[3790] | 1 | #!/bin/bash |
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| 2 | |
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[3791] | 3 | # inifor - The Mesoscale Interface for Initializing and Forcing PALM |
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[3790] | 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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[4843] | 19 | # Copyright 2017-2021 Leibniz Universitaet Hannover |
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[3790] | 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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[3792] | 25 | # |
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[3790] | 26 | # Former revisions: |
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| 27 | # ----------------- |
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| 28 | # $Id$ |
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[3792] | 29 | # initial revision |
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[3790] | 30 | # |
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[3792] | 31 | # |
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| 32 | # |
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[3790] | 33 | #--------------------------------------------------------------------------------# |
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[3791] | 34 | # inifor - script for running the inifor executable |
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[3790] | 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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[3791] | 46 | typeset -i i iec=0 |
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[3790] | 47 | |
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[3791] | 48 | activation_string_list="inifor" |
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[3790] | 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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[3791] | 55 | version="inifor 0.1 Rev$Rev$" |
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[3790] | 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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[3791] | 73 | printf "\n\n+++ inifor crashed \n\n" |
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[3790] | 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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[3791] | 78 | printf "\n+++ inifor killed by \"^C\" \n\n" |
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[3790] | 79 | exit 2 |
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| 80 | else |
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[3791] | 81 | printf "\n --> inifor finished\n\n" |
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[3790] | 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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[3791] | 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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[3790] | 95 | do |
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| 96 | case $option in |
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[3791] | 97 | (a) activation_string_list=$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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[3790] | 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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[3791] | 115 | # TODO: add description of additional inifor options |
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[3790] | 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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[3791] | 149 | |
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[3790] | 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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[3791] | 153 | locat=connect; exit |
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| 154 | |
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[3790] | 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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[3791] | 163 | if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]] |
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[3790] | 164 | then |
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[3791] | 165 | printf "\n\n +++ WARNING: A file connection file has been found in your" |
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| 166 | printf "\n working directory, but its revision does not match" |
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| 167 | printf "\n the revision of the default (trunk) version." |
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| 168 | printf "\n You may need to update your connection file" |
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| 169 | printf "\n \"${working_directory}/.palm.iofiles\" !" |
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[3790] | 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 $fileconnection_file" |
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| 182 | printf "\n does not exist" |
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| 183 | locat=connect; exit |
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| 184 | fi |
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| 185 | |
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| 186 | |
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| 187 | # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN |
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[3791] | 188 | # TODO: I suggest to use/extend the .palm.iofiles file to set the inifor I/O files, |
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| 189 | # activation string could be "inifor" |
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[3790] | 190 | if [[ "$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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[3791] | 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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[3790] | 202 | [[ $silent = false ]] && printf "\n\n Reading the configuration file... " |
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| 203 | |
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[3791] | 204 | |
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[3790] | 205 | # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE |
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| 206 | while read line |
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| 207 | do |
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| 208 | |
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| 209 | # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES |
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| 210 | eval line=\"$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 < $config_file |
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| 300 | |
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| 301 | |
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| 302 | # CHECK SETTING OF REQUIRED PARAMETERS |
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[3791] | 303 | # TODO: we probably need to include such a line in the configuration file |
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| 304 | if [[ "$execute_command_inifor" = "" ]] |
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[3790] | 305 | then |
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[3791] | 306 | printf "\n +++ no execute command found for inifor in $config_file" |
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| 307 | printf "\n Please add line \"execute_command_inifor ...\" to that file." |
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[3790] | 308 | locat=config_file; exit |
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| 309 | fi |
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| 310 | |
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| 311 | |
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| 312 | # DETERMINE THE CALL STATUS |
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[3791] | 313 | if [[ "$remote_ip" != "" ]] |
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[3790] | 314 | then |
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[3791] | 315 | run_on_remote=true |
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[3790] | 316 | else |
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[3791] | 317 | run_on_remote=false |
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[3790] | 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 | [[ $silent = false ]] && printf "\n Reading the I/O files... " |
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| 323 | |
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[3791] | 324 | |
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[3790] | 325 | # READ THE FILE CONNECTION FILE LINE BY LINE |
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| 326 | while read line |
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| 327 | do |
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| 328 | |
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| 329 | # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE |
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| 330 | # HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY |
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| 331 | line=`echo "$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 |
---|
| 466 | printf "\n +++ I/O-attribute in file $fileconnection_file has invalid" |
---|
| 467 | printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!" |
---|
| 468 | locat=connect; exit |
---|
| 469 | fi |
---|
| 470 | IFS="$IFSALT" |
---|
| 471 | fi |
---|
| 472 | |
---|
| 473 | done < $fileconnection_file |
---|
| 474 | |
---|
| 475 | |
---|
| 476 | |
---|
[3791] | 477 | # VALUES OF INIFOR-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE |
---|
| 478 | # next line is just an example |
---|
| 479 | # TODO: default values for inifor script options could be set in the configuration file |
---|
| 480 | # (if it makes sense) |
---|
| 481 | [[ "$inifor_cores" != "" ]] && cores=$inifor_cores |
---|
[3790] | 482 | |
---|
| 483 | |
---|
| 484 | |
---|
[3791] | 485 | # CHECK IF INIFOR EXECUTABLE EXISTS |
---|
| 486 | if [[ $run_on_remote = false ]] |
---|
[3790] | 487 | then |
---|
| 488 | |
---|
[3791] | 489 | if [[ ! -f ${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}/inifor ]] |
---|
[3790] | 490 | then |
---|
[3791] | 491 | printf "\n +++ no inifor executable found in folder" |
---|
| 492 | printf "\n \"${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}\" " |
---|
| 493 | printf "\n You may run \"palmbuild -c ${configuration_identifier}\" to create" |
---|
| 494 | printf "\n the utility routines." |
---|
| 495 | locat=connect; exit |
---|
[3790] | 496 | fi |
---|
| 497 | |
---|
| 498 | else |
---|
| 499 | |
---|
[3791] | 500 | printf "\n +++ remote call of inifor not realized yet" |
---|
| 501 | locat=inifor_remote; exit |
---|
[3790] | 502 | |
---|
[3791] | 503 | fi |
---|
[3790] | 504 | |
---|
| 505 | |
---|
| 506 | |
---|
| 507 | # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY |
---|
| 508 | # (HANDED OVER TO RESTART-RUNS USING OPTION -G) |
---|
| 509 | if [[ "$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 $filename" |
---|
| 825 | printf "\n cannot be created, although directory exists" |
---|
| 826 | printf "\n" |
---|
| 827 | locat=output ; exit |
---|
| 828 | fi |
---|
| 829 | fi 2>/dev/null |
---|
| 830 | |
---|
| 831 | fi |
---|
| 832 | |
---|
| 833 | fi |
---|
| 834 | done |
---|
| 835 | |
---|
| 836 | |
---|
[3791] | 837 | # DETERMINE THE NAME OF INIFOR'S TEMPORARY WORKING DIRECTORY |
---|
| 838 | run_id_number=$RANDOM |
---|
| 839 | run_id=${run_identifier}.$run_id_number |
---|
| 840 | tempdir=$fast_io_catalog/$run_id |
---|
[3790] | 841 | |
---|
| 842 | |
---|
| 843 | |
---|
| 844 | |
---|
[3791] | 845 | # OUTPUT OF THE INIFOR-HEADER |
---|
[3790] | 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" |
---|
[3791] | 854 | if [[ $run_on_remote = true ]] |
---|
[3790] | 855 | then |
---|
[3791] | 856 | column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)" |
---|
[3790] | 857 | else |
---|
[3791] | 858 | column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)" |
---|
[3790] | 859 | fi |
---|
| 860 | printf "| %-25s%-45s | \n" "$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 |
---|
[3791] | 902 | if [[ $silent = false ]] |
---|
[3790] | 903 | then |
---|
| 904 | antwort=dummy |
---|
| 905 | printf "\n\n" |
---|
| 906 | printf " >>> everything o.k. (y/n) ? " |
---|
| 907 | while read antwort |
---|
| 908 | do |
---|
| 909 | if [[ "$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 |
---|
[3791] | 920 | if [[ $run_on_remote ]] |
---|
[3790] | 921 | then |
---|
[3791] | 922 | printf "\n *** inifor will now run on remote" |
---|
[3790] | 923 | else |
---|
[3791] | 924 | printf "\n *** inifor will now continue to execute on this machine" |
---|
[3790] | 925 | fi |
---|
| 926 | fi |
---|
| 927 | |
---|
| 928 | |
---|
[3791] | 929 | # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE INIFOR ON THIS MACHINE (COPYING I/O FILES) |
---|
| 930 | # CHANGE TO THE TEMPORARY WORKING DIRECTORY |
---|
[3790] | 931 | |
---|
[3791] | 932 | mkdir -p $tempdir |
---|
| 933 | chmod go+rx $tempdir |
---|
| 934 | cd $tempdir |
---|
[3790] | 935 | |
---|
[3791] | 936 | printf "\n *** changed to temporary directory: $tempdir" |
---|
[3790] | 937 | |
---|
| 938 | |
---|
| 939 | |
---|
[3791] | 940 | # PROVIDE THE INPUT FILES |
---|
| 941 | # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE) |
---|
| 942 | optional_files_missing=false |
---|
| 943 | (( i = 0 )) |
---|
| 944 | while (( i < nr_of_input_files )) |
---|
| 945 | do |
---|
| 946 | (( i = i + 1 )) |
---|
| 947 | if (( i == 1 )) |
---|
[3790] | 948 | then |
---|
[3791] | 949 | printf "\n\n *** providing INPUT-files:\n$dashes" |
---|
[3790] | 950 | fi |
---|
| 951 | |
---|
| 952 | |
---|
[3791] | 953 | # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST |
---|
| 954 | if [[ "${actionin[$i]}" = unavailable ]] |
---|
[3790] | 955 | then |
---|
[3791] | 956 | optional_files_missing=true |
---|
| 957 | continue |
---|
[3790] | 958 | fi |
---|
| 959 | |
---|
[3791] | 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 $cores ]] |
---|
[3790] | 963 | then |
---|
[3791] | 964 | files_for_cores=true; filetype=files |
---|
| 965 | actionin[$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" |
---|
[3790] | 976 | fi |
---|
| 977 | |
---|
[3791] | 978 | if [[ $files_for_cores = true ]] |
---|
[3790] | 979 | then |
---|
[3791] | 980 | printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}" |
---|
[3790] | 981 | else |
---|
[3791] | 982 | printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}" |
---|
[3790] | 983 | fi |
---|
| 984 | |
---|
[3791] | 985 | # INPUT-FILES TO BE LINKED |
---|
| 986 | if [[ "${actionin[$i]}" = ln ]] |
---|
| 987 | then |
---|
[3790] | 988 | |
---|
[3791] | 989 | printf "\n $filetype will be linked" |
---|
| 990 | if [[ $files_for_cores = false ]] |
---|
[3790] | 991 | then |
---|
[3791] | 992 | if [[ -f "${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 $tempdir |
---|
| 1007 | fi |
---|
[3790] | 1008 | |
---|
[3791] | 1009 | # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r" |
---|
| 1010 | if [[ ! -f "${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 |
---|
[3790] | 1015 | |
---|
[3791] | 1016 | got_tmp[$i]=true |
---|
[3790] | 1017 | fi |
---|
[3791] | 1018 | fi |
---|
[3790] | 1019 | |
---|
[3791] | 1020 | # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE |
---|
| 1021 | if [[ "${actionin[$i]}" = "" || "${actionin[$i]}" = "di" || "${actionin[$i]}" = "tr" || "${actionin[$i]}" = "npe" ]] |
---|
| 1022 | then |
---|
| 1023 | |
---|
| 1024 | if [[ "${actionin[$i]}" = "npe" && -n $cores ]] |
---|
[3790] | 1025 | then |
---|
| 1026 | |
---|
[3791] | 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 | |
---|
[3790] | 1050 | else |
---|
| 1051 | |
---|
[3791] | 1052 | if [[ $files_for_cores = true ]] |
---|
| 1053 | then |
---|
[3790] | 1054 | |
---|
[3791] | 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 ]] |
---|
[3790] | 1061 | then |
---|
[3791] | 1062 | printf " files will be linked\n" |
---|
[3790] | 1063 | cd ${absnamein[$i]} |
---|
| 1064 | for file in $(ls *) |
---|
| 1065 | do |
---|
[3791] | 1066 | ln -f $file ${localin[$i]} |
---|
| 1067 | done |
---|
[3790] | 1068 | cd $tempdir |
---|
| 1069 | fi |
---|
| 1070 | |
---|
[3791] | 1071 | # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r" |
---|
[3790] | 1072 | if [[ ! -f "${localin[$i]}/_000000" ]] |
---|
| 1073 | then |
---|
[3791] | 1074 | if [[ $link_local_input = true ]] |
---|
| 1075 | then |
---|
| 1076 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
| 1077 | fi |
---|
[3790] | 1078 | cp -r ${absnamein[$i]}/* ${localin[$i]} |
---|
| 1079 | fi |
---|
| 1080 | |
---|
[3791] | 1081 | else |
---|
[3790] | 1082 | |
---|
[3791] | 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 ]] |
---|
[3790] | 1093 | then |
---|
[3791] | 1094 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
| 1095 | fi |
---|
| 1096 | if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]] |
---|
[3790] | 1097 | then |
---|
[3791] | 1098 | mv ${absnamein[$i]} ${localin[$i]} |
---|
[3790] | 1099 | else |
---|
[3791] | 1100 | cp ${absnamein[$i]} ${localin[$i]} |
---|
[3790] | 1101 | fi |
---|
| 1102 | fi |
---|
| 1103 | fi |
---|
| 1104 | fi |
---|
[3791] | 1105 | fi |
---|
[3790] | 1106 | |
---|
[3791] | 1107 | done |
---|
| 1108 | if (( i != 0 )) |
---|
| 1109 | then |
---|
| 1110 | if [[ $optional_files_missing = true ]] |
---|
[3790] | 1111 | then |
---|
[3791] | 1112 | printf "\n *** INFORMATIVE: some optional INPUT-files are not present" |
---|
[3790] | 1113 | fi |
---|
[3791] | 1114 | printf "\n$dashes\n *** all INPUT-files provided \n" |
---|
| 1115 | fi |
---|
[3790] | 1116 | |
---|
| 1117 | |
---|
[3791] | 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 )) |
---|
[3790] | 1124 | then |
---|
[3791] | 1125 | printf "\n\n *** execution of INPUT-commands:\n$dashes" |
---|
[3790] | 1126 | fi |
---|
[3791] | 1127 | printf "\n >>> ${in_command[$i]}" |
---|
| 1128 | eval ${in_command[$i]} |
---|
| 1129 | if (( i == iic )) |
---|
| 1130 | then |
---|
| 1131 | printf "\n$dashes\n" |
---|
| 1132 | fi |
---|
| 1133 | done |
---|
[3790] | 1134 | |
---|
| 1135 | |
---|
| 1136 | # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM |
---|
| 1137 | # (FILE ENVPAR WILL BE READ BY PALM) |
---|
[3791] | 1138 | # TODO: this has to be adjusted for inifor, i.e. the values of the script options |
---|
| 1139 | # have to be converted to NAMELIST variables which are then read by inifor. |
---|
| 1140 | # Required PALM parameters could also be extracted from local file PARIN |
---|
| 1141 | # and added here |
---|
[3790] | 1142 | cat > ENVPAR << EOF |
---|
| 1143 | &envpar run_identifier = '$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 | |
---|
[3791] | 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 |
---|
[3790] | 1155 | |
---|
[3791] | 1156 | # COPY EXECUTABLE TO THIS TEMPORARY FOLDER |
---|
| 1157 | cp ${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}/inifor . |
---|
[3790] | 1158 | |
---|
[3791] | 1159 | # STARTING THE EXECUTABLE |
---|
| 1160 | printf "\n\n *** inifor starts in directory\n \"`pwd`\"\n$dashes\n" |
---|
| 1161 | PATH=$PATH:$tempdir |
---|
[3790] | 1162 | |
---|
| 1163 | |
---|
[3791] | 1164 | # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES |
---|
| 1165 | line=`echo "${execute_command_inifor}" | sed 's/{{/$/g' | sed 's/}}//g'` |
---|
| 1166 | eval line=\"$line\" |
---|
| 1167 | execute_command="$line" |
---|
[3790] | 1168 | |
---|
| 1169 | |
---|
| 1170 | |
---|
[3791] | 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: $OMP_NUM_THREADS" |
---|
| 1176 | else |
---|
| 1177 | export OMP_NUM_THREADS=1 |
---|
| 1178 | fi |
---|
[3790] | 1179 | |
---|
| 1180 | |
---|
[3791] | 1181 | printf "\n *** execute command:" |
---|
| 1182 | printf "\n \"$execute_command\" \n\n" |
---|
[3790] | 1183 | |
---|
| 1184 | |
---|
[3791] | 1185 | $execute_command &> >(tee STDOUT) |
---|
| 1186 | exit_code=${PIPESTATUS[0]} |
---|
[3790] | 1187 | |
---|
[3791] | 1188 | if [[ ${exit_code} != 0 ]] |
---|
| 1189 | then |
---|
[3790] | 1190 | |
---|
[3791] | 1191 | # ABORT IN CASE OF RUNTIME ERRORS |
---|
| 1192 | printf "\n +++ runtime error occured" |
---|
| 1193 | locat=execution |
---|
| 1194 | exit |
---|
[3790] | 1195 | |
---|
[3791] | 1196 | else |
---|
[3790] | 1197 | |
---|
[3791] | 1198 | printf "\n$dashes\n *** execution finished \n" |
---|
[3790] | 1199 | |
---|
[3791] | 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 )) |
---|
[3790] | 1209 | then |
---|
[3791] | 1210 | printf "\n\n *** execution of OUTPUT-commands:\n$dashes" |
---|
[3790] | 1211 | fi |
---|
| 1212 | |
---|
[3791] | 1213 | # REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES |
---|
| 1214 | out_command[$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 )) |
---|
[3790] | 1219 | then |
---|
[3791] | 1220 | printf "\n$dashes\n" |
---|
| 1221 | fi |
---|
| 1222 | done |
---|
[3790] | 1223 | |
---|
| 1224 | |
---|
[3791] | 1225 | # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF |
---|
| 1226 | # WILDCARDS |
---|
| 1227 | (( i = 0 )) |
---|
| 1228 | (( nr_of_output_files = 0 )) |
---|
[3790] | 1229 | |
---|
[3791] | 1230 | while (( i < iout )) |
---|
| 1231 | do |
---|
[3790] | 1232 | |
---|
[3791] | 1233 | (( i = i + 1 )) |
---|
[3790] | 1234 | |
---|
[3791] | 1235 | # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND |
---|
| 1236 | # CREATE A LIST FOR THE DETECTED ENDINGS |
---|
| 1237 | if [[ "${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 |
---|
[3790] | 1242 | |
---|
[3791] | 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:${length_localname}} |
---|
[3790] | 1250 | |
---|
[3791] | 1251 | if [[ "$ending" != "" ]] |
---|
| 1252 | then |
---|
| 1253 | endings="$endings $ending" |
---|
| 1254 | fi |
---|
| 1255 | |
---|
| 1256 | done <filelist |
---|
[3790] | 1257 | |
---|
[3791] | 1258 | rm filelist |
---|
[3790] | 1259 | |
---|
[3791] | 1260 | else |
---|
[3790] | 1261 | |
---|
[3791] | 1262 | # SINGLE NAME |
---|
| 1263 | endings=DEFAULT |
---|
[3790] | 1264 | |
---|
[3791] | 1265 | fi |
---|
[3790] | 1266 | |
---|
[3791] | 1267 | # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST |
---|
| 1268 | for ending in $endings |
---|
| 1269 | do |
---|
[3790] | 1270 | |
---|
[3791] | 1271 | # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED |
---|
| 1272 | if [[ $ending = DEFAULT ]] |
---|
[3790] | 1273 | then |
---|
[3791] | 1274 | ending="" |
---|
[3790] | 1275 | fi |
---|
| 1276 | |
---|
[3791] | 1277 | # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!) |
---|
| 1278 | (( nr_of_output_files = nr_of_output_files + 1 )) |
---|
| 1279 | localout[$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]}" |
---|
[3790] | 1286 | |
---|
| 1287 | done |
---|
| 1288 | |
---|
[3791] | 1289 | done |
---|
[3790] | 1290 | |
---|
| 1291 | |
---|
[3791] | 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:" |
---|
[3790] | 1300 | |
---|
[3791] | 1301 | # GET RUN NUMBER ASSIGNED BY PALM |
---|
| 1302 | if [[ -f RUN_NUMBER ]] |
---|
[3790] | 1303 | then |
---|
[3791] | 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" |
---|
[3790] | 1307 | else |
---|
[3791] | 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 |
---|
[3790] | 1318 | |
---|
[3791] | 1319 | if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]] |
---|
| 1320 | then |
---|
[3790] | 1321 | |
---|
[3791] | 1322 | eval filename=${pathout[$i]}/${run_identifier}${endout[$i]} |
---|
[3790] | 1323 | |
---|
[3791] | 1324 | # DETERMINE THE CYCLE NUMBER |
---|
| 1325 | ls -1 -d $filename > filelist 2>/dev/null |
---|
| 1326 | ls -1 -d $filename.* >> filelist 2>/dev/null |
---|
| 1327 | while read line |
---|
[3790] | 1328 | do |
---|
[3791] | 1329 | |
---|
| 1330 | # filename without path (i.e. after the last "/") |
---|
| 1331 | basefilename=$(basename ${line}) |
---|
| 1332 | |
---|
| 1333 | # check if there is an extension |
---|
| 1334 | extension=${basefilename##*.} |
---|
| 1335 | if [[ "$extension" = "${extout[$i]}" ]] |
---|
[3790] | 1336 | then |
---|
[3791] | 1337 | basefilename=${basefilename%.*} |
---|
[3790] | 1338 | fi |
---|
[3791] | 1339 | |
---|
| 1340 | # check for an existing cycle number |
---|
| 1341 | cycle=${basefilename##*.} |
---|
| 1342 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
[3790] | 1343 | then |
---|
[3791] | 1344 | # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS |
---|
| 1345 | # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 |
---|
| 1346 | (( icycle = $((10#$cycle)) + 1 )) |
---|
[3790] | 1347 | else |
---|
[3791] | 1348 | (( icycle = 1 )) |
---|
[3790] | 1349 | fi |
---|
[3791] | 1350 | |
---|
| 1351 | if (( icycle > maxcycle )) |
---|
[3790] | 1352 | then |
---|
[3791] | 1353 | (( maxcycle = icycle )) |
---|
[3790] | 1354 | fi |
---|
| 1355 | |
---|
[3791] | 1356 | done <filelist |
---|
| 1357 | rm filelist |
---|
[3790] | 1358 | |
---|
| 1359 | |
---|
[3791] | 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 |
---|
[3790] | 1366 | |
---|
[3791] | 1367 | (( cycnum[$i] = maxcycle )) |
---|
| 1368 | pathout[$i]=$filename |
---|
[3790] | 1369 | |
---|
| 1370 | |
---|
[3791] | 1371 | # ADD CYCLE NUMBER TO FILENAME |
---|
| 1372 | # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER |
---|
| 1373 | if [[ "${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] )) |
---|
[3790] | 1378 | then |
---|
[3791] | 1379 | (( cycnum[$i] = run_number )) |
---|
| 1380 | else |
---|
| 1381 | if (( run_number > 0 )) |
---|
[3790] | 1382 | then |
---|
[3791] | 1383 | printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number" |
---|
[3790] | 1384 | fi |
---|
| 1385 | fi |
---|
[3791] | 1386 | fi |
---|
| 1387 | if (( cycnum[$i] > 0 )) |
---|
| 1388 | then |
---|
| 1389 | cyclestring=`printf "%03d" ${cycnum[$i]}` |
---|
| 1390 | pathout[$i]=${pathout[$i]}.$cyclestring |
---|
| 1391 | fi |
---|
| 1392 | fi |
---|
[3790] | 1393 | |
---|
[3791] | 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 ]] |
---|
[3790] | 1425 | then |
---|
[3791] | 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 ]] |
---|
[3790] | 1431 | then |
---|
[3791] | 1432 | printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n" |
---|
[3790] | 1433 | fi |
---|
[3791] | 1434 | else |
---|
[3790] | 1435 | |
---|
[3791] | 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 ]] |
---|
[3790] | 1440 | then |
---|
[3791] | 1441 | if [[ $running_on_remote = true ]] |
---|
[3790] | 1442 | then |
---|
| 1443 | |
---|
[3791] | 1444 | # SET OPTIONS FOR TRANSFER |
---|
| 1445 | if [[ "${actionout[$i]}" = tr ]] |
---|
[3790] | 1446 | then |
---|
[3791] | 1447 | if [[ $files_for_cores = false ]] |
---|
[3790] | 1448 | then |
---|
[3791] | 1449 | catalog_option="" |
---|
| 1450 | catalog_string="" |
---|
[3790] | 1451 | else |
---|
[3791] | 1452 | catalog_option="-c" |
---|
| 1453 | catalog_string="/" |
---|
[3790] | 1454 | fi |
---|
[3791] | 1455 | append_option="" |
---|
| 1456 | append_string="" |
---|
[3790] | 1457 | else |
---|
[3791] | 1458 | append_option="-A" |
---|
| 1459 | append_string="append" |
---|
[3790] | 1460 | fi |
---|
| 1461 | |
---|
[3791] | 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]}$catalog_string\n" |
---|
[3790] | 1465 | |
---|
[3791] | 1466 | # TRANSFER VIA SCP |
---|
| 1467 | if [[ "$remote_loginnode" != "" ]] |
---|
[3790] | 1468 | then |
---|
[3791] | 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]}" |
---|
[3790] | 1470 | else |
---|
[3791] | 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]} |
---|
[3790] | 1472 | fi |
---|
[3791] | 1473 | [[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true |
---|
[3790] | 1474 | |
---|
| 1475 | |
---|
[3791] | 1476 | # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE |
---|
| 1477 | if [[ $transfer_failed = true ]] |
---|
[3790] | 1478 | then |
---|
[3791] | 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 ]] |
---|
[3790] | 1485 | then |
---|
[3791] | 1486 | printf " *** local directory does not exist. Trying to create:\n" |
---|
| 1487 | printf " $local_catalog \n" |
---|
| 1488 | mkdir -p $local_catalog |
---|
[3790] | 1489 | fi |
---|
[3791] | 1490 | eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number |
---|
| 1491 | transfer_problems=true |
---|
[3790] | 1492 | fi |
---|
| 1493 | |
---|
[3791] | 1494 | else |
---|
[3790] | 1495 | |
---|
[3791] | 1496 | # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST |
---|
| 1497 | # BE COPIED OR APPENDED ON THIS MACHINE |
---|
| 1498 | if [[ "${actionout[$i]}" = tr ]] |
---|
[3790] | 1499 | then |
---|
[3791] | 1500 | actionout[$i]="" |
---|
| 1501 | else |
---|
| 1502 | actionout[$i]="a" |
---|
| 1503 | fi |
---|
[3790] | 1504 | fi |
---|
| 1505 | fi |
---|
| 1506 | |
---|
| 1507 | |
---|
[3791] | 1508 | # APPEND ON THIS MACHINE |
---|
| 1509 | if [[ "${actionout[$i]}" = "a" ]] |
---|
[3790] | 1510 | then |
---|
[3791] | 1511 | if [[ "${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 |
---|
[3790] | 1521 | fi |
---|
| 1522 | |
---|
[3791] | 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]}" = "" && $files_for_cores = false ]] |
---|
[3790] | 1527 | then |
---|
| 1528 | |
---|
[3791] | 1529 | # COPY IN CASE OF RUNS ON SINGLE CORES |
---|
| 1530 | if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] |
---|
[3790] | 1531 | then |
---|
[3791] | 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 |
---|
[3790] | 1550 | else |
---|
[3791] | 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 |
---|
[3790] | 1569 | fi |
---|
| 1570 | |
---|
[3791] | 1571 | elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]] |
---|
[3790] | 1572 | then |
---|
| 1573 | |
---|
[3791] | 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 ]] |
---|
[3790] | 1579 | then |
---|
[3791] | 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 $tempdir |
---|
[3790] | 1588 | fi |
---|
| 1589 | |
---|
[3791] | 1590 | # IF "ln -f" HAS FAILED OR IF "$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 |
---|
[3790] | 1600 | |
---|
| 1601 | fi |
---|
| 1602 | fi |
---|
[3791] | 1603 | done |
---|
[3790] | 1604 | |
---|
[3791] | 1605 | if (( i != 0 )) |
---|
| 1606 | then |
---|
| 1607 | if [[ $transfer_problems = true ]] |
---|
[3790] | 1608 | then |
---|
[3791] | 1609 | printf "\n$dashes\n *** OUTPUT-files saved" |
---|
| 1610 | printf "\n +++ WARNING: some data transfers failed! \n" |
---|
[3790] | 1611 | else |
---|
[3791] | 1612 | printf "\n$dashes\n *** all OUTPUT-files saved \n" |
---|
[3790] | 1613 | fi |
---|
[3791] | 1614 | fi |
---|
[3790] | 1615 | |
---|
| 1616 | |
---|
| 1617 | |
---|
| 1618 | |
---|
[3791] | 1619 | # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED |
---|
| 1620 | cd - |
---|
| 1621 | [[ $delete_temporary_catalog = true ]] && rm -rf $tempdir |
---|