1 | #!/bin/bash |
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2 | |
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3 | # inifor - The Mesoscale Interface for Initializing and Forcing PALM |
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4 | |
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5 | #--------------------------------------------------------------------------------# |
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6 | # This file is part of the PALM model system. |
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7 | # |
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8 | # PALM is free software: you can redistribute it and/or modify it under the terms |
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9 | # of the GNU General Public License as published by the Free Software Foundation, |
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10 | # either version 3 of the License, or (at your option) any later version. |
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11 | # |
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12 | # PALM is distributed in the hope that it will be useful, but WITHOUT ANY |
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13 | # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR |
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14 | # A PARTICULAR PURPOSE. See the GNU General Public License for more details. |
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15 | # |
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16 | # You should have received a copy of the GNU General Public License along with |
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17 | # PALM. If not, see <http://www.gnu.org/licenses/>. |
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18 | # |
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19 | # Copyright 2017-2018 Leibniz Universitaet Hannover |
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20 | #--------------------------------------------------------------------------------# |
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21 | # |
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22 | # Current revisions: |
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23 | # ------------------ |
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24 | # |
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25 | # |
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26 | # Former revisions: |
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27 | # ----------------- |
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28 | # $Id$ |
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29 | # initial revision |
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30 | # |
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31 | # |
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32 | # |
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33 | #--------------------------------------------------------------------------------# |
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34 | # inifor - script for running the inifor executable |
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35 | #--------------------------------------------------------------------------------# |
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36 | |
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37 | |
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38 | |
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39 | # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES |
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40 | |
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41 | set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS |
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42 | # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN |
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43 | # (TOO MANY ARGUMENTS - PROBLEM) |
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44 | set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN |
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45 | |
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46 | typeset -i i iec=0 |
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47 | |
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48 | activation_string_list="inifor" |
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49 | configuration_identifier="default" |
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50 | delete_temporary_catalog=true |
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51 | fileconnection_file=trunk/SCRIPTS/.palm.iofiles |
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52 | locat=normal |
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53 | run_identifier=test |
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54 | silent=false |
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55 | version="inifor 0.1 Rev$Rev$" |
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56 | working_directory=`pwd` |
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57 | |
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58 | |
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59 | # ERROR HANDLING IN CASE OF EXIT |
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60 | trap 'if [[ $locat != normal && $locat != control_c ]] |
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61 | then |
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62 | |
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63 | # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:) |
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64 | (( i = 0 )) |
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65 | while (( i < iec )) |
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66 | do |
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67 | (( i = i + 1 )) |
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68 | printf "\n *** Execution of ERROR-command:\n" |
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69 | printf " >>> ${err_command[$i]}\n" |
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70 | eval ${err_command[$i]} |
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71 | done |
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72 | [[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir) |
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73 | printf "\n\n+++ inifor crashed \n\n" |
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74 | exit 1 |
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75 | elif [[ $locat != normal ]] |
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76 | then |
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77 | [[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir) |
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78 | printf "\n+++ inifor killed by \"^C\" \n\n" |
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79 | exit 2 |
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80 | else |
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81 | printf "\n --> inifor finished\n\n" |
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82 | exit 0 |
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83 | fi' exit |
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84 | |
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85 | |
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86 | # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C): |
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87 | trap 'locat=control_c |
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88 | exit 1 |
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89 | ' 2 |
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90 | |
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91 | |
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92 | # READ SHELLSCRIPT-OPTIONS |
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93 | # TODO: add additional inifor options |
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94 | while getopts :a:Bc:r:v option |
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95 | do |
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96 | case $option in |
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97 | (a) activation_string_list=$OPTARG;; |
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98 | (B) delete_temporary_catalog=false;; |
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99 | (c) configuration_identifier=$OPTARG;; |
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100 | (r) run_identifier=$OPTARG;; |
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101 | (v) silent=true;; |
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102 | (\?) printf "\n +++ unknown option $OPTARG \n" |
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103 | printf "\n --> type \"$0 ?\" for available options \n" |
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104 | locat=parameter;exit;; |
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105 | esac |
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106 | done |
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107 | |
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108 | |
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109 | # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN |
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110 | # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED |
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111 | (( to_shift = $OPTIND - 1 )) |
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112 | shift $to_shift |
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113 | |
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114 | # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS |
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115 | # TODO: add description of additional inifor options |
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116 | if [[ "$1" = "?" ]] |
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117 | then |
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118 | (printf "\n *** Description of available palmrun options:\n" |
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119 | printf "\n Option Description Default-Value" |
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120 | printf "\n -a activation string list \"\" " |
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121 | printf "\n -c configuration identifier \"default\" " |
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122 | printf "\n -r run identifier test" |
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123 | printf "\n -v no prompt for confirmation ---" |
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124 | printf "\n " |
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125 | printf "\n Possible values of positional parameter <modus>:" |
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126 | printf "\n \"?\" - this outline \n\n") | more |
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127 | exit |
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128 | elif [[ "$1" != "" ]] |
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129 | then |
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130 | printf "\n +++ positional parameter $1 unknown \n" |
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131 | locat=parameter; exit |
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132 | fi |
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133 | |
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134 | |
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135 | |
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136 | # SHORT STARTING MESSAGE |
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137 | printf "\n*** $version " |
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138 | printf "\n will be executed. Please wait ..." |
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139 | |
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140 | |
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141 | # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME |
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142 | config_file=.palm.config.$configuration_identifier |
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143 | sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier |
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144 | |
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145 | |
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146 | # CHECK, IF CONFIGURATION FILE EXISTS |
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147 | if [[ ! -f $config_file ]] |
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148 | then |
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149 | |
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150 | printf "\n\n +++ configuration file: " |
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151 | printf "\n $config_file" |
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152 | printf "\n does not exist" |
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153 | locat=connect; exit |
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154 | |
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155 | fi |
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156 | |
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157 | |
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158 | # CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE |
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159 | if [[ -f .palm.iofiles ]] |
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160 | then |
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161 | |
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162 | # CHECK VERSION MISMATCH |
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163 | if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]] |
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164 | then |
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165 | printf "\n\n +++ WARNING: A file connection file has been found in your" |
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166 | printf "\n working directory, but its revision does not match" |
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167 | printf "\n the revision of the default (trunk) version." |
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168 | printf "\n You may need to update your connection file" |
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169 | printf "\n \"${working_directory}/.palm.iofiles\" !" |
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170 | fi |
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171 | |
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172 | fileconnection_file=.palm.iofiles |
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173 | |
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174 | fi |
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175 | |
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176 | |
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177 | # CHECK, IF FILE CONNECTION FILE EXISTS |
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178 | if [[ ! -f $fileconnection_file ]] |
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179 | then |
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180 | printf "\n\n +++ file connection file: " |
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181 | printf "\n $fileconnection_file" |
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182 | printf "\n does not exist" |
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183 | locat=connect; exit |
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184 | fi |
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185 | |
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186 | |
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187 | # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN |
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188 | # TODO: I suggest to use/extend the .palm.iofiles file to set the inifor I/O files, |
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189 | # activation string could be "inifor" |
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190 | if [[ "$activation_string_list" = "" ]] |
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191 | then |
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192 | printf "\n\n +++ no activation string list given: " |
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193 | printf "\n please set palmrun option \"-a\" " |
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194 | locat=palmrun_option; exit |
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195 | fi |
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196 | |
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197 | |
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198 | # READ AND EVALUATE THE CONFIGURATION-FILE |
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199 | # TODO: we can think about if it is really required tio read and interpret the whole file |
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200 | # since many settings are not relevant for inifor. Instead, we could read only lines |
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201 | # inifor-specific variables are set (like it is done in palmbuild) |
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202 | [[ $silent = false ]] && printf "\n\n Reading the configuration file... " |
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203 | |
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204 | |
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205 | # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE |
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206 | while read line |
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207 | do |
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208 | |
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209 | # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES |
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210 | eval line=\"$line\" |
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211 | |
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212 | |
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213 | # INTERPRET THE LINE |
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214 | if [[ "$(echo $line)" = "" ]] |
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215 | then |
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216 | |
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217 | # EMPTY LINE, NO ACTION |
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218 | continue |
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219 | |
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220 | elif [[ "$(echo $line | cut -c1)" = "#" ]] |
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221 | then |
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222 | |
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223 | # LINE IS A COMMENT LINE |
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224 | continue |
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225 | |
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226 | elif [[ "$(echo $line | cut -c1)" = "%" ]] |
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227 | then |
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228 | |
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229 | # LINE DEFINES AN ENVIRONMENT-VARIABLE |
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230 | var=`echo $line | cut -d" " -s -f1 | cut -c2-` |
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231 | value=`echo $line | cut -d" " -s -f2-` |
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232 | |
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233 | |
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234 | # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE |
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235 | # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY |
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236 | # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS). |
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237 | # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER). |
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238 | # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE |
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239 | # CONFIGURATION-FILE. |
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240 | if [[ "$(eval echo \$$var)" = "" || "$(eval echo \$$var)" = "0" ]] |
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241 | then |
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242 | eval export $var="\$value" |
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243 | |
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244 | # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on |
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245 | if [[ $do_trace = true ]] |
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246 | then |
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247 | printf "\n*** ENVIRONMENT-VARIABLE $var = $value" |
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248 | fi |
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249 | fi |
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250 | |
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251 | elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]] |
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252 | then |
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253 | |
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254 | # LINE DEFINES BATCH-DIRECTIVE |
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255 | (( ibd = ibd + 1 )) |
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256 | line=$(echo $line | cut -c4-) |
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257 | batch_directive[$ibd]="$line" |
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258 | |
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259 | elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]] |
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260 | then |
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261 | |
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262 | # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A |
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263 | # REMOTE TO A LOCAL HOST |
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264 | (( ibdt = ibdt + 1 )) |
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265 | line=$(echo $line | cut -c5-) |
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266 | batch_directive_transfer[$ibdt]="$line" |
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267 | |
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268 | elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]] |
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269 | then |
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270 | |
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271 | # LINE DEFINES ERROR-COMMAND |
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272 | (( iec = iec + 1 )) |
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273 | line=$(echo $line | cut -c4-) |
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274 | err_command[$iec]="$line" |
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275 | |
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276 | elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]] |
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277 | then |
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278 | |
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279 | # LINE DEFINES INPUT-COMMAND |
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280 | (( iic = iic + 1 )) |
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281 | line=$(echo $line | cut -c4-) |
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282 | in_command[$iic]="$line" |
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283 | |
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284 | elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]] |
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285 | then |
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286 | |
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287 | # LINE DEFINES OUTPUT-COMMAND |
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288 | (( ioc = ioc + 1 )) |
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289 | line=$(echo $line | cut -c4-) |
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290 | out_command[$ioc]="$line" |
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291 | |
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292 | else |
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293 | |
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294 | # SKIP ALL OTHER LINES |
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295 | continue |
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296 | |
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297 | fi |
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298 | |
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299 | done < $config_file |
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300 | |
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301 | |
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302 | # CHECK SETTING OF REQUIRED PARAMETERS |
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303 | # TODO: we probably need to include such a line in the configuration file |
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304 | if [[ "$execute_command_inifor" = "" ]] |
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305 | then |
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306 | printf "\n +++ no execute command found for inifor in $config_file" |
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307 | printf "\n Please add line \"execute_command_inifor ...\" to that file." |
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308 | locat=config_file; exit |
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309 | fi |
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310 | |
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311 | |
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312 | # DETERMINE THE CALL STATUS |
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313 | if [[ "$remote_ip" != "" ]] |
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314 | then |
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315 | run_on_remote=true |
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316 | else |
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317 | run_on_remote=false |
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318 | fi |
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319 | |
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320 | |
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321 | # READ AND EVALUATE THE I/O-FILE LIST |
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322 | [[ $silent = false ]] && printf "\n Reading the I/O files... " |
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323 | |
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324 | |
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325 | # READ THE FILE CONNECTION FILE LINE BY LINE |
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326 | while read line |
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327 | do |
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328 | |
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329 | # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE |
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330 | # HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY |
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331 | line=`echo "$line" | tr -s " "` |
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332 | |
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333 | # INTERPRET THE LINE |
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334 | if [[ "$(echo $line)" = "" ]] |
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335 | then |
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336 | # EMPTY LINE, NO ACTION |
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337 | continue |
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338 | |
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339 | elif [[ "$(echo $line | cut -c1)" = "#" ]] |
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340 | then |
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341 | |
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342 | # LINE IS A COMMENT LINE |
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343 | true |
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344 | |
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345 | else |
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346 | |
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347 | # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES. |
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348 | # s2a: in/out - field |
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349 | # s2b: action - field (optional) |
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350 | s1=`echo "$line" | cut -d" " -f1` |
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351 | s2=`echo "$line" | cut -d" " -s -f2` |
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352 | if [[ $(echo $s2 | grep -c ":") = 0 ]] |
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353 | then |
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354 | s2a=$s2 |
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355 | s2b="" |
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356 | else |
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357 | s2a=`echo $s2 | cut -d":" -f1` |
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358 | s2b=`echo $s2 | cut -d":" -f2` |
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359 | fi |
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360 | s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'` |
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361 | s4=`echo "$line" | cut -d" " -s -f4` |
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362 | eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES |
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363 | s5=`echo "$line" | cut -d" " -s -f5` |
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364 | s6=`echo "$line" | cut -d" " -s -f6` |
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365 | |
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366 | |
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367 | # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM |
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368 | # INPUT- OR OUTPUT-LIST. |
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369 | # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":"). |
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370 | # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY |
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371 | # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION |
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372 | # IS NOT CHECKED AND STORED. |
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373 | IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR |
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374 | if [[ ( "$s2a" = in || "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]] |
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375 | then |
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376 | found=false |
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377 | for actual in $activation_string_list |
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378 | do |
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379 | for formal in $s3 |
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380 | do |
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381 | [[ $actual = $formal || "$formal" = "-" ]] && found=true |
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382 | done |
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383 | done |
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384 | if [[ $found = true ]] |
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385 | then |
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386 | (( iin = iin + 1 )) |
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387 | localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b; |
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388 | pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6 |
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389 | if [[ "$s2a" = inopt ]] |
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390 | then |
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391 | optin_pre[$iin]=yes |
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392 | else |
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393 | optin_pre[$iin]=no |
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394 | fi |
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395 | |
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396 | # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN |
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397 | # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST |
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398 | if [[ $running_on_remote = true && "$s2b" = tr ]] |
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399 | then |
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400 | pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog} |
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401 | fi |
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402 | |
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403 | # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE |
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404 | # THE WILDCARD FROM THE ENDING |
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405 | if [[ "${s5: -1}" = "*" ]] |
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406 | then |
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407 | if [[ "$s2b" = "di" ]] |
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408 | then |
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409 | printf "\n +++ wildcards (*) not allowed with \"di\" file attribute." |
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410 | printf "\n see file \"$fileconnection_file\", line" |
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411 | printf "\n$line" |
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412 | locat=iofiles_file; exit |
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413 | fi |
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414 | multin[$iin]=true |
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415 | string=${endin_pre[$iin]} |
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416 | endin_pre[$iin]="${string%?}" |
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417 | else |
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418 | multin[$iin]=false |
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419 | fi |
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420 | fi |
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421 | elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]] |
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422 | then |
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423 | found=false |
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424 | for actual in $activation_string_list |
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425 | do |
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426 | for formal in $s3 |
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427 | do |
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428 | [[ $actual = $formal || $formal = wildcard ]] && found=true |
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429 | done |
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430 | done |
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431 | if [[ $found = true ]] |
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432 | then |
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433 | (( iout = iout + 1 )) |
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434 | localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b |
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435 | pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6 |
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436 | |
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437 | # CHECK IF WILDCARD IS USED AS ACTIVATION STRING |
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438 | # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST |
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439 | if [[ $formal = wildcard ]] |
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440 | then |
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441 | warnout_pre[$iout]=false |
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442 | else |
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443 | warnout_pre[$iout]=true |
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444 | fi |
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445 | |
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446 | # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE |
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447 | # THE WILDCARD FROM THE LOCAL FILENAME |
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448 | if [[ "${s1: -1}" = "*" ]] |
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449 | then |
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450 | if [[ "$s2b" = "di" ]] |
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451 | then |
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452 | printf "\n +++ wildcards (*) not allowed with \"di\" file attribute." |
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453 | printf "\n see file \"$fileconnection_file\", line" |
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454 | printf "\n$line" |
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455 | locat=iofiles_file; exit |
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456 | fi |
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457 | multout[$iout]=true |
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458 | string=${localout_pre[$iout]} |
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459 | localout_pre[$iout]="${string%?}" |
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460 | else |
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461 | multout[$iout]=false |
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462 | fi |
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463 | fi |
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464 | elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]] |
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465 | then |
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466 | printf "\n +++ I/O-attribute in file $fileconnection_file has invalid" |
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467 | printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!" |
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468 | locat=connect; exit |
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469 | fi |
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470 | IFS="$IFSALT" |
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471 | fi |
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472 | |
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473 | done < $fileconnection_file |
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474 | |
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475 | |
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476 | |
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477 | # VALUES OF INIFOR-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE |
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478 | # next line is just an example |
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479 | # TODO: default values for inifor script options could be set in the configuration file |
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480 | # (if it makes sense) |
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481 | [[ "$inifor_cores" != "" ]] && cores=$inifor_cores |
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482 | |
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483 | |
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484 | |
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485 | # CHECK IF INIFOR EXECUTABLE EXISTS |
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486 | if [[ $run_on_remote = false ]] |
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487 | then |
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488 | |
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489 | if [[ ! -f ${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}/inifor ]] |
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490 | then |
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491 | printf "\n +++ no inifor executable found in folder" |
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492 | printf "\n \"${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}\" " |
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493 | printf "\n You may run \"palmbuild -c ${configuration_identifier}\" to create" |
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494 | printf "\n the utility routines." |
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495 | locat=connect; exit |
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496 | fi |
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497 | |
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498 | else |
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499 | |
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500 | printf "\n +++ remote call of inifor not realized yet" |
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501 | locat=inifor_remote; exit |
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502 | |
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503 | fi |
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504 | |
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505 | |
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506 | |
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507 | # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY |
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508 | # (HANDED OVER TO RESTART-RUNS USING OPTION -G) |
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509 | if [[ "$global_revision" = "" ]] |
---|
510 | then |
---|
511 | global_revision=`svnversion $source_path 2>/dev/null` |
---|
512 | global_revision="Rev: $global_revision" |
---|
513 | fi |
---|
514 | |
---|
515 | |
---|
516 | |
---|
517 | # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT |
---|
518 | if [[ "$scp_port" != "" ]] |
---|
519 | then |
---|
520 | PORTOPT="-P $scp_port" |
---|
521 | SSH_PORTOPT="-p $scp_port" |
---|
522 | fi |
---|
523 | |
---|
524 | |
---|
525 | # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE |
---|
526 | # CONFIG-FILE |
---|
527 | if [[ "$ssh_key" != "" ]] |
---|
528 | then |
---|
529 | ssh_key="-i $HOME/.ssh/$ssh_key" |
---|
530 | fi |
---|
531 | |
---|
532 | |
---|
533 | # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH |
---|
534 | # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST) |
---|
535 | (( i = 0 )) |
---|
536 | (( nr_of_input_files = 0 )) |
---|
537 | while (( i < iin )) |
---|
538 | do |
---|
539 | (( i = i + 1 )) |
---|
540 | |
---|
541 | # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE |
---|
542 | # FILE IDENTIFIER IS NOT PART OF THE FILENAME)) |
---|
543 | if [[ "${actionin_pre[$i]}" = di ]] |
---|
544 | then |
---|
545 | eval filename=${pathin_pre[$i]}/${endin_pre[$i]} |
---|
546 | else |
---|
547 | eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]} |
---|
548 | fi |
---|
549 | |
---|
550 | |
---|
551 | # CHECK IF FILE EXISTS |
---|
552 | if ! ls $filename* 1>/dev/null 2>&1 |
---|
553 | then |
---|
554 | |
---|
555 | # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST. |
---|
556 | if [[ "${optin_pre[$i]}" != "yes" ]] |
---|
557 | then |
---|
558 | printf "\n\n +++ INPUT-file: " |
---|
559 | if [[ "${extin_pre[$i]}" = "" || "${extin_pre[$i]}" = " " ]] |
---|
560 | then |
---|
561 | printf "\n $filename" |
---|
562 | else |
---|
563 | printf "\n $filename.${extin_pre[$i]}" |
---|
564 | fi |
---|
565 | printf "\n does not exist\n" |
---|
566 | locat=input; exit |
---|
567 | else |
---|
568 | (( nr_of_input_files = nr_of_input_files + 1 )) |
---|
569 | localin[$nr_of_input_files]="${localin_pre[$i]}" |
---|
570 | optin[$nr_of_input_files]="${optin_pre[$i]}" |
---|
571 | actionin[$nr_of_input_files]="unavailable" |
---|
572 | pathin[$nr_of_input_files]="${pathin_pre[$i]}" |
---|
573 | endin[$nr_of_input_files]="${endin_pre[$i]}" |
---|
574 | extin[$nr_of_input_files]="${extin_pre[$i]}" |
---|
575 | fi |
---|
576 | |
---|
577 | else |
---|
578 | |
---|
579 | # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME |
---|
580 | # ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME |
---|
581 | # ENDINGS |
---|
582 | if [[ "${multin[$i]}" = true ]] |
---|
583 | then |
---|
584 | # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES |
---|
585 | ls -1 -d ${filename} > filelist 2>/dev/null |
---|
586 | ls -1 -d ${filename}.* >> filelist 2>/dev/null |
---|
587 | ls -1 -d ${filename}_* >> filelist 2>/dev/null |
---|
588 | |
---|
589 | endings="" |
---|
590 | while read line |
---|
591 | do |
---|
592 | # filename without path (i.e. after the last "/") |
---|
593 | basefilename=$(basename ${line}) |
---|
594 | |
---|
595 | # check if there is an extension and remove it |
---|
596 | ext=${basefilename##*.} |
---|
597 | if [[ "$ext" = "${extin_pre[$i]}" ]] |
---|
598 | then |
---|
599 | basefilename=${basefilename%.*} |
---|
600 | fi |
---|
601 | |
---|
602 | # check for an existing cycle number and remove it |
---|
603 | cycle=${basefilename##*.} |
---|
604 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
605 | then |
---|
606 | basefilename=${basefilename%.*} |
---|
607 | fi |
---|
608 | |
---|
609 | # remove the run_identifier from the beginning |
---|
610 | length_run_identifier=${#run_identifier} |
---|
611 | ending=${basefilename:${length_run_identifier}} |
---|
612 | |
---|
613 | # remove the ending given in the .iofiles from the beginning |
---|
614 | endingstring="${endin_pre[$i]}" |
---|
615 | length_ending=${#endingstring} |
---|
616 | ending=${ending:${length_ending}} |
---|
617 | |
---|
618 | if [[ "$ending" = "" ]] |
---|
619 | then |
---|
620 | # standard ending as given in the .iofiles |
---|
621 | if [[ $(echo $endings | grep -c DEFAULT) = 0 ]] |
---|
622 | then |
---|
623 | endings="$endings DEFAULT" |
---|
624 | fi |
---|
625 | else |
---|
626 | # ending must start with "_", otherwise its a different file |
---|
627 | if [[ "${ending:0:1}" = "_" ]] |
---|
628 | then |
---|
629 | if [[ $(echo $endings | grep -c "$ending") = 0 ]] |
---|
630 | then |
---|
631 | endings="$endings $ending" |
---|
632 | fi |
---|
633 | fi |
---|
634 | fi |
---|
635 | |
---|
636 | done <filelist |
---|
637 | |
---|
638 | rm filelist |
---|
639 | |
---|
640 | else |
---|
641 | |
---|
642 | # SINGLE NAME |
---|
643 | endings=DEFAULT |
---|
644 | |
---|
645 | fi |
---|
646 | |
---|
647 | # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST |
---|
648 | for ending in $endings |
---|
649 | do |
---|
650 | |
---|
651 | # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED |
---|
652 | if [[ $ending = DEFAULT ]] |
---|
653 | then |
---|
654 | ending="" |
---|
655 | fi |
---|
656 | |
---|
657 | # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!) |
---|
658 | (( nr_of_input_files = nr_of_input_files + 1 )) |
---|
659 | localin[$nr_of_input_files]="${localin_pre[$i]}"$ending |
---|
660 | optin[$nr_of_input_files]="${optin_pre[$i]}" |
---|
661 | actionin[$nr_of_input_files]="${actionin_pre[$i]}" |
---|
662 | pathin[$nr_of_input_files]="${pathin_pre[$i]}" |
---|
663 | endin[$nr_of_input_files]="${endin_pre[$i]}"$ending |
---|
664 | extin[$nr_of_input_files]="${extin_pre[$i]}" |
---|
665 | |
---|
666 | |
---|
667 | # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE |
---|
668 | # FILE IDENTIFIER IS NOT PART OF THE FILENAME)) |
---|
669 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
670 | then |
---|
671 | eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]} |
---|
672 | else |
---|
673 | eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]} |
---|
674 | fi |
---|
675 | |
---|
676 | # DETERMINE THE FILE'S CYCLE NUMBER |
---|
677 | (( maxcycle = 0 )) |
---|
678 | ls -1 -d $filename > filelist 2>/dev/null |
---|
679 | ls -1 -d $filename.* >> filelist 2>/dev/null |
---|
680 | while read line |
---|
681 | do |
---|
682 | # filename without path (i.e. after the last "/") |
---|
683 | basefilename=$(basename ${line}) |
---|
684 | |
---|
685 | # check if there is an extension |
---|
686 | extension=${basefilename##*.} |
---|
687 | if [[ "$extension" = "${extin[$nr_of_input_files]}" ]] |
---|
688 | then |
---|
689 | basefilename=${basefilename%.*} |
---|
690 | fi |
---|
691 | |
---|
692 | # check for an existing cycle number |
---|
693 | cycle=${basefilename##*.} |
---|
694 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
695 | then |
---|
696 | # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS |
---|
697 | # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 |
---|
698 | (( icycle = $((10#$cycle)) )) |
---|
699 | else |
---|
700 | (( icycle = 0 )) |
---|
701 | fi |
---|
702 | |
---|
703 | if (( icycle > maxcycle )) |
---|
704 | then |
---|
705 | (( maxcycle = icycle )) |
---|
706 | |
---|
707 | # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS |
---|
708 | # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS |
---|
709 | if [[ $(echo $cycle | cut -c1) = 0 ]] |
---|
710 | then |
---|
711 | leading_zero=true |
---|
712 | else |
---|
713 | leading_zero=false |
---|
714 | fi |
---|
715 | fi |
---|
716 | |
---|
717 | done <filelist |
---|
718 | rm filelist |
---|
719 | |
---|
720 | # MAKE CYCLE NUMBER THREE DIGITS WIDE |
---|
721 | if [[ $leading_zero = true ]] |
---|
722 | then |
---|
723 | cyclestring=`printf "%03d" $maxcycle` |
---|
724 | else |
---|
725 | cyclestring=$maxcycle |
---|
726 | fi |
---|
727 | |
---|
728 | # APPEND CYCLE NUMBER TO FILENAME |
---|
729 | if (( maxcycle > 0 )) |
---|
730 | then |
---|
731 | if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]] |
---|
732 | then |
---|
733 | filename=${filename}.$cyclestring.${extin[$nr_of_input_files]} |
---|
734 | else |
---|
735 | filename=${filename}.$cyclestring |
---|
736 | fi |
---|
737 | else |
---|
738 | if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]] |
---|
739 | then |
---|
740 | filename=${filename}.${extin[$nr_of_input_files]} |
---|
741 | fi |
---|
742 | fi |
---|
743 | |
---|
744 | # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER, |
---|
745 | # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE) |
---|
746 | absnamein[$nr_of_input_files]=$filename |
---|
747 | if (( maxcycle > 0 )) |
---|
748 | then |
---|
749 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
750 | then |
---|
751 | frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring |
---|
752 | else |
---|
753 | frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring |
---|
754 | fi |
---|
755 | else |
---|
756 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
757 | then |
---|
758 | frelin[$nr_of_input_files]=${endin[$nr_of_input_files]} |
---|
759 | else |
---|
760 | frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]} |
---|
761 | fi |
---|
762 | fi |
---|
763 | |
---|
764 | done |
---|
765 | |
---|
766 | fi |
---|
767 | |
---|
768 | done |
---|
769 | |
---|
770 | |
---|
771 | # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~), |
---|
772 | # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST), |
---|
773 | # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED |
---|
774 | # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO |
---|
775 | # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE |
---|
776 | # REMOTE HOST) |
---|
777 | (( i = 0 )) |
---|
778 | while (( i < iout )) |
---|
779 | do |
---|
780 | (( i = i + 1 )) |
---|
781 | if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]] |
---|
782 | then |
---|
783 | if [[ "${actionout_pre[$i]}" = tr ]] |
---|
784 | then |
---|
785 | actionout_pre[$i]="" |
---|
786 | elif [[ "${actionout_pre[$i]}" = trpe ]] |
---|
787 | then |
---|
788 | actionout_pre[$i]=pe |
---|
789 | elif [[ "${actionout_pre[$i]}" = tra ]] |
---|
790 | then |
---|
791 | actionout_pre[$i]=a |
---|
792 | fi |
---|
793 | (( maxcycle = 0 )) |
---|
794 | eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]} |
---|
795 | eval catalogname=${pathout_pre[$i]} |
---|
796 | if ! ls $filename* 1>/dev/null 2>&1 |
---|
797 | then |
---|
798 | |
---|
799 | # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED |
---|
800 | if cat /dev/null > $filename |
---|
801 | then |
---|
802 | rm $filename |
---|
803 | else |
---|
804 | |
---|
805 | # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS |
---|
806 | # IF IT DOES NOT EXIST, TRY TO CREATE IT |
---|
807 | if [[ ! -d $catalogname ]] |
---|
808 | then |
---|
809 | if mkdir -p $catalogname |
---|
810 | then |
---|
811 | printf "\n\n *** directory:" |
---|
812 | printf "\n $catalogname" |
---|
813 | printf "\n was created\n" |
---|
814 | else |
---|
815 | printf "\n\n +++ OUTPUT-file:" |
---|
816 | printf "\n $filename" |
---|
817 | printf "\n cannot be created, because directory does not exist" |
---|
818 | printf "\n and cannot be created either" |
---|
819 | printf "\n" |
---|
820 | locat=output ; exit |
---|
821 | fi 2>/dev/null |
---|
822 | else |
---|
823 | printf "\n\n +++ OUTPUT-file:" |
---|
824 | printf "\n $filename" |
---|
825 | printf "\n cannot be created, although directory exists" |
---|
826 | printf "\n" |
---|
827 | locat=output ; exit |
---|
828 | fi |
---|
829 | fi 2>/dev/null |
---|
830 | |
---|
831 | fi |
---|
832 | |
---|
833 | fi |
---|
834 | done |
---|
835 | |
---|
836 | |
---|
837 | # DETERMINE THE NAME OF INIFOR'S TEMPORARY WORKING DIRECTORY |
---|
838 | run_id_number=$RANDOM |
---|
839 | run_id=${run_identifier}.$run_id_number |
---|
840 | tempdir=$fast_io_catalog/$run_id |
---|
841 | |
---|
842 | |
---|
843 | |
---|
844 | |
---|
845 | # OUTPUT OF THE INIFOR-HEADER |
---|
846 | calltime=$(date) |
---|
847 | printf "\n" |
---|
848 | printf "#------------------------------------------------------------------------# \n" |
---|
849 | printf "| %-35s%35s | \n" "$version" "$calltime" |
---|
850 | printf "| %-35s%35s | \n" "PALM code $global_revision" " " |
---|
851 | printf "| | \n" |
---|
852 | column1="called on:"; column2=$(hostname) |
---|
853 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
854 | if [[ $run_on_remote = true ]] |
---|
855 | then |
---|
856 | column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)" |
---|
857 | else |
---|
858 | column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)" |
---|
859 | fi |
---|
860 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
861 | |
---|
862 | |
---|
863 | if [[ "$login_init_cmd" != "" ]] |
---|
864 | then |
---|
865 | column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45) |
---|
866 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
867 | line=$(echo "$login_init_cmd" | cut -c46-) |
---|
868 | while [[ "$line" != "" ]] |
---|
869 | do |
---|
870 | column1="" |
---|
871 | column2=$(echo "$line" | cut -c-45) |
---|
872 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
873 | line=$(echo "$line" | cut -c46-) |
---|
874 | done |
---|
875 | fi |
---|
876 | |
---|
877 | if [[ "$module_commands" != "" ]] |
---|
878 | then |
---|
879 | column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45) |
---|
880 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
881 | line=$(echo "$module_commands" | cut -c46-) |
---|
882 | while [[ "$line" != "" ]] |
---|
883 | do |
---|
884 | column1="" |
---|
885 | column2=$(echo "$line" | cut -c-45) |
---|
886 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
887 | line=$(echo "$line" | cut -c46-) |
---|
888 | done |
---|
889 | fi |
---|
890 | printf "| | \n" |
---|
891 | column1="run identifier:"; column2=$run_identifier |
---|
892 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
893 | column1="activation string list:"; column2=$(echo $activation_string_list) |
---|
894 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
895 | |
---|
896 | printf "#------------------------------------------------------------------------#" |
---|
897 | |
---|
898 | |
---|
899 | |
---|
900 | |
---|
901 | # QUERY FOR CONTINUE |
---|
902 | if [[ $silent = false ]] |
---|
903 | then |
---|
904 | antwort=dummy |
---|
905 | printf "\n\n" |
---|
906 | printf " >>> everything o.k. (y/n) ? " |
---|
907 | while read antwort |
---|
908 | do |
---|
909 | if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]] |
---|
910 | then |
---|
911 | printf " >>> everything o.k. (y/n) ? " |
---|
912 | else |
---|
913 | break |
---|
914 | fi |
---|
915 | done |
---|
916 | if [[ $antwort = n || $antwort = N ]] |
---|
917 | then |
---|
918 | locat=user_abort; (( iec = 0 )); exit |
---|
919 | fi |
---|
920 | if [[ $run_on_remote ]] |
---|
921 | then |
---|
922 | printf "\n *** inifor will now run on remote" |
---|
923 | else |
---|
924 | printf "\n *** inifor will now continue to execute on this machine" |
---|
925 | fi |
---|
926 | fi |
---|
927 | |
---|
928 | |
---|
929 | # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE INIFOR ON THIS MACHINE (COPYING I/O FILES) |
---|
930 | # CHANGE TO THE TEMPORARY WORKING DIRECTORY |
---|
931 | |
---|
932 | mkdir -p $tempdir |
---|
933 | chmod go+rx $tempdir |
---|
934 | cd $tempdir |
---|
935 | |
---|
936 | printf "\n *** changed to temporary directory: $tempdir" |
---|
937 | |
---|
938 | |
---|
939 | |
---|
940 | # PROVIDE THE INPUT FILES |
---|
941 | # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE) |
---|
942 | optional_files_missing=false |
---|
943 | (( i = 0 )) |
---|
944 | while (( i < nr_of_input_files )) |
---|
945 | do |
---|
946 | (( i = i + 1 )) |
---|
947 | if (( i == 1 )) |
---|
948 | then |
---|
949 | printf "\n\n *** providing INPUT-files:\n$dashes" |
---|
950 | fi |
---|
951 | |
---|
952 | |
---|
953 | # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST |
---|
954 | if [[ "${actionin[$i]}" = unavailable ]] |
---|
955 | then |
---|
956 | optional_files_missing=true |
---|
957 | continue |
---|
958 | fi |
---|
959 | |
---|
960 | # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION) |
---|
961 | files_for_cores=false; filetype=file |
---|
962 | if [[ "${actionin[$i]}" = pe && -n $cores ]] |
---|
963 | then |
---|
964 | files_for_cores=true; filetype=files |
---|
965 | actionin[$i]="" |
---|
966 | elif [[ "${actionin[$i]}" = pe && ! -n $cores ]] |
---|
967 | then |
---|
968 | actionin[$i]="" |
---|
969 | elif [[ "${actionin[$i]}" = lnpe && -n $cores ]] |
---|
970 | then |
---|
971 | files_for_cores=true; filetype=files |
---|
972 | actionin[$i]="ln" |
---|
973 | elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]] |
---|
974 | then |
---|
975 | actionin[$i]="ln" |
---|
976 | fi |
---|
977 | |
---|
978 | if [[ $files_for_cores = true ]] |
---|
979 | then |
---|
980 | printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}" |
---|
981 | else |
---|
982 | printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}" |
---|
983 | fi |
---|
984 | |
---|
985 | # INPUT-FILES TO BE LINKED |
---|
986 | if [[ "${actionin[$i]}" = ln ]] |
---|
987 | then |
---|
988 | |
---|
989 | printf "\n $filetype will be linked" |
---|
990 | if [[ $files_for_cores = false ]] |
---|
991 | then |
---|
992 | if [[ -f "${absnamein[$i]}" ]] |
---|
993 | then |
---|
994 | ln ${absnamein[$i]} ${localin[$i]} |
---|
995 | got_tmp[$i]=true |
---|
996 | fi |
---|
997 | else |
---|
998 | if [[ -d "${absnamein[$i]}" ]] |
---|
999 | then |
---|
1000 | mkdir -p ${localin[$i]} |
---|
1001 | cd ${absnamein[$i]} |
---|
1002 | for file in $(ls *) |
---|
1003 | do |
---|
1004 | ln $file $tempdir/${localin[$i]} |
---|
1005 | done >|/dev/null 2>&1 |
---|
1006 | cd $tempdir |
---|
1007 | fi |
---|
1008 | |
---|
1009 | # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r" |
---|
1010 | if [[ ! -f "${localin[$i]}/_000000" ]] |
---|
1011 | then |
---|
1012 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
1013 | cp -r ${absnamein[$i]}/* ${localin[$i]} |
---|
1014 | fi |
---|
1015 | |
---|
1016 | got_tmp[$i]=true |
---|
1017 | fi |
---|
1018 | fi |
---|
1019 | |
---|
1020 | # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE |
---|
1021 | if [[ "${actionin[$i]}" = "" || "${actionin[$i]}" = "di" || "${actionin[$i]}" = "tr" || "${actionin[$i]}" = "npe" ]] |
---|
1022 | then |
---|
1023 | |
---|
1024 | if [[ "${actionin[$i]}" = "npe" && -n $cores ]] |
---|
1025 | then |
---|
1026 | |
---|
1027 | # FILE COPIES ARE PROVIDED FOR ALL CORES |
---|
1028 | # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER |
---|
1029 | printf "\n file will be provided for $cores processors" |
---|
1030 | mkdir -p ${localin[$i]} |
---|
1031 | ival=$cores |
---|
1032 | (( ii = 0 )) |
---|
1033 | while (( ii <= ival-1 )) |
---|
1034 | do |
---|
1035 | if (( ii < 10 )) |
---|
1036 | then |
---|
1037 | cp ${absnamein[$i]} ${localin[$i]}/_000$ii |
---|
1038 | elif (( ii < 100 )) |
---|
1039 | then |
---|
1040 | cp ${absnamein[$i]} ${localin[$i]}/_00$ii |
---|
1041 | elif (( ii < 1000 )) |
---|
1042 | then |
---|
1043 | cp ${absnamein[$i]} ${localin[$i]}/_0$ii |
---|
1044 | else |
---|
1045 | cp ${absnamein[$i]} ${localin[$i]}/_$ii |
---|
1046 | fi |
---|
1047 | (( ii = ii + 1 )) |
---|
1048 | done |
---|
1049 | |
---|
1050 | else |
---|
1051 | |
---|
1052 | if [[ $files_for_cores = true ]] |
---|
1053 | then |
---|
1054 | |
---|
1055 | # PROVIDE FILES FOR EACH CORE |
---|
1056 | # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES |
---|
1057 | # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE |
---|
1058 | printf "\n providing $cores files for the respective cores" |
---|
1059 | mkdir -p ${localin[$i]} |
---|
1060 | if [[ $link_local_input = true ]] |
---|
1061 | then |
---|
1062 | printf " files will be linked\n" |
---|
1063 | cd ${absnamein[$i]} |
---|
1064 | for file in $(ls *) |
---|
1065 | do |
---|
1066 | ln -f $file ${localin[$i]} |
---|
1067 | done |
---|
1068 | cd $tempdir |
---|
1069 | fi |
---|
1070 | |
---|
1071 | # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r" |
---|
1072 | if [[ ! -f "${localin[$i]}/_000000" ]] |
---|
1073 | then |
---|
1074 | if [[ $link_local_input = true ]] |
---|
1075 | then |
---|
1076 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
1077 | fi |
---|
1078 | cp -r ${absnamein[$i]}/* ${localin[$i]} |
---|
1079 | fi |
---|
1080 | |
---|
1081 | else |
---|
1082 | |
---|
1083 | # PROVIDE FILE FOR RUNS ON A SINGLE CORE |
---|
1084 | if [[ $link_local_input = true ]] |
---|
1085 | then |
---|
1086 | printf " file will be linked\n" |
---|
1087 | ln -f ${absnamein[$i]} ${localin[$i]} |
---|
1088 | fi |
---|
1089 | # If "ln -f" fails or if "$link_local_input = false" do a normal "cp" |
---|
1090 | if [[ ! -f "${localin[$i]}" ]] |
---|
1091 | then |
---|
1092 | if [[ $link_local_input = true ]] |
---|
1093 | then |
---|
1094 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
1095 | fi |
---|
1096 | if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]] |
---|
1097 | then |
---|
1098 | mv ${absnamein[$i]} ${localin[$i]} |
---|
1099 | else |
---|
1100 | cp ${absnamein[$i]} ${localin[$i]} |
---|
1101 | fi |
---|
1102 | fi |
---|
1103 | fi |
---|
1104 | fi |
---|
1105 | fi |
---|
1106 | |
---|
1107 | done |
---|
1108 | if (( i != 0 )) |
---|
1109 | then |
---|
1110 | if [[ $optional_files_missing = true ]] |
---|
1111 | then |
---|
1112 | printf "\n *** INFORMATIVE: some optional INPUT-files are not present" |
---|
1113 | fi |
---|
1114 | printf "\n$dashes\n *** all INPUT-files provided \n" |
---|
1115 | fi |
---|
1116 | |
---|
1117 | |
---|
1118 | # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE |
---|
1119 | (( i = 0 )) |
---|
1120 | while (( i < iic )) |
---|
1121 | do |
---|
1122 | (( i = i + 1 )) |
---|
1123 | if (( i == 1 )) |
---|
1124 | then |
---|
1125 | printf "\n\n *** execution of INPUT-commands:\n$dashes" |
---|
1126 | fi |
---|
1127 | printf "\n >>> ${in_command[$i]}" |
---|
1128 | eval ${in_command[$i]} |
---|
1129 | if (( i == iic )) |
---|
1130 | then |
---|
1131 | printf "\n$dashes\n" |
---|
1132 | fi |
---|
1133 | done |
---|
1134 | |
---|
1135 | |
---|
1136 | # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM |
---|
1137 | # (FILE ENVPAR WILL BE READ BY PALM) |
---|
1138 | # TODO: this has to be adjusted for inifor, i.e. the values of the script options |
---|
1139 | # have to be converted to NAMELIST variables which are then read by inifor. |
---|
1140 | # Required PALM parameters could also be extracted from local file PARIN |
---|
1141 | # and added here |
---|
1142 | cat > ENVPAR << EOF |
---|
1143 | &envpar run_identifier = '$run_identifier', host = '$configuration_identifier', |
---|
1144 | write_svf = .${write_svf}., write_binary = .${write_binary}., |
---|
1145 | read_svf = .${read_svf}., tasks_per_node = $tasks_per_node, |
---|
1146 | maximum_parallel_io_streams = $maximum_parallel_io_streams, |
---|
1147 | maximum_cpu_time_allowed = ${cpumax}., |
---|
1148 | revision = '$global_revision', |
---|
1149 | progress_bar_disabled = .${progress_bar_disabled}. / |
---|
1150 | |
---|
1151 | EOF |
---|
1152 | |
---|
1153 | # TODO: this is just an example for a possible access of the PALM parameters |
---|
1154 | grep -Eo '(\s*\&(initialization_parameters|inipar|runtime_parameters|d3par)\s*)|(([nd][xyz]|end_time|longitude|latitude|dz_stretch_level|dz_stretch_factor|dz_max)\s*\=\s*[0-9]*\.*\,*)|((dz_stretch_level_start|dz_stretch_level_end)\s*\=(\s*[0-9]*\.*\,*)*)|\/' PARIN |
---|
1155 | |
---|
1156 | # COPY EXECUTABLE TO THIS TEMPORARY FOLDER |
---|
1157 | cp ${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}/inifor . |
---|
1158 | |
---|
1159 | # STARTING THE EXECUTABLE |
---|
1160 | printf "\n\n *** inifor starts in directory\n \"`pwd`\"\n$dashes\n" |
---|
1161 | PATH=$PATH:$tempdir |
---|
1162 | |
---|
1163 | |
---|
1164 | # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES |
---|
1165 | line=`echo "${execute_command_inifor}" | sed 's/{{/$/g' | sed 's/}}//g'` |
---|
1166 | eval line=\"$line\" |
---|
1167 | execute_command="$line" |
---|
1168 | |
---|
1169 | |
---|
1170 | |
---|
1171 | # SET THE NUMBER OF OPENMP-THREADS |
---|
1172 | if [[ $use_openmp = true ]] |
---|
1173 | then |
---|
1174 | export OMP_NUM_THREADS=$threads_per_task |
---|
1175 | printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS" |
---|
1176 | else |
---|
1177 | export OMP_NUM_THREADS=1 |
---|
1178 | fi |
---|
1179 | |
---|
1180 | |
---|
1181 | printf "\n *** execute command:" |
---|
1182 | printf "\n \"$execute_command\" \n\n" |
---|
1183 | |
---|
1184 | |
---|
1185 | $execute_command &> >(tee STDOUT) |
---|
1186 | exit_code=${PIPESTATUS[0]} |
---|
1187 | |
---|
1188 | if [[ ${exit_code} != 0 ]] |
---|
1189 | then |
---|
1190 | |
---|
1191 | # ABORT IN CASE OF RUNTIME ERRORS |
---|
1192 | printf "\n +++ runtime error occured" |
---|
1193 | locat=execution |
---|
1194 | exit |
---|
1195 | |
---|
1196 | else |
---|
1197 | |
---|
1198 | printf "\n$dashes\n *** execution finished \n" |
---|
1199 | |
---|
1200 | fi |
---|
1201 | |
---|
1202 | |
---|
1203 | # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE |
---|
1204 | (( i = 0 )) |
---|
1205 | while (( i < ioc )) |
---|
1206 | do |
---|
1207 | (( i = i + 1 )) |
---|
1208 | if (( i == 1 )) |
---|
1209 | then |
---|
1210 | printf "\n\n *** execution of OUTPUT-commands:\n$dashes" |
---|
1211 | fi |
---|
1212 | |
---|
1213 | # REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES |
---|
1214 | out_command[$i]=`echo "${out_command[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'` |
---|
1215 | |
---|
1216 | printf "\n >>> ${out_command[$i]}" |
---|
1217 | eval ${out_command[$i]} |
---|
1218 | if (( i == ioc )) |
---|
1219 | then |
---|
1220 | printf "\n$dashes\n" |
---|
1221 | fi |
---|
1222 | done |
---|
1223 | |
---|
1224 | |
---|
1225 | # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF |
---|
1226 | # WILDCARDS |
---|
1227 | (( i = 0 )) |
---|
1228 | (( nr_of_output_files = 0 )) |
---|
1229 | |
---|
1230 | while (( i < iout )) |
---|
1231 | do |
---|
1232 | |
---|
1233 | (( i = i + 1 )) |
---|
1234 | |
---|
1235 | # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND |
---|
1236 | # CREATE A LIST FOR THE DETECTED ENDINGS |
---|
1237 | if [[ "${multout[$i]}" = true ]] |
---|
1238 | then |
---|
1239 | # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES |
---|
1240 | ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null |
---|
1241 | ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null |
---|
1242 | |
---|
1243 | endings="DEFAULT" |
---|
1244 | while read line |
---|
1245 | do |
---|
1246 | # remove the local name from the beginning |
---|
1247 | localnamestring="${localout_pre[$i]}" |
---|
1248 | length_localname=${#localnamestring} |
---|
1249 | ending=${line:${length_localname}} |
---|
1250 | |
---|
1251 | if [[ "$ending" != "" ]] |
---|
1252 | then |
---|
1253 | endings="$endings $ending" |
---|
1254 | fi |
---|
1255 | |
---|
1256 | done <filelist |
---|
1257 | |
---|
1258 | rm filelist |
---|
1259 | |
---|
1260 | else |
---|
1261 | |
---|
1262 | # SINGLE NAME |
---|
1263 | endings=DEFAULT |
---|
1264 | |
---|
1265 | fi |
---|
1266 | |
---|
1267 | # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST |
---|
1268 | for ending in $endings |
---|
1269 | do |
---|
1270 | |
---|
1271 | # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED |
---|
1272 | if [[ $ending = DEFAULT ]] |
---|
1273 | then |
---|
1274 | ending="" |
---|
1275 | fi |
---|
1276 | |
---|
1277 | # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!) |
---|
1278 | (( nr_of_output_files = nr_of_output_files + 1 )) |
---|
1279 | localout[$nr_of_output_files]="${localout_pre[$i]}"$ending |
---|
1280 | transout[$nr_of_output_files]="${transout_pre[$i]}" |
---|
1281 | actionout[$nr_of_output_files]="${actionout_pre[$i]}" |
---|
1282 | pathout[$nr_of_output_files]="${pathout_pre[$i]}" |
---|
1283 | endout[$nr_of_output_files]="${endout_pre[$i]}"$ending |
---|
1284 | extout[$nr_of_output_files]="${extout_pre[$i]}" |
---|
1285 | warnout[$nr_of_output_files]="${warnout_pre[$i]}" |
---|
1286 | |
---|
1287 | done |
---|
1288 | |
---|
1289 | done |
---|
1290 | |
---|
1291 | |
---|
1292 | # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS |
---|
1293 | (( i = 0 )) |
---|
1294 | while (( i < nr_of_output_files )) |
---|
1295 | do |
---|
1296 | (( i = i + 1 )) |
---|
1297 | if (( i == 1 )) |
---|
1298 | then |
---|
1299 | printf "\n\n *** saving OUTPUT-files:" |
---|
1300 | |
---|
1301 | # GET RUN NUMBER ASSIGNED BY PALM |
---|
1302 | if [[ -f RUN_NUMBER ]] |
---|
1303 | then |
---|
1304 | read run_number < RUN_NUMBER |
---|
1305 | printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files" |
---|
1306 | usecycle_option="-U $run_number" |
---|
1307 | else |
---|
1308 | run_number=0 |
---|
1309 | usecycle_option="" |
---|
1310 | fi |
---|
1311 | if [[ $running_on_remote = true && "$remote_loginnode" != "" ]] |
---|
1312 | then |
---|
1313 | printf "\n *** in case of SCP transfers to local host" |
---|
1314 | printf "\n they will be done via remote login-node \"$remote_loginnode\" " |
---|
1315 | fi |
---|
1316 | printf "\n$dashes" |
---|
1317 | fi |
---|
1318 | |
---|
1319 | if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]] |
---|
1320 | then |
---|
1321 | |
---|
1322 | eval filename=${pathout[$i]}/${run_identifier}${endout[$i]} |
---|
1323 | |
---|
1324 | # DETERMINE THE CYCLE NUMBER |
---|
1325 | ls -1 -d $filename > filelist 2>/dev/null |
---|
1326 | ls -1 -d $filename.* >> filelist 2>/dev/null |
---|
1327 | while read line |
---|
1328 | do |
---|
1329 | |
---|
1330 | # filename without path (i.e. after the last "/") |
---|
1331 | basefilename=$(basename ${line}) |
---|
1332 | |
---|
1333 | # check if there is an extension |
---|
1334 | extension=${basefilename##*.} |
---|
1335 | if [[ "$extension" = "${extout[$i]}" ]] |
---|
1336 | then |
---|
1337 | basefilename=${basefilename%.*} |
---|
1338 | fi |
---|
1339 | |
---|
1340 | # check for an existing cycle number |
---|
1341 | cycle=${basefilename##*.} |
---|
1342 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
1343 | then |
---|
1344 | # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS |
---|
1345 | # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 |
---|
1346 | (( icycle = $((10#$cycle)) + 1 )) |
---|
1347 | else |
---|
1348 | (( icycle = 1 )) |
---|
1349 | fi |
---|
1350 | |
---|
1351 | if (( icycle > maxcycle )) |
---|
1352 | then |
---|
1353 | (( maxcycle = icycle )) |
---|
1354 | fi |
---|
1355 | |
---|
1356 | done <filelist |
---|
1357 | rm filelist |
---|
1358 | |
---|
1359 | |
---|
1360 | # SET THE CYCLE NUMBER |
---|
1361 | # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER |
---|
1362 | if [[ "${actionout[$i]}" = a ]] |
---|
1363 | then |
---|
1364 | (( maxcycle = maxcycle - 1 )) |
---|
1365 | fi |
---|
1366 | |
---|
1367 | (( cycnum[$i] = maxcycle )) |
---|
1368 | pathout[$i]=$filename |
---|
1369 | |
---|
1370 | |
---|
1371 | # ADD CYCLE NUMBER TO FILENAME |
---|
1372 | # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER |
---|
1373 | if [[ "${actionout[$i]}" != "a" ]] |
---|
1374 | then |
---|
1375 | # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT |
---|
1376 | # WITH AN EXISTING CYCLE NUMBER |
---|
1377 | if (( run_number >= cycnum[$i] )) |
---|
1378 | then |
---|
1379 | (( cycnum[$i] = run_number )) |
---|
1380 | else |
---|
1381 | if (( run_number > 0 )) |
---|
1382 | then |
---|
1383 | printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number" |
---|
1384 | fi |
---|
1385 | fi |
---|
1386 | fi |
---|
1387 | if (( cycnum[$i] > 0 )) |
---|
1388 | then |
---|
1389 | cyclestring=`printf "%03d" ${cycnum[$i]}` |
---|
1390 | pathout[$i]=${pathout[$i]}.$cyclestring |
---|
1391 | fi |
---|
1392 | fi |
---|
1393 | |
---|
1394 | # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION) |
---|
1395 | files_for_cores=false; filetype=file |
---|
1396 | link_local_output=false |
---|
1397 | if [[ "${actionout[$i]}" = pe && -n $cores ]] |
---|
1398 | then |
---|
1399 | files_for_cores=true; filetype=directory |
---|
1400 | actionout[$i]="" |
---|
1401 | elif [[ "${actionout[$i]}" = pe && ! -n $cores ]] |
---|
1402 | then |
---|
1403 | actionout[$i]="" |
---|
1404 | elif [[ "${actionout[$i]}" = lnpe && -n $cores ]] |
---|
1405 | then |
---|
1406 | files_for_cores=true; filetype=directory |
---|
1407 | link_local_output=true |
---|
1408 | actionout[$i]="" |
---|
1409 | elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]] |
---|
1410 | then |
---|
1411 | link_local_output |
---|
1412 | actionout[$i]="" |
---|
1413 | elif [[ "${actionout[$i]}" = trpe && -n $cores ]] |
---|
1414 | then |
---|
1415 | files_for_cores=true; filetype=directory |
---|
1416 | actionout[$i]="tr" |
---|
1417 | elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]] |
---|
1418 | then |
---|
1419 | actionout[$i]="tr" |
---|
1420 | fi |
---|
1421 | |
---|
1422 | if [[ ! -f ${localout[$i]} && $files_for_cores = false ]] |
---|
1423 | then |
---|
1424 | if [[ ${warnout[$i]} = true ]] |
---|
1425 | then |
---|
1426 | printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n" |
---|
1427 | fi |
---|
1428 | elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]] |
---|
1429 | then |
---|
1430 | if [[ ${warnout[$i]} = true ]] |
---|
1431 | then |
---|
1432 | printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n" |
---|
1433 | fi |
---|
1434 | else |
---|
1435 | |
---|
1436 | |
---|
1437 | # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m) |
---|
1438 | # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT |
---|
1439 | if [[ "${actionout[$i]}" = tr || "${actionout[$i]}" = tra ]] |
---|
1440 | then |
---|
1441 | if [[ $running_on_remote = true ]] |
---|
1442 | then |
---|
1443 | |
---|
1444 | # SET OPTIONS FOR TRANSFER |
---|
1445 | if [[ "${actionout[$i]}" = tr ]] |
---|
1446 | then |
---|
1447 | if [[ $files_for_cores = false ]] |
---|
1448 | then |
---|
1449 | catalog_option="" |
---|
1450 | catalog_string="" |
---|
1451 | else |
---|
1452 | catalog_option="-c" |
---|
1453 | catalog_string="/" |
---|
1454 | fi |
---|
1455 | append_option="" |
---|
1456 | append_string="" |
---|
1457 | else |
---|
1458 | append_option="-A" |
---|
1459 | append_string="append" |
---|
1460 | fi |
---|
1461 | |
---|
1462 | transfer_failed=false |
---|
1463 | printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to" |
---|
1464 | printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n" |
---|
1465 | |
---|
1466 | # TRANSFER VIA SCP |
---|
1467 | if [[ "$remote_loginnode" != "" ]] |
---|
1468 | then |
---|
1469 | ssh -q $remote_username@$remote_loginnode "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" |
---|
1470 | else |
---|
1471 | batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]} |
---|
1472 | fi |
---|
1473 | [[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true |
---|
1474 | |
---|
1475 | |
---|
1476 | # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE |
---|
1477 | if [[ $transfer_failed = true ]] |
---|
1478 | then |
---|
1479 | printf " +++ transfer failed. Trying to save a copy on this host under:\n" |
---|
1480 | printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n" |
---|
1481 | |
---|
1482 | # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY |
---|
1483 | eval local_catalog=${pathout[$i]} |
---|
1484 | if [[ ! -d $local_catalog ]] |
---|
1485 | then |
---|
1486 | printf " *** local directory does not exist. Trying to create:\n" |
---|
1487 | printf " $local_catalog \n" |
---|
1488 | mkdir -p $local_catalog |
---|
1489 | fi |
---|
1490 | eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number |
---|
1491 | transfer_problems=true |
---|
1492 | fi |
---|
1493 | |
---|
1494 | else |
---|
1495 | |
---|
1496 | # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST |
---|
1497 | # BE COPIED OR APPENDED ON THIS MACHINE |
---|
1498 | if [[ "${actionout[$i]}" = tr ]] |
---|
1499 | then |
---|
1500 | actionout[$i]="" |
---|
1501 | else |
---|
1502 | actionout[$i]="a" |
---|
1503 | fi |
---|
1504 | fi |
---|
1505 | fi |
---|
1506 | |
---|
1507 | |
---|
1508 | # APPEND ON THIS MACHINE |
---|
1509 | if [[ "${actionout[$i]}" = "a" ]] |
---|
1510 | then |
---|
1511 | if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] |
---|
1512 | then |
---|
1513 | printf "\n >>> OUTPUT: ${localout[$i]} append to" |
---|
1514 | printf "\n ${pathout[$i]}.${extout[$i]}\n" |
---|
1515 | cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]} |
---|
1516 | else |
---|
1517 | printf "\n >>> OUTPUT: ${localout[$i]} append to" |
---|
1518 | printf "\n ${pathout[$i]}\n" |
---|
1519 | cat ${localout[$i]} >> ${pathout[$i]} |
---|
1520 | fi |
---|
1521 | fi |
---|
1522 | |
---|
1523 | # COPY ON THIS MACHINE |
---|
1524 | # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE |
---|
1525 | # ON DIFFERENT FILE-SYSTEMS |
---|
1526 | if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]] |
---|
1527 | then |
---|
1528 | |
---|
1529 | # COPY IN CASE OF RUNS ON SINGLE CORES |
---|
1530 | if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] |
---|
1531 | then |
---|
1532 | printf "\n >>> OUTPUT: ${localout[$i]} to" |
---|
1533 | printf "\n ${pathout[$i]}.${extout[$i]}\n" |
---|
1534 | if [[ $link_local_output = true ]] |
---|
1535 | then |
---|
1536 | printf " file will be linked\n" |
---|
1537 | ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]} |
---|
1538 | fi |
---|
1539 | # If "ln -f" fails of if "$link_local_output = false" do a normal "cp" |
---|
1540 | if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]] |
---|
1541 | then |
---|
1542 | if [[ $link_local_output = true ]] |
---|
1543 | then |
---|
1544 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
1545 | fi |
---|
1546 | cp ${localout[$i]} ${pathout[$i]}.${extout[$i]} |
---|
1547 | else |
---|
1548 | printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n" |
---|
1549 | fi |
---|
1550 | else |
---|
1551 | printf "\n >>> OUTPUT: ${localout[$i]} to" |
---|
1552 | printf "\n ${pathout[$i]}\n" |
---|
1553 | if [[ $link_local_output = true ]] |
---|
1554 | then |
---|
1555 | printf " file will be linked\n" |
---|
1556 | ln -f ${localout[$i]} ${pathout[$i]} |
---|
1557 | fi |
---|
1558 | # If "ln -f" fails of if "$link_local_output = false" do a normal "cp" |
---|
1559 | if [[ ! -f "${pathout[$i]}" ]] |
---|
1560 | then |
---|
1561 | if [[ $link_local_output = true ]] |
---|
1562 | then |
---|
1563 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
1564 | fi |
---|
1565 | cp ${localout[$i]} ${pathout[$i]} |
---|
1566 | else |
---|
1567 | printf "+++ no copy because file ${pathout[$i]} exists\n" |
---|
1568 | fi |
---|
1569 | fi |
---|
1570 | |
---|
1571 | elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]] |
---|
1572 | then |
---|
1573 | |
---|
1574 | # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY |
---|
1575 | # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED |
---|
1576 | printf "\n >>> OUTPUT: ${localout[$i]}/_.... to" |
---|
1577 | printf "\n ${pathout[$i]}\n" |
---|
1578 | if [[ $link_local_output = true ]] |
---|
1579 | then |
---|
1580 | printf " files will be linked\n" |
---|
1581 | mkdir -p ${pathout[$i]} |
---|
1582 | cd ${localout[$i]} |
---|
1583 | for file in $(ls *) |
---|
1584 | do |
---|
1585 | ln -f $file ${pathout[$i]} |
---|
1586 | done >|/dev/null 2>&1 |
---|
1587 | cd $tempdir |
---|
1588 | fi |
---|
1589 | |
---|
1590 | # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r" |
---|
1591 | if [[ ! -f "${pathout[$i]}/_000000" ]] |
---|
1592 | then |
---|
1593 | if [[ $link_local_output = true ]] |
---|
1594 | then |
---|
1595 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
1596 | fi |
---|
1597 | [[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]} |
---|
1598 | cp -r ${localout[$i]}/* ${pathout[$i]} |
---|
1599 | fi |
---|
1600 | |
---|
1601 | fi |
---|
1602 | fi |
---|
1603 | done |
---|
1604 | |
---|
1605 | if (( i != 0 )) |
---|
1606 | then |
---|
1607 | if [[ $transfer_problems = true ]] |
---|
1608 | then |
---|
1609 | printf "\n$dashes\n *** OUTPUT-files saved" |
---|
1610 | printf "\n +++ WARNING: some data transfers failed! \n" |
---|
1611 | else |
---|
1612 | printf "\n$dashes\n *** all OUTPUT-files saved \n" |
---|
1613 | fi |
---|
1614 | fi |
---|
1615 | |
---|
1616 | |
---|
1617 | |
---|
1618 | |
---|
1619 | # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED |
---|
1620 | cd - |
---|
1621 | [[ $delete_temporary_catalog = true ]] && rm -rf $tempdir |
---|