys ) ; then |
---|
720 | echo "IGCM_sys_Dods_Cp :" $@ |
---|
721 | fi |
---|
722 | return 0 |
---|
723 | } |
---|
724 | |
---|
725 | #D-#================================================== |
---|
726 | #D-function IGCM_sys_Put_Dods |
---|
727 | #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here |
---|
728 | #D-* Examples: |
---|
729 | #D- |
---|
730 | function IGCM_sys_Put_Dods { |
---|
731 | IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ |
---|
732 | if ( $DEBUG_sys ) ; then |
---|
733 | echo "IGCM_sys_Put_Dods :" $@ |
---|
734 | fi |
---|
735 | IGCM_debug_PopStack "IGCM_sys_Put_Dods" |
---|
736 | } |
---|
737 | |
---|
738 | ############################################################## |
---|
739 | # REBUILD OPERATOR |
---|
740 | |
---|
741 | #D-#================================================== |
---|
742 | #D-function IGCM_sys_sync |
---|
743 | #D-* Purpose: flush buffer on disk (dummy function on Ciclad) |
---|
744 | #D-* Examples: |
---|
745 | #D- |
---|
746 | function IGCM_sys_sync { |
---|
747 | IGCM_debug_PushStack "IGCM_sys_sync" $@ |
---|
748 | if ( $DEBUG_sys ) ; then |
---|
749 | echo "IGCM_sys_sync :" $@ |
---|
750 | echo "Dummy call, let the system do that." |
---|
751 | fi |
---|
752 | IGCM_debug_PopStack "IGCM_sys_sync" |
---|
753 | } |
---|
754 | |
---|
755 | ############################################################ |
---|
756 | # Activate Running Environnment Variables |
---|
757 | |
---|
758 | #D-#================================================== |
---|
759 | #D-function IGCM_sys_activ_variables |
---|
760 | #D-* Purpose: set environement variables prior to execution |
---|
761 | #D-* Examples: |
---|
762 | #D- |
---|
763 | function IGCM_sys_activ_variables { |
---|
764 | IGCM_debug_PushStack "IGCM_sys_activ_variables" |
---|
765 | if ( $DEBUG_sys ) ; then |
---|
766 | echo "IGCM_sys_activ_variables" |
---|
767 | fi |
---|
768 | |
---|
769 | # -------------------------------------------------------------------- |
---|
770 | #D- MPI specifications |
---|
771 | # -------------------------------------------------------------------- |
---|
772 | |
---|
773 | # -------------------------------------------------------------------- |
---|
774 | #D- Other specifications |
---|
775 | # -------------------------------------------------------------------- |
---|
776 | |
---|
777 | ulimit -s unlimited |
---|
778 | |
---|
779 | IGCM_debug_PopStack "IGCM_sys_activ_variables" |
---|
780 | } |
---|
781 | |
---|
782 | ############################################################ |
---|
783 | # Desactivate Running Environnment Variables |
---|
784 | |
---|
785 | #D-#================================================== |
---|
786 | #D-function IGCM_sys_desactiv_variables |
---|
787 | #D-* Purpose: unset environement variables after execution |
---|
788 | #D-* Examples: |
---|
789 | #D- |
---|
790 | function IGCM_sys_desactiv_variables { |
---|
791 | IGCM_debug_PushStack "IGCM_sys_desactiv_variables" |
---|
792 | if ( $DEBUG_sys ) ; then |
---|
793 | echo "IGCM_sys_desactiv_variables" |
---|
794 | fi |
---|
795 | # -------------------------------------------------------------------- |
---|
796 | #D- MPI specifications |
---|
797 | # -------------------------------------------------------------------- |
---|
798 | |
---|
799 | # -------------------------------------------------------------------- |
---|
800 | #D- Other specifications |
---|
801 | # -------------------------------------------------------------------- |
---|
802 | |
---|
803 | IGCM_debug_PopStack "IGCM_sys_desactiv_variables" |
---|
804 | } |
---|
805 | |
---|
806 | ############################################################ |
---|
807 | # Update job headers to be used by the scheduler |
---|
808 | |
---|
809 | #D-#================================================== |
---|
810 | #D-function IGCM_sys_updateHeaders |
---|
811 | #D-* Purpose: Update job headers to be used by the scheduler |
---|
812 | #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP |
---|
813 | #D- |
---|
814 | function IGCM_sys_updateHeaders { |
---|
815 | IGCM_debug_PushStack "IGCM_sys_updateHeaders" |
---|
816 | if ( $DEBUG_sys ) ; then |
---|
817 | echo "IGCM_sys_updateHeaders" |
---|
818 | fi |
---|
819 | typeset file |
---|
820 | file=$1 |
---|
821 | |
---|
822 | if [ ${executionType} -eq 1 ] ; then |
---|
823 | # MPMD + MPI |
---|
824 | sed -e "/::openMPthreads::/d" \ |
---|
825 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
826 | ${file} > ${file}.tmp |
---|
827 | |
---|
828 | elif [ ${executionType} -eq 2 ] ; then |
---|
829 | # MPMD + MPI + OMP |
---|
830 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
831 | -e "s/::JobNumProcTot::/${coreNumber}/" \ |
---|
832 | ${file} > ${file}.tmp |
---|
833 | |
---|
834 | elif [ ${executionType} -eq 3 ] ; then |
---|
835 | # SPMD + MPI/OMP |
---|
836 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
837 | -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
838 | ${file} > ${file}.tmp |
---|
839 | |
---|
840 | elif [ ${executionType} -eq 4 ] ; then |
---|
841 | # SPMD + MPI only |
---|
842 | sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ |
---|
843 | -e "/::openMPthreads::/d" \ |
---|
844 | ${file} > ${file}.tmp |
---|
845 | |
---|
846 | elif [ ${executionType} -eq 5 ] ; then |
---|
847 | # SPMD + OMP only |
---|
848 | sed -e "s/::openMPthreads::/${openMPthreads}/" \ |
---|
849 | -e "/::JobNumProcTot::/d" \ |
---|
850 | ${file} > ${file}.tmp |
---|
851 | |
---|
852 | elif [ ${executionType} -eq 6 ] ; then |
---|
853 | # SEQUENTIAL THEN |
---|
854 | sed -e "s/::JobNumProcTot::/1/" \ |
---|
855 | -e "/::openMPthreads::/d" \ |
---|
856 | ${file} > ${file}.tmp |
---|
857 | |
---|
858 | fi |
---|
859 | |
---|
860 | IGCM_sys_Mv ${file}.tmp ${file} |
---|
861 | |
---|
862 | IGCM_debug_PopStack "IGCM_sys_updateHeaders" |
---|
863 | } |
---|
864 | |
---|
865 | ############################################################ |
---|
866 | # Build MPI/OMP scripts run file (dummy function) |
---|
867 | |
---|
868 | #D-#================================================== |
---|
869 | #D-function IGCM_sys_build_run_file |
---|
870 | #D-* Purpose: build run file (deprecated) |
---|
871 | #D-* Examples: |
---|
872 | #D- |
---|
873 | function IGCM_sys_build_run_file { |
---|
874 | IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " |
---|
875 | } |
---|
876 | |
---|
877 | ############################################################ |
---|
878 | # Build MPI/OMP scripts |
---|
879 | |
---|
880 | #D-#================================================== |
---|
881 | #D-function IGCM_sys_build_execution_scripts |
---|
882 | #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} |
---|
883 | #D-* Examples: |
---|
884 | #D- |
---|
885 | function IGCM_sys_build_execution_scripts |
---|
886 | { |
---|
887 | IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ |
---|
888 | if ( $DEBUG_sys ) ; then |
---|
889 | echo "IGCM_sys_build_execution_scripts " $@ |
---|
890 | fi |
---|
891 | |
---|
892 | EXECUTION=${HOST_MPIRUN_COMMAND} |
---|
893 | |
---|
894 | # MPMD mode |
---|
895 | if ( ${OK_PARA_MPMD} ) ; then |
---|
896 | |
---|
897 | # Only MPI (MPMD) |
---|
898 | if ( ! ${OK_PARA_OMP} ) ; then |
---|
899 | |
---|
900 | if [ -f run_file ] ; then |
---|
901 | IGCM_sys_Rm -f run_file |
---|
902 | fi |
---|
903 | touch run_file |
---|
904 | |
---|
905 | # Build run_file |
---|
906 | |
---|
907 | # First loop on the components for the coupler ie oasis (only if oasis3) |
---|
908 | # the coupler ie oasis3 must be the first one |
---|
909 | for comp in ${config_ListOfComponents[*]} ; do |
---|
910 | |
---|
911 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
912 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
913 | |
---|
914 | # for CPL component only |
---|
915 | if [ "X${comp}" = "XCPL" ] && [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
916 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
917 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
918 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut} " >> run_file |
---|
919 | fi |
---|
920 | done |
---|
921 | |
---|
922 | # Then second loop on the components |
---|
923 | for comp in ${config_ListOfComponents[*]} ; do |
---|
924 | |
---|
925 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
926 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
927 | |
---|
928 | # Only if we really have an executable for the component and not the coupler ie oasis: |
---|
929 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then |
---|
930 | |
---|
931 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
932 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
933 | echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file |
---|
934 | fi |
---|
935 | done |
---|
936 | |
---|
937 | EXECUTION="${HOST_MPIRUN_COMMAND} --app ./run_file" |
---|
938 | |
---|
939 | IGCM_sys_Chmod u+x run_file |
---|
940 | if ( $DEBUG_sys ) ; then |
---|
941 | echo "run_file contains : " |
---|
942 | cat run_file |
---|
943 | fi |
---|
944 | |
---|
945 | # MPI-OpenMP (MPMD) |
---|
946 | else |
---|
947 | |
---|
948 | # Hosts treatment |
---|
949 | ${HOST_MPIRUN_COMMAND} hostname | sort | uniq > hosts.tmp |
---|
950 | |
---|
951 | i=0 |
---|
952 | rm -f hosts |
---|
953 | IGCM_debug_Print 1 "sys Ciclad, Hosts available :" |
---|
954 | for nodes in `cat hosts.tmp` ; do |
---|
955 | host[$i]=$nodes |
---|
956 | echo "${host[$i]} slots=1 max_slots=1" >> hosts |
---|
957 | IGCM_debug_Print 1 ${host[$i]} |
---|
958 | i=$((i+1)) |
---|
959 | done |
---|
960 | rm -f hosts.tmp |
---|
961 | |
---|
962 | listnodes=${host[*]} |
---|
963 | |
---|
964 | EXECUTION="${HOST_MPIRUN_COMMAND} -hostfile hosts" |
---|
965 | |
---|
966 | # Initialisation |
---|
967 | rank=0 |
---|
968 | current_core=0 |
---|
969 | core_per_node=8 |
---|
970 | init_exec=n |
---|
971 | |
---|
972 | # Loop on the components |
---|
973 | for comp in ${config_ListOfComponents[*]} ; do |
---|
974 | |
---|
975 | eval ExeNameIn=\${config_Executable_${comp}[0]} |
---|
976 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
977 | |
---|
978 | # Not possible if oasis has an executable (i.e old version of oasis3) |
---|
979 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" = "XCPL" ] ) ; then |
---|
980 | IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version" |
---|
981 | IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler" |
---|
982 | IGCM_debug_Verif_Exit |
---|
983 | fi |
---|
984 | |
---|
985 | # Only if we really have an executable for the component : |
---|
986 | if [ "X${ExeNameOut}" != X\"\" ] ; then |
---|
987 | |
---|
988 | eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} |
---|
989 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
990 | |
---|
991 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
992 | echo "" >> script_${ExeNameOut}.ksh |
---|
993 | if [ ${comp_proc_omp_loc} -gt 1 ] ; then |
---|
994 | |
---|
995 | # Check if the number of threads is correct |
---|
996 | case ${comp_proc_omp_loc} in |
---|
997 | 2|4|8) |
---|
998 | IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads" |
---|
999 | ;; |
---|
1000 | *) |
---|
1001 | IGCM_debug_Exit "ERROR with OMP parameters !" |
---|
1002 | IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads" |
---|
1003 | IGCM_debug_Print 2 "Only 2,4,8 as number of OMP threads are possible " |
---|
1004 | IGCM_debug_Verif_Exit |
---|
1005 | ;; |
---|
1006 | esac |
---|
1007 | #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh |
---|
1008 | #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh |
---|
1009 | #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh |
---|
1010 | echo "export OMP_STACKSIZE=200M" >> script_${ExeNameOut}.ksh |
---|
1011 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
1012 | fi |
---|
1013 | |
---|
1014 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
1015 | echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK )) " >> script_${ExeNameOut}.ksh |
---|
1016 | echo "MYMPIRANK=\$(printf '%3.3d\n' \${MYMPIRANK})" >> script_${ExeNameOut}.ksh |
---|
1017 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh |
---|
1018 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
1019 | |
---|
1020 | if [ ${init_exec} = y ] ; then |
---|
1021 | EXECUTION="${EXECUTION} : -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
1022 | else |
---|
1023 | EXECUTION="${EXECUTION} -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh" |
---|
1024 | init_exec=y |
---|
1025 | fi |
---|
1026 | |
---|
1027 | # Build rankfile : method used to assign cores and nodes for the MPI process |
---|
1028 | # Ex : |
---|
1029 | #rank 0=curie5296 slot=0,1,2,3 |
---|
1030 | #rank 1=curie5296 slot=4,5,6,7 |
---|
1031 | # Example of final command : |
---|
1032 | # mpirun -hostfile hosts -rankfile rankfile -np 27 ./script_lmdz.x.ksh : -np 5 ./script_opa.xx.ksh |
---|
1033 | # with script_lmdz.x.ksh : |
---|
1034 | # #!/bin/ksh |
---|
1035 | #export OMP_STACKSIZE=200M |
---|
1036 | #export OMP_NUM_THREADS=4 |
---|
1037 | #./lmdz.x |
---|
1038 | |
---|
1039 | for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do |
---|
1040 | (( index_host = current_core / core_per_node )) |
---|
1041 | host_value=${host[${index_host}]} |
---|
1042 | (( slot = current_core % core_per_node )) |
---|
1043 | virg="," |
---|
1044 | string_final="" |
---|
1045 | for index in `seq $slot $(($slot+$comp_proc_omp_loc-1))`; do |
---|
1046 | string=$index$virg |
---|
1047 | string_final=$string_final$string |
---|
1048 | done |
---|
1049 | string_final=$( echo $string_final | sed "s/.$//" ) |
---|
1050 | echo "rank $rank=$host_value slot=$string_final" >> rankfile |
---|
1051 | (( rank = rank + 1 )) |
---|
1052 | (( current_core = current_core + comp_proc_omp_loc )) |
---|
1053 | done |
---|
1054 | fi |
---|
1055 | done |
---|
1056 | fi |
---|
1057 | |
---|
1058 | # Only one executable (SPMD mode). |
---|
1059 | else |
---|
1060 | |
---|
1061 | for comp in ${config_ListOfComponents[*]} ; do |
---|
1062 | |
---|
1063 | # Only if we really have an executable for the component : |
---|
1064 | eval ExeNameOut=\${config_Executable_${comp}[1]} |
---|
1065 | if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then |
---|
1066 | |
---|
1067 | echo "#!/bin/ksh" > script_${ExeNameOut}.ksh |
---|
1068 | echo "" >> script_${ExeNameOut}.ksh |
---|
1069 | if ( ${OK_PARA_OMP} ) ; then |
---|
1070 | eval comp_proc_omp_loc=\${${comp}_PROC_OMP} |
---|
1071 | echo "export OMP_STACKSIZE=200M" >> script_${ExeNameOut}.ksh |
---|
1072 | echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh |
---|
1073 | fi |
---|
1074 | if ( ${OK_PARA_MPI} ) ; then |
---|
1075 | # Default : mpirun used if nb_proc gt 1 |
---|
1076 | # pour sortie out/err par process |
---|
1077 | echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${OMPI_COMM_WORLD_RANK} 2>out_${ExeNameOut}.err.\${OMPI_COMM_WORLD_RANK}" >> script_${ExeNameOut}.ksh |
---|
1078 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
1079 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
1080 | EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh" |
---|
1081 | else |
---|
1082 | # Default : mpirun is NOT used if nb_proc eq 1 |
---|
1083 | # pour sortie out/err par process |
---|
1084 | echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh |
---|
1085 | #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh |
---|
1086 | IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh |
---|
1087 | EXECUTION="time ./script_${ExeNameOut}.ksh" |
---|
1088 | fi |
---|
1089 | |
---|
1090 | IGCM_debug_Print 1 "sys Ciclad : script_${ExeNameOut}.ksh contains" |
---|
1091 | cat script_${ExeNameOut}.ksh |
---|
1092 | |
---|
1093 | fi |
---|
1094 | |
---|
1095 | done |
---|
1096 | |
---|
1097 | fi |
---|
1098 | |
---|
1099 | IGCM_debug_Print 1 "sys Ciclad : execution command is" |
---|
1100 | IGCM_debug_Print 1 "$EXECUTION" |
---|
1101 | |
---|
1102 | IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" |
---|
1103 | } |
---|
1104 | |
---|
1105 | #D-#================================================== |
---|
1106 | #D-function IGCM_sys_check_path |
---|
1107 | #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine |
---|
1108 | #D-* do not point to an important use directory. Stop immediately in that case. |
---|
1109 | #D-* Examples: |
---|
1110 | #D- |
---|
1111 | function IGCM_sys_check_path { |
---|
1112 | IGCM_debug_PushStack "IGCM_sys_check_path" |
---|
1113 | if ( $DEBUG_sys ) ; then |
---|
1114 | echo "IGCM_sys_check_path" |
---|
1115 | fi |
---|
1116 | |
---|
1117 | if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then |
---|
1118 | IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" |
---|
1119 | IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" |
---|
1120 | IGCM_debug_Exit "This will stop the job" |
---|
1121 | fi |
---|
1122 | IGCM_debug_PopStack "IGCM_sys_check_path" |
---|
1123 | } |
---|
1124 | |
---|
1125 | #D-#================================================== |
---|
1126 | #D-function IGCM_sys_check_quota. Dummy call here |
---|
1127 | #D-* Purpose: check user quota. Stop the simulation if quota above 90% |
---|
1128 | #D-* Examples: |
---|
1129 | #D- |
---|
1130 | function IGCM_sys_check_quota { |
---|
1131 | IGCM_debug_PushStack "IGCM_sys_check_quota" |
---|
1132 | if ( $DEBUG_sys ) ; then |
---|
1133 | echo "IGCM_sys_check_quota" |
---|
1134 | fi |
---|
1135 | |
---|
1136 | # TO BE IMPLEMENTED |
---|
1137 | |
---|
1138 | IGCM_debug_PopStack "IGCM_sys_check_quota" |
---|
1139 | } |
---|
1140 | |
---|
1141 | #D-#================================================== |
---|
1142 | #D-function IGCM_sys_projectAccounting |
---|
1143 | #D-* Purpose: store project accounting information in a file |
---|
1144 | #D-* Examples: |
---|
1145 | #D- |
---|
1146 | function IGCM_sys_projectAccounting { |
---|
1147 | IGCM_debug_PushStack "IGCM_sys_projectAccounting" |
---|
1148 | if ( $DEBUG_sys ) ; then |
---|
1149 | echo "IGCM_sys_check_quota" |
---|
1150 | fi |
---|
1151 | |
---|
1152 | touch $1 |
---|
1153 | |
---|
1154 | IGCM_debug_PopStack "IGCM_sys_projectAccounting" |
---|
1155 | } |
---|
1156 | |
---|
1157 | #D-#================================================== |
---|
1158 | #D-function IGCM_sys_getJobSchedulerID |
---|
1159 | #D-* Purpose: Get the job ID during execution |
---|
1160 | #D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID |
---|
1161 | #D- |
---|
1162 | function IGCM_sys_getJobSchedulerID { |
---|
1163 | IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID" |
---|
1164 | if ( $DEBUG_sys ) ; then |
---|
1165 | echo "IGCM_sys_getJobSchedulerID" |
---|
1166 | fi |
---|
1167 | |
---|
1168 | eval ${1}=$( echo ${PBS_JOBID} | awk -F. '{print $1}' ) |
---|
1169 | |
---|
1170 | IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID" |
---|
1171 | } |
---|
1172 | |
---|
1173 | #D-#================================================== |
---|
1174 | #D-function IGCM_sys_GetJobID |
---|
1175 | #D-* Purpose: Get the job ID from the JobName |
---|
1176 | #D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID |
---|
1177 | #D- |
---|
1178 | function IGCM_sys_GetJobID { |
---|
1179 | IGCM_debug_PushStack "IGCM_sys_GetJobID" |
---|
1180 | if ( $DEBUG_sys ) ; then |
---|
1181 | echo "IGCM_sys_GetJobID" |
---|
1182 | fi |
---|
1183 | |
---|
1184 | # With -f option, the full job name is given in the last column |
---|
1185 | ID="$( qstat -u $2 | grep -w $1 | gawk '-F ' '{print $10}' )" |
---|
1186 | |
---|
1187 | eval ${3}=${ID} |
---|
1188 | IGCM_debug_PopStack "IGCM_sys_GetJobID" |
---|
1189 | } |
---|
1190 | |
---|
1191 | #D-#================================================== |
---|
1192 | #D-function IGCM_sys_CountJobInQueue |
---|
1193 | #D-* Purpose: Count number of users job |
---|
1194 | #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun |
---|
1195 | #D- |
---|
1196 | function IGCM_sys_CountJobInQueue { |
---|
1197 | IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" |
---|
1198 | if ( $DEBUG_sys ) ; then |
---|
1199 | echo "IGCM_sys_CountJobInQueue" |
---|
1200 | fi |
---|
1201 | IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" |
---|
1202 | } |
---|
1203 | |
---|
1204 | #D-#================================================== |
---|
1205 | #D-function IGCM_sys_atlas |
---|
1206 | #D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity |
---|
1207 | #D-* Examples: |
---|
1208 | #D- |
---|
1209 | function IGCM_sys_atlas { |
---|
1210 | IGCM_debug_PushStack "IGCM_sys_atlas" $@ |
---|
1211 | if ( $DEBUG_sys ) ; then |
---|
1212 | echo "IGCM_sys_atlas :" $@ |
---|
1213 | fi |
---|
1214 | |
---|
1215 | typeset status |
---|
1216 | |
---|
1217 | \atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 |
---|
1218 | status=$? |
---|
1219 | if [ ${status} -gt 0 ] ; then |
---|
1220 | echo "IGCM_sys_atlas : error code ${status}" |
---|
1221 | cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
1222 | \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ |
---|
1223 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1224 | return 1 |
---|
1225 | else |
---|
1226 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1227 | return 0 |
---|
1228 | fi |
---|
1229 | |
---|
1230 | IGCM_debug_PopStack "IGCM_sys_atlas" |
---|
1231 | } |
---|
1232 | |
---|