[2380] | 1 | #!/bin/bash |
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| 2 | |
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| 3 | # palmrun - script for running PALM jobs |
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| 4 | |
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| 5 | #--------------------------------------------------------------------------------# |
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| 6 | # This file is part of PALM. |
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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 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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[2410] | 25 | # |
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[2380] | 26 | # Former revisions: |
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| 27 | # ----------------- |
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| 28 | # $Id: palmrun 2669 2017-12-06 16:03:27Z raasch $ |
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[2669] | 29 | # file attributes in .palm.iofiles restructured, "loc" attribute completely |
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| 30 | # removed, |
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| 31 | # wildcard (*) allowed in .palm.iofiles as file activation string for output |
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| 32 | # files, |
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| 33 | # informative messages in case of missing optional input files shortened |
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| 34 | # bugfix: variable cycle explicitly interpreted with 10 as the number base |
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| 35 | # |
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| 36 | # 2638 2017-11-23 12:44:23Z raasch |
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[2610] | 37 | # use of wildcards in file connection statements enabled |
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| 38 | # |
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| 39 | # 2605 2017-11-09 15:31:46Z raasch |
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[2605] | 40 | # in case of remote jobs, input files with "job" or "jobopt" (new) attribute |
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| 41 | # will not be sent with the job file any more, but copied into the |
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[2610] | 42 | # SOURCES_FOR_RUN... folder on the remote host, before the job is submitted |
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[2605] | 43 | # |
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| 44 | # 2600 2017-11-01 14:11:20Z raasch |
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[2600] | 45 | # cycle numbers are made three digits wide |
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| 46 | # |
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| 47 | # 2566 2017-10-20 08:50:47Z raasch |
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[2566] | 48 | # execute command for combine_plot_fields added |
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| 49 | # "TEMPDIR" renamed "tempdir" |
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| 50 | # temporary working directory for local batch jobs is created immediately within |
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| 51 | # the user's palmrun call, due to a requirement of the "grid engine" batch |
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| 52 | # system, where the working directory is given with batch directive -wd and must |
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| 53 | # already exist when the job is submitted, |
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| 54 | # informative messages in non-trace mode reduced and partly reformatted |
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| 55 | # |
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| 56 | # 2551 2017-10-18 07:25:11Z raasch |
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[2551] | 57 | # TEMPDIR added as replacement string to be used in batch directives |
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| 58 | # |
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| 59 | # 2512 2017-10-04 08:26:59Z raasch |
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[2507] | 60 | # bugfix for determining cycle numbers of NetCDF input files |
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| 61 | # |
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| 62 | # 2506 2017-09-29 08:30:37Z raasch |
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[2506] | 63 | # option -V added to check for an existing SOURCES_FOR_RUN_... folder |
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| 64 | # host configuration added to SOURCES_FOR_RUN_... folder name |
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| 65 | # host_identifier renamed host_configuration |
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| 66 | # option -W added to allow for job dependencies |
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| 67 | # |
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| 68 | # 2501 2017-09-26 11:41:55Z raasch |
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[2501] | 69 | # default value for number of cores (option -X) set to 1 |
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| 70 | # bugfix for mechanism which overwrites configuration file settings with values |
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| 71 | # provided by palmrun options |
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| 72 | # |
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| 73 | # 2499 2017-09-22 16:47:58Z kanani |
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[2499] | 74 | # option -h named configuration identifier |
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| 75 | # |
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| 76 | # 2480 2017-09-19 06:24:14Z maronga |
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[2480] | 77 | # bugfix for last revision |
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| 78 | # |
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| 79 | # 2479 2017-09-19 06:12:16Z raasch |
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[2479] | 80 | # option -A (project account number) added |
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| 81 | # |
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| 82 | # 2422 2017-09-08 08:25:41Z raasch |
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[2410] | 83 | # initial revision |
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[2380] | 84 | # |
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| 85 | #--------------------------------------------------------------------------------# |
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| 86 | # palmrun - script for running PALM jobs on local and remote hosts |
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| 87 | #--------------------------------------------------------------------------------# |
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| 88 | |
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| 89 | |
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| 90 | |
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| 91 | # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES |
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| 92 | |
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| 93 | set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS |
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| 94 | # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN |
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| 95 | # (TOO MANY ARGUMENTS - PROBLEM) |
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| 96 | set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN |
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| 97 | |
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[2610] | 98 | typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0 |
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| 99 | typeset -i nr_of_output_files=0 |
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[2380] | 100 | typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE |
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| 101 | # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE |
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| 102 | # SCRIPT-OPTION ARGUMENTS |
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| 103 | typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio |
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| 104 | typeset -i icycle inode ival maxcycle mpi_tasks |
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| 105 | typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task |
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| 106 | |
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| 107 | activation_string_list="" |
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| 108 | AddFilenames="" |
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| 109 | combine_plot_fields=true |
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| 110 | compiler_name="" |
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| 111 | compiler_name_ser="" |
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| 112 | compiler_options="" |
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[2501] | 113 | cores=1 |
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[2380] | 114 | cores_atmos=0 |
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| 115 | cores_ocean=0 |
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| 116 | coupled_dist="" |
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| 117 | cpp_options="" |
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| 118 | cpumax=0 |
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[2506] | 119 | create_batch_job=false |
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[2380] | 120 | create_jobfile_only=false |
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| 121 | create_remote_batch_job=false |
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| 122 | dashes=" ----------------------------------------------------------------------------" |
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| 123 | defaultqueue="" |
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[2506] | 124 | delete_temporary_catalog=true |
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[2380] | 125 | do_compile=true |
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| 126 | do_trace=false |
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| 127 | executable="" |
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| 128 | execute_command="" |
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| 129 | execution_error=false |
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| 130 | fileconnection_file=.palm.iofiles |
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| 131 | fname=test |
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| 132 | global_revision="" |
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[2506] | 133 | host_configuration="default" |
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[2380] | 134 | hostfile="" |
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| 135 | hp="" |
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| 136 | keep_data_from_previous_run=false |
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| 137 | link_local_input=false |
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| 138 | link_local_output=false |
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[2388] | 139 | linker_options="" |
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[2385] | 140 | local_jobcatalog="" |
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[2380] | 141 | locat=normal |
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| 142 | makefile="" |
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| 143 | max_par_io_str="" |
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| 144 | prc=$0 |
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| 145 | while [[ $(echo $prc | grep -c "/") != 0 ]] |
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| 146 | do |
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| 147 | prc=`echo $prc | cut -f2- -d"/"` |
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| 148 | done |
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| 149 | module_calls="" |
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[2506] | 150 | palmrun_memory="" |
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[2380] | 151 | palmrun_script_name=$prc |
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| 152 | openmp=false |
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[2506] | 153 | previous_job="" |
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[2479] | 154 | project_account="" |
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[2380] | 155 | queue=none |
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| 156 | restart_run=false |
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| 157 | return_address="" |
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[2385] | 158 | remote_jobcatalog="" |
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[2380] | 159 | remote_username="" |
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| 160 | running_in_batch_mode=false |
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| 161 | run_coupled_model=false |
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| 162 | run_id="" |
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| 163 | silent=false |
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| 164 | source_list="" |
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| 165 | source_path="" |
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[2501] | 166 | tasks_per_node=0 |
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[2380] | 167 | threads_per_task=1 |
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| 168 | transfer_problems=false |
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[2384] | 169 | user_source_path="" |
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[2506] | 170 | use_existing_sources_folder="" |
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[2380] | 171 | use_openmp=false |
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[2422] | 172 | version="palmrun 1.0 Rev$Rev: 2303 $" |
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[2380] | 173 | working_directory=`pwd` |
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| 174 | write_binary="" |
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| 175 | TOPT="" |
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| 176 | |
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| 177 | |
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| 178 | # ERROR HANDLING IN CASE OF EXIT |
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[2404] | 179 | trap 'if [[ $locat != normal && $locat != control_c ]] |
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[2380] | 180 | then |
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| 181 | |
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| 182 | # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:) |
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| 183 | (( i = 0 )) |
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| 184 | while (( i < iec )) |
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| 185 | do |
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| 186 | (( i = i + 1 )) |
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| 187 | printf "\n *** Execution of ERROR-command:\n" |
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| 188 | printf " >>> ${err_command[$i]}\n" |
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| 189 | eval ${err_command[$i]} |
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| 190 | done |
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[2566] | 191 | [[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir) |
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[2380] | 192 | printf "\n\n+++ palmrun killed \n\n" |
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| 193 | elif [[ $locat != control_c ]] |
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| 194 | then |
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[2566] | 195 | printf "\n --> palmrun finished\n\n" |
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[2380] | 196 | fi' exit |
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| 197 | |
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| 198 | |
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| 199 | # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C): |
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[2566] | 200 | trap 'cd; rm -rf $tempdir |
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[2380] | 201 | printf "\n+++ palmrun killed by \"^C\" \n\n" |
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| 202 | locat=control_c |
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| 203 | exit |
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| 204 | ' 2 |
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| 205 | |
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| 206 | |
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| 207 | # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc), |
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| 208 | # WHICH WILL BE USED TO START RESTART-JOBS |
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[2506] | 209 | while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option |
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[2380] | 210 | do |
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| 211 | case $option in |
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| 212 | (a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";; |
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[2479] | 213 | (A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";; |
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[2380] | 214 | (b) create_batch_job=true; prc="$prc -b";; |
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| 215 | (B) delete_temporary_catalog=false; prc="$prc -B";; |
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| 216 | (C) restart_run=true; prc="$prc -C";; |
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| 217 | (d) fname=$OPTARG; prc="$prc -d$OPTARG";; |
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| 218 | (F) create_jobfile_only=true;; |
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| 219 | (G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";; |
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[2506] | 220 | (h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";; |
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[2380] | 221 | (j) running_in_batch_mode=true;; |
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| 222 | (k) keep_data_from_previous_run=true; prc="$prc -k";; |
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[2501] | 223 | (m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";; |
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[2380] | 224 | (M) makefile=$OPTARG; prc="$prc -M$OPTARG";; |
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| 225 | (O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";; |
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| 226 | (q) queue=$OPTARG; prc="$prc -q$OPTARG";; |
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| 227 | (r) run_id=$OPTARG;; |
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| 228 | (R) return_address=$OPTARG;; |
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| 229 | (s) source_list=$OPTARG;; |
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[2501] | 230 | (t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";; |
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[2380] | 231 | (T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";; |
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| 232 | (u) remote_username=$OPTARG; prc="$prc -u$OPTARG";; |
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| 233 | (U) return_username=$OPTARG; prc="$prc -U$OPTARG";; |
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| 234 | (v) silent=true; prc="$prc -v";; |
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[2506] | 235 | (V) use_existing_sources_folder="-V";; |
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[2380] | 236 | (w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";; |
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[2506] | 237 | (W) previous_job=$OPTARG;; |
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[2380] | 238 | (x) do_trace=true;set -x; prc="$prc -x";; |
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[2501] | 239 | (X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";; |
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[2380] | 240 | (y) ocean_file_appendix=true; prc="$prc -y";; |
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| 241 | (Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";; |
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| 242 | (Z) combine_plot_fields=false; prc="$prc -Z";; |
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| 243 | (\?) printf "\n +++ unknown option $OPTARG \n" |
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| 244 | printf "\n --> type \"$0 ?\" for available options \n" |
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| 245 | locat=parameter;exit;; |
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| 246 | esac |
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| 247 | done |
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| 248 | |
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| 249 | |
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| 250 | # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN |
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| 251 | # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED |
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| 252 | (( to_shift = $OPTIND - 1 )) |
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| 253 | shift $to_shift |
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| 254 | |
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| 255 | # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS |
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| 256 | if [[ "$1" = "?" ]] |
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| 257 | then |
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| 258 | (printf "\n *** Description of available palmrun options:\n" |
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| 259 | printf "\n Option Description Default-Value" |
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| 260 | printf "\n -a activation string list \"\" " |
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[2479] | 261 | printf "\n -A project account number ---" |
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[2380] | 262 | printf "\n -b batch-job on local machine ---" |
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| 263 | printf "\n -B do not delete temporary directory at end ---" |
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| 264 | printf "\n -d base name of files attached to program test" |
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| 265 | printf "\n -F create batch job file only ---" |
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[2506] | 266 | printf "\n -h host configuration \"default\" " |
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[2380] | 267 | printf "\n -k keep data from previous run" |
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| 268 | printf "\n -m memory demand in MB (batch-jobs) 0 MB" |
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| 269 | printf "\n -M Makefile name Makefile" |
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| 270 | printf "\n -O threads per openMP task ---" |
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| 271 | printf "\n -q queue \"$queue\" " |
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| 272 | printf "\n -s filenames of routines to be compiled \"\" " |
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| 273 | printf "\n must end with .f, .f90, .F, or .c !" |
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| 274 | printf "\n use \"..\" for more than one file and wildcards" |
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| 275 | printf "\n -s LM compiles all locally modified files" |
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| 276 | printf "\n -t allowed cpu-time in seconds (batch) 0" |
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[2384] | 277 | printf "\n -T tasks per node ---" |
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[2380] | 278 | printf "\n -u username on remote machine \"\" " |
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| 279 | printf "\n -v no prompt for confirmation ---" |
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[2506] | 280 | printf "\n -V check if SOURCES_FOR_RUN_... exists ---" |
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[2380] | 281 | printf "\n -w maximum parallel io streams as given by -X" |
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[2506] | 282 | printf "\n -W name of job to wait for ---" |
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[2380] | 283 | printf "\n -x tracing of palmrun for debug purposes ---" |
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| 284 | printf "\n -X # of processors (on parallel machines) 1" |
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| 285 | printf "\n -y add appendix \"_O\" to all local output" |
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| 286 | printf "\n files (ocean precursor runs followed by" |
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| 287 | printf "\n coupled atmosphere-ocean runs) ---" |
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| 288 | printf "\n -Y run coupled model, \"#1 #2\" with" |
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| 289 | printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X" |
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| 290 | printf "\n -Z skip combine_plot_fields at the end of " |
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| 291 | printf "\n the simulation ---" |
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| 292 | printf "\n " |
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| 293 | printf "\n Possible values of positional parameter <modus>:" |
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| 294 | printf "\n \"?\" - this outline \n\n") | more |
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| 295 | exit |
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| 296 | elif [[ "$1" != "" ]] |
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| 297 | then |
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| 298 | printf "\n +++ positional parameter $1 unknown \n" |
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| 299 | locat=parameter; exit |
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| 300 | fi |
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| 301 | |
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| 302 | |
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| 303 | |
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| 304 | # SHORT STARTING MESSAGE |
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| 305 | printf "\n*** $version " |
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| 306 | printf "\n will be executed. Please wait ..." |
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| 307 | |
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| 308 | |
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[2506] | 309 | # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME |
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| 310 | config_file=.palm.config.$host_configuration |
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| 311 | sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname |
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[2380] | 312 | |
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| 313 | |
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| 314 | # CHECK, IF CONFIGURATION FILE EXISTS |
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| 315 | if [[ ! -f $config_file ]] |
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| 316 | then |
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| 317 | printf "\n\n +++ configuration file: " |
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| 318 | printf "\n $config_file" |
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| 319 | printf "\n does not exist" |
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| 320 | locat=connect; exit |
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| 321 | fi |
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| 322 | |
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| 323 | |
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| 324 | # CHECK, IF FILE CONNECTION FILE EXISTS |
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| 325 | if [[ ! -f $fileconnection_file ]] |
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| 326 | then |
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| 327 | printf "\n\n +++ file connection file: " |
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| 328 | printf "\n $fileconnection_file" |
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| 329 | printf "\n does not exist" |
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| 330 | locat=connect; exit |
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| 331 | fi |
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| 332 | |
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| 333 | |
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[2404] | 334 | # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN |
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| 335 | if [[ "$activation_string_list" = "" ]] |
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| 336 | then |
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| 337 | printf "\n\n +++ no activation string list given: " |
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| 338 | printf "\n please set palmrun option \"-a\" " |
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| 339 | locat=palmrun_option; exit |
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| 340 | fi |
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| 341 | |
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| 342 | |
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| 343 | # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS |
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| 344 | if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]] |
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| 345 | then |
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| 346 | write_binary=true |
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| 347 | else |
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| 348 | write_binary=false |
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| 349 | fi |
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| 350 | |
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| 351 | |
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[2380] | 352 | # READ AND EVALUATE THE CONFIGURATION-FILE |
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| 353 | [[ $silent = false ]] && printf "\n\n Reading the configuration file... " |
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| 354 | |
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| 355 | # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE |
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| 356 | while read line |
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| 357 | do |
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| 358 | |
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| 359 | # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES |
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| 360 | eval line=\"$line\" |
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| 361 | |
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| 362 | |
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| 363 | # INTERPRET THE LINE |
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| 364 | if [[ "$(echo $line)" = "" ]] |
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| 365 | then |
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| 366 | |
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| 367 | # EMPTY LINE, NO ACTION |
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| 368 | continue |
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| 369 | |
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| 370 | elif [[ "$(echo $line | cut -c1)" = "#" ]] |
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| 371 | then |
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| 372 | |
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| 373 | # LINE IS A COMMENT LINE |
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| 374 | continue |
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| 375 | |
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| 376 | elif [[ "$(echo $line | cut -c1)" = "%" ]] |
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| 377 | then |
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| 378 | |
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| 379 | # LINE DEFINES AN ENVIRONMENT-VARIABLE |
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| 380 | var=`echo $line | cut -d" " -s -f1 | cut -c2-` |
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| 381 | value=`echo $line | cut -d" " -s -f2-` |
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| 382 | |
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| 383 | |
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| 384 | # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE |
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| 385 | # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY |
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| 386 | # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS). |
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| 387 | # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER). |
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| 388 | # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE |
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| 389 | # CONFIGURATION-FILE. |
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| 390 | if [[ "$(eval echo \$$var)" = "" || "$(eval echo \$$var)" = "0" ]] |
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| 391 | then |
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| 392 | eval export $var="\$value" |
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| 393 | |
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| 394 | # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on |
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| 395 | if [[ $do_trace = true ]] |
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| 396 | then |
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| 397 | printf "\n*** ENVIRONMENT-VARIABLE $var = $value" |
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| 398 | fi |
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| 399 | fi |
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| 400 | |
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| 401 | elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]] |
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| 402 | then |
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| 403 | |
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| 404 | # LINE DEFINES BATCH-DIRECTIVE |
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| 405 | (( ibd = ibd + 1 )) |
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| 406 | line=$(echo $line | cut -c4-) |
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| 407 | batch_directive[$ibd]="$line" |
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| 408 | |
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| 409 | elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]] |
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| 410 | then |
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| 411 | |
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| 412 | # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A |
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| 413 | # REMOTE TO A LOCAL HOST |
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| 414 | (( ibdt = ibdt + 1 )) |
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| 415 | line=$(echo $line | cut -c5-) |
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| 416 | batch_directive_transfer[$ibdt]="$line" |
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| 417 | |
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| 418 | elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]] |
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| 419 | then |
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| 420 | |
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| 421 | # LINE DEFINES ERROR-COMMAND |
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| 422 | (( iec = iec + 1 )) |
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| 423 | line=$(echo $line | cut -c4-) |
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| 424 | err_command[$iec]="$line" |
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| 425 | |
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| 426 | elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]] |
---|
| 427 | then |
---|
| 428 | |
---|
| 429 | # LINE DEFINES INPUT-COMMAND |
---|
| 430 | (( iic = iic + 1 )) |
---|
| 431 | line=$(echo $line | cut -c4-) |
---|
| 432 | in_command[$iic]="$line" |
---|
| 433 | |
---|
| 434 | elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]] |
---|
| 435 | then |
---|
| 436 | |
---|
| 437 | # LINE DEFINES OUTPUT-COMMAND |
---|
| 438 | (( ioc = ioc + 1 )) |
---|
| 439 | line=$(echo $line | cut -c4-) |
---|
| 440 | out_command[$ioc]="$line" |
---|
| 441 | |
---|
| 442 | else |
---|
| 443 | |
---|
| 444 | # SKIP ALL OTHER LINES |
---|
| 445 | continue |
---|
| 446 | |
---|
| 447 | fi |
---|
| 448 | |
---|
| 449 | done < $config_file |
---|
| 450 | |
---|
| 451 | |
---|
| 452 | # CHECK SETTING OF REQUIRED PARAMETERS |
---|
| 453 | if [[ "$compiler_name" = "" ]] |
---|
| 454 | then |
---|
| 455 | printf "\n +++ no compiler name found in $config_file" |
---|
| 456 | printf "\n Please add line \"compiler_name ...\" to that file." |
---|
| 457 | locat=config_file; exit |
---|
| 458 | fi |
---|
| 459 | if [[ "$compiler_name_ser" = "" ]] |
---|
| 460 | then |
---|
| 461 | printf "\n +++ no compiler name for non-paralle compilation found in $config_file" |
---|
| 462 | printf "\n Please add line \"compiler_name_ser ...\" to that file." |
---|
| 463 | locat=config_file; exit |
---|
| 464 | fi |
---|
| 465 | if [[ "$compiler_options" = "" ]] |
---|
| 466 | then |
---|
| 467 | printf "\n +++ no compiler options found in $config_file" |
---|
| 468 | printf "\n Please add line \"compiler_options ...\" to that file." |
---|
| 469 | locat=config_file; exit |
---|
| 470 | fi |
---|
[2388] | 471 | if [[ "$linker_options" = "" ]] |
---|
[2380] | 472 | then |
---|
[2388] | 473 | printf "\n +++ no linker options found in $config_file" |
---|
| 474 | printf "\n Please add line \"linker_options ...\" to that file." |
---|
[2380] | 475 | locat=config_file; exit |
---|
| 476 | fi |
---|
| 477 | if [[ "$execute_command" = "" ]] |
---|
| 478 | then |
---|
| 479 | printf "\n +++ no execute command found in $config_file" |
---|
| 480 | printf "\n Please add line \"execute_command ...\" to that file." |
---|
| 481 | locat=config_file; exit |
---|
| 482 | fi |
---|
| 483 | |
---|
| 484 | if [[ "$hostfile" != "" ]] |
---|
| 485 | then |
---|
| 486 | if [[ $hostfile != auto && ! -f $hostfile ]] |
---|
| 487 | then |
---|
| 488 | printf "\n +++ no hostfile \"$hostfile\" found" |
---|
| 489 | printf "\n Please check line \"hostfile ...\" in $config_file" |
---|
| 490 | locat=config_file; exit |
---|
| 491 | fi |
---|
| 492 | fi |
---|
| 493 | |
---|
| 494 | |
---|
| 495 | # DETERMINE THE CALL STATUS |
---|
| 496 | if [[ "$return_address" != "" ]] |
---|
| 497 | then |
---|
| 498 | |
---|
| 499 | # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN |
---|
| 500 | # BATCH MODE AND ... |
---|
| 501 | running_on_remote=true |
---|
| 502 | |
---|
| 503 | else |
---|
| 504 | |
---|
| 505 | # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST |
---|
| 506 | if [[ "$remote_ip" != "" ]] |
---|
| 507 | then |
---|
| 508 | |
---|
| 509 | # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST |
---|
| 510 | create_remote_batch_job=true |
---|
| 511 | |
---|
| 512 | fi |
---|
| 513 | running_on_remote=false |
---|
| 514 | fi |
---|
| 515 | |
---|
| 516 | |
---|
| 517 | |
---|
| 518 | # READ AND EVALUATE THE I/O-FILE LIST |
---|
| 519 | [[ $silent = false ]] && printf "\n Reading the I/O files... " |
---|
| 520 | |
---|
| 521 | # READ THE FILE CONNECTION FILE LINE BY LINE |
---|
| 522 | while read line |
---|
| 523 | do |
---|
| 524 | |
---|
[2669] | 525 | # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE |
---|
| 526 | line=`echo "$line" | sed -e "s/\s\{1,\}/ /g"` |
---|
[2380] | 527 | |
---|
| 528 | # INTERPRET THE LINE |
---|
| 529 | if [[ "$(echo $line)" = "" ]] |
---|
| 530 | then |
---|
| 531 | # EMPTY LINE, NO ACTION |
---|
| 532 | continue |
---|
| 533 | |
---|
| 534 | elif [[ "$(echo $line | cut -c1)" = "#" ]] |
---|
| 535 | then |
---|
| 536 | |
---|
| 537 | # LINE IS A COMMENT LINE |
---|
| 538 | true |
---|
| 539 | |
---|
| 540 | else |
---|
| 541 | |
---|
| 542 | # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES. |
---|
| 543 | # s2a: in/out - field |
---|
[2669] | 544 | # s2b: action - field (optional) |
---|
| 545 | s1=`echo "$line" | cut -d" " -f1` |
---|
| 546 | s2=`echo "$line" | cut -d" " -s -f2` |
---|
| 547 | # s2a=$(echo $s2 | cut -d":" -f1) |
---|
[2380] | 548 | if [[ $(echo $s2 | grep -c ":") = 0 ]] |
---|
| 549 | then |
---|
[2669] | 550 | s2a=$s2 |
---|
[2380] | 551 | s2b="" |
---|
| 552 | else |
---|
[2669] | 553 | s2a=`echo $s2 | cut -d":" -f1` |
---|
| 554 | s2b=`echo $s2 | cut -d":" -f2` |
---|
[2380] | 555 | fi |
---|
[2669] | 556 | s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'` |
---|
| 557 | s4=`echo "$line" | cut -d" " -s -f4` |
---|
| 558 | eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES |
---|
| 559 | echo "### s4=\"$s4\" " |
---|
| 560 | s5=`echo "$line" | cut -d" " -s -f5` |
---|
| 561 | s6=`echo "$line" | cut -d" " -s -f6` |
---|
[2380] | 562 | |
---|
| 563 | |
---|
| 564 | # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM |
---|
| 565 | # INPUT- OR OUTPUT-LIST. |
---|
| 566 | # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":"). |
---|
| 567 | # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY |
---|
[2669] | 568 | # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION |
---|
[2380] | 569 | # IS NOT CHECKED AND STORED. |
---|
[2610] | 570 | IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR |
---|
[2669] | 571 | if [[ ( "$s2a" = in || "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]] |
---|
[2380] | 572 | then |
---|
| 573 | found=false |
---|
| 574 | for actual in $activation_string_list |
---|
| 575 | do |
---|
| 576 | for formal in $s3 |
---|
| 577 | do |
---|
| 578 | [[ $actual = $formal || "$formal" = "-" ]] && found=true |
---|
| 579 | done |
---|
| 580 | done |
---|
| 581 | if [[ $found = true ]] |
---|
| 582 | then |
---|
| 583 | (( iin = iin + 1 )) |
---|
[2669] | 584 | localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b; |
---|
[2610] | 585 | pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6 |
---|
[2669] | 586 | if [[ "$s2a" = inopt ]] |
---|
| 587 | then |
---|
| 588 | optin_pre[$iin]=yes |
---|
| 589 | else |
---|
| 590 | optin_pre[$iin]=no |
---|
| 591 | fi |
---|
[2605] | 592 | |
---|
| 593 | # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN |
---|
| 594 | # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST |
---|
[2669] | 595 | if [[ $running_on_remote = true && "$s2b" = tr ]] |
---|
[2605] | 596 | then |
---|
[2610] | 597 | pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog} |
---|
[2605] | 598 | fi |
---|
| 599 | |
---|
[2610] | 600 | # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE |
---|
| 601 | # THE WILDCARD FROM THE ENDING |
---|
| 602 | if [[ "${s5: -1}" = "*" ]] |
---|
| 603 | then |
---|
[2669] | 604 | if [[ "$s2b" = "di" ]] |
---|
[2610] | 605 | then |
---|
| 606 | printf "\n +++ wildcards (*) not allowed with \"di\" file attribute." |
---|
| 607 | printf "\n see file \"$fileconnection_file\", line" |
---|
| 608 | printf "\n$line" |
---|
| 609 | locat=iofiles_file; exit |
---|
| 610 | fi |
---|
| 611 | multin[$iin]=true |
---|
| 612 | string=${endin_pre[$iin]} |
---|
| 613 | endin_pre[$iin]="${string%?}" |
---|
| 614 | else |
---|
| 615 | multin[$iin]=false |
---|
| 616 | fi |
---|
[2380] | 617 | fi |
---|
[2669] | 618 | elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]] |
---|
[2380] | 619 | then |
---|
| 620 | found=false |
---|
[2669] | 621 | echo "### line=\"$line\" " |
---|
[2380] | 622 | for actual in $activation_string_list |
---|
| 623 | do |
---|
| 624 | for formal in $s3 |
---|
| 625 | do |
---|
[2669] | 626 | echo "--- actual=\"$actual\" formal=\"$formal\" s3=\"$s3\" " |
---|
| 627 | if [[ $actual = $formal || $formal = wildcard ]] |
---|
| 628 | then |
---|
| 629 | found=true |
---|
| 630 | echo "--- found" |
---|
| 631 | else |
---|
| 632 | echo "--- not found" |
---|
| 633 | fi |
---|
[2380] | 634 | done |
---|
| 635 | done |
---|
| 636 | if [[ $found = true ]] |
---|
| 637 | then |
---|
| 638 | (( iout = iout + 1 )) |
---|
[2669] | 639 | localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b |
---|
[2610] | 640 | pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6 |
---|
[2669] | 641 | echo "### pathout_pre[$iout]=\"${pathout_pre[$iout]}\" " |
---|
[2610] | 642 | |
---|
[2669] | 643 | # CHECK IF WILDCARD IS USED AS ACTIVATION STRING |
---|
| 644 | # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST |
---|
| 645 | if [[ $formal = wildcard ]] |
---|
| 646 | then |
---|
| 647 | warnout_pre[$iout]=false |
---|
| 648 | else |
---|
| 649 | warnout_pre[$iout]=true |
---|
| 650 | fi |
---|
| 651 | |
---|
[2610] | 652 | # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE |
---|
| 653 | # THE WILDCARD FROM THE LOCAL FILENAME |
---|
| 654 | if [[ "${s1: -1}" = "*" ]] |
---|
| 655 | then |
---|
[2669] | 656 | if [[ "$s2b" = "di" ]] |
---|
[2610] | 657 | then |
---|
| 658 | printf "\n +++ wildcards (*) not allowed with \"di\" file attribute." |
---|
| 659 | printf "\n see file \"$fileconnection_file\", line" |
---|
| 660 | printf "\n$line" |
---|
| 661 | locat=iofiles_file; exit |
---|
| 662 | fi |
---|
| 663 | multout[$iout]=true |
---|
| 664 | string=${localout_pre[$iout]} |
---|
| 665 | localout_pre[$iout]="${string%?}" |
---|
| 666 | else |
---|
| 667 | multout[$iout]=false |
---|
| 668 | fi |
---|
[2380] | 669 | fi |
---|
[2669] | 670 | elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]] |
---|
[2380] | 671 | then |
---|
[2669] | 672 | printf "\n +++ I/O-attribute in file $fileconnection_file has invalid" |
---|
| 673 | printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!" |
---|
[2380] | 674 | locat=connect; exit |
---|
| 675 | fi |
---|
| 676 | IFS="$IFSALT" |
---|
| 677 | fi |
---|
| 678 | |
---|
| 679 | done < $fileconnection_file |
---|
| 680 | |
---|
| 681 | |
---|
| 682 | |
---|
[2501] | 683 | # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE |
---|
[2506] | 684 | [[ $palmrun_memory != "" ]] && memory=$palmrun_memory |
---|
[2501] | 685 | [[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax |
---|
| 686 | [[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores |
---|
| 687 | [[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str |
---|
| 688 | [[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node |
---|
| 689 | |
---|
| 690 | |
---|
| 691 | |
---|
[2380] | 692 | # EVALUATE MODEL COUPLING FEATURES (OPTION -Y) |
---|
| 693 | if [[ $run_coupled_model = true ]] |
---|
| 694 | then |
---|
| 695 | |
---|
| 696 | cores_atmos=`echo $coupled_dist | cut -d" " -s -f1` |
---|
| 697 | cores_ocean=`echo $coupled_dist | cut -d" " -s -f2` |
---|
| 698 | |
---|
| 699 | if (( $cores_ocean + $cores_atmos != $cores )) |
---|
| 700 | then |
---|
| 701 | |
---|
| 702 | printf "\n +++ number of processors does not fit to specification by \"-Y\"." |
---|
| 703 | printf "\n PEs (total) : $cores" |
---|
| 704 | printf "\n PEs (atmosphere): $cores_atmos" |
---|
| 705 | printf "\n PEs (ocean) : $cores_ocean" |
---|
| 706 | locat=coupling; exit |
---|
| 707 | |
---|
| 708 | fi |
---|
| 709 | |
---|
| 710 | fi |
---|
| 711 | |
---|
| 712 | |
---|
| 713 | # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES |
---|
| 714 | # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_... |
---|
| 715 | # FOLDER |
---|
| 716 | if [[ $running_in_batch_mode = true ]] |
---|
| 717 | then |
---|
| 718 | |
---|
[2506] | 719 | if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]] |
---|
[2380] | 720 | then |
---|
[2506] | 721 | printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing" |
---|
[2380] | 722 | printf "\n Please check the output of the palmrun-call" |
---|
| 723 | printf "\n that you did on your local host." |
---|
| 724 | locat=SOURCES_FOR_RUN; exit |
---|
| 725 | fi |
---|
| 726 | |
---|
| 727 | else |
---|
| 728 | |
---|
| 729 | # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN |
---|
| 730 | # AUTOMATIC RESTART RUN |
---|
| 731 | # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN |
---|
| 732 | if [[ $restart_run = false ]] |
---|
| 733 | then |
---|
| 734 | |
---|
| 735 | # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON |
---|
| 736 | # THE LOCAL HOST |
---|
| 737 | if [[ ! -d $source_path ]] |
---|
| 738 | then |
---|
| 739 | printf "\n\n +++ source path \"$source_path\" on local host" |
---|
| 740 | printf "\n \"$(hostname)\" does not exist" |
---|
| 741 | locat=source_path; exit |
---|
| 742 | fi |
---|
| 743 | |
---|
[2506] | 744 | rm -rf $sources_for_run_catalog |
---|
| 745 | mkdir -p $sources_for_run_catalog |
---|
[2380] | 746 | |
---|
| 747 | if [[ "$source_list" = LM ]] |
---|
| 748 | then |
---|
| 749 | |
---|
| 750 | # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY |
---|
| 751 | source_list="" |
---|
| 752 | cd $source_path |
---|
| 753 | |
---|
| 754 | |
---|
[2512] | 755 | # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL |
---|
| 756 | if [[ ! -d ../.svn ]] |
---|
[2380] | 757 | then |
---|
| 758 | printf "\n\n +++ source directory" |
---|
| 759 | printf "\n \"$source_path\" " |
---|
| 760 | printf "\n is not under control of \"subversion\"." |
---|
[2512] | 761 | printf "\n Please do not use palmrun-option \"-s LM\"\n" |
---|
[2380] | 762 | fi |
---|
| 763 | |
---|
| 764 | |
---|
| 765 | # LIST ALL MODIFIED SOURCE CODE FILES |
---|
| 766 | Filenames="" |
---|
[2404] | 767 | svn status > tmp_svnstatus |
---|
[2380] | 768 | while read line |
---|
| 769 | do |
---|
| 770 | firstc=`echo $line | cut -c1` |
---|
| 771 | if [[ $firstc = M || $firstc = "?" ]] |
---|
| 772 | then |
---|
| 773 | Name=`echo "$line" | cut -c8-` |
---|
| 774 | extension=`echo $Name | cut -d. -f2` |
---|
| 775 | if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]] |
---|
| 776 | then |
---|
| 777 | Filenames="$Filenames "$Name |
---|
| 778 | fi |
---|
| 779 | fi |
---|
[2404] | 780 | done < tmp_svnstatus |
---|
| 781 | rm -rf tmp_svnstatus |
---|
[2380] | 782 | |
---|
| 783 | |
---|
| 784 | # COPY FILES TO SOURCES_FOR_RUN_... |
---|
| 785 | for filename in $Filenames |
---|
| 786 | do |
---|
[2506] | 787 | cp $filename ${working_directory}/${sources_for_run_catalog} |
---|
[2380] | 788 | source_list=$source_list"$filename " |
---|
| 789 | done |
---|
| 790 | |
---|
| 791 | cd - > /dev/null |
---|
| 792 | |
---|
| 793 | |
---|
| 794 | # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_... |
---|
| 795 | elif [[ "$source_list" != "" ]] |
---|
| 796 | then |
---|
| 797 | |
---|
| 798 | cd $source_path |
---|
| 799 | |
---|
| 800 | for filename in $source_list |
---|
| 801 | do |
---|
| 802 | |
---|
| 803 | # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH |
---|
| 804 | if [[ $(echo $filename | grep -c "/") != 0 ]] |
---|
| 805 | then |
---|
| 806 | printf "\n +++ source code file: $filename" |
---|
| 807 | printf "\n must not contain (\"/\") " |
---|
| 808 | locat=source; exit |
---|
| 809 | fi |
---|
| 810 | |
---|
| 811 | if [[ ! -f $filename ]] |
---|
| 812 | then |
---|
| 813 | printf "\n +++ source code file: $filename" |
---|
| 814 | printf "\n does not exist" |
---|
| 815 | locat=source; exit |
---|
| 816 | else |
---|
[2506] | 817 | cp $filename ${working_directory}/${sources_for_run_catalog} |
---|
[2380] | 818 | fi |
---|
| 819 | |
---|
| 820 | done |
---|
| 821 | |
---|
| 822 | cd - > /dev/null |
---|
| 823 | |
---|
| 824 | fi |
---|
| 825 | |
---|
| 826 | # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY |
---|
| 827 | [[ "$makefile" = "" ]] && makefile=$source_path/Makefile |
---|
| 828 | if [[ ! -f $makefile ]] |
---|
| 829 | then |
---|
| 830 | printf "\n +++ file \"$makefile\" does not exist" |
---|
| 831 | locat=make; exit |
---|
| 832 | else |
---|
[2506] | 833 | cp $makefile ${sources_for_run_catalog}/Makefile |
---|
[2380] | 834 | fi |
---|
| 835 | |
---|
| 836 | |
---|
| 837 | # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE |
---|
[2384] | 838 | if [[ "$user_source_path" != "" ]] |
---|
[2380] | 839 | then |
---|
| 840 | |
---|
| 841 | # DOES THE DIRECTORY EXIST? |
---|
[2384] | 842 | if [[ ! -d $user_source_path ]] |
---|
[2380] | 843 | then |
---|
| 844 | |
---|
| 845 | printf "\n\n *** INFORMATIVE: additional source code directory" |
---|
[2384] | 846 | printf "\n \"$user_source_path\" " |
---|
[2380] | 847 | printf "\n does not exist or is not a directory." |
---|
| 848 | printf "\n No source code will be used from this directory!\n" |
---|
[2384] | 849 | user_source_path="" |
---|
[2380] | 850 | if [[ $silent == false ]] |
---|
| 851 | then |
---|
| 852 | sleep 2 |
---|
| 853 | fi |
---|
| 854 | |
---|
| 855 | else |
---|
| 856 | |
---|
[2384] | 857 | cd $user_source_path |
---|
[2380] | 858 | found=false |
---|
| 859 | |
---|
| 860 | Names=$(ls -1 *.f90 2>&1) |
---|
| 861 | [[ $(echo $Names | grep -c '*.f90') = 0 ]] && AddFilenames="$Names" |
---|
| 862 | Names=$(ls -1 *.F90 2>&1) |
---|
| 863 | [[ $(echo $Names | grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names" |
---|
| 864 | Names=$(ls -1 *.F 2>&1) |
---|
| 865 | [[ $(echo $Names | grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names" |
---|
| 866 | Names=$(ls -1 *.f 2>&1) |
---|
| 867 | [[ $(echo $Names | grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names" |
---|
| 868 | Names=$(ls -1 *.c 2>&1) |
---|
| 869 | [[ $(echo $Names | grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names" |
---|
| 870 | |
---|
| 871 | cd - > /dev/null |
---|
[2506] | 872 | cd $sources_for_run_catalog |
---|
[2380] | 873 | |
---|
| 874 | # COPY MAKEFILE IF EXISTING |
---|
[2384] | 875 | if [[ -f $user_source_path/Makefile ]] |
---|
[2380] | 876 | then |
---|
| 877 | printf "\n\n *** user Makefile from directory" |
---|
[2384] | 878 | printf "\n \"$user_source_path\" is used \n" |
---|
[2380] | 879 | if [[ $silent == false ]] |
---|
| 880 | then |
---|
| 881 | sleep 1 |
---|
| 882 | fi |
---|
[2384] | 883 | cp $user_source_path/Makefile . |
---|
[2380] | 884 | fi |
---|
| 885 | |
---|
| 886 | for filename in $AddFilenames |
---|
| 887 | do |
---|
| 888 | if [[ -f $filename ]] |
---|
| 889 | then |
---|
| 890 | printf "\n +++ source code file \"$filename\" found in additional" |
---|
[2384] | 891 | printf "\n source code directory \"$user_source_path\" " |
---|
[2380] | 892 | printf "\n but was also given with option \"-s\" which means that it should be taken" |
---|
| 893 | printf "\n from directory \"$source_path\"." |
---|
| 894 | locat=source; exit |
---|
| 895 | fi |
---|
| 896 | |
---|
[2384] | 897 | cp $user_source_path/$filename . |
---|
[2380] | 898 | source_list="$source_list $filename" |
---|
| 899 | |
---|
| 900 | # CHECK IF FILE IS CONTAINED IN MAKEFILE |
---|
| 901 | if [[ $(grep -c $filename Makefile) = 0 ]] |
---|
| 902 | then |
---|
| 903 | printf "\n\n +++ user file \"$filename\" " |
---|
| 904 | printf "\n is not listed in Makefile \n" |
---|
| 905 | locat=source; exit |
---|
| 906 | else |
---|
| 907 | |
---|
| 908 | if [[ $found = false ]] |
---|
| 909 | then |
---|
| 910 | found=true |
---|
| 911 | printf "\n\n *** following user file(s) added to the" |
---|
| 912 | printf " files to be translated:\n " |
---|
| 913 | fi |
---|
| 914 | printf "$filename " |
---|
| 915 | if [[ $silent == false ]] |
---|
| 916 | then |
---|
| 917 | sleep 0.5 |
---|
| 918 | fi |
---|
| 919 | |
---|
| 920 | fi |
---|
| 921 | done |
---|
| 922 | [[ $found = true ]] && printf "\n" |
---|
| 923 | cd - > /dev/null |
---|
| 924 | fi |
---|
| 925 | fi |
---|
| 926 | |
---|
| 927 | # COPY CONFIGURATION FILES |
---|
[2506] | 928 | cp $config_file $sources_for_run_catalog |
---|
| 929 | cp $fileconnection_file $sources_for_run_catalog |
---|
[2380] | 930 | |
---|
| 931 | # COPY SHELLSCRIPTS |
---|
[2506] | 932 | cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog |
---|
| 933 | cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog |
---|
[2380] | 934 | |
---|
| 935 | fi |
---|
| 936 | |
---|
| 937 | fi |
---|
| 938 | |
---|
[2605] | 939 | |
---|
[2380] | 940 | # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY |
---|
| 941 | # (HANDED OVER TO RESTART-RUNS USING OPTION -G) |
---|
| 942 | if [[ "$global_revision" = "" ]] |
---|
| 943 | then |
---|
| 944 | global_revision=`svnversion $source_path 2>/dev/null` |
---|
| 945 | global_revision="Rev: $global_revision" |
---|
| 946 | fi |
---|
| 947 | |
---|
| 948 | |
---|
| 949 | # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS |
---|
| 950 | if [[ -n $cores ]] |
---|
| 951 | then |
---|
| 952 | |
---|
| 953 | # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN |
---|
| 954 | # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X |
---|
[2501] | 955 | if [[ $tasks_per_node = 0 ]] |
---|
[2380] | 956 | then |
---|
| 957 | printf "\n" |
---|
| 958 | printf "\n +++ option \"-T\" (tasks per node) is missing" |
---|
| 959 | printf "\n set -T option or define tasks_per_node in the config file" |
---|
| 960 | locat=tasks_per_node; (( iec = 0 )); exit |
---|
| 961 | fi |
---|
| 962 | |
---|
| 963 | if (( cores < tasks_per_node )) |
---|
| 964 | then |
---|
| 965 | printf "\n" |
---|
| 966 | printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)" |
---|
| 967 | printf "\n given values: -T $tasks_per_node -X $cores" |
---|
| 968 | locat=tasks_per_node; (( iec = 0 )); exit |
---|
| 969 | fi |
---|
| 970 | |
---|
| 971 | (( nodes = cores / ( tasks_per_node * threads_per_task ) )) |
---|
| 972 | (( mpi_tasks = cores / threads_per_task )) |
---|
| 973 | [[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 )) |
---|
| 974 | (( ii = cores / tasks_per_node )) |
---|
| 975 | (( remaining_cores = cores - ii * tasks_per_node )) |
---|
| 976 | if (( remaining_cores > 0 )) |
---|
| 977 | then |
---|
| 978 | printf "\n" |
---|
| 979 | printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral" |
---|
| 980 | printf "\n divisor of the total number of cores (option \"-X\")" |
---|
| 981 | printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\"" |
---|
| 982 | printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks" |
---|
| 983 | (( nodes = nodes + 1 )) |
---|
| 984 | fi |
---|
| 985 | |
---|
| 986 | # SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW) |
---|
| 987 | if [[ "$tasks_per_node" != "" ]] |
---|
| 988 | then |
---|
| 989 | TOPT="-T $tasks_per_node" |
---|
| 990 | fi |
---|
| 991 | |
---|
| 992 | fi |
---|
| 993 | |
---|
| 994 | |
---|
| 995 | # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS |
---|
| 996 | if [[ "$maximum_parallel_io_streams" = "" ]] |
---|
| 997 | then |
---|
| 998 | maximum_parallel_io_streams=$cores |
---|
| 999 | fi |
---|
| 1000 | |
---|
| 1001 | |
---|
| 1002 | # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT |
---|
| 1003 | if [[ "$scp_port" != "" ]] |
---|
| 1004 | then |
---|
| 1005 | PORTOPT="-P $scp_port" |
---|
| 1006 | SSH_PORTOPT="-p $scp_port" |
---|
| 1007 | fi |
---|
| 1008 | |
---|
| 1009 | |
---|
| 1010 | # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE |
---|
| 1011 | # CONFIG-FILE |
---|
| 1012 | if [[ "$ssh_key" != "" ]] |
---|
| 1013 | then |
---|
| 1014 | ssh_key="-i $HOME/.ssh/$ssh_key" |
---|
| 1015 | fi |
---|
| 1016 | |
---|
| 1017 | |
---|
| 1018 | # SET QUEUE, IF NOT GIVEN |
---|
| 1019 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1020 | then |
---|
| 1021 | |
---|
| 1022 | if [[ $queue = none && "$defaultqueue" = "" ]] |
---|
| 1023 | then |
---|
| 1024 | printf "\n" |
---|
| 1025 | printf "\n +++ no default queue given in configuration file and no queue" |
---|
| 1026 | printf "\n given with option -q" |
---|
| 1027 | fi |
---|
| 1028 | if [[ $queue = none ]] |
---|
| 1029 | then |
---|
| 1030 | queue=$defaultqueue |
---|
| 1031 | fi |
---|
| 1032 | |
---|
| 1033 | fi |
---|
| 1034 | |
---|
| 1035 | |
---|
| 1036 | # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH |
---|
| 1037 | # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST) |
---|
| 1038 | (( i = 0 )) |
---|
[2610] | 1039 | (( nr_of_input_files = 0 )) |
---|
[2380] | 1040 | while (( i < iin )) |
---|
| 1041 | do |
---|
| 1042 | (( i = i + 1 )) |
---|
| 1043 | |
---|
| 1044 | # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE |
---|
| 1045 | # FILE IDENTIFIER IS NOT PART OF THE FILENAME)) |
---|
[2610] | 1046 | if [[ "${actionin_pre[$i]}" = di ]] |
---|
[2380] | 1047 | then |
---|
[2610] | 1048 | eval filename=${pathin_pre[$i]}/${endin_pre[$i]} |
---|
[2380] | 1049 | else |
---|
[2610] | 1050 | eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]} |
---|
[2380] | 1051 | fi |
---|
| 1052 | |
---|
[2610] | 1053 | |
---|
[2380] | 1054 | # CHECK IF FILE EXISTS |
---|
| 1055 | if ! ls $filename* 1>/dev/null 2>&1 |
---|
| 1056 | then |
---|
| 1057 | |
---|
[2669] | 1058 | # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST. |
---|
| 1059 | if [[ "${optin_pre[$i]}" != "yes" ]] |
---|
[2380] | 1060 | then |
---|
| 1061 | printf "\n\n +++ INPUT-file: " |
---|
[2610] | 1062 | if [[ "${extin_pre[$i]}" = "" || "${extin_pre[$i]}" = " " ]] |
---|
[2380] | 1063 | then |
---|
| 1064 | printf "\n $filename" |
---|
| 1065 | else |
---|
[2610] | 1066 | printf "\n $filename.${extin_pre[$i]}" |
---|
[2380] | 1067 | fi |
---|
| 1068 | printf "\n does not exist\n" |
---|
| 1069 | locat=input; exit |
---|
| 1070 | else |
---|
[2610] | 1071 | (( nr_of_input_files = nr_of_input_files + 1 )) |
---|
| 1072 | localin[$nr_of_input_files]="${localin_pre[$i]}" |
---|
[2669] | 1073 | optin[$nr_of_input_files]="${optin_pre[$i]}" |
---|
| 1074 | actionin[$nr_of_input_files]="unavailable" |
---|
[2610] | 1075 | pathin[$nr_of_input_files]="${pathin_pre[$i]}" |
---|
| 1076 | endin[$nr_of_input_files]="${endin_pre[$i]}" |
---|
| 1077 | extin[$nr_of_input_files]="${extin_pre[$i]}" |
---|
[2380] | 1078 | fi |
---|
[2605] | 1079 | |
---|
[2380] | 1080 | else |
---|
| 1081 | |
---|
[2610] | 1082 | # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND |
---|
| 1083 | # CREATE A LIST FOR THE DETECTED BASENAME ENDINGS |
---|
| 1084 | if [[ "${multin[$i]}" = true ]] |
---|
| 1085 | then |
---|
| 1086 | # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES |
---|
| 1087 | ls -1 -d ${filename} > filelist 2>/dev/null |
---|
| 1088 | ls -1 -d ${filename}.* >> filelist 2>/dev/null |
---|
| 1089 | ls -1 -d ${filename}_* >> filelist 2>/dev/null |
---|
[2380] | 1090 | |
---|
[2610] | 1091 | endings="" |
---|
| 1092 | while read line |
---|
| 1093 | do |
---|
| 1094 | # filename without path (i.e. after the last "/") |
---|
| 1095 | basefilename=$(basename ${line}) |
---|
[2380] | 1096 | |
---|
[2610] | 1097 | # check if there is an extension and remove it |
---|
| 1098 | ext=${basefilename##*.} |
---|
| 1099 | if [[ "$ext" = "${extin_pre[$i]}" ]] |
---|
| 1100 | then |
---|
| 1101 | basefilename=${basefilename%.*} |
---|
| 1102 | fi |
---|
[2380] | 1103 | |
---|
[2610] | 1104 | # check for an existing cycle number and remove it |
---|
| 1105 | cycle=${basefilename##*.} |
---|
| 1106 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
| 1107 | then |
---|
| 1108 | basefilename=${basefilename%.*} |
---|
| 1109 | fi |
---|
[2600] | 1110 | |
---|
[2610] | 1111 | # remove the fname from the beginning |
---|
| 1112 | length_fname=${#fname} |
---|
| 1113 | ending=${basefilename:${length_fname}} |
---|
| 1114 | |
---|
| 1115 | # remove the ending given in the .iofiles from the beginning |
---|
| 1116 | endingstring="${endin_pre[$i]}" |
---|
| 1117 | length_ending=${#endingstring} |
---|
| 1118 | ending=${ending:${length_ending}} |
---|
| 1119 | |
---|
| 1120 | if [[ "$ending" = "" ]] |
---|
[2600] | 1121 | then |
---|
[2610] | 1122 | # standard ending as given in the .iofiles |
---|
| 1123 | if [[ $(echo $endings | grep -c DEFAULT) = 0 ]] |
---|
| 1124 | then |
---|
| 1125 | endings="$endings DEFAULT" |
---|
| 1126 | fi |
---|
[2600] | 1127 | else |
---|
[2610] | 1128 | # ending must start with "_", otherwise its a different file |
---|
| 1129 | if [[ "${ending:0:1}" = "_" ]] |
---|
| 1130 | then |
---|
| 1131 | if [[ $(echo $endings | grep -c "$ending") = 0 ]] |
---|
| 1132 | then |
---|
| 1133 | endings="$endings $ending" |
---|
| 1134 | fi |
---|
| 1135 | fi |
---|
[2600] | 1136 | fi |
---|
[2610] | 1137 | |
---|
| 1138 | done <filelist |
---|
[2380] | 1139 | |
---|
[2610] | 1140 | rm filelist |
---|
[2380] | 1141 | |
---|
[2600] | 1142 | else |
---|
[2610] | 1143 | |
---|
| 1144 | # SINGLE NAME |
---|
| 1145 | endings=DEFAULT |
---|
| 1146 | |
---|
[2600] | 1147 | fi |
---|
| 1148 | |
---|
[2610] | 1149 | # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST |
---|
| 1150 | for ending in $endings |
---|
| 1151 | do |
---|
| 1152 | |
---|
| 1153 | # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED |
---|
| 1154 | if [[ $ending = DEFAULT ]] |
---|
[2380] | 1155 | then |
---|
[2610] | 1156 | ending="" |
---|
| 1157 | fi |
---|
| 1158 | |
---|
| 1159 | # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!) |
---|
| 1160 | (( nr_of_input_files = nr_of_input_files + 1 )) |
---|
| 1161 | localin[$nr_of_input_files]="${localin_pre[$i]}"$ending |
---|
[2669] | 1162 | optin[$nr_of_input_files]="${optin_pre[$i]}" |
---|
[2610] | 1163 | actionin[$nr_of_input_files]="${actionin_pre[$i]}" |
---|
| 1164 | pathin[$nr_of_input_files]="${pathin_pre[$i]}" |
---|
| 1165 | endin[$nr_of_input_files]="${endin_pre[$i]}"$ending |
---|
| 1166 | extin[$nr_of_input_files]="${extin_pre[$i]}" |
---|
| 1167 | |
---|
| 1168 | |
---|
| 1169 | # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE |
---|
| 1170 | # FILE IDENTIFIER IS NOT PART OF THE FILENAME)) |
---|
| 1171 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
| 1172 | then |
---|
| 1173 | eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]} |
---|
[2380] | 1174 | else |
---|
[2610] | 1175 | eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]} |
---|
[2380] | 1176 | fi |
---|
[2610] | 1177 | |
---|
| 1178 | # DETERMINE THE FILE'S CYCLE NUMBER |
---|
| 1179 | (( maxcycle = 0 )) |
---|
| 1180 | ls -1 -d $filename > filelist 2>/dev/null |
---|
| 1181 | ls -1 -d $filename.* >> filelist 2>/dev/null |
---|
| 1182 | while read line |
---|
| 1183 | do |
---|
| 1184 | # filename without path (i.e. after the last "/") |
---|
| 1185 | basefilename=$(basename ${line}) |
---|
| 1186 | |
---|
| 1187 | # check if there is an extension |
---|
| 1188 | extension=${basefilename##*.} |
---|
| 1189 | if [[ "$extension" = "${extin[$nr_of_input_files]}" ]] |
---|
| 1190 | then |
---|
| 1191 | basefilename=${basefilename%.*} |
---|
| 1192 | fi |
---|
| 1193 | |
---|
| 1194 | # check for an existing cycle number |
---|
| 1195 | cycle=${basefilename##*.} |
---|
| 1196 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
| 1197 | then |
---|
[2669] | 1198 | # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS |
---|
| 1199 | # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 |
---|
| 1200 | (( icycle = $((10#$cycle)) )) |
---|
[2610] | 1201 | else |
---|
| 1202 | (( icycle = 0 )) |
---|
| 1203 | fi |
---|
| 1204 | |
---|
| 1205 | if (( icycle > maxcycle )) |
---|
| 1206 | then |
---|
| 1207 | (( maxcycle = icycle )) |
---|
| 1208 | |
---|
| 1209 | # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS |
---|
| 1210 | # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS |
---|
| 1211 | if [[ $(echo $cycle | cut -c1) = 0 ]] |
---|
| 1212 | then |
---|
| 1213 | leading_zero=true |
---|
| 1214 | else |
---|
| 1215 | leading_zero=false |
---|
| 1216 | fi |
---|
| 1217 | fi |
---|
| 1218 | |
---|
| 1219 | done <filelist |
---|
| 1220 | rm filelist |
---|
| 1221 | |
---|
| 1222 | # MAKE CYCLE NUMBER THREE DIGITS WIDE |
---|
| 1223 | if [[ $leading_zero = true ]] |
---|
[2380] | 1224 | then |
---|
[2610] | 1225 | cyclestring=`printf "%03d" $maxcycle` |
---|
| 1226 | else |
---|
| 1227 | cyclestring=$maxcycle |
---|
[2380] | 1228 | fi |
---|
[2610] | 1229 | |
---|
| 1230 | # APPEND CYCLE NUMBER TO FILENAME |
---|
| 1231 | if (( maxcycle > 0 )) |
---|
[2380] | 1232 | then |
---|
[2610] | 1233 | if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]] |
---|
| 1234 | then |
---|
| 1235 | filename=${filename}.$cyclestring.${extin[$nr_of_input_files]} |
---|
| 1236 | else |
---|
| 1237 | filename=${filename}.$cyclestring |
---|
| 1238 | fi |
---|
[2380] | 1239 | else |
---|
[2610] | 1240 | if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]] |
---|
| 1241 | then |
---|
| 1242 | filename=${filename}.${extin[$nr_of_input_files]} |
---|
| 1243 | fi |
---|
[2380] | 1244 | fi |
---|
[2610] | 1245 | |
---|
| 1246 | # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER, |
---|
| 1247 | # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE) |
---|
| 1248 | absnamein[$nr_of_input_files]=$filename |
---|
| 1249 | if (( maxcycle > 0 )) |
---|
[2380] | 1250 | then |
---|
[2610] | 1251 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
| 1252 | then |
---|
| 1253 | frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring |
---|
| 1254 | else |
---|
| 1255 | frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring |
---|
| 1256 | fi |
---|
[2380] | 1257 | else |
---|
[2610] | 1258 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
| 1259 | then |
---|
| 1260 | frelin[$nr_of_input_files]=${endin[$nr_of_input_files]} |
---|
| 1261 | else |
---|
| 1262 | frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]} |
---|
| 1263 | fi |
---|
[2380] | 1264 | fi |
---|
| 1265 | |
---|
[2610] | 1266 | done |
---|
| 1267 | |
---|
[2380] | 1268 | fi |
---|
[2610] | 1269 | |
---|
[2380] | 1270 | done |
---|
| 1271 | |
---|
[2610] | 1272 | |
---|
[2380] | 1273 | # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~), |
---|
| 1274 | # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST), |
---|
| 1275 | # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED |
---|
[2610] | 1276 | # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO |
---|
[2380] | 1277 | # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE |
---|
| 1278 | # REMOTE HOST) |
---|
| 1279 | (( i = 0 )) |
---|
| 1280 | while (( i < iout )) |
---|
| 1281 | do |
---|
| 1282 | (( i = i + 1 )) |
---|
[2610] | 1283 | if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]] |
---|
[2380] | 1284 | then |
---|
[2610] | 1285 | if [[ "${actionout_pre[$i]}" = tr ]] |
---|
[2380] | 1286 | then |
---|
[2610] | 1287 | actionout_pre[$i]="" |
---|
| 1288 | elif [[ "${actionout_pre[$i]}" = trpe ]] |
---|
[2380] | 1289 | then |
---|
[2610] | 1290 | actionout_pre[$i]=pe |
---|
| 1291 | elif [[ "${actionout_pre[$i]}" = tra ]] |
---|
[2380] | 1292 | then |
---|
[2610] | 1293 | actionout_pre[$i]=a |
---|
[2380] | 1294 | fi |
---|
| 1295 | (( maxcycle = 0 )) |
---|
[2610] | 1296 | eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]} |
---|
| 1297 | eval catalogname=${pathout_pre[$i]} |
---|
[2380] | 1298 | if ! ls $filename* 1>/dev/null 2>&1 |
---|
| 1299 | then |
---|
| 1300 | |
---|
| 1301 | # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED |
---|
| 1302 | if cat /dev/null > $filename |
---|
| 1303 | then |
---|
| 1304 | rm $filename |
---|
| 1305 | else |
---|
| 1306 | |
---|
| 1307 | # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS |
---|
| 1308 | # IF IT DOES NOT EXIST, TRY TO CREATE IT |
---|
| 1309 | if [[ ! -d $catalogname ]] |
---|
| 1310 | then |
---|
| 1311 | if mkdir -p $catalogname |
---|
| 1312 | then |
---|
| 1313 | printf "\n\n *** directory:" |
---|
| 1314 | printf "\n $catalogname" |
---|
| 1315 | printf "\n was created\n" |
---|
| 1316 | else |
---|
| 1317 | printf "\n\n +++ OUTPUT-file:" |
---|
| 1318 | printf "\n $filename" |
---|
| 1319 | printf "\n cannot be created, because directory does not exist" |
---|
| 1320 | printf "\n and cannot be created either" |
---|
| 1321 | printf "\n" |
---|
| 1322 | locat=output ; exit |
---|
| 1323 | fi 2>/dev/null |
---|
| 1324 | else |
---|
| 1325 | printf "\n\n +++ OUTPUT-file:" |
---|
| 1326 | printf "\n $filename" |
---|
| 1327 | printf "\n cannot be created, although directory exists" |
---|
| 1328 | printf "\n" |
---|
| 1329 | locat=output ; exit |
---|
| 1330 | fi |
---|
| 1331 | fi 2>/dev/null |
---|
| 1332 | |
---|
| 1333 | fi |
---|
| 1334 | |
---|
| 1335 | fi |
---|
| 1336 | done |
---|
| 1337 | |
---|
| 1338 | |
---|
| 1339 | # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY |
---|
| 1340 | if [[ $running_in_batch_mode = false ]] |
---|
| 1341 | then |
---|
| 1342 | run_id=$RANDOM |
---|
| 1343 | job_id=${fname}.$run_id |
---|
| 1344 | |
---|
[2566] | 1345 | tempdir=$fast_io_catalog/$job_id |
---|
[2380] | 1346 | fi |
---|
| 1347 | |
---|
| 1348 | |
---|
| 1349 | # CHECK SETTINGS REQUIRED FOR BATCH JOBS |
---|
| 1350 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1351 | then |
---|
| 1352 | |
---|
| 1353 | # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE |
---|
| 1354 | if [[ $ibd = 0 ]] |
---|
| 1355 | then |
---|
| 1356 | printf "\n" |
---|
| 1357 | printf "\n +++ no batch directives found in configuration file" |
---|
| 1358 | locat=config_file_batch_directives; (( iec = 0 )); exit |
---|
| 1359 | fi |
---|
| 1360 | |
---|
| 1361 | # CHECK IF CPUTIME IS GIVEN FOR JOB |
---|
| 1362 | done=false |
---|
[2384] | 1363 | cputime=$cpumax |
---|
[2380] | 1364 | while [[ $done = false ]] |
---|
| 1365 | do |
---|
[2384] | 1366 | if (( cputime == 0 )) |
---|
[2380] | 1367 | then |
---|
| 1368 | printf "\n +++ cpu-time is undefined" |
---|
| 1369 | printf "\n >>> Please type CPU-time in seconds as INTEGER:" |
---|
| 1370 | printf "\n >>> " |
---|
[2384] | 1371 | read cputime 1>/dev/null 2>&1 |
---|
[2380] | 1372 | else |
---|
| 1373 | done=true |
---|
| 1374 | fi |
---|
| 1375 | done |
---|
[2420] | 1376 | cpumax=$cputime |
---|
[2380] | 1377 | |
---|
| 1378 | # CHECK THE MEMORY DEMAND |
---|
| 1379 | done=false |
---|
| 1380 | while [[ $done = false ]] |
---|
| 1381 | do |
---|
| 1382 | if (( memory == 0 )) |
---|
| 1383 | then |
---|
| 1384 | printf "\n +++ memory demand is undefined" |
---|
| 1385 | printf "\n >>> Please type memory in MByte per process as INTEGER:" |
---|
| 1386 | printf "\n >>> " |
---|
| 1387 | read memory 1>/dev/null 2>&1 |
---|
| 1388 | else |
---|
| 1389 | done=true |
---|
| 1390 | fi |
---|
| 1391 | done |
---|
| 1392 | |
---|
| 1393 | # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN |
---|
| 1394 | if [[ $create_remote_batch_job = true && -z $remote_username ]] |
---|
| 1395 | then |
---|
| 1396 | while [[ -z $remote_username ]] |
---|
| 1397 | do |
---|
[2420] | 1398 | printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined" |
---|
[2380] | 1399 | printf "\n >>> Please type username:" |
---|
| 1400 | printf "\n >>> " |
---|
| 1401 | read remote_username |
---|
| 1402 | done |
---|
| 1403 | fi |
---|
| 1404 | |
---|
| 1405 | else |
---|
| 1406 | |
---|
[2420] | 1407 | if [[ $running_in_batch_mode = false ]] |
---|
| 1408 | then |
---|
| 1409 | cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS |
---|
| 1410 | cpumax=$cputime |
---|
| 1411 | else |
---|
| 1412 | cputime=$cpumax |
---|
| 1413 | fi |
---|
[2380] | 1414 | |
---|
| 1415 | fi |
---|
| 1416 | |
---|
| 1417 | |
---|
| 1418 | # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES |
---|
| 1419 | (( cpu_hours = cputime / 3600 )) |
---|
| 1420 | (( resttime = cputime - cpu_hours * 3600 )) |
---|
| 1421 | (( cpu_minutes = resttime / 60 )) |
---|
| 1422 | (( cpu_seconds = resttime - cpu_minutes * 60 )) |
---|
| 1423 | timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds} |
---|
| 1424 | |
---|
| 1425 | |
---|
| 1426 | # OUTPUT OF THE PALMRUN-HEADER |
---|
| 1427 | calltime=$(date) |
---|
| 1428 | printf "\n" |
---|
| 1429 | printf "#------------------------------------------------------------------------# \n" |
---|
| 1430 | printf "| %-35s%35s | \n" "$version" "$calltime" |
---|
| 1431 | printf "| | \n" |
---|
| 1432 | column1="called on:"; column2=$(hostname) |
---|
| 1433 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1434 | if [[ $create_remote_batch_job = true ]] |
---|
| 1435 | then |
---|
[2506] | 1436 | column1="execution on:"; column2="$host_configuration (username: $remote_username)" |
---|
[2380] | 1437 | else |
---|
| 1438 | if [[ $running_on_remote = true ]] |
---|
| 1439 | then |
---|
[2506] | 1440 | column1="execution on:"; column2="$host_configuration (IP:$remote_ip)" |
---|
[2380] | 1441 | else |
---|
[2506] | 1442 | column1="execution on:"; column2="$host_configuration (IP:$local_ip)" |
---|
[2380] | 1443 | fi |
---|
| 1444 | fi |
---|
| 1445 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1446 | |
---|
| 1447 | column1="running in:" |
---|
| 1448 | if [[ $running_in_batch_mode = true ]] |
---|
| 1449 | then |
---|
| 1450 | column2="batch job mode" |
---|
| 1451 | else |
---|
| 1452 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1453 | then |
---|
| 1454 | column2="job creation mode" |
---|
| 1455 | else |
---|
| 1456 | column2="interactive run mode" |
---|
| 1457 | fi |
---|
| 1458 | fi |
---|
| 1459 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1460 | |
---|
[2479] | 1461 | if [[ $running_in_batch_mode = true || $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1462 | then |
---|
[2480] | 1463 | if [[ "$project_account" != "" ]] |
---|
[2479] | 1464 | then |
---|
| 1465 | column1="project account number:" |
---|
| 1466 | column2="$project_account" |
---|
| 1467 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1468 | fi |
---|
| 1469 | fi |
---|
| 1470 | |
---|
[2380] | 1471 | if [[ -n $cores ]] |
---|
| 1472 | then |
---|
| 1473 | if [[ $run_coupled_model = false ]] |
---|
| 1474 | then |
---|
| 1475 | column1="number of cores:"; column2=$cores |
---|
| 1476 | else |
---|
| 1477 | column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)" |
---|
| 1478 | fi |
---|
| 1479 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1480 | fi |
---|
| 1481 | if [[ -n $tasks_per_node ]] |
---|
| 1482 | then |
---|
| 1483 | column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)" |
---|
| 1484 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1485 | if (( remaining_cores > 0 )) |
---|
| 1486 | then |
---|
| 1487 | column1=" "; column2="one of the nodes only filled with $remaining_cores tasks" |
---|
| 1488 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1489 | fi |
---|
| 1490 | fi |
---|
| 1491 | if [[ $maximum_parallel_io_streams != $cores ]] |
---|
| 1492 | then |
---|
| 1493 | column1="max par io streams:"; column2="$maximum_parallel_io_streams" |
---|
| 1494 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1495 | fi |
---|
| 1496 | if [[ $use_openmp = true ]] |
---|
| 1497 | then |
---|
| 1498 | column1="threads per task:"; column2="$threads_per_task" |
---|
| 1499 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1500 | fi |
---|
[2384] | 1501 | if [[ $create_batch_job = true || $create_remote_batch_job = true || $running_in_batch_mode = true ]] |
---|
| 1502 | then |
---|
[2506] | 1503 | column1="memory demand / PE":; column2="$memory MB" |
---|
| 1504 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
[2384] | 1505 | column1="job cpu time (h:m:s):"; column2="$timestring" |
---|
| 1506 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1507 | fi |
---|
[2380] | 1508 | printf "| | \n" |
---|
| 1509 | if [[ "$source_list" != "" ]] |
---|
| 1510 | then |
---|
| 1511 | if [[ "$make_options" != "" ]] |
---|
| 1512 | then |
---|
| 1513 | column1="make options:"; column2=$(echo "$make_options" | cut -c-45) |
---|
| 1514 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1515 | line=$(echo "$make_options" | cut -c46-) |
---|
| 1516 | while [[ "$line" != "" ]] |
---|
| 1517 | do |
---|
| 1518 | column1="" |
---|
| 1519 | column2=$(echo "$line" | cut -c-45) |
---|
| 1520 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1521 | line=$(echo "$line" | cut -c46-) |
---|
| 1522 | done |
---|
| 1523 | fi |
---|
| 1524 | fi |
---|
| 1525 | |
---|
| 1526 | column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45) |
---|
| 1527 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1528 | line=$(echo "$cpp_options" | cut -c46-) |
---|
| 1529 | while [[ "$line" != "" ]] |
---|
| 1530 | do |
---|
| 1531 | column1="" |
---|
| 1532 | column2=$(echo "$line" | cut -c-45) |
---|
| 1533 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1534 | line=$(echo "$line" | cut -c46-) |
---|
| 1535 | done |
---|
| 1536 | |
---|
| 1537 | column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45) |
---|
| 1538 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1539 | line=$(echo "$compiler_options" | cut -c46-) |
---|
| 1540 | while [[ "$line" != "" ]] |
---|
| 1541 | do |
---|
| 1542 | column1="" |
---|
| 1543 | column2=$(echo "$line" | cut -c-45) |
---|
| 1544 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1545 | line=$(echo "$line" | cut -c46-) |
---|
| 1546 | done |
---|
| 1547 | |
---|
[2388] | 1548 | column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45) |
---|
[2380] | 1549 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
[2388] | 1550 | line=$(echo "$linker_options" | cut -c46-) |
---|
[2380] | 1551 | while [[ "$line" != "" ]] |
---|
| 1552 | do |
---|
| 1553 | column1="" |
---|
| 1554 | column2=$(echo "$line" | cut -c-45) |
---|
| 1555 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1556 | line=$(echo "$line" | cut -c46-) |
---|
| 1557 | done |
---|
| 1558 | |
---|
| 1559 | if [[ "$login_init_cmd" != "" ]] |
---|
| 1560 | then |
---|
| 1561 | column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45) |
---|
| 1562 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1563 | line=$(echo "$login_init_cmd" | cut -c46-) |
---|
| 1564 | while [[ "$line" != "" ]] |
---|
| 1565 | do |
---|
| 1566 | column1="" |
---|
| 1567 | column2=$(echo "$line" | cut -c-45) |
---|
| 1568 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1569 | line=$(echo "$line" | cut -c46-) |
---|
| 1570 | done |
---|
| 1571 | fi |
---|
| 1572 | |
---|
| 1573 | if [[ "$module_commands" != "" ]] |
---|
| 1574 | then |
---|
| 1575 | column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45) |
---|
| 1576 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1577 | line=$(echo "$module_commands" | cut -c46-) |
---|
| 1578 | while [[ "$line" != "" ]] |
---|
| 1579 | do |
---|
| 1580 | column1="" |
---|
| 1581 | column2=$(echo "$line" | cut -c-45) |
---|
| 1582 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1583 | line=$(echo "$line" | cut -c46-) |
---|
| 1584 | done |
---|
| 1585 | fi |
---|
| 1586 | printf "| | \n" |
---|
| 1587 | column1="base name of files:"; column2=$fname |
---|
| 1588 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1589 | column1="activation string list:"; column2=$(echo $activation_string_list) |
---|
| 1590 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1591 | |
---|
| 1592 | if [[ "$ocean_file_appendix" = true ]] |
---|
| 1593 | then |
---|
| 1594 | printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " " |
---|
| 1595 | fi |
---|
| 1596 | |
---|
| 1597 | if [[ "$source_list" != "" ]] |
---|
| 1598 | then |
---|
| 1599 | printf "| | \n" |
---|
| 1600 | printf "| Files to be compiled: | \n" |
---|
| 1601 | line=$source_list |
---|
| 1602 | while [[ "$line" != "" ]] |
---|
| 1603 | do |
---|
| 1604 | linestart=$(echo $line | cut -c-70) |
---|
| 1605 | printf "| %-70s | \n" "$linestart" |
---|
| 1606 | line=$(echo "$line" | cut -c71-) |
---|
| 1607 | done |
---|
| 1608 | fi |
---|
| 1609 | printf "#------------------------------------------------------------------------#" |
---|
| 1610 | |
---|
| 1611 | |
---|
| 1612 | |
---|
| 1613 | # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK |
---|
| 1614 | if [[ $do_trace = true ]] |
---|
| 1615 | then |
---|
| 1616 | (( i = 0 )) |
---|
[2610] | 1617 | while (( i < nr_of_input_files )) |
---|
[2380] | 1618 | do |
---|
| 1619 | (( i = i + 1 )) |
---|
| 1620 | if (( i == 1 )) |
---|
| 1621 | then |
---|
| 1622 | printf "\n\n >>> INPUT-file assignments:\n" |
---|
| 1623 | fi |
---|
| 1624 | printf "\n ${localin[$i]} : ${absnamein[$i]}" |
---|
| 1625 | done |
---|
| 1626 | (( i = 0 )) |
---|
| 1627 | while (( i < iout )) |
---|
| 1628 | do |
---|
| 1629 | (( i = i + 1 )) |
---|
| 1630 | if (( i == 1 )) |
---|
| 1631 | then |
---|
| 1632 | printf "\n\n >>> OUTPUT-file assignments:\n" |
---|
| 1633 | fi |
---|
| 1634 | printf "\n ${localout[$i]} : ${pathout[$i]}" |
---|
| 1635 | done |
---|
| 1636 | (( i = 0 )) |
---|
| 1637 | while (( i < iic )) |
---|
| 1638 | do |
---|
| 1639 | (( i = i + 1 )) |
---|
| 1640 | if (( i == 1 )) |
---|
| 1641 | then |
---|
| 1642 | printf "\n\n >>> INPUT-commands:\n" |
---|
| 1643 | fi |
---|
| 1644 | printf "\n ${in_command[$i]}" |
---|
| 1645 | done |
---|
| 1646 | (( i = 0 )) |
---|
| 1647 | while (( i < ioc )) |
---|
| 1648 | do |
---|
| 1649 | (( i = i + 1 )) |
---|
| 1650 | if (( i == 1 )) |
---|
| 1651 | then |
---|
| 1652 | printf "\n\n >>> OUTPUT-commands:\n" |
---|
| 1653 | fi |
---|
| 1654 | printf "\n ${out_command[$i]}" |
---|
| 1655 | done |
---|
| 1656 | fi |
---|
| 1657 | |
---|
| 1658 | # QUERY FOR CONTINUE |
---|
| 1659 | if [[ $silent = false && $running_in_batch_mode = false ]] |
---|
| 1660 | then |
---|
| 1661 | antwort=dummy |
---|
| 1662 | printf "\n\n" |
---|
| 1663 | printf " >>> everything o.k. (y/n) ? " |
---|
| 1664 | while read antwort |
---|
| 1665 | do |
---|
| 1666 | if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]] |
---|
| 1667 | then |
---|
| 1668 | printf " >>> everything o.k. (y/n) ? " |
---|
| 1669 | else |
---|
| 1670 | break |
---|
| 1671 | fi |
---|
| 1672 | done |
---|
| 1673 | if [[ $antwort = n || $antwort = N ]] |
---|
| 1674 | then |
---|
| 1675 | locat=user_abort; (( iec = 0 )); exit |
---|
| 1676 | fi |
---|
| 1677 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1678 | then |
---|
[2566] | 1679 | printf "\n *** batch-job will be created and submitted" |
---|
[2380] | 1680 | else |
---|
[2566] | 1681 | printf "\n *** PALMRUN will now continue to execute on this machine" |
---|
[2380] | 1682 | fi |
---|
| 1683 | fi |
---|
| 1684 | |
---|
| 1685 | |
---|
| 1686 | |
---|
| 1687 | # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE |
---|
| 1688 | if [[ $restart_run = false && $running_in_batch_mode = false ]] |
---|
| 1689 | then |
---|
| 1690 | |
---|
| 1691 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1692 | then |
---|
[2566] | 1693 | printf "\n\n *** creating executable and other sources for the remote host\n" |
---|
[2380] | 1694 | else |
---|
[2566] | 1695 | printf "\n\n *** creating executable and other sources for the local host\n" |
---|
[2380] | 1696 | fi |
---|
| 1697 | |
---|
[2422] | 1698 | # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF |
---|
| 1699 | # IT SHALL BE CREATED |
---|
| 1700 | ask_for_make_depository=false |
---|
| 1701 | if [[ $create_remote_batch_job = true ]] |
---|
| 1702 | then |
---|
| 1703 | |
---|
| 1704 | line=`grep %base_directory $config_file` |
---|
[2506] | 1705 | make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration} |
---|
| 1706 | echo "[[ ! -d ${make_depository} ]] && echo depository not found" | ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 | tee ${host_configuration}_last_make_protokoll |
---|
[2422] | 1707 | |
---|
[2506] | 1708 | if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]] |
---|
[2422] | 1709 | then |
---|
| 1710 | printf "\n\n +++ make depository \"${make_depository}\"" |
---|
| 1711 | printf "\n on remote host not found!" |
---|
| 1712 | ask_for_make_depository=true |
---|
| 1713 | fi |
---|
[2506] | 1714 | rm ${host_configuration}_last_make_protokoll |
---|
[2422] | 1715 | |
---|
| 1716 | else |
---|
| 1717 | |
---|
| 1718 | # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST |
---|
[2506] | 1719 | make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration} |
---|
[2422] | 1720 | if [[ ! -d ${make_depository} ]] |
---|
| 1721 | then |
---|
| 1722 | printf "\n\n +++ make depository \"${make_depository}\"" |
---|
| 1723 | printf "\n on local host not found!" |
---|
| 1724 | ask_for_make_depository=true |
---|
| 1725 | fi |
---|
| 1726 | |
---|
| 1727 | fi |
---|
| 1728 | |
---|
| 1729 | if [[ $ask_for_make_depository = true ]] |
---|
| 1730 | then |
---|
| 1731 | |
---|
| 1732 | antwort=dummy |
---|
| 1733 | printf "\n\n" |
---|
| 1734 | printf " >>> Create a new one (y/n) ? " |
---|
| 1735 | while read antwort |
---|
| 1736 | do |
---|
| 1737 | if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]] |
---|
| 1738 | then |
---|
| 1739 | printf " >>> Create a new one (y/n) ? " |
---|
| 1740 | else |
---|
| 1741 | break |
---|
| 1742 | fi |
---|
| 1743 | done |
---|
| 1744 | if [[ $antwort = n || $antwort = N ]] |
---|
| 1745 | then |
---|
| 1746 | locat=user_abort; (( iec = 0 )); exit |
---|
| 1747 | fi |
---|
| 1748 | |
---|
[2566] | 1749 | if [[ $do_trace = true ]] |
---|
| 1750 | then |
---|
| 1751 | palmbuild -h $host_configuration |
---|
| 1752 | else |
---|
| 1753 | palmbuild -v -h $host_configuration |
---|
| 1754 | fi |
---|
[2422] | 1755 | |
---|
| 1756 | if [[ $? != 0 ]] |
---|
| 1757 | then |
---|
| 1758 | |
---|
| 1759 | # ABORT IN CASE OF COMPILATION PROBLEMS |
---|
| 1760 | printf "\n +++ error while compiling for the MAKE_DEPOSITORY" |
---|
| 1761 | locat=make_depository |
---|
| 1762 | exit |
---|
| 1763 | else |
---|
| 1764 | echo " *** now continue with creating executable and other sources" |
---|
| 1765 | fi |
---|
| 1766 | |
---|
| 1767 | fi |
---|
| 1768 | |
---|
[2566] | 1769 | # NOW CREATE THE SOURCES_FOR_RUN FOLDER |
---|
[2506] | 1770 | palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname |
---|
[2380] | 1771 | |
---|
| 1772 | if [[ $? != 0 ]] |
---|
| 1773 | then |
---|
| 1774 | |
---|
| 1775 | # ABORT IN CASE OF COMPILATION PROBLEMS |
---|
| 1776 | printf "\n +++ error while creating executable and/or other sources" |
---|
| 1777 | locat=execution |
---|
[2506] | 1778 | rm -rf $sources_for_run_catalog |
---|
[2380] | 1779 | exit |
---|
| 1780 | |
---|
| 1781 | else |
---|
| 1782 | |
---|
[2566] | 1783 | printf " *** executable and other sources created\n" |
---|
[2506] | 1784 | rm -rf $sources_for_run_catalog |
---|
[2380] | 1785 | |
---|
| 1786 | fi |
---|
| 1787 | |
---|
| 1788 | fi |
---|
| 1789 | |
---|
| 1790 | |
---|
[2669] | 1791 | # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT |
---|
| 1792 | # WILL BE COPIED TO THE REMOTE HOST |
---|
[2605] | 1793 | if [[ $create_remote_batch_job = true ]] |
---|
| 1794 | then |
---|
| 1795 | (( i = 0 )) |
---|
[2610] | 1796 | while (( i < nr_of_input_files )) |
---|
[2605] | 1797 | do |
---|
| 1798 | (( i = i + 1 )) |
---|
[2669] | 1799 | if [[ "${actionin[$i]}" = tr ]] |
---|
[2605] | 1800 | then |
---|
| 1801 | eval inputfile=${pathin[$i]}/${frelin[$i]} |
---|
| 1802 | scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]} |
---|
| 1803 | fi |
---|
| 1804 | done |
---|
| 1805 | if (( i > 0 )) |
---|
| 1806 | then |
---|
| 1807 | printf " *** input files have been copied to the remote host\n" |
---|
| 1808 | fi |
---|
| 1809 | fi |
---|
| 1810 | |
---|
| 1811 | |
---|
[2380] | 1812 | # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE |
---|
| 1813 | # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES) |
---|
| 1814 | if [[ $create_batch_job = false && $create_remote_batch_job = false ]] |
---|
| 1815 | then |
---|
| 1816 | |
---|
| 1817 | # CHANGE TO THE TEMPORARY WORKING DIRECTORY |
---|
| 1818 | if [[ $running_in_batch_mode = false ]] |
---|
| 1819 | then |
---|
| 1820 | # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT |
---|
| 1821 | # FOLDER |
---|
[2566] | 1822 | mkdir -p $tempdir |
---|
| 1823 | chmod go+rx $tempdir |
---|
| 1824 | cd $tempdir |
---|
| 1825 | cp ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*} $tempdir |
---|
| 1826 | printf "\n *** changed to temporary directory: $tempdir" |
---|
[2380] | 1827 | |
---|
| 1828 | else |
---|
| 1829 | |
---|
| 1830 | # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR |
---|
[2566] | 1831 | printf "\n *** running in temporary directory: $tempdir" |
---|
[2380] | 1832 | |
---|
| 1833 | fi |
---|
| 1834 | |
---|
| 1835 | |
---|
| 1836 | # PROVIDE THE INPUT FILES |
---|
| 1837 | # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE) |
---|
[2669] | 1838 | optional_files_missing=false |
---|
[2380] | 1839 | (( i = 0 )) |
---|
[2610] | 1840 | while (( i < nr_of_input_files )) |
---|
[2380] | 1841 | do |
---|
| 1842 | (( i = i + 1 )) |
---|
| 1843 | if (( i == 1 )) |
---|
| 1844 | then |
---|
| 1845 | printf "\n\n *** providing INPUT-files:\n$dashes" |
---|
| 1846 | fi |
---|
| 1847 | |
---|
| 1848 | |
---|
| 1849 | # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST |
---|
[2669] | 1850 | if [[ "${actionin[$i]}" = unavailable ]] |
---|
[2380] | 1851 | then |
---|
[2669] | 1852 | optional_files_missing=true |
---|
[2380] | 1853 | continue |
---|
| 1854 | fi |
---|
| 1855 | |
---|
| 1856 | # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION) |
---|
| 1857 | files_for_cores=false; filetype=file |
---|
| 1858 | if [[ "${actionin[$i]}" = pe && -n $cores ]] |
---|
| 1859 | then |
---|
| 1860 | files_for_cores=true; filetype=files |
---|
| 1861 | actionin[$i]="" |
---|
| 1862 | elif [[ "${actionin[$i]}" = pe && ! -n $cores ]] |
---|
| 1863 | then |
---|
| 1864 | actionin[$i]="" |
---|
| 1865 | elif [[ "${actionin[$i]}" = lnpe && -n $cores ]] |
---|
| 1866 | then |
---|
| 1867 | files_for_cores=true; filetype=files |
---|
| 1868 | actionin[$i]="ln" |
---|
| 1869 | elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]] |
---|
| 1870 | then |
---|
| 1871 | actionin[$i]="ln" |
---|
| 1872 | fi |
---|
| 1873 | |
---|
| 1874 | if [[ $files_for_cores = true ]] |
---|
| 1875 | then |
---|
| 1876 | printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}" |
---|
| 1877 | else |
---|
| 1878 | printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}" |
---|
| 1879 | fi |
---|
| 1880 | |
---|
| 1881 | # INPUT-FILES TO BE LINKED |
---|
| 1882 | if [[ "${actionin[$i]}" = ln ]] |
---|
| 1883 | then |
---|
| 1884 | |
---|
| 1885 | printf "\n $filetype will be linked" |
---|
| 1886 | if [[ $files_for_cores = false ]] |
---|
| 1887 | then |
---|
| 1888 | if [[ -f "${absnamein[$i]}" ]] |
---|
| 1889 | then |
---|
| 1890 | ln ${absnamein[$i]} ${localin[$i]} |
---|
| 1891 | got_tmp[$i]=true |
---|
| 1892 | fi |
---|
| 1893 | else |
---|
| 1894 | if [[ -d "${absnamein[$i]}" ]] |
---|
| 1895 | then |
---|
[2396] | 1896 | mkdir -p ${localin[$i]} |
---|
[2380] | 1897 | cd ${absnamein[$i]} |
---|
| 1898 | for file in $(ls *) |
---|
| 1899 | do |
---|
[2566] | 1900 | ln $file $tempdir/${localin[$i]} |
---|
[2380] | 1901 | done >|/dev/null 2>&1 |
---|
[2566] | 1902 | cd $tempdir |
---|
[2380] | 1903 | fi |
---|
| 1904 | |
---|
| 1905 | # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r" |
---|
| 1906 | if [[ ! -f "${localin[$i]}/_000000" ]] |
---|
| 1907 | then |
---|
| 1908 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
| 1909 | cp -r ${absnamein[$i]}/* ${localin[$i]} |
---|
| 1910 | fi |
---|
| 1911 | |
---|
| 1912 | got_tmp[$i]=true |
---|
| 1913 | fi |
---|
| 1914 | fi |
---|
| 1915 | |
---|
| 1916 | # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE |
---|
[2669] | 1917 | if [[ "${actionin[$i]}" = "" || "${actionin[$i]}" = "di" || "${actionin[$i]}" = "tr" || "${actionin[$i]}" = "npe" ]] |
---|
[2380] | 1918 | then |
---|
| 1919 | |
---|
| 1920 | if [[ "${actionin[$i]}" = "npe" && -n $cores ]] |
---|
| 1921 | then |
---|
| 1922 | |
---|
| 1923 | # FILE COPIES ARE PROVIDED FOR ALL CORES |
---|
| 1924 | # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER |
---|
| 1925 | printf "\n file will be provided for $cores processors" |
---|
[2396] | 1926 | mkdir -p ${localin[$i]} |
---|
[2380] | 1927 | ival=$cores |
---|
| 1928 | (( ii = 0 )) |
---|
| 1929 | while (( ii <= ival-1 )) |
---|
| 1930 | do |
---|
| 1931 | if (( ii < 10 )) |
---|
| 1932 | then |
---|
| 1933 | cp ${absnamein[$i]} ${localin[$i]}/_000$ii |
---|
| 1934 | elif (( ii < 100 )) |
---|
| 1935 | then |
---|
| 1936 | cp ${absnamein[$i]} ${localin[$i]}/_00$ii |
---|
| 1937 | elif (( ii < 1000 )) |
---|
| 1938 | then |
---|
| 1939 | cp ${absnamein[$i]} ${localin[$i]}/_0$ii |
---|
| 1940 | else |
---|
| 1941 | cp ${absnamein[$i]} ${localin[$i]}/_$ii |
---|
| 1942 | fi |
---|
| 1943 | (( ii = ii + 1 )) |
---|
| 1944 | done |
---|
| 1945 | |
---|
| 1946 | else |
---|
| 1947 | |
---|
| 1948 | if [[ $files_for_cores = true ]] |
---|
| 1949 | then |
---|
| 1950 | |
---|
| 1951 | # PROVIDE FILES FOR EACH CORE |
---|
| 1952 | # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES |
---|
| 1953 | # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE |
---|
| 1954 | printf "\n providing $cores files for the respective cores" |
---|
[2396] | 1955 | mkdir -p ${localin[$i]} |
---|
[2380] | 1956 | if [[ $link_local_input = true ]] |
---|
| 1957 | then |
---|
| 1958 | printf " files will be linked\n" |
---|
| 1959 | cd ${absnamein[$i]} |
---|
| 1960 | for file in $(ls *) |
---|
| 1961 | do |
---|
| 1962 | ln -f $file ${localin[$i]} |
---|
| 1963 | done |
---|
[2566] | 1964 | cd $tempdir |
---|
[2380] | 1965 | fi |
---|
| 1966 | |
---|
| 1967 | # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r" |
---|
| 1968 | if [[ ! -f "${localin[$i]}/_000000" ]] |
---|
| 1969 | then |
---|
| 1970 | if [[ $link_local_input = true ]] |
---|
| 1971 | then |
---|
| 1972 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
| 1973 | fi |
---|
| 1974 | cp -r ${absnamein[$i]}/* ${localin[$i]} |
---|
| 1975 | fi |
---|
| 1976 | |
---|
| 1977 | else |
---|
| 1978 | |
---|
| 1979 | # PROVIDE FILE FOR RUNS ON A SINGLE CORE |
---|
| 1980 | if [[ $link_local_input = true ]] |
---|
| 1981 | then |
---|
| 1982 | printf " file will be linked\n" |
---|
| 1983 | ln -f ${absnamein[$i]} ${localin[$i]} |
---|
| 1984 | fi |
---|
[2605] | 1985 | # If "ln -f" fails or if "$link_local_input = false" do a normal "cp" |
---|
[2380] | 1986 | if [[ ! -f "${localin[$i]}" ]] |
---|
| 1987 | then |
---|
| 1988 | if [[ $link_local_input = true ]] |
---|
| 1989 | then |
---|
| 1990 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
| 1991 | fi |
---|
[2669] | 1992 | if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]] |
---|
[2605] | 1993 | then |
---|
| 1994 | mv ${absnamein[$i]} ${localin[$i]} |
---|
| 1995 | else |
---|
| 1996 | cp ${absnamein[$i]} ${localin[$i]} |
---|
| 1997 | fi |
---|
[2380] | 1998 | fi |
---|
| 1999 | fi |
---|
| 2000 | fi |
---|
| 2001 | fi |
---|
| 2002 | |
---|
| 2003 | done |
---|
| 2004 | if (( i != 0 )) |
---|
| 2005 | then |
---|
[2669] | 2006 | if [[ $optional_files_missing = true ]] |
---|
| 2007 | then |
---|
| 2008 | printf "\n *** INFORMATIVE: some optional INPUT-files are not present" |
---|
| 2009 | fi |
---|
[2380] | 2010 | printf "\n$dashes\n *** all INPUT-files provided \n" |
---|
| 2011 | fi |
---|
| 2012 | |
---|
| 2013 | |
---|
| 2014 | # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE |
---|
| 2015 | (( i = 0 )) |
---|
| 2016 | while (( i < iic )) |
---|
| 2017 | do |
---|
| 2018 | (( i = i + 1 )) |
---|
| 2019 | if (( i == 1 )) |
---|
| 2020 | then |
---|
| 2021 | printf "\n\n *** execution of INPUT-commands:\n$dashes" |
---|
| 2022 | fi |
---|
| 2023 | printf "\n >>> ${in_command[$i]}" |
---|
| 2024 | eval ${in_command[$i]} |
---|
| 2025 | if (( i == iic )) |
---|
| 2026 | then |
---|
| 2027 | printf "\n$dashes\n" |
---|
| 2028 | fi |
---|
| 2029 | done |
---|
| 2030 | |
---|
| 2031 | |
---|
| 2032 | # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM |
---|
| 2033 | # (FILE ENVPAR WILL BE READ BY PALM) |
---|
| 2034 | cat > ENVPAR << EOF |
---|
[2506] | 2035 | &envpar run_identifier = '$fname', host = '$host_configuration', |
---|
[2380] | 2036 | write_binary = .${write_binary}., tasks_per_node = $tasks_per_node, |
---|
| 2037 | maximum_parallel_io_streams = $maximum_parallel_io_streams, |
---|
| 2038 | maximum_cpu_time_allowed = ${cpumax}., |
---|
| 2039 | revision = '$global_revision', |
---|
| 2040 | batch_job = .${running_in_batch_mode}. / |
---|
| 2041 | |
---|
| 2042 | EOF |
---|
| 2043 | |
---|
| 2044 | |
---|
| 2045 | # STARTING THE EXECUTABLE |
---|
| 2046 | printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n" |
---|
[2566] | 2047 | PATH=$PATH:$tempdir |
---|
[2380] | 2048 | |
---|
| 2049 | |
---|
| 2050 | # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES |
---|
[2393] | 2051 | line=`echo "${execute_command}" | sed 's/{{MPI_TASKS}}/$mpi_tasks/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'` |
---|
| 2052 | line2=`echo "${execute_command}" | sed 's/{{MPI_TASKS}}/1/g' | sed 's/{{TASKS_PER_NODE}}/1/g' | sed 's/palm/combine_plot_fields.x/g'` |
---|
[2380] | 2053 | eval line=\"$line\" |
---|
| 2054 | execute_command="$line" |
---|
| 2055 | |
---|
| 2056 | |
---|
| 2057 | # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS |
---|
[2566] | 2058 | if [[ "$execute_command_for_combine" = "" ]] |
---|
| 2059 | then |
---|
| 2060 | eval line2=\"$line2\" |
---|
| 2061 | execute_command_for_combine="$line2" |
---|
| 2062 | fi |
---|
| 2063 | |
---|
[2380] | 2064 | |
---|
| 2065 | |
---|
| 2066 | # PROVIDE A HOSTFILE, IF REQUIRED |
---|
| 2067 | if [[ "$hostfile" != "" ]] |
---|
| 2068 | then |
---|
| 2069 | |
---|
| 2070 | if [[ $hostfile = auto ]] |
---|
| 2071 | then |
---|
| 2072 | # CREATE A NEW HOSTFILE |
---|
| 2073 | (( ii = 1 )) |
---|
| 2074 | while (( ii <= cores / threads_per_task )) |
---|
| 2075 | do |
---|
| 2076 | echo $(hostname) >> hostfile |
---|
| 2077 | (( ii = ii + 1 )) |
---|
| 2078 | done |
---|
| 2079 | if (( cores / threads_per_task == 0 )) |
---|
| 2080 | then |
---|
| 2081 | echo $(hostname) >> hostfile |
---|
| 2082 | fi |
---|
| 2083 | |
---|
| 2084 | else |
---|
| 2085 | cp $hostfile hostfile |
---|
| 2086 | fi |
---|
| 2087 | eval line=\"`head -n $ii hostfile`\" |
---|
| 2088 | printf "\n *** running on: $line" |
---|
| 2089 | fi |
---|
| 2090 | |
---|
| 2091 | |
---|
| 2092 | |
---|
| 2093 | # SET THE NUMBER OF OPENMP-THREADS |
---|
| 2094 | if [[ $use_openmp = true ]] |
---|
| 2095 | then |
---|
| 2096 | export OMP_NUM_THREADS=$threads_per_task |
---|
| 2097 | printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS" |
---|
| 2098 | else |
---|
| 2099 | export OMP_NUM_THREADS=1 |
---|
| 2100 | fi |
---|
| 2101 | |
---|
| 2102 | |
---|
[2610] | 2103 | # PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING |
---|
[2380] | 2104 | if [[ $run_coupled_model = false ]] |
---|
| 2105 | then |
---|
| 2106 | if [[ "$ocean_file_appendix" = true ]] |
---|
| 2107 | then |
---|
| 2108 | echo "precursor_ocean" > coupling_steering |
---|
| 2109 | else |
---|
| 2110 | echo "precursor_atmos" > coupling_steering |
---|
| 2111 | fi |
---|
| 2112 | else |
---|
| 2113 | (( iia = $cores_atmos / $threads_per_task )) |
---|
| 2114 | (( iio = $cores_ocean / $threads_per_task )) |
---|
| 2115 | printf "\n coupled run ($iia atmosphere, $iio ocean)" |
---|
| 2116 | printf "\n\n" |
---|
| 2117 | echo "coupled_run $iia $iio" > coupling_steering |
---|
| 2118 | fi |
---|
| 2119 | |
---|
| 2120 | printf "\n *** execute command:" |
---|
| 2121 | printf "\n \"$execute_command\" \n\n" |
---|
| 2122 | |
---|
| 2123 | $execute_command < coupling_steering |
---|
| 2124 | |
---|
| 2125 | if [[ $? != 0 ]] |
---|
| 2126 | then |
---|
| 2127 | |
---|
| 2128 | # ABORT IN CASE OF RUNTIME ERRORS |
---|
| 2129 | printf "\n +++ runtime error occured" |
---|
| 2130 | locat=execution |
---|
| 2131 | exit |
---|
| 2132 | |
---|
| 2133 | else |
---|
| 2134 | |
---|
| 2135 | printf "\n$dashes\n *** execution finished \n" |
---|
| 2136 | |
---|
| 2137 | fi |
---|
| 2138 | |
---|
| 2139 | |
---|
| 2140 | # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN |
---|
| 2141 | # BY EACH CORE INTO ONE FILE |
---|
| 2142 | if [[ ! -f combine_plot_fields.x ]] |
---|
| 2143 | then |
---|
| 2144 | |
---|
| 2145 | printf "\n\n\n +++ WARNING: no combine_plot_fields found" |
---|
| 2146 | printf "\n 2d- and/or 3d-data may be incomplete!" |
---|
| 2147 | printf "\n Your previous palmbuild may have failed. Please check.\n" |
---|
| 2148 | |
---|
| 2149 | elif [[ "$combine_plot_fields" == true ]] |
---|
| 2150 | then |
---|
| 2151 | |
---|
| 2152 | printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..." |
---|
| 2153 | $execute_command_for_combine |
---|
| 2154 | |
---|
| 2155 | else |
---|
| 2156 | |
---|
| 2157 | # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF |
---|
[2605] | 2158 | # DATA OUTPUT |
---|
[2380] | 2159 | printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..." |
---|
| 2160 | fi |
---|
| 2161 | |
---|
| 2162 | |
---|
| 2163 | |
---|
| 2164 | # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE |
---|
| 2165 | (( i = 0 )) |
---|
| 2166 | while (( i < ioc )) |
---|
| 2167 | do |
---|
| 2168 | (( i = i + 1 )) |
---|
| 2169 | if (( i == 1 )) |
---|
| 2170 | then |
---|
| 2171 | printf "\n\n *** execution of OUTPUT-commands:\n$dashes" |
---|
| 2172 | fi |
---|
| 2173 | printf "\n >>> ${out_command[$i]}" |
---|
| 2174 | eval ${out_command[$i]} |
---|
| 2175 | if (( i == ioc )) |
---|
| 2176 | then |
---|
| 2177 | printf "\n$dashes\n" |
---|
| 2178 | fi |
---|
| 2179 | done |
---|
| 2180 | |
---|
| 2181 | |
---|
[2610] | 2182 | # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF |
---|
| 2183 | # WILDCARDS |
---|
[2380] | 2184 | (( i = 0 )) |
---|
[2610] | 2185 | (( nr_of_output_files = 0 )) |
---|
| 2186 | |
---|
[2380] | 2187 | while (( i < iout )) |
---|
| 2188 | do |
---|
[2610] | 2189 | |
---|
[2380] | 2190 | (( i = i + 1 )) |
---|
[2610] | 2191 | |
---|
| 2192 | # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND |
---|
| 2193 | # CREATE A LIST FOR THE DETECTED ENDINGS |
---|
| 2194 | if [[ "${multout[$i]}" = true ]] |
---|
| 2195 | then |
---|
| 2196 | # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES |
---|
| 2197 | ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null |
---|
| 2198 | ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null |
---|
| 2199 | |
---|
| 2200 | endings="DEFAULT" |
---|
| 2201 | while read line |
---|
| 2202 | do |
---|
| 2203 | # remove the local name from the beginning |
---|
| 2204 | localnamestring="${localout_pre[$i]}" |
---|
| 2205 | length_localname=${#localnamestring} |
---|
| 2206 | ending=${line:${length_localname}} |
---|
| 2207 | |
---|
| 2208 | if [[ "$ending" != "" ]] |
---|
| 2209 | then |
---|
| 2210 | endings="$endings $ending" |
---|
| 2211 | fi |
---|
| 2212 | |
---|
| 2213 | done <filelist |
---|
| 2214 | |
---|
| 2215 | rm filelist |
---|
| 2216 | |
---|
| 2217 | else |
---|
| 2218 | |
---|
| 2219 | # SINGLE NAME |
---|
| 2220 | endings=DEFAULT |
---|
| 2221 | |
---|
| 2222 | fi |
---|
| 2223 | |
---|
| 2224 | # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST |
---|
| 2225 | for ending in $endings |
---|
| 2226 | do |
---|
| 2227 | |
---|
| 2228 | # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED |
---|
| 2229 | if [[ $ending = DEFAULT ]] |
---|
| 2230 | then |
---|
| 2231 | ending="" |
---|
| 2232 | fi |
---|
| 2233 | |
---|
| 2234 | # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!) |
---|
| 2235 | (( nr_of_output_files = nr_of_output_files + 1 )) |
---|
| 2236 | localout[$nr_of_output_files]="${localout_pre[$i]}"$ending |
---|
| 2237 | transout[$nr_of_output_files]="${transout_pre[$i]}" |
---|
| 2238 | actionout[$nr_of_output_files]="${actionout_pre[$i]}" |
---|
| 2239 | pathout[$nr_of_output_files]="${pathout_pre[$i]}" |
---|
| 2240 | endout[$nr_of_output_files]="${endout_pre[$i]}"$ending |
---|
| 2241 | extout[$nr_of_output_files]="${extout_pre[$i]}" |
---|
[2669] | 2242 | warnout[$nr_of_output_files]="${warnout_pre[$i]}" |
---|
[2610] | 2243 | |
---|
| 2244 | done |
---|
| 2245 | |
---|
| 2246 | done |
---|
| 2247 | |
---|
| 2248 | |
---|
| 2249 | |
---|
| 2250 | |
---|
| 2251 | # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS |
---|
| 2252 | (( i = 0 )) |
---|
| 2253 | while (( i < nr_of_output_files )) |
---|
| 2254 | do |
---|
| 2255 | (( i = i + 1 )) |
---|
[2380] | 2256 | if (( i == 1 )) |
---|
| 2257 | then |
---|
| 2258 | printf "\n\n *** saving OUTPUT-files:" |
---|
| 2259 | |
---|
| 2260 | # GET RUN NUMBER ASSIGNED BY PALM |
---|
| 2261 | if [[ -f RUN_NUMBER ]] |
---|
| 2262 | then |
---|
| 2263 | read run_number < RUN_NUMBER |
---|
| 2264 | printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files" |
---|
| 2265 | usecycle_option="-U $run_number" |
---|
| 2266 | else |
---|
| 2267 | run_number=0 |
---|
| 2268 | usecycle_option="" |
---|
| 2269 | fi |
---|
| 2270 | if [[ $running_on_remote = true && "$remote_loginnode" != "" ]] |
---|
| 2271 | then |
---|
[2404] | 2272 | printf "\n *** in case of SCP transfers to local host" |
---|
| 2273 | printf "\n they will be done via remote login-node \"$remote_loginnode\" " |
---|
[2380] | 2274 | fi |
---|
| 2275 | printf "\n$dashes" |
---|
| 2276 | fi |
---|
| 2277 | |
---|
| 2278 | if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]] |
---|
| 2279 | then |
---|
| 2280 | |
---|
[2610] | 2281 | eval filename=${pathout[$i]}/${fname}${endout[$i]} |
---|
| 2282 | |
---|
| 2283 | # DETERMINE THE CYCLE NUMBER |
---|
| 2284 | ls -1 -d $filename > filelist 2>/dev/null |
---|
| 2285 | ls -1 -d $filename.* >> filelist 2>/dev/null |
---|
| 2286 | while read line |
---|
| 2287 | do |
---|
| 2288 | |
---|
| 2289 | # filename without path (i.e. after the last "/") |
---|
| 2290 | basefilename=$(basename ${line}) |
---|
| 2291 | |
---|
| 2292 | # check if there is an extension |
---|
| 2293 | extension=${basefilename##*.} |
---|
| 2294 | if [[ "$extension" = "${extout[$i]}" ]] |
---|
| 2295 | then |
---|
| 2296 | basefilename=${basefilename%.*} |
---|
| 2297 | fi |
---|
| 2298 | |
---|
| 2299 | # check for an existing cycle number |
---|
| 2300 | cycle=${basefilename##*.} |
---|
| 2301 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
| 2302 | then |
---|
[2669] | 2303 | # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS |
---|
| 2304 | # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 |
---|
| 2305 | (( icycle = $((10#$cycle)) + 1 )) |
---|
[2610] | 2306 | else |
---|
| 2307 | (( icycle = 1 )) |
---|
| 2308 | fi |
---|
| 2309 | |
---|
| 2310 | if (( icycle > maxcycle )) |
---|
| 2311 | then |
---|
| 2312 | (( maxcycle = icycle )) |
---|
| 2313 | fi |
---|
| 2314 | |
---|
| 2315 | done <filelist |
---|
| 2316 | rm filelist |
---|
| 2317 | |
---|
| 2318 | |
---|
| 2319 | # SET THE CYCLE NUMBER |
---|
| 2320 | # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER |
---|
| 2321 | if [[ "${actionout[$i]}" = a ]] |
---|
| 2322 | then |
---|
| 2323 | (( maxcycle = maxcycle - 1 )) |
---|
| 2324 | fi |
---|
| 2325 | |
---|
| 2326 | (( cycnum[$i] = maxcycle )) |
---|
| 2327 | pathout[$i]=$filename |
---|
| 2328 | |
---|
| 2329 | |
---|
| 2330 | # ADD CYCLE NUMBER TO FILENAME |
---|
| 2331 | # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER |
---|
[2380] | 2332 | if [[ "${actionout[$i]}" != "a" ]] |
---|
| 2333 | then |
---|
| 2334 | # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT |
---|
| 2335 | # WITH AN EXISTING CYCLE NUMBER |
---|
| 2336 | if (( run_number >= cycnum[$i] )) |
---|
| 2337 | then |
---|
| 2338 | (( cycnum[$i] = run_number )) |
---|
| 2339 | else |
---|
| 2340 | if (( run_number > 0 )) |
---|
| 2341 | then |
---|
| 2342 | printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number" |
---|
| 2343 | fi |
---|
| 2344 | fi |
---|
| 2345 | fi |
---|
| 2346 | if (( cycnum[$i] > 0 )) |
---|
| 2347 | then |
---|
[2600] | 2348 | cyclestring=`printf "%03d" ${cycnum[$i]}` |
---|
| 2349 | pathout[$i]=${pathout[$i]}.$cyclestring |
---|
[2380] | 2350 | fi |
---|
| 2351 | fi |
---|
| 2352 | |
---|
| 2353 | # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION) |
---|
| 2354 | files_for_cores=false; filetype=file |
---|
| 2355 | link_local_output=false |
---|
| 2356 | if [[ "${actionout[$i]}" = pe && -n $cores ]] |
---|
| 2357 | then |
---|
| 2358 | files_for_cores=true; filetype=directory |
---|
| 2359 | actionout[$i]="" |
---|
| 2360 | elif [[ "${actionout[$i]}" = pe && ! -n $cores ]] |
---|
| 2361 | then |
---|
| 2362 | actionout[$i]="" |
---|
| 2363 | elif [[ "${actionout[$i]}" = lnpe && -n $cores ]] |
---|
| 2364 | then |
---|
| 2365 | files_for_cores=true; filetype=directory |
---|
| 2366 | link_local_output=true |
---|
| 2367 | actionout[$i]="" |
---|
| 2368 | elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]] |
---|
| 2369 | then |
---|
| 2370 | link_local_output |
---|
| 2371 | actionout[$i]="" |
---|
| 2372 | elif [[ "${actionout[$i]}" = trpe && -n $cores ]] |
---|
| 2373 | then |
---|
| 2374 | files_for_cores=true; filetype=directory |
---|
| 2375 | actionout[$i]="tr" |
---|
| 2376 | elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]] |
---|
| 2377 | then |
---|
| 2378 | actionout[$i]="tr" |
---|
| 2379 | fi |
---|
| 2380 | |
---|
| 2381 | if [[ ! -f ${localout[$i]} && $files_for_cores = false ]] |
---|
| 2382 | then |
---|
[2669] | 2383 | if [[ ${warnout[$i]} = true ]] |
---|
| 2384 | then |
---|
| 2385 | printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n" |
---|
| 2386 | fi |
---|
[2380] | 2387 | elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]] |
---|
| 2388 | then |
---|
[2669] | 2389 | if [[ ${warnout[$i]} = true ]] |
---|
| 2390 | then |
---|
| 2391 | printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n" |
---|
| 2392 | fi |
---|
[2380] | 2393 | else |
---|
| 2394 | |
---|
| 2395 | |
---|
| 2396 | # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m) |
---|
| 2397 | # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT |
---|
| 2398 | if [[ "${actionout[$i]}" = tr || "${actionout[$i]}" = tra ]] |
---|
| 2399 | then |
---|
| 2400 | if [[ $running_on_remote = true ]] |
---|
| 2401 | then |
---|
| 2402 | |
---|
| 2403 | # SET OPTIONS FOR TRANSFER |
---|
| 2404 | if [[ "${actionout[$i]}" = tr ]] |
---|
| 2405 | then |
---|
| 2406 | if [[ $files_for_cores = false ]] |
---|
| 2407 | then |
---|
| 2408 | catalog_option="" |
---|
| 2409 | catalog_string="" |
---|
| 2410 | else |
---|
| 2411 | catalog_option="-c" |
---|
| 2412 | catalog_string="/" |
---|
| 2413 | fi |
---|
| 2414 | append_option="" |
---|
| 2415 | append_string="" |
---|
| 2416 | else |
---|
| 2417 | append_option="-A" |
---|
| 2418 | append_string="append" |
---|
| 2419 | fi |
---|
| 2420 | |
---|
| 2421 | transfer_failed=false |
---|
| 2422 | printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to" |
---|
[2506] | 2423 | printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n" |
---|
[2380] | 2424 | |
---|
| 2425 | # TRANSFER VIA SCP |
---|
| 2426 | if [[ "$remote_loginnode" != "" ]] |
---|
| 2427 | then |
---|
[2566] | 2428 | echo "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]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" | ssh -q $remote_username@$remote_loginnode |
---|
[2380] | 2429 | else |
---|
[2506] | 2430 | batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]} |
---|
[2380] | 2431 | fi |
---|
| 2432 | [[ $? != 0 ]] && transfer_failed=true |
---|
| 2433 | |
---|
| 2434 | |
---|
| 2435 | # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE |
---|
| 2436 | if [[ $transfer_failed = true ]] |
---|
| 2437 | then |
---|
| 2438 | printf " +++ transfer failed. Trying to save a copy on this host under:\n" |
---|
[2506] | 2439 | printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n" |
---|
[2380] | 2440 | |
---|
| 2441 | # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY |
---|
| 2442 | eval local_catalog=${pathout[$i]} |
---|
| 2443 | if [[ ! -d $local_catalog ]] |
---|
| 2444 | then |
---|
| 2445 | printf " *** local directory does not exist. Trying to create:\n" |
---|
| 2446 | printf " $local_catalog \n" |
---|
| 2447 | mkdir -p $local_catalog |
---|
| 2448 | fi |
---|
[2506] | 2449 | eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id |
---|
[2380] | 2450 | transfer_problems=true |
---|
| 2451 | fi |
---|
| 2452 | |
---|
| 2453 | else |
---|
| 2454 | |
---|
| 2455 | # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST |
---|
| 2456 | # BE COPIED OR APPENDED ON THIS MACHINE |
---|
| 2457 | if [[ "${actionout[$i]}" = tr ]] |
---|
| 2458 | then |
---|
| 2459 | actionout[$i]="" |
---|
| 2460 | else |
---|
| 2461 | actionout[$i]="a" |
---|
| 2462 | fi |
---|
| 2463 | fi |
---|
| 2464 | fi |
---|
| 2465 | |
---|
| 2466 | |
---|
| 2467 | # APPEND ON THIS MACHINE |
---|
| 2468 | if [[ "${actionout[$i]}" = "a" ]] |
---|
| 2469 | then |
---|
| 2470 | if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] |
---|
| 2471 | then |
---|
| 2472 | printf "\n >>> OUTPUT: ${localout[$i]} append to" |
---|
| 2473 | printf "\n ${pathout[$i]}.${extout[$i]}\n" |
---|
| 2474 | cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]} |
---|
| 2475 | else |
---|
| 2476 | printf "\n >>> OUTPUT: ${localout[$i]} append to" |
---|
| 2477 | printf "\n ${pathout[$i]}\n" |
---|
| 2478 | cat ${localout[$i]} >> ${pathout[$i]} |
---|
| 2479 | fi |
---|
| 2480 | fi |
---|
| 2481 | |
---|
| 2482 | # COPY ON THIS MACHINE |
---|
| 2483 | # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE |
---|
| 2484 | # ON DIFFERENT FILE-SYSTEMS |
---|
| 2485 | if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]] |
---|
| 2486 | then |
---|
| 2487 | |
---|
| 2488 | # COPY IN CASE OF RUNS ON SINGLE CORES |
---|
| 2489 | if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] |
---|
| 2490 | then |
---|
| 2491 | printf "\n >>> OUTPUT: ${localout[$i]} to" |
---|
| 2492 | printf "\n ${pathout[$i]}.${extout[$i]}\n" |
---|
| 2493 | if [[ $link_local_output = true ]] |
---|
| 2494 | then |
---|
| 2495 | printf " file will be linked\n" |
---|
| 2496 | ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]} |
---|
| 2497 | fi |
---|
| 2498 | # If "ln -f" fails of if "$link_local_output = false" do a normal "cp" |
---|
| 2499 | if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]] |
---|
| 2500 | then |
---|
| 2501 | if [[ $link_local_output = true ]] |
---|
| 2502 | then |
---|
| 2503 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
| 2504 | fi |
---|
| 2505 | cp ${localout[$i]} ${pathout[$i]}.${extout[$i]} |
---|
| 2506 | else |
---|
| 2507 | printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n" |
---|
| 2508 | fi |
---|
| 2509 | else |
---|
| 2510 | printf "\n >>> OUTPUT: ${localout[$i]} to" |
---|
| 2511 | printf "\n ${pathout[$i]}\n" |
---|
| 2512 | if [[ $link_local_output = true ]] |
---|
| 2513 | then |
---|
| 2514 | printf " file will be linked\n" |
---|
| 2515 | ln -f ${localout[$i]} ${pathout[$i]} |
---|
| 2516 | fi |
---|
| 2517 | # If "ln -f" fails of if "$link_local_output = false" do a normal "cp" |
---|
| 2518 | if [[ ! -f "${pathout[$i]}" ]] |
---|
| 2519 | then |
---|
| 2520 | if [[ $link_local_output = true ]] |
---|
| 2521 | then |
---|
| 2522 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
| 2523 | fi |
---|
| 2524 | cp ${localout[$i]} ${pathout[$i]} |
---|
| 2525 | else |
---|
| 2526 | printf "+++ no copy because file ${pathout[$i]} exists\n" |
---|
| 2527 | fi |
---|
| 2528 | fi |
---|
| 2529 | |
---|
| 2530 | elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]] |
---|
| 2531 | then |
---|
| 2532 | |
---|
| 2533 | # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY |
---|
| 2534 | # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED |
---|
| 2535 | printf "\n >>> OUTPUT: ${localout[$i]}/_.... to" |
---|
| 2536 | printf "\n ${pathout[$i]}\n" |
---|
| 2537 | if [[ $link_local_output = true ]] |
---|
| 2538 | then |
---|
| 2539 | printf " files will be linked\n" |
---|
[2396] | 2540 | mkdir -p ${pathout[$i]} |
---|
[2380] | 2541 | cd ${localout[$i]} |
---|
| 2542 | for file in $(ls *) |
---|
| 2543 | do |
---|
| 2544 | ln -f $file ${pathout[$i]} |
---|
| 2545 | done >|/dev/null 2>&1 |
---|
[2566] | 2546 | cd $tempdir |
---|
[2380] | 2547 | fi |
---|
| 2548 | |
---|
| 2549 | # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r" |
---|
| 2550 | if [[ ! -f "${pathout[$i]}/_000000" ]] |
---|
| 2551 | then |
---|
| 2552 | if [[ $link_local_output = true ]] |
---|
| 2553 | then |
---|
| 2554 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
| 2555 | fi |
---|
| 2556 | cp -r ${localout[$i]}/* ${pathout[$i]} |
---|
| 2557 | fi |
---|
| 2558 | |
---|
| 2559 | fi |
---|
| 2560 | fi |
---|
| 2561 | done |
---|
| 2562 | |
---|
| 2563 | if (( i != 0 )) |
---|
| 2564 | then |
---|
| 2565 | if [[ $transfer_problems = true ]] |
---|
| 2566 | then |
---|
| 2567 | printf "\n$dashes\n *** OUTPUT-files saved" |
---|
| 2568 | printf "\n +++ WARNING: some data transfers failed! \n" |
---|
| 2569 | else |
---|
| 2570 | printf "\n$dashes\n *** all OUTPUT-files saved \n" |
---|
| 2571 | fi |
---|
| 2572 | fi |
---|
| 2573 | |
---|
| 2574 | |
---|
| 2575 | # IF REQUIRED, START A RESTART-JOB |
---|
| 2576 | # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM) |
---|
| 2577 | if [[ -f CONTINUE_RUN ]] |
---|
| 2578 | then |
---|
| 2579 | |
---|
| 2580 | # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY): |
---|
| 2581 | # -C TELLS PALMRUN THAT IT IS A RESTART-RUN |
---|
| 2582 | # -v SILENT MODE WITHOUT INTERACTIVE QUERIES |
---|
| 2583 | # -b START A BATCH JOB |
---|
| 2584 | [[ $(echo $prc | grep -c "\-C") = 0 ]] && prc="$prc -C" |
---|
| 2585 | [[ $(echo $prc | grep -c "\-v") = 0 ]] && prc="$prc -v" |
---|
| 2586 | [[ $(echo $prc | grep -c "\-b") = 0 ]] && prc="$prc -b" |
---|
| 2587 | |
---|
| 2588 | |
---|
| 2589 | # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a) |
---|
| 2590 | # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN |
---|
| 2591 | if [[ $(echo $prc | grep -c "#") != 0 ]] |
---|
| 2592 | then |
---|
[2381] | 2593 | prc=`echo $prc | sed 's/#/r/g'` |
---|
[2380] | 2594 | fi |
---|
| 2595 | |
---|
| 2596 | |
---|
| 2597 | # START THE RESTART-JOB |
---|
| 2598 | printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n" |
---|
| 2599 | echo " $prc" |
---|
| 2600 | printf "\n$dashes\n" |
---|
| 2601 | if [[ $running_on_remote = true ]] |
---|
| 2602 | then |
---|
| 2603 | |
---|
| 2604 | echo "*** ssh will be used to initiate restart-runs!" |
---|
| 2605 | echo " return_address=\"$return_address\" " |
---|
| 2606 | echo " return_username=\"$local_username\" " |
---|
| 2607 | |
---|
| 2608 | if [[ "$remote_loginnode" != "" ]] |
---|
| 2609 | then |
---|
[2420] | 2610 | echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" | ssh -q $SSH_PORTOPT $local_username@$return_address " | ssh -q $remote_username@$remote_loginnode |
---|
[2380] | 2611 | else |
---|
[2420] | 2612 | echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" | ssh -q $SSH_PORTOPT $local_username@$return_address |
---|
[2380] | 2613 | fi |
---|
| 2614 | |
---|
| 2615 | # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED |
---|
| 2616 | sleep 30 |
---|
| 2617 | |
---|
| 2618 | else |
---|
| 2619 | |
---|
| 2620 | # START THE RESTART JOB ON THE LOCAL HOST |
---|
| 2621 | eval $prc # THE ' MUST BE EVALUATED |
---|
| 2622 | cd - > /dev/null |
---|
| 2623 | |
---|
| 2624 | fi |
---|
| 2625 | printf "\n$dashes\n *** restart-run initiated \n" |
---|
| 2626 | |
---|
| 2627 | |
---|
| 2628 | # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA |
---|
| 2629 | # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB. |
---|
| 2630 | # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES |
---|
| 2631 | # MAY BE VERY HUGE) |
---|
| 2632 | (( i = 0 )) |
---|
[2610] | 2633 | while (( i < nr_of_input_files )) |
---|
[2380] | 2634 | do |
---|
| 2635 | (( i = i + 1 )) |
---|
| 2636 | if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]] |
---|
| 2637 | then |
---|
| 2638 | rm -r ${absnamein[$i]} |
---|
| 2639 | fi |
---|
| 2640 | done |
---|
| 2641 | |
---|
| 2642 | fi |
---|
| 2643 | |
---|
| 2644 | |
---|
| 2645 | # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED |
---|
| 2646 | cd $HOME |
---|
[2566] | 2647 | [[ $delete_temporary_catalog = true ]] && rm -rf $tempdir |
---|
[2380] | 2648 | |
---|
| 2649 | |
---|
| 2650 | else |
---|
| 2651 | |
---|
| 2652 | |
---|
| 2653 | # PREPARING ACTIONS, |
---|
| 2654 | # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE |
---|
| 2655 | |
---|
| 2656 | # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB |
---|
[2506] | 2657 | palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username" |
---|
[2380] | 2658 | [[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\"" |
---|
| 2659 | [[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\"" |
---|
| 2660 | [[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k" |
---|
| 2661 | [[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x" |
---|
| 2662 | [[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores" |
---|
| 2663 | [[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task" |
---|
[2501] | 2664 | [[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node" |
---|
[2380] | 2665 | [[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B" |
---|
| 2666 | [[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y" |
---|
| 2667 | [[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\"" |
---|
| 2668 | [[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z" |
---|
| 2669 | [[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str" |
---|
[2479] | 2670 | [[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account" |
---|
[2380] | 2671 | if [[ $create_remote_batch_job = true ]] |
---|
| 2672 | then |
---|
| 2673 | palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip" |
---|
[2420] | 2674 | if [[ $do_trace = true ]] |
---|
| 2675 | then |
---|
| 2676 | printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n" |
---|
| 2677 | fi |
---|
[2380] | 2678 | elif [[ $create_batch_job = true ]] |
---|
| 2679 | then |
---|
| 2680 | palmrun_com=${palmrun_com}" -j" |
---|
[2420] | 2681 | if [[ $do_trace = true ]] |
---|
| 2682 | then |
---|
| 2683 | printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n" |
---|
| 2684 | fi |
---|
[2380] | 2685 | fi |
---|
| 2686 | |
---|
| 2687 | |
---|
| 2688 | # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND |
---|
| 2689 | # REMOTE HOST |
---|
[2506] | 2690 | job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id} |
---|
[2380] | 2691 | job_protocol_file=$job_protocol_file_local |
---|
| 2692 | if [[ $create_remote_batch_job = true ]] |
---|
| 2693 | then |
---|
[2506] | 2694 | job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id} |
---|
[2380] | 2695 | job_protocol_file=$job_protocol_file_remote |
---|
| 2696 | job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol |
---|
| 2697 | scpjob_file=${remote_jobcatalog}/scpjob.$run_id |
---|
| 2698 | fi |
---|
| 2699 | |
---|
| 2700 | |
---|
| 2701 | # BUILD THE JOB-SCRIPTS ON FILE jobfile |
---|
| 2702 | jobfile=jobfile.$run_id |
---|
| 2703 | |
---|
| 2704 | |
---|
| 2705 | # FIRST CREATE THE BATCH DIRECTIVES |
---|
| 2706 | (( i = 0 )) |
---|
| 2707 | while (( i < ibd )) |
---|
| 2708 | do |
---|
| 2709 | (( i = i + 1 )) |
---|
[2566] | 2710 | line=`echo "${batch_directive[$i]}" | sed 's/{{JOB_ID}}/$job_id/g' | sed 's/{{JOBFILE}}/$job_protocol_file/g' | sed 's/{{CPU_HOURS}}/$cpu_hours/g' | sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' | sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' | sed 's/{{NODES}}/$nodes/g' | sed 's/{{CORES}}/$cores/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' | sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' | sed 's/{{FNAME}}/$fname/g' | sed 's/{{QUEUE}}/$queue/g' | sed 's/{{MEMORY}}/$memory/g' | sed 's/{{PROJECT_ACCOUNT}}/$project_account/g' | sed 's/{{PREVIOUS_JOB}}/$previous_job/g' | sed 's/{{TEMPDIR}}/$tempdir/g'` |
---|
[2380] | 2711 | eval line=\"$line\" |
---|
| 2712 | echo "$line" >> $jobfile |
---|
| 2713 | done |
---|
| 2714 | echo " " >> $jobfile |
---|
| 2715 | |
---|
| 2716 | |
---|
| 2717 | # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB |
---|
| 2718 | # PROTOCOL |
---|
| 2719 | if [[ $create_remote_batch_job = true ]] |
---|
| 2720 | then |
---|
| 2721 | echo "set +vx" >> $jobfile |
---|
| 2722 | echo "trap '" >> $jobfile |
---|
| 2723 | echo "set +vx" >> $jobfile |
---|
| 2724 | echo "cd ${remote_jobcatalog}" >> $jobfile |
---|
| 2725 | echo "cat > scpjob.$run_id << %%END%%" >> $jobfile |
---|
| 2726 | |
---|
| 2727 | # ADD THE BATCH DIRECTIVES |
---|
| 2728 | (( i = 0 )) |
---|
| 2729 | while (( i < ibdt )) |
---|
| 2730 | do |
---|
| 2731 | (( i = i + 1 )) |
---|
[2506] | 2732 | line=`echo "${batch_directive_transfer[$i]}" | sed 's/{{JOB_ID}}/$job_id/g' | sed 's/{{JOBFILE}}/$job_protocol_file/g' | sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' | sed 's/{{CPU_HOURS}}/$cpu_hours/g' | sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' | sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' | sed 's/{{NODES}}/$nodes/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' | sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' | sed 's/{{FNAME}}/$fname/g' | sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'` |
---|
[2380] | 2733 | eval line=\"$line\" |
---|
| 2734 | echo "$line" >> $jobfile |
---|
| 2735 | done |
---|
| 2736 | echo " " >> $jobfile |
---|
| 2737 | |
---|
| 2738 | echo "set -x" >> $jobfile |
---|
[2506] | 2739 | echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile |
---|
[2380] | 2740 | echo "%%END%%" >> $jobfile |
---|
| 2741 | echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile |
---|
| 2742 | echo "$submit_command $scpjob_file" >> $jobfile |
---|
| 2743 | echo "rm $scpjob_file" >> $jobfile |
---|
[2404] | 2744 | echo "rm -rf $job_transfer_protocol_file" >> $jobfile |
---|
[2380] | 2745 | echo "set -x" >> $jobfile |
---|
| 2746 | echo " ' exit" >> $jobfile |
---|
| 2747 | fi |
---|
| 2748 | |
---|
| 2749 | |
---|
| 2750 | # ACTIVATE ERROR-TRACEBACK |
---|
| 2751 | if [[ $do_trace = true ]] |
---|
| 2752 | then |
---|
| 2753 | echo "set -x" >> $jobfile |
---|
| 2754 | else |
---|
| 2755 | echo "set +vx" >> $jobfile |
---|
| 2756 | fi |
---|
| 2757 | |
---|
| 2758 | |
---|
| 2759 | # INITIALIZE THE ENVIRONMENT AND LOAD MODULES |
---|
| 2760 | if [[ "$login_init_cmd" != "" ]] |
---|
| 2761 | then |
---|
| 2762 | echo "$login_init_cmd" >> $jobfile |
---|
| 2763 | fi |
---|
| 2764 | if [[ "$module_commands" != "" ]] |
---|
| 2765 | then |
---|
| 2766 | echo "$module_commands" >> $jobfile |
---|
| 2767 | fi |
---|
| 2768 | |
---|
| 2769 | |
---|
| 2770 | # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT |
---|
[2566] | 2771 | if [[ $create_remote_batch_job = true ]] |
---|
| 2772 | then |
---|
| 2773 | echo "mkdir $tempdir" >> $jobfile |
---|
| 2774 | echo "chmod go+rx $tempdir" >> $jobfile |
---|
| 2775 | else |
---|
| 2776 | # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A |
---|
| 2777 | # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN |
---|
| 2778 | # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED) |
---|
| 2779 | mkdir $tempdir |
---|
| 2780 | chmod go+rx $tempdir |
---|
| 2781 | fi |
---|
| 2782 | echo "cd $tempdir" >> $jobfile |
---|
| 2783 | echo "export tempdir=$tempdir" >> $jobfile |
---|
[2506] | 2784 | echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*} ." >> $jobfile |
---|
[2380] | 2785 | echo "export PATH=.:\$PATH" >> $jobfile |
---|
| 2786 | echo "export execute_palmrun=true" >> $jobfile |
---|
| 2787 | |
---|
| 2788 | |
---|
| 2789 | # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS |
---|
| 2790 | # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN |
---|
| 2791 | # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED |
---|
| 2792 | echo "LOCAL_PWD=$working_directory" >> $jobfile |
---|
| 2793 | echo "export LOCAL_PWD" >> $jobfile |
---|
| 2794 | |
---|
| 2795 | |
---|
| 2796 | # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON |
---|
[2420] | 2797 | echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile |
---|
[2380] | 2798 | echo "export LOCAL_PALMRUN_PATH" >> $jobfile |
---|
| 2799 | |
---|
| 2800 | |
---|
| 2801 | # CALL PALMRUN WITHIN THE JOB |
---|
| 2802 | # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB |
---|
| 2803 | echo "set -x" >> $jobfile |
---|
| 2804 | echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile |
---|
| 2805 | |
---|
| 2806 | |
---|
| 2807 | # TRANSFER JOBFILE TO THE TARGET HOST |
---|
| 2808 | if [[ $create_jobfile_only = false ]] |
---|
| 2809 | then |
---|
| 2810 | |
---|
| 2811 | if [[ $create_remote_batch_job = true ]] |
---|
| 2812 | then |
---|
| 2813 | |
---|
[2420] | 2814 | echo " " |
---|
[2566] | 2815 | echo " *** transfer of job to remote host via scp" |
---|
[2420] | 2816 | if [[ $do_trace = true ]] |
---|
| 2817 | then |
---|
[2506] | 2818 | echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}" |
---|
[2420] | 2819 | fi |
---|
[2566] | 2820 | scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null |
---|
[2380] | 2821 | |
---|
[2566] | 2822 | printf " *** submit the job (output of submit command, e.g. the job-id, may follow)" |
---|
[2420] | 2823 | if [[ $do_trace = true ]] |
---|
| 2824 | then |
---|
[2506] | 2825 | echo " cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id} | ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1" |
---|
[2420] | 2826 | fi |
---|
[2506] | 2827 | echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}" | ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1 |
---|
[2380] | 2828 | |
---|
| 2829 | elif [[ $create_batch_job = true ]] |
---|
| 2830 | then |
---|
| 2831 | |
---|
[2385] | 2832 | eval local_jobcatalog=$local_jobcatalog |
---|
[2506] | 2833 | cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id} |
---|
[2385] | 2834 | cd $local_jobcatalog |
---|
[2380] | 2835 | echo " " |
---|
[2420] | 2836 | echo " *** submit the job" |
---|
| 2837 | if [[ $do_trace = true ]] |
---|
| 2838 | then |
---|
[2506] | 2839 | echo "$submit_command ${host_configuration}_${job_id}" |
---|
[2420] | 2840 | fi |
---|
[2506] | 2841 | $submit_command ${host_configuration}_${job_id} |
---|
| 2842 | rm ${host_configuration}_${job_id} |
---|
[2380] | 2843 | cd - > /dev/null |
---|
| 2844 | |
---|
| 2845 | fi |
---|
| 2846 | |
---|
| 2847 | rm -rf $jobfile |
---|
| 2848 | |
---|
| 2849 | else |
---|
| 2850 | |
---|
| 2851 | printf "\n *** jobfile created under name \"$jobfile\" " |
---|
| 2852 | printf "\n no batch-job has been sent!" |
---|
| 2853 | |
---|
| 2854 | fi |
---|
| 2855 | |
---|
| 2856 | fi # END OF REMOTE-PART |
---|