[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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[2696] | 6 | # This file is part of the PALM model system. |
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[2380] | 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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[2718] | 19 | # Copyright 2017-2018 Leibniz Universitaet Hannover |
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[2380] | 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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[3032] | 28 | # $Id: palmrun 4303 2019-11-25 08:55:18Z maronga $ |
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[4303] | 29 | # Abort if temporary working catalog cannot be created |
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| 30 | # |
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| 31 | # 3982 2019-05-16 11:07:31Z raasch |
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[3982] | 32 | # bugfix: -b is not added in automatically generated batch jobs for remote hosts |
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| 33 | # |
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| 34 | # 3917 2019-04-18 11:46:37Z raasch |
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[3917] | 35 | # in case of batch jobs on remote machines, copying files from SOURCES_FOR_RUN folder has |
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| 36 | # been rearranged to avoid that input files with original names (e.g. ..._p3d) are copied |
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| 37 | # into the temporary working catalog |
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| 38 | # |
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| 39 | # 3860 2019-04-04 06:23:27Z raasch |
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[3860] | 40 | # check added, that it is not allowed to set option -b if the configuration file has been setup |
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| 41 | # for running batch jobs on remote hosts, |
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| 42 | # local time added to terminal output before and after saving output files |
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| 43 | # |
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| 44 | # 3725 2019-02-07 10:11:02Z raasch |
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[3725] | 45 | # error messages for failed restarts extended |
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| 46 | # |
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| 47 | # 3682 2019-01-18 17:01:54Z knoop |
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[3665] | 48 | # ssh-call for submitting batch jobs on remote systems modified again to avoid output |
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| 49 | # of login messages on specific systems |
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| 50 | # |
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| 51 | # 3574 2018-11-28 13:14:39Z raasch |
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[3574] | 52 | # syntax-error in last commit fixed |
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| 53 | # |
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| 54 | # 3573 2018-11-28 13:03:44Z raasch |
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[3573] | 55 | # bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command |
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| 56 | # removed, |
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| 57 | # r3570 reverted |
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| 58 | # |
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| 59 | # 3570 2018-11-27 17:44:21Z kanani |
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[3570] | 60 | # Rename job-id by run_id |
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| 61 | # |
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| 62 | # 3555 2018-11-22 13:50:37Z raasch |
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[3555] | 63 | # sed-command to remove repeated space-characters replaced by tr-command, to |
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| 64 | # guarantee mac compatible |
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| 65 | # |
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| 66 | # 3549 2018-11-21 15:44:44Z raasch |
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[3549] | 67 | # ssh-call for submitting batch jobs on remote systems modified to avoid output |
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| 68 | # of login messages on specific systems |
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| 69 | # |
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| 70 | # 3534 2018-11-19 15:35:16Z raasch |
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[3534] | 71 | # batch_scp for sending back the job protocol file is called via login-node if |
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| 72 | # a login-node has been set in the config-file |
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| 73 | # ssh-calls rearranged to avoid output of system/user-profile messages |
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| 74 | # |
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| 75 | # 3505 2018-11-08 09:14:30Z raasch |
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[3505] | 76 | # job folders are created in case that they do not exist |
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| 77 | # |
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| 78 | # 3455 2018-10-30 14:12:31Z raasch |
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[3455] | 79 | # options -h and -d renamed -c and -r, respectively |
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| 80 | # |
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| 81 | # 3402 2018-10-23 11:49:24Z knoop |
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[3346] | 82 | # job_id is set for compatibility reasons with older versions of config files |
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| 83 | # |
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| 84 | # 3313 2018-10-06 15:22:48Z knoop |
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[3294] | 85 | # more detailed error message for outdated fileconnection file |
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| 86 | # |
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| 87 | # 3236 2018-09-10 09:07:06Z raasch |
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[3236] | 88 | # warning issued in case of file connection file version mismatch, |
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| 89 | # host_configuration renamed configuration_identifier, |
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| 90 | # "host identifier" in header output renamed "config. identifier", |
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| 91 | # jobname renamed run_identifier, |
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| 92 | # run_id renamed run_id_number |
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| 93 | # job_id renamed run_id |
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| 94 | # option -r renamed -i |
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| 95 | # |
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| 96 | # 3151 2018-07-19 08:45:38Z raasch |
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[3151] | 97 | # removed additional listing of files to be compiled, print PALM code revision |
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| 98 | # in header |
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| 99 | # |
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| 100 | # 3132 2018-07-16 11:44:58Z raasch |
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[3132] | 101 | # create consistent error messages in case of failed restarts, |
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| 102 | # check existence of remote job catalog |
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| 103 | # |
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| 104 | # 3043 2018-05-25 10:47:54Z raasch |
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[3043] | 105 | # check for setting of fast_io_catalog |
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| 106 | # |
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| 107 | # 3033 2018-05-23 15:26:19Z raasch |
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[3025] | 108 | # -T option not required for interactive runs (tasks per node = |
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| 109 | # total number of cores is assumed as default, if option is not given), |
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| 110 | # reformatting of a few messages, |
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| 111 | # bugfix: destination output directory is created if attribute "pe" is set in |
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| 112 | # .palm.iofiles |
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| 113 | # |
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| 114 | # 2718 2018-01-02 08:49:38Z maronga |
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[2993] | 115 | # bugfix of r2990 |
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| 116 | # |
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| 117 | # 2718 2018-01-02 08:49:38Z maronga |
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[2990] | 118 | # bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and |
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| 119 | # not in the working directory from where palmrun is called |
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| 120 | # |
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| 121 | # 2718 2018-01-02 08:49:38Z maronga |
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[2957] | 122 | # svfout in the activation string will be replaced now by svfin in case of |
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| 123 | # automatic restarts |
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| 124 | # |
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| 125 | # 2718 2018-01-02 08:49:38Z maronga |
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[2906] | 126 | # Introduction of new ENVIRONMENT variables read_svf and write_svf to consider |
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| 127 | # the possible output or input of sky view factors |
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| 128 | # |
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| 129 | # 2718 2018-01-02 08:49:38Z maronga |
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[2834] | 130 | # "fname" renamed to "jobname" |
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| 131 | # |
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| 132 | # 2718 2018-01-02 08:49:38Z maronga |
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[2799] | 133 | # parameters are allowed in output commands (OC:) |
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| 134 | # |
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| 135 | # 2718 2018-01-02 08:49:38Z maronga |
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[2789] | 136 | # bugfix: exit if no queue has been given neither with option -q nor in the |
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| 137 | # configuration file |
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| 138 | # |
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| 139 | # 2718 2018-01-02 08:49:38Z maronga |
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[2762] | 140 | # file connection file from trunk/SCRIPTS is taken by default |
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| 141 | # |
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| 142 | # 2718 2018-01-02 08:49:38Z maronga |
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[2716] | 143 | # Corrected "Former revisions" section |
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| 144 | # |
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| 145 | # 2696 2017-12-14 17:12:51Z kanani |
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| 146 | # Change in file header (GPL part) |
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| 147 | # |
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| 148 | # 2693 2017-12-13 12:33:49Z raasch |
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[2693] | 149 | # replacement of variables given by {{<variable>}} in configuration file is now |
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| 150 | # done in a more general way, variable names are written in small letters |
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| 151 | # |
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| 152 | # 2670 2017-12-06 16:32:19Z raasch |
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[2670] | 153 | # test printouts removed |
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| 154 | # |
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| 155 | # 2669 2017-12-06 16:03:27Z raasch |
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[2669] | 156 | # file attributes in .palm.iofiles restructured, "loc" attribute completely |
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| 157 | # removed, |
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| 158 | # wildcard (*) allowed in .palm.iofiles as file activation string for output |
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| 159 | # files, |
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| 160 | # informative messages in case of missing optional input files shortened |
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| 161 | # bugfix: variable cycle explicitly interpreted with 10 as the number base |
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| 162 | # |
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| 163 | # 2638 2017-11-23 12:44:23Z raasch |
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[2610] | 164 | # use of wildcards in file connection statements enabled |
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| 165 | # |
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| 166 | # 2605 2017-11-09 15:31:46Z raasch |
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[2605] | 167 | # in case of remote jobs, input files with "job" or "jobopt" (new) attribute |
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| 168 | # will not be sent with the job file any more, but copied into the |
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[2610] | 169 | # SOURCES_FOR_RUN... folder on the remote host, before the job is submitted |
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[2605] | 170 | # |
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| 171 | # 2600 2017-11-01 14:11:20Z raasch |
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[2600] | 172 | # cycle numbers are made three digits wide |
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| 173 | # |
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| 174 | # 2566 2017-10-20 08:50:47Z raasch |
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[2566] | 175 | # execute command for combine_plot_fields added |
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| 176 | # "TEMPDIR" renamed "tempdir" |
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| 177 | # temporary working directory for local batch jobs is created immediately within |
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| 178 | # the user's palmrun call, due to a requirement of the "grid engine" batch |
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| 179 | # system, where the working directory is given with batch directive -wd and must |
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| 180 | # already exist when the job is submitted, |
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| 181 | # informative messages in non-trace mode reduced and partly reformatted |
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| 182 | # |
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| 183 | # 2551 2017-10-18 07:25:11Z raasch |
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[2551] | 184 | # TEMPDIR added as replacement string to be used in batch directives |
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| 185 | # |
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| 186 | # 2512 2017-10-04 08:26:59Z raasch |
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[2507] | 187 | # bugfix for determining cycle numbers of NetCDF input files |
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| 188 | # |
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| 189 | # 2506 2017-09-29 08:30:37Z raasch |
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[2506] | 190 | # option -V added to check for an existing SOURCES_FOR_RUN_... folder |
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| 191 | # host configuration added to SOURCES_FOR_RUN_... folder name |
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| 192 | # host_identifier renamed host_configuration |
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| 193 | # option -W added to allow for job dependencies |
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| 194 | # |
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| 195 | # 2501 2017-09-26 11:41:55Z raasch |
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[2501] | 196 | # default value for number of cores (option -X) set to 1 |
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| 197 | # bugfix for mechanism which overwrites configuration file settings with values |
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| 198 | # provided by palmrun options |
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| 199 | # |
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| 200 | # 2499 2017-09-22 16:47:58Z kanani |
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[2499] | 201 | # option -h named configuration identifier |
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| 202 | # |
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| 203 | # 2480 2017-09-19 06:24:14Z maronga |
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[2480] | 204 | # bugfix for last revision |
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| 205 | # |
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| 206 | # 2479 2017-09-19 06:12:16Z raasch |
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[2479] | 207 | # option -A (project account number) added |
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| 208 | # |
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| 209 | # 2422 2017-09-08 08:25:41Z raasch |
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[2410] | 210 | # initial revision |
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[2380] | 211 | # |
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| 212 | #--------------------------------------------------------------------------------# |
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| 213 | # palmrun - script for running PALM jobs on local and remote hosts |
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| 214 | #--------------------------------------------------------------------------------# |
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| 215 | |
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| 216 | |
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| 217 | |
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| 218 | # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES |
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| 219 | |
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| 220 | set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS |
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| 221 | # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN |
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| 222 | # (TOO MANY ARGUMENTS - PROBLEM) |
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| 223 | set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN |
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| 224 | |
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[2610] | 225 | 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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| 226 | typeset -i nr_of_output_files=0 |
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[2380] | 227 | typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE |
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| 228 | # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE |
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| 229 | # SCRIPT-OPTION ARGUMENTS |
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| 230 | typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio |
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| 231 | typeset -i icycle inode ival maxcycle mpi_tasks |
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| 232 | typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task |
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| 233 | |
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| 234 | activation_string_list="" |
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| 235 | AddFilenames="" |
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| 236 | combine_plot_fields=true |
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| 237 | compiler_name="" |
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| 238 | compiler_name_ser="" |
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| 239 | compiler_options="" |
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[3236] | 240 | configuration_identifier="default" |
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[2501] | 241 | cores=1 |
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[2380] | 242 | cores_atmos=0 |
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| 243 | cores_ocean=0 |
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| 244 | coupled_dist="" |
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| 245 | cpp_options="" |
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| 246 | cpumax=0 |
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[2506] | 247 | create_batch_job=false |
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[2380] | 248 | create_jobfile_only=false |
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| 249 | create_remote_batch_job=false |
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| 250 | dashes=" ----------------------------------------------------------------------------" |
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| 251 | defaultqueue="" |
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[2506] | 252 | delete_temporary_catalog=true |
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[2380] | 253 | do_compile=true |
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| 254 | do_trace=false |
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| 255 | executable="" |
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| 256 | execute_command="" |
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| 257 | execution_error=false |
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[2762] | 258 | fileconnection_file=trunk/SCRIPTS/.palm.iofiles |
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[2380] | 259 | global_revision="" |
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| 260 | hostfile="" |
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| 261 | hp="" |
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| 262 | keep_data_from_previous_run=false |
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| 263 | link_local_input=false |
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| 264 | link_local_output=false |
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[2388] | 265 | linker_options="" |
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[2385] | 266 | local_jobcatalog="" |
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[2380] | 267 | locat=normal |
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| 268 | makefile="" |
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| 269 | max_par_io_str="" |
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| 270 | prc=$0 |
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| 271 | while [[ $(echo $prc | grep -c "/") != 0 ]] |
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| 272 | do |
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| 273 | prc=`echo $prc | cut -f2- -d"/"` |
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| 274 | done |
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| 275 | module_calls="" |
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[2506] | 276 | palmrun_memory="" |
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[2380] | 277 | palmrun_script_name=$prc |
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| 278 | openmp=false |
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[2506] | 279 | previous_job="" |
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[2479] | 280 | project_account="" |
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[2380] | 281 | queue=none |
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[2906] | 282 | read_svf="" |
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[2380] | 283 | restart_run=false |
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| 284 | return_address="" |
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[2385] | 285 | remote_jobcatalog="" |
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[2380] | 286 | remote_username="" |
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| 287 | running_in_batch_mode=false |
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[3313] | 288 | running_in_test_mode=false |
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[2380] | 289 | run_coupled_model=false |
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| 290 | run_id="" |
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[3236] | 291 | run_id_number="" |
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| 292 | run_identifier=test |
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[2380] | 293 | silent=false |
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| 294 | source_list="" |
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| 295 | source_path="" |
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[2501] | 296 | tasks_per_node=0 |
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[2380] | 297 | threads_per_task=1 |
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| 298 | transfer_problems=false |
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[2384] | 299 | user_source_path="" |
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[2506] | 300 | use_existing_sources_folder="" |
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[2380] | 301 | use_openmp=false |
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[3033] | 302 | version="palmrun 1.0 Rev$Rev: 4303 $" |
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[2380] | 303 | working_directory=`pwd` |
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| 304 | write_binary="" |
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[2906] | 305 | write_svf="" |
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[2380] | 306 | |
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| 307 | |
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| 308 | # ERROR HANDLING IN CASE OF EXIT |
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[2404] | 309 | trap 'if [[ $locat != normal && $locat != control_c ]] |
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[2380] | 310 | then |
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| 311 | |
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| 312 | # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:) |
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| 313 | (( i = 0 )) |
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| 314 | while (( i < iec )) |
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| 315 | do |
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| 316 | (( i = i + 1 )) |
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| 317 | printf "\n *** Execution of ERROR-command:\n" |
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| 318 | printf " >>> ${err_command[$i]}\n" |
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| 319 | eval ${err_command[$i]} |
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| 320 | done |
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[2566] | 321 | [[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir) |
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[3312] | 322 | printf "\n\n+++ palmrun crashed \n\n" |
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| 323 | exit 1 |
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| 324 | elif [[ $locat != normal ]] |
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[2380] | 325 | then |
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[3312] | 326 | [[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir) |
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| 327 | printf "\n+++ palmrun killed by \"^C\" \n\n" |
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| 328 | exit 2 |
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| 329 | else |
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[2566] | 330 | printf "\n --> palmrun finished\n\n" |
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[3312] | 331 | exit 0 |
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[2380] | 332 | fi' exit |
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| 333 | |
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| 334 | |
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| 335 | # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C): |
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[3312] | 336 | trap 'locat=control_c |
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| 337 | exit 1 |
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[2380] | 338 | ' 2 |
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| 339 | |
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| 340 | |
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| 341 | # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc), |
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| 342 | # WHICH WILL BE USED TO START RESTART-JOBS |
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[3455] | 343 | while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option |
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[2380] | 344 | do |
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| 345 | case $option in |
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| 346 | (a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";; |
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[2479] | 347 | (A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";; |
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[2380] | 348 | (b) create_batch_job=true; prc="$prc -b";; |
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| 349 | (B) delete_temporary_catalog=false; prc="$prc -B";; |
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[3455] | 350 | (c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";; |
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[2380] | 351 | (C) restart_run=true; prc="$prc -C";; |
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| 352 | (F) create_jobfile_only=true;; |
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| 353 | (G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";; |
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[3236] | 354 | (i) run_id_number=$OPTARG;; |
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[2380] | 355 | (j) running_in_batch_mode=true;; |
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| 356 | (k) keep_data_from_previous_run=true; prc="$prc -k";; |
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[2501] | 357 | (m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";; |
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[2380] | 358 | (M) makefile=$OPTARG; prc="$prc -M$OPTARG";; |
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| 359 | (O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";; |
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| 360 | (q) queue=$OPTARG; prc="$prc -q$OPTARG";; |
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[3455] | 361 | (r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";; |
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[2380] | 362 | (R) return_address=$OPTARG;; |
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| 363 | (s) source_list=$OPTARG;; |
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[2501] | 364 | (t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";; |
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[2380] | 365 | (T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";; |
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| 366 | (u) remote_username=$OPTARG; prc="$prc -u$OPTARG";; |
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| 367 | (U) return_username=$OPTARG; prc="$prc -U$OPTARG";; |
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| 368 | (v) silent=true; prc="$prc -v";; |
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[2506] | 369 | (V) use_existing_sources_folder="-V";; |
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[2380] | 370 | (w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";; |
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[2506] | 371 | (W) previous_job=$OPTARG;; |
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[2380] | 372 | (x) do_trace=true;set -x; prc="$prc -x";; |
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[2501] | 373 | (X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";; |
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[2380] | 374 | (y) ocean_file_appendix=true; prc="$prc -y";; |
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| 375 | (Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";; |
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[3313] | 376 | (z) running_in_test_mode=true;; |
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[2380] | 377 | (Z) combine_plot_fields=false; prc="$prc -Z";; |
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| 378 | (\?) printf "\n +++ unknown option $OPTARG \n" |
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| 379 | printf "\n --> type \"$0 ?\" for available options \n" |
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| 380 | locat=parameter;exit;; |
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| 381 | esac |
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| 382 | done |
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| 383 | |
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| 384 | |
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| 385 | # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN |
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| 386 | # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED |
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| 387 | (( to_shift = $OPTIND - 1 )) |
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| 388 | shift $to_shift |
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| 389 | |
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| 390 | # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS |
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| 391 | if [[ "$1" = "?" ]] |
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| 392 | then |
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| 393 | (printf "\n *** Description of available palmrun options:\n" |
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| 394 | printf "\n Option Description Default-Value" |
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| 395 | printf "\n -a activation string list \"\" " |
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[2479] | 396 | printf "\n -A project account number ---" |
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[2380] | 397 | printf "\n -b batch-job on local machine ---" |
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| 398 | printf "\n -B do not delete temporary directory at end ---" |
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[3455] | 399 | printf "\n -c configuration identifier \"default\" " |
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[2380] | 400 | printf "\n -F create batch job file only ---" |
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| 401 | printf "\n -k keep data from previous run" |
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| 402 | printf "\n -m memory demand in MB (batch-jobs) 0 MB" |
---|
| 403 | printf "\n -M Makefile name Makefile" |
---|
| 404 | printf "\n -O threads per openMP task ---" |
---|
| 405 | printf "\n -q queue \"$queue\" " |
---|
[3455] | 406 | printf "\n -r run identifier test" |
---|
[2380] | 407 | printf "\n -s filenames of routines to be compiled \"\" " |
---|
| 408 | printf "\n must end with .f, .f90, .F, or .c !" |
---|
| 409 | printf "\n use \"..\" for more than one file and wildcards" |
---|
| 410 | printf "\n -s LM compiles all locally modified files" |
---|
| 411 | printf "\n -t allowed cpu-time in seconds (batch) 0" |
---|
[2384] | 412 | printf "\n -T tasks per node ---" |
---|
[2380] | 413 | printf "\n -u username on remote machine \"\" " |
---|
| 414 | printf "\n -v no prompt for confirmation ---" |
---|
[2506] | 415 | printf "\n -V check if SOURCES_FOR_RUN_... exists ---" |
---|
[2380] | 416 | printf "\n -w maximum parallel io streams as given by -X" |
---|
[2506] | 417 | printf "\n -W name of job to wait for ---" |
---|
[2380] | 418 | printf "\n -x tracing of palmrun for debug purposes ---" |
---|
| 419 | printf "\n -X # of processors (on parallel machines) 1" |
---|
| 420 | printf "\n -y add appendix \"_O\" to all local output" |
---|
| 421 | printf "\n files (ocean precursor runs followed by" |
---|
| 422 | printf "\n coupled atmosphere-ocean runs) ---" |
---|
| 423 | printf "\n -Y run coupled model, \"#1 #2\" with" |
---|
| 424 | printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X" |
---|
| 425 | printf "\n -Z skip combine_plot_fields at the end of " |
---|
| 426 | printf "\n the simulation ---" |
---|
| 427 | printf "\n " |
---|
| 428 | printf "\n Possible values of positional parameter <modus>:" |
---|
| 429 | printf "\n \"?\" - this outline \n\n") | more |
---|
| 430 | exit |
---|
| 431 | elif [[ "$1" != "" ]] |
---|
| 432 | then |
---|
| 433 | printf "\n +++ positional parameter $1 unknown \n" |
---|
| 434 | locat=parameter; exit |
---|
| 435 | fi |
---|
| 436 | |
---|
| 437 | |
---|
| 438 | |
---|
| 439 | # SHORT STARTING MESSAGE |
---|
| 440 | printf "\n*** $version " |
---|
| 441 | printf "\n will be executed. Please wait ..." |
---|
| 442 | |
---|
| 443 | |
---|
[2506] | 444 | # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME |
---|
[3236] | 445 | config_file=.palm.config.$configuration_identifier |
---|
| 446 | sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier |
---|
[2380] | 447 | |
---|
| 448 | |
---|
| 449 | # CHECK, IF CONFIGURATION FILE EXISTS |
---|
| 450 | if [[ ! -f $config_file ]] |
---|
| 451 | then |
---|
| 452 | printf "\n\n +++ configuration file: " |
---|
| 453 | printf "\n $config_file" |
---|
| 454 | printf "\n does not exist" |
---|
| 455 | locat=connect; exit |
---|
| 456 | fi |
---|
| 457 | |
---|
| 458 | |
---|
[2762] | 459 | # CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE |
---|
| 460 | if [[ -f .palm.iofiles ]] |
---|
| 461 | then |
---|
[3236] | 462 | |
---|
| 463 | # CHECK VERSION MISMATCH |
---|
[3573] | 464 | # RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT |
---|
| 465 | # FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL |
---|
| 466 | if [[ $running_in_batch_mode != true && $restart_run != true ]] |
---|
[3236] | 467 | then |
---|
| 468 | if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]] |
---|
| 469 | then |
---|
| 470 | printf "\n\n +++ WARNING: A file connection file has been found in your" |
---|
| 471 | printf "\n working directory, but its revision does not match" |
---|
| 472 | printf "\n the revision of the default (trunk) version." |
---|
[3294] | 473 | printf "\n You may need to update your connection file" |
---|
| 474 | printf "\n \"${working_directory}/.palm.iofiles\" !" |
---|
[3236] | 475 | fi |
---|
| 476 | fi |
---|
| 477 | |
---|
[2762] | 478 | fileconnection_file=.palm.iofiles |
---|
[3236] | 479 | |
---|
[2762] | 480 | fi |
---|
| 481 | |
---|
| 482 | |
---|
[2380] | 483 | # CHECK, IF FILE CONNECTION FILE EXISTS |
---|
| 484 | if [[ ! -f $fileconnection_file ]] |
---|
| 485 | then |
---|
| 486 | printf "\n\n +++ file connection file: " |
---|
| 487 | printf "\n $fileconnection_file" |
---|
| 488 | printf "\n does not exist" |
---|
| 489 | locat=connect; exit |
---|
| 490 | fi |
---|
| 491 | |
---|
| 492 | |
---|
[2404] | 493 | # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN |
---|
| 494 | if [[ "$activation_string_list" = "" ]] |
---|
| 495 | then |
---|
| 496 | printf "\n\n +++ no activation string list given: " |
---|
| 497 | printf "\n please set palmrun option \"-a\" " |
---|
| 498 | locat=palmrun_option; exit |
---|
| 499 | fi |
---|
| 500 | |
---|
| 501 | |
---|
| 502 | # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS |
---|
| 503 | if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]] |
---|
| 504 | then |
---|
| 505 | write_binary=true |
---|
| 506 | else |
---|
| 507 | write_binary=false |
---|
| 508 | fi |
---|
| 509 | |
---|
[2906] | 510 | # SET VARIABLE TO ACTIVATE WRITING OF SVF DATA |
---|
| 511 | if [[ $(echo $activation_string_list | grep -c "svfout") != 0 ]] |
---|
| 512 | then |
---|
| 513 | write_svf=true |
---|
| 514 | else |
---|
| 515 | write_svf=false |
---|
| 516 | fi |
---|
[2404] | 517 | |
---|
[2906] | 518 | # SET VARIABLE TO ACTIVATE READING OF SVF DATA |
---|
| 519 | if [[ $(echo $activation_string_list | grep -c "svfin") != 0 ]] |
---|
| 520 | then |
---|
| 521 | read_svf=true |
---|
| 522 | else |
---|
| 523 | read_svf=false |
---|
| 524 | fi |
---|
| 525 | |
---|
| 526 | |
---|
[2380] | 527 | # READ AND EVALUATE THE CONFIGURATION-FILE |
---|
| 528 | [[ $silent = false ]] && printf "\n\n Reading the configuration file... " |
---|
| 529 | |
---|
| 530 | # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE |
---|
| 531 | while read line |
---|
| 532 | do |
---|
| 533 | |
---|
| 534 | # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES |
---|
| 535 | eval line=\"$line\" |
---|
| 536 | |
---|
| 537 | |
---|
| 538 | # INTERPRET THE LINE |
---|
| 539 | if [[ "$(echo $line)" = "" ]] |
---|
| 540 | then |
---|
| 541 | |
---|
| 542 | # EMPTY LINE, NO ACTION |
---|
| 543 | continue |
---|
| 544 | |
---|
| 545 | elif [[ "$(echo $line | cut -c1)" = "#" ]] |
---|
| 546 | then |
---|
| 547 | |
---|
| 548 | # LINE IS A COMMENT LINE |
---|
| 549 | continue |
---|
| 550 | |
---|
| 551 | elif [[ "$(echo $line | cut -c1)" = "%" ]] |
---|
| 552 | then |
---|
| 553 | |
---|
| 554 | # LINE DEFINES AN ENVIRONMENT-VARIABLE |
---|
| 555 | var=`echo $line | cut -d" " -s -f1 | cut -c2-` |
---|
| 556 | value=`echo $line | cut -d" " -s -f2-` |
---|
| 557 | |
---|
| 558 | |
---|
| 559 | # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE |
---|
| 560 | # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY |
---|
| 561 | # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS). |
---|
| 562 | # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER). |
---|
| 563 | # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE |
---|
| 564 | # CONFIGURATION-FILE. |
---|
| 565 | if [[ "$(eval echo \$$var)" = "" || "$(eval echo \$$var)" = "0" ]] |
---|
| 566 | then |
---|
| 567 | eval export $var="\$value" |
---|
| 568 | |
---|
| 569 | # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on |
---|
| 570 | if [[ $do_trace = true ]] |
---|
| 571 | then |
---|
| 572 | printf "\n*** ENVIRONMENT-VARIABLE $var = $value" |
---|
| 573 | fi |
---|
| 574 | fi |
---|
| 575 | |
---|
| 576 | elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]] |
---|
| 577 | then |
---|
| 578 | |
---|
| 579 | # LINE DEFINES BATCH-DIRECTIVE |
---|
| 580 | (( ibd = ibd + 1 )) |
---|
| 581 | line=$(echo $line | cut -c4-) |
---|
| 582 | batch_directive[$ibd]="$line" |
---|
| 583 | |
---|
| 584 | elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]] |
---|
| 585 | then |
---|
| 586 | |
---|
| 587 | # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A |
---|
| 588 | # REMOTE TO A LOCAL HOST |
---|
| 589 | (( ibdt = ibdt + 1 )) |
---|
| 590 | line=$(echo $line | cut -c5-) |
---|
| 591 | batch_directive_transfer[$ibdt]="$line" |
---|
| 592 | |
---|
| 593 | elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]] |
---|
| 594 | then |
---|
| 595 | |
---|
| 596 | # LINE DEFINES ERROR-COMMAND |
---|
| 597 | (( iec = iec + 1 )) |
---|
| 598 | line=$(echo $line | cut -c4-) |
---|
| 599 | err_command[$iec]="$line" |
---|
| 600 | |
---|
| 601 | elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]] |
---|
| 602 | then |
---|
| 603 | |
---|
| 604 | # LINE DEFINES INPUT-COMMAND |
---|
| 605 | (( iic = iic + 1 )) |
---|
| 606 | line=$(echo $line | cut -c4-) |
---|
| 607 | in_command[$iic]="$line" |
---|
| 608 | |
---|
| 609 | elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]] |
---|
| 610 | then |
---|
| 611 | |
---|
| 612 | # LINE DEFINES OUTPUT-COMMAND |
---|
| 613 | (( ioc = ioc + 1 )) |
---|
| 614 | line=$(echo $line | cut -c4-) |
---|
| 615 | out_command[$ioc]="$line" |
---|
| 616 | |
---|
| 617 | else |
---|
| 618 | |
---|
| 619 | # SKIP ALL OTHER LINES |
---|
| 620 | continue |
---|
| 621 | |
---|
| 622 | fi |
---|
| 623 | |
---|
| 624 | done < $config_file |
---|
| 625 | |
---|
| 626 | |
---|
| 627 | # CHECK SETTING OF REQUIRED PARAMETERS |
---|
[3043] | 628 | if [[ "$fast_io_catalog" = "" ]] |
---|
| 629 | then |
---|
[3860] | 630 | printf "\n\n +++ no fast_io_catalog found in $config_file" |
---|
[3043] | 631 | printf "\n Please add line \"fast_io_catalog ...\" to that file." |
---|
| 632 | locat=config_file; exit |
---|
| 633 | fi |
---|
[2380] | 634 | if [[ "$compiler_name" = "" ]] |
---|
| 635 | then |
---|
[3860] | 636 | printf "\n\n +++ no compiler name found in $config_file" |
---|
[2380] | 637 | printf "\n Please add line \"compiler_name ...\" to that file." |
---|
| 638 | locat=config_file; exit |
---|
| 639 | fi |
---|
| 640 | if [[ "$compiler_name_ser" = "" ]] |
---|
| 641 | then |
---|
[3860] | 642 | printf "\n\n +++ no compiler name for non-paralle compilation found in $config_file" |
---|
[2380] | 643 | printf "\n Please add line \"compiler_name_ser ...\" to that file." |
---|
| 644 | locat=config_file; exit |
---|
| 645 | fi |
---|
| 646 | if [[ "$compiler_options" = "" ]] |
---|
| 647 | then |
---|
[3860] | 648 | printf "\n\n +++ no compiler options found in $config_file" |
---|
[2380] | 649 | printf "\n Please add line \"compiler_options ...\" to that file." |
---|
| 650 | locat=config_file; exit |
---|
| 651 | fi |
---|
| 652 | if [[ "$execute_command" = "" ]] |
---|
| 653 | then |
---|
[3860] | 654 | printf "\n\n +++ no execute command found in $config_file" |
---|
[2380] | 655 | printf "\n Please add line \"execute_command ...\" to that file." |
---|
| 656 | locat=config_file; exit |
---|
| 657 | fi |
---|
| 658 | |
---|
| 659 | if [[ "$hostfile" != "" ]] |
---|
| 660 | then |
---|
| 661 | if [[ $hostfile != auto && ! -f $hostfile ]] |
---|
| 662 | then |
---|
[3860] | 663 | printf "\n\n +++ no hostfile \"$hostfile\" found" |
---|
[3151] | 664 | printf "\n Please check line \"hostfile ...\" in $config_file" |
---|
[2380] | 665 | locat=config_file; exit |
---|
| 666 | fi |
---|
| 667 | fi |
---|
| 668 | |
---|
| 669 | |
---|
| 670 | # DETERMINE THE CALL STATUS |
---|
| 671 | if [[ "$return_address" != "" ]] |
---|
| 672 | then |
---|
| 673 | |
---|
| 674 | # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN |
---|
| 675 | # BATCH MODE AND ... |
---|
| 676 | running_on_remote=true |
---|
| 677 | |
---|
| 678 | else |
---|
| 679 | |
---|
| 680 | # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST |
---|
| 681 | if [[ "$remote_ip" != "" ]] |
---|
| 682 | then |
---|
| 683 | |
---|
| 684 | # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST |
---|
| 685 | create_remote_batch_job=true |
---|
| 686 | |
---|
[3132] | 687 | # CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET |
---|
| 688 | if [[ "$remote_jobcatalog" = "" ]] |
---|
| 689 | then |
---|
[3860] | 690 | printf "\n\n +++ no remote jobcatalog found in $config_file" |
---|
[3132] | 691 | printf "\n Please add line \"remote_jobcatalog ...\" to that file." |
---|
| 692 | locat=config_file; exit |
---|
| 693 | fi |
---|
| 694 | |
---|
[3860] | 695 | # CHECK THAT OPTION -b (SUBMITTING BATCH JOB ON LOCAL HOST) HASN'T BEEN SET |
---|
| 696 | if [[ $create_batch_job = true ]] |
---|
| 697 | then |
---|
| 698 | printf "\n\n +++ option -b must not be set because configuration file has been setup" |
---|
| 699 | printf "\n for running jobs on a remote host" |
---|
| 700 | locat=config_file; exit |
---|
| 701 | fi |
---|
| 702 | |
---|
[2380] | 703 | fi |
---|
| 704 | running_on_remote=false |
---|
| 705 | fi |
---|
| 706 | |
---|
| 707 | |
---|
| 708 | |
---|
| 709 | # READ AND EVALUATE THE I/O-FILE LIST |
---|
| 710 | [[ $silent = false ]] && printf "\n Reading the I/O files... " |
---|
| 711 | |
---|
| 712 | # READ THE FILE CONNECTION FILE LINE BY LINE |
---|
| 713 | while read line |
---|
| 714 | do |
---|
| 715 | |
---|
[2669] | 716 | # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE |
---|
[3555] | 717 | # HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY |
---|
| 718 | line=`echo "$line" | tr -s " "` |
---|
[2380] | 719 | |
---|
| 720 | # INTERPRET THE LINE |
---|
| 721 | if [[ "$(echo $line)" = "" ]] |
---|
| 722 | then |
---|
| 723 | # EMPTY LINE, NO ACTION |
---|
| 724 | continue |
---|
| 725 | |
---|
| 726 | elif [[ "$(echo $line | cut -c1)" = "#" ]] |
---|
| 727 | then |
---|
| 728 | |
---|
| 729 | # LINE IS A COMMENT LINE |
---|
| 730 | true |
---|
| 731 | |
---|
| 732 | else |
---|
| 733 | |
---|
| 734 | # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES. |
---|
| 735 | # s2a: in/out - field |
---|
[2669] | 736 | # s2b: action - field (optional) |
---|
| 737 | s1=`echo "$line" | cut -d" " -f1` |
---|
| 738 | s2=`echo "$line" | cut -d" " -s -f2` |
---|
[2380] | 739 | if [[ $(echo $s2 | grep -c ":") = 0 ]] |
---|
| 740 | then |
---|
[2669] | 741 | s2a=$s2 |
---|
[2380] | 742 | s2b="" |
---|
| 743 | else |
---|
[2669] | 744 | s2a=`echo $s2 | cut -d":" -f1` |
---|
| 745 | s2b=`echo $s2 | cut -d":" -f2` |
---|
[2380] | 746 | fi |
---|
[2669] | 747 | s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'` |
---|
| 748 | s4=`echo "$line" | cut -d" " -s -f4` |
---|
| 749 | eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES |
---|
| 750 | s5=`echo "$line" | cut -d" " -s -f5` |
---|
| 751 | s6=`echo "$line" | cut -d" " -s -f6` |
---|
[2380] | 752 | |
---|
| 753 | |
---|
| 754 | # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM |
---|
| 755 | # INPUT- OR OUTPUT-LIST. |
---|
| 756 | # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":"). |
---|
| 757 | # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY |
---|
[2669] | 758 | # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION |
---|
[2380] | 759 | # IS NOT CHECKED AND STORED. |
---|
[2610] | 760 | IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR |
---|
[2669] | 761 | if [[ ( "$s2a" = in || "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]] |
---|
[2380] | 762 | then |
---|
| 763 | found=false |
---|
| 764 | for actual in $activation_string_list |
---|
| 765 | do |
---|
| 766 | for formal in $s3 |
---|
| 767 | do |
---|
| 768 | [[ $actual = $formal || "$formal" = "-" ]] && found=true |
---|
| 769 | done |
---|
| 770 | done |
---|
| 771 | if [[ $found = true ]] |
---|
| 772 | then |
---|
| 773 | (( iin = iin + 1 )) |
---|
[2669] | 774 | localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b; |
---|
[2610] | 775 | pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6 |
---|
[2669] | 776 | if [[ "$s2a" = inopt ]] |
---|
| 777 | then |
---|
| 778 | optin_pre[$iin]=yes |
---|
| 779 | else |
---|
| 780 | optin_pre[$iin]=no |
---|
| 781 | fi |
---|
[2605] | 782 | |
---|
| 783 | # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN |
---|
| 784 | # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST |
---|
[2669] | 785 | if [[ $running_on_remote = true && "$s2b" = tr ]] |
---|
[2605] | 786 | then |
---|
[2610] | 787 | pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog} |
---|
[2605] | 788 | fi |
---|
| 789 | |
---|
[2610] | 790 | # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE |
---|
| 791 | # THE WILDCARD FROM THE ENDING |
---|
| 792 | if [[ "${s5: -1}" = "*" ]] |
---|
| 793 | then |
---|
[2669] | 794 | if [[ "$s2b" = "di" ]] |
---|
[2610] | 795 | then |
---|
| 796 | printf "\n +++ wildcards (*) not allowed with \"di\" file attribute." |
---|
| 797 | printf "\n see file \"$fileconnection_file\", line" |
---|
| 798 | printf "\n$line" |
---|
| 799 | locat=iofiles_file; exit |
---|
| 800 | fi |
---|
| 801 | multin[$iin]=true |
---|
| 802 | string=${endin_pre[$iin]} |
---|
| 803 | endin_pre[$iin]="${string%?}" |
---|
| 804 | else |
---|
| 805 | multin[$iin]=false |
---|
| 806 | fi |
---|
[2380] | 807 | fi |
---|
[2669] | 808 | elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]] |
---|
[2380] | 809 | then |
---|
| 810 | found=false |
---|
| 811 | for actual in $activation_string_list |
---|
| 812 | do |
---|
| 813 | for formal in $s3 |
---|
| 814 | do |
---|
[2670] | 815 | [[ $actual = $formal || $formal = wildcard ]] && found=true |
---|
[2380] | 816 | done |
---|
| 817 | done |
---|
| 818 | if [[ $found = true ]] |
---|
| 819 | then |
---|
| 820 | (( iout = iout + 1 )) |
---|
[2669] | 821 | localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b |
---|
[2610] | 822 | pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6 |
---|
| 823 | |
---|
[2669] | 824 | # CHECK IF WILDCARD IS USED AS ACTIVATION STRING |
---|
| 825 | # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST |
---|
| 826 | if [[ $formal = wildcard ]] |
---|
| 827 | then |
---|
| 828 | warnout_pre[$iout]=false |
---|
| 829 | else |
---|
| 830 | warnout_pre[$iout]=true |
---|
| 831 | fi |
---|
| 832 | |
---|
[2610] | 833 | # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE |
---|
| 834 | # THE WILDCARD FROM THE LOCAL FILENAME |
---|
| 835 | if [[ "${s1: -1}" = "*" ]] |
---|
| 836 | then |
---|
[2669] | 837 | if [[ "$s2b" = "di" ]] |
---|
[2610] | 838 | then |
---|
| 839 | printf "\n +++ wildcards (*) not allowed with \"di\" file attribute." |
---|
| 840 | printf "\n see file \"$fileconnection_file\", line" |
---|
| 841 | printf "\n$line" |
---|
| 842 | locat=iofiles_file; exit |
---|
| 843 | fi |
---|
| 844 | multout[$iout]=true |
---|
| 845 | string=${localout_pre[$iout]} |
---|
| 846 | localout_pre[$iout]="${string%?}" |
---|
| 847 | else |
---|
| 848 | multout[$iout]=false |
---|
| 849 | fi |
---|
[2380] | 850 | fi |
---|
[2669] | 851 | elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]] |
---|
[2380] | 852 | then |
---|
[2669] | 853 | printf "\n +++ I/O-attribute in file $fileconnection_file has invalid" |
---|
| 854 | printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!" |
---|
[2380] | 855 | locat=connect; exit |
---|
| 856 | fi |
---|
| 857 | IFS="$IFSALT" |
---|
| 858 | fi |
---|
| 859 | |
---|
| 860 | done < $fileconnection_file |
---|
| 861 | |
---|
| 862 | |
---|
| 863 | |
---|
[2501] | 864 | # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE |
---|
[3025] | 865 | [[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory |
---|
| 866 | [[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax |
---|
| 867 | [[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores |
---|
[2501] | 868 | [[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str |
---|
| 869 | [[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node |
---|
| 870 | |
---|
| 871 | |
---|
| 872 | |
---|
[2380] | 873 | # EVALUATE MODEL COUPLING FEATURES (OPTION -Y) |
---|
| 874 | if [[ $run_coupled_model = true ]] |
---|
| 875 | then |
---|
| 876 | |
---|
| 877 | cores_atmos=`echo $coupled_dist | cut -d" " -s -f1` |
---|
| 878 | cores_ocean=`echo $coupled_dist | cut -d" " -s -f2` |
---|
| 879 | |
---|
| 880 | if (( $cores_ocean + $cores_atmos != $cores )) |
---|
| 881 | then |
---|
| 882 | |
---|
| 883 | printf "\n +++ number of processors does not fit to specification by \"-Y\"." |
---|
| 884 | printf "\n PEs (total) : $cores" |
---|
| 885 | printf "\n PEs (atmosphere): $cores_atmos" |
---|
| 886 | printf "\n PEs (ocean) : $cores_ocean" |
---|
| 887 | locat=coupling; exit |
---|
| 888 | |
---|
| 889 | fi |
---|
| 890 | |
---|
| 891 | fi |
---|
| 892 | |
---|
| 893 | |
---|
| 894 | # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES |
---|
| 895 | # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_... |
---|
| 896 | # FOLDER |
---|
| 897 | if [[ $running_in_batch_mode = true ]] |
---|
| 898 | then |
---|
| 899 | |
---|
[2506] | 900 | if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]] |
---|
[2380] | 901 | then |
---|
[2506] | 902 | printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing" |
---|
[2380] | 903 | printf "\n Please check the output of the palmrun-call" |
---|
| 904 | printf "\n that you did on your local host." |
---|
| 905 | locat=SOURCES_FOR_RUN; exit |
---|
| 906 | fi |
---|
| 907 | |
---|
| 908 | else |
---|
| 909 | |
---|
| 910 | # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN |
---|
| 911 | # AUTOMATIC RESTART RUN |
---|
| 912 | # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN |
---|
| 913 | if [[ $restart_run = false ]] |
---|
| 914 | then |
---|
| 915 | |
---|
| 916 | # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON |
---|
| 917 | # THE LOCAL HOST |
---|
| 918 | if [[ ! -d $source_path ]] |
---|
| 919 | then |
---|
| 920 | printf "\n\n +++ source path \"$source_path\" on local host" |
---|
| 921 | printf "\n \"$(hostname)\" does not exist" |
---|
| 922 | locat=source_path; exit |
---|
| 923 | fi |
---|
| 924 | |
---|
[2990] | 925 | rm -rf ${base_directory}/${sources_for_run_catalog} |
---|
| 926 | mkdir -p ${base_directory}/${sources_for_run_catalog} |
---|
[2380] | 927 | |
---|
| 928 | if [[ "$source_list" = LM ]] |
---|
| 929 | then |
---|
| 930 | |
---|
| 931 | # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY |
---|
| 932 | source_list="" |
---|
| 933 | cd $source_path |
---|
| 934 | |
---|
| 935 | |
---|
[2512] | 936 | # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL |
---|
| 937 | if [[ ! -d ../.svn ]] |
---|
[2380] | 938 | then |
---|
| 939 | printf "\n\n +++ source directory" |
---|
| 940 | printf "\n \"$source_path\" " |
---|
| 941 | printf "\n is not under control of \"subversion\"." |
---|
[2512] | 942 | printf "\n Please do not use palmrun-option \"-s LM\"\n" |
---|
[2380] | 943 | fi |
---|
| 944 | |
---|
| 945 | |
---|
| 946 | # LIST ALL MODIFIED SOURCE CODE FILES |
---|
| 947 | Filenames="" |
---|
[2404] | 948 | svn status > tmp_svnstatus |
---|
[2380] | 949 | while read line |
---|
| 950 | do |
---|
| 951 | firstc=`echo $line | cut -c1` |
---|
| 952 | if [[ $firstc = M || $firstc = "?" ]] |
---|
| 953 | then |
---|
| 954 | Name=`echo "$line" | cut -c8-` |
---|
| 955 | extension=`echo $Name | cut -d. -f2` |
---|
| 956 | if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]] |
---|
| 957 | then |
---|
| 958 | Filenames="$Filenames "$Name |
---|
| 959 | fi |
---|
| 960 | fi |
---|
[2404] | 961 | done < tmp_svnstatus |
---|
| 962 | rm -rf tmp_svnstatus |
---|
[2380] | 963 | |
---|
| 964 | |
---|
| 965 | # COPY FILES TO SOURCES_FOR_RUN_... |
---|
| 966 | for filename in $Filenames |
---|
| 967 | do |
---|
[2990] | 968 | cp $filename ${base_directory}/${sources_for_run_catalog} |
---|
[2380] | 969 | source_list=$source_list"$filename " |
---|
| 970 | done |
---|
| 971 | |
---|
| 972 | cd - > /dev/null |
---|
| 973 | |
---|
| 974 | |
---|
| 975 | # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_... |
---|
| 976 | elif [[ "$source_list" != "" ]] |
---|
| 977 | then |
---|
| 978 | |
---|
| 979 | cd $source_path |
---|
| 980 | |
---|
| 981 | for filename in $source_list |
---|
| 982 | do |
---|
| 983 | |
---|
| 984 | # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH |
---|
| 985 | if [[ $(echo $filename | grep -c "/") != 0 ]] |
---|
| 986 | then |
---|
| 987 | printf "\n +++ source code file: $filename" |
---|
| 988 | printf "\n must not contain (\"/\") " |
---|
| 989 | locat=source; exit |
---|
| 990 | fi |
---|
| 991 | |
---|
| 992 | if [[ ! -f $filename ]] |
---|
| 993 | then |
---|
| 994 | printf "\n +++ source code file: $filename" |
---|
| 995 | printf "\n does not exist" |
---|
| 996 | locat=source; exit |
---|
| 997 | else |
---|
[2990] | 998 | cp $filename ${base_directory}/${sources_for_run_catalog} |
---|
[2380] | 999 | fi |
---|
| 1000 | |
---|
| 1001 | done |
---|
| 1002 | |
---|
| 1003 | cd - > /dev/null |
---|
| 1004 | |
---|
| 1005 | fi |
---|
| 1006 | |
---|
| 1007 | # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY |
---|
| 1008 | [[ "$makefile" = "" ]] && makefile=$source_path/Makefile |
---|
| 1009 | if [[ ! -f $makefile ]] |
---|
| 1010 | then |
---|
| 1011 | printf "\n +++ file \"$makefile\" does not exist" |
---|
| 1012 | locat=make; exit |
---|
| 1013 | else |
---|
[2990] | 1014 | cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile |
---|
[2380] | 1015 | fi |
---|
| 1016 | |
---|
| 1017 | |
---|
| 1018 | # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE |
---|
[2384] | 1019 | if [[ "$user_source_path" != "" ]] |
---|
[2380] | 1020 | then |
---|
| 1021 | |
---|
| 1022 | # DOES THE DIRECTORY EXIST? |
---|
[2384] | 1023 | if [[ ! -d $user_source_path ]] |
---|
[2380] | 1024 | then |
---|
| 1025 | |
---|
| 1026 | printf "\n\n *** INFORMATIVE: additional source code directory" |
---|
[2384] | 1027 | printf "\n \"$user_source_path\" " |
---|
[2380] | 1028 | printf "\n does not exist or is not a directory." |
---|
| 1029 | printf "\n No source code will be used from this directory!\n" |
---|
[2384] | 1030 | user_source_path="" |
---|
[2380] | 1031 | if [[ $silent == false ]] |
---|
| 1032 | then |
---|
| 1033 | sleep 2 |
---|
| 1034 | fi |
---|
| 1035 | |
---|
| 1036 | else |
---|
| 1037 | |
---|
[2384] | 1038 | cd $user_source_path |
---|
[2380] | 1039 | |
---|
| 1040 | Names=$(ls -1 *.f90 2>&1) |
---|
| 1041 | [[ $(echo $Names | grep -c '*.f90') = 0 ]] && AddFilenames="$Names" |
---|
| 1042 | Names=$(ls -1 *.F90 2>&1) |
---|
| 1043 | [[ $(echo $Names | grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names" |
---|
| 1044 | Names=$(ls -1 *.F 2>&1) |
---|
| 1045 | [[ $(echo $Names | grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names" |
---|
| 1046 | Names=$(ls -1 *.f 2>&1) |
---|
| 1047 | [[ $(echo $Names | grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names" |
---|
| 1048 | Names=$(ls -1 *.c 2>&1) |
---|
| 1049 | [[ $(echo $Names | grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names" |
---|
| 1050 | |
---|
| 1051 | cd - > /dev/null |
---|
[2990] | 1052 | cd ${base_directory}/${sources_for_run_catalog} |
---|
[2380] | 1053 | |
---|
| 1054 | # COPY MAKEFILE IF EXISTING |
---|
[2384] | 1055 | if [[ -f $user_source_path/Makefile ]] |
---|
[2380] | 1056 | then |
---|
| 1057 | printf "\n\n *** user Makefile from directory" |
---|
[2384] | 1058 | printf "\n \"$user_source_path\" is used \n" |
---|
[2380] | 1059 | if [[ $silent == false ]] |
---|
| 1060 | then |
---|
| 1061 | sleep 1 |
---|
| 1062 | fi |
---|
[2384] | 1063 | cp $user_source_path/Makefile . |
---|
[2380] | 1064 | fi |
---|
| 1065 | |
---|
| 1066 | for filename in $AddFilenames |
---|
| 1067 | do |
---|
| 1068 | if [[ -f $filename ]] |
---|
| 1069 | then |
---|
| 1070 | printf "\n +++ source code file \"$filename\" found in additional" |
---|
[2384] | 1071 | printf "\n source code directory \"$user_source_path\" " |
---|
[2380] | 1072 | printf "\n but was also given with option \"-s\" which means that it should be taken" |
---|
| 1073 | printf "\n from directory \"$source_path\"." |
---|
| 1074 | locat=source; exit |
---|
| 1075 | fi |
---|
| 1076 | |
---|
[2384] | 1077 | cp $user_source_path/$filename . |
---|
[2380] | 1078 | source_list="$source_list $filename" |
---|
| 1079 | |
---|
| 1080 | # CHECK IF FILE IS CONTAINED IN MAKEFILE |
---|
| 1081 | if [[ $(grep -c $filename Makefile) = 0 ]] |
---|
| 1082 | then |
---|
| 1083 | printf "\n\n +++ user file \"$filename\" " |
---|
| 1084 | printf "\n is not listed in Makefile \n" |
---|
| 1085 | locat=source; exit |
---|
| 1086 | fi |
---|
| 1087 | done |
---|
| 1088 | cd - > /dev/null |
---|
| 1089 | fi |
---|
| 1090 | fi |
---|
| 1091 | |
---|
| 1092 | # COPY CONFIGURATION FILES |
---|
[2990] | 1093 | cp $config_file ${base_directory}/${sources_for_run_catalog} |
---|
| 1094 | cp $fileconnection_file ${base_directory}/${sources_for_run_catalog} |
---|
[2380] | 1095 | |
---|
| 1096 | # COPY SHELLSCRIPTS |
---|
[2990] | 1097 | cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog} |
---|
| 1098 | cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog} |
---|
[2380] | 1099 | |
---|
| 1100 | fi |
---|
| 1101 | |
---|
| 1102 | fi |
---|
| 1103 | |
---|
[2605] | 1104 | |
---|
[2380] | 1105 | # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY |
---|
| 1106 | # (HANDED OVER TO RESTART-RUNS USING OPTION -G) |
---|
| 1107 | if [[ "$global_revision" = "" ]] |
---|
| 1108 | then |
---|
| 1109 | global_revision=`svnversion $source_path 2>/dev/null` |
---|
| 1110 | global_revision="Rev: $global_revision" |
---|
| 1111 | fi |
---|
| 1112 | |
---|
| 1113 | |
---|
| 1114 | # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS |
---|
| 1115 | if [[ -n $cores ]] |
---|
| 1116 | then |
---|
| 1117 | |
---|
| 1118 | # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN |
---|
| 1119 | # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X |
---|
[2501] | 1120 | if [[ $tasks_per_node = 0 ]] |
---|
[2380] | 1121 | then |
---|
[3025] | 1122 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1123 | then |
---|
| 1124 | printf "\n" |
---|
| 1125 | printf "\n +++ option \"-T\" (tasks per node) is missing" |
---|
| 1126 | printf "\n set -T option or define tasks_per_node in the config file" |
---|
| 1127 | locat=tasks_per_node; (( iec = 0 )); exit |
---|
| 1128 | else |
---|
| 1129 | # DEFAULT FOR INTERACTIVE RUN |
---|
| 1130 | tasks_per_node=$cores |
---|
| 1131 | fi |
---|
[2380] | 1132 | fi |
---|
| 1133 | |
---|
| 1134 | if (( cores < tasks_per_node )) |
---|
| 1135 | then |
---|
| 1136 | printf "\n" |
---|
| 1137 | printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)" |
---|
| 1138 | printf "\n given values: -T $tasks_per_node -X $cores" |
---|
| 1139 | locat=tasks_per_node; (( iec = 0 )); exit |
---|
| 1140 | fi |
---|
| 1141 | |
---|
| 1142 | (( nodes = cores / ( tasks_per_node * threads_per_task ) )) |
---|
| 1143 | (( mpi_tasks = cores / threads_per_task )) |
---|
| 1144 | [[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 )) |
---|
| 1145 | (( ii = cores / tasks_per_node )) |
---|
| 1146 | (( remaining_cores = cores - ii * tasks_per_node )) |
---|
| 1147 | if (( remaining_cores > 0 )) |
---|
| 1148 | then |
---|
| 1149 | printf "\n" |
---|
| 1150 | printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral" |
---|
| 1151 | printf "\n divisor of the total number of cores (option \"-X\")" |
---|
| 1152 | printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\"" |
---|
| 1153 | printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks" |
---|
| 1154 | (( nodes = nodes + 1 )) |
---|
| 1155 | fi |
---|
| 1156 | |
---|
| 1157 | fi |
---|
| 1158 | |
---|
| 1159 | |
---|
| 1160 | # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS |
---|
| 1161 | if [[ "$maximum_parallel_io_streams" = "" ]] |
---|
| 1162 | then |
---|
| 1163 | maximum_parallel_io_streams=$cores |
---|
| 1164 | fi |
---|
| 1165 | |
---|
| 1166 | |
---|
| 1167 | # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT |
---|
| 1168 | if [[ "$scp_port" != "" ]] |
---|
| 1169 | then |
---|
| 1170 | PORTOPT="-P $scp_port" |
---|
| 1171 | SSH_PORTOPT="-p $scp_port" |
---|
| 1172 | fi |
---|
| 1173 | |
---|
| 1174 | |
---|
| 1175 | # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE |
---|
| 1176 | # CONFIG-FILE |
---|
| 1177 | if [[ "$ssh_key" != "" ]] |
---|
| 1178 | then |
---|
| 1179 | ssh_key="-i $HOME/.ssh/$ssh_key" |
---|
| 1180 | fi |
---|
| 1181 | |
---|
| 1182 | |
---|
| 1183 | # SET QUEUE, IF NOT GIVEN |
---|
| 1184 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1185 | then |
---|
| 1186 | |
---|
| 1187 | if [[ $queue = none && "$defaultqueue" = "" ]] |
---|
| 1188 | then |
---|
| 1189 | printf "\n" |
---|
| 1190 | printf "\n +++ no default queue given in configuration file and no queue" |
---|
| 1191 | printf "\n given with option -q" |
---|
[2789] | 1192 | locat=queue; exit |
---|
[2380] | 1193 | fi |
---|
| 1194 | if [[ $queue = none ]] |
---|
| 1195 | then |
---|
| 1196 | queue=$defaultqueue |
---|
| 1197 | fi |
---|
| 1198 | |
---|
| 1199 | fi |
---|
| 1200 | |
---|
| 1201 | |
---|
| 1202 | # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH |
---|
| 1203 | # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST) |
---|
| 1204 | (( i = 0 )) |
---|
[2610] | 1205 | (( nr_of_input_files = 0 )) |
---|
[2380] | 1206 | while (( i < iin )) |
---|
| 1207 | do |
---|
| 1208 | (( i = i + 1 )) |
---|
| 1209 | |
---|
| 1210 | # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE |
---|
| 1211 | # FILE IDENTIFIER IS NOT PART OF THE FILENAME)) |
---|
[2610] | 1212 | if [[ "${actionin_pre[$i]}" = di ]] |
---|
[2380] | 1213 | then |
---|
[2610] | 1214 | eval filename=${pathin_pre[$i]}/${endin_pre[$i]} |
---|
[2380] | 1215 | else |
---|
[3236] | 1216 | eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]} |
---|
[2380] | 1217 | fi |
---|
| 1218 | |
---|
[2610] | 1219 | |
---|
[2380] | 1220 | # CHECK IF FILE EXISTS |
---|
| 1221 | if ! ls $filename* 1>/dev/null 2>&1 |
---|
| 1222 | then |
---|
| 1223 | |
---|
[2669] | 1224 | # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST. |
---|
| 1225 | if [[ "${optin_pre[$i]}" != "yes" ]] |
---|
[2380] | 1226 | then |
---|
| 1227 | printf "\n\n +++ INPUT-file: " |
---|
[2610] | 1228 | if [[ "${extin_pre[$i]}" = "" || "${extin_pre[$i]}" = " " ]] |
---|
[2380] | 1229 | then |
---|
| 1230 | printf "\n $filename" |
---|
| 1231 | else |
---|
[2610] | 1232 | printf "\n $filename.${extin_pre[$i]}" |
---|
[2380] | 1233 | fi |
---|
| 1234 | printf "\n does not exist\n" |
---|
| 1235 | locat=input; exit |
---|
| 1236 | else |
---|
[2610] | 1237 | (( nr_of_input_files = nr_of_input_files + 1 )) |
---|
| 1238 | localin[$nr_of_input_files]="${localin_pre[$i]}" |
---|
[2669] | 1239 | optin[$nr_of_input_files]="${optin_pre[$i]}" |
---|
| 1240 | actionin[$nr_of_input_files]="unavailable" |
---|
[2610] | 1241 | pathin[$nr_of_input_files]="${pathin_pre[$i]}" |
---|
| 1242 | endin[$nr_of_input_files]="${endin_pre[$i]}" |
---|
| 1243 | extin[$nr_of_input_files]="${extin_pre[$i]}" |
---|
[2380] | 1244 | fi |
---|
[2605] | 1245 | |
---|
[2380] | 1246 | else |
---|
| 1247 | |
---|
[3236] | 1248 | # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME |
---|
| 1249 | # ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME |
---|
| 1250 | # ENDINGS |
---|
[2610] | 1251 | if [[ "${multin[$i]}" = true ]] |
---|
| 1252 | then |
---|
| 1253 | # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES |
---|
| 1254 | ls -1 -d ${filename} > filelist 2>/dev/null |
---|
| 1255 | ls -1 -d ${filename}.* >> filelist 2>/dev/null |
---|
| 1256 | ls -1 -d ${filename}_* >> filelist 2>/dev/null |
---|
[2380] | 1257 | |
---|
[2610] | 1258 | endings="" |
---|
| 1259 | while read line |
---|
| 1260 | do |
---|
| 1261 | # filename without path (i.e. after the last "/") |
---|
| 1262 | basefilename=$(basename ${line}) |
---|
[2380] | 1263 | |
---|
[2610] | 1264 | # check if there is an extension and remove it |
---|
| 1265 | ext=${basefilename##*.} |
---|
| 1266 | if [[ "$ext" = "${extin_pre[$i]}" ]] |
---|
| 1267 | then |
---|
| 1268 | basefilename=${basefilename%.*} |
---|
| 1269 | fi |
---|
[2380] | 1270 | |
---|
[2610] | 1271 | # check for an existing cycle number and remove it |
---|
| 1272 | cycle=${basefilename##*.} |
---|
| 1273 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
| 1274 | then |
---|
| 1275 | basefilename=${basefilename%.*} |
---|
| 1276 | fi |
---|
[2600] | 1277 | |
---|
[3236] | 1278 | # remove the run_identifier from the beginning |
---|
| 1279 | length_run_identifier=${#run_identifier} |
---|
| 1280 | ending=${basefilename:${length_run_identifier}} |
---|
[2610] | 1281 | |
---|
| 1282 | # remove the ending given in the .iofiles from the beginning |
---|
| 1283 | endingstring="${endin_pre[$i]}" |
---|
| 1284 | length_ending=${#endingstring} |
---|
| 1285 | ending=${ending:${length_ending}} |
---|
| 1286 | |
---|
| 1287 | if [[ "$ending" = "" ]] |
---|
[2600] | 1288 | then |
---|
[2610] | 1289 | # standard ending as given in the .iofiles |
---|
| 1290 | if [[ $(echo $endings | grep -c DEFAULT) = 0 ]] |
---|
| 1291 | then |
---|
| 1292 | endings="$endings DEFAULT" |
---|
| 1293 | fi |
---|
[2600] | 1294 | else |
---|
[2610] | 1295 | # ending must start with "_", otherwise its a different file |
---|
| 1296 | if [[ "${ending:0:1}" = "_" ]] |
---|
| 1297 | then |
---|
| 1298 | if [[ $(echo $endings | grep -c "$ending") = 0 ]] |
---|
| 1299 | then |
---|
| 1300 | endings="$endings $ending" |
---|
| 1301 | fi |
---|
| 1302 | fi |
---|
[2600] | 1303 | fi |
---|
[2610] | 1304 | |
---|
| 1305 | done <filelist |
---|
[2380] | 1306 | |
---|
[2610] | 1307 | rm filelist |
---|
[2380] | 1308 | |
---|
[2600] | 1309 | else |
---|
[2610] | 1310 | |
---|
| 1311 | # SINGLE NAME |
---|
| 1312 | endings=DEFAULT |
---|
| 1313 | |
---|
[2600] | 1314 | fi |
---|
| 1315 | |
---|
[2610] | 1316 | # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST |
---|
| 1317 | for ending in $endings |
---|
| 1318 | do |
---|
| 1319 | |
---|
| 1320 | # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED |
---|
| 1321 | if [[ $ending = DEFAULT ]] |
---|
[2380] | 1322 | then |
---|
[2610] | 1323 | ending="" |
---|
| 1324 | fi |
---|
| 1325 | |
---|
| 1326 | # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!) |
---|
| 1327 | (( nr_of_input_files = nr_of_input_files + 1 )) |
---|
| 1328 | localin[$nr_of_input_files]="${localin_pre[$i]}"$ending |
---|
[2669] | 1329 | optin[$nr_of_input_files]="${optin_pre[$i]}" |
---|
[2610] | 1330 | actionin[$nr_of_input_files]="${actionin_pre[$i]}" |
---|
| 1331 | pathin[$nr_of_input_files]="${pathin_pre[$i]}" |
---|
| 1332 | endin[$nr_of_input_files]="${endin_pre[$i]}"$ending |
---|
| 1333 | extin[$nr_of_input_files]="${extin_pre[$i]}" |
---|
| 1334 | |
---|
| 1335 | |
---|
| 1336 | # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE |
---|
| 1337 | # FILE IDENTIFIER IS NOT PART OF THE FILENAME)) |
---|
| 1338 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
| 1339 | then |
---|
| 1340 | eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]} |
---|
[2380] | 1341 | else |
---|
[3236] | 1342 | eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]} |
---|
[2380] | 1343 | fi |
---|
[2610] | 1344 | |
---|
| 1345 | # DETERMINE THE FILE'S CYCLE NUMBER |
---|
| 1346 | (( maxcycle = 0 )) |
---|
| 1347 | ls -1 -d $filename > filelist 2>/dev/null |
---|
| 1348 | ls -1 -d $filename.* >> filelist 2>/dev/null |
---|
| 1349 | while read line |
---|
| 1350 | do |
---|
| 1351 | # filename without path (i.e. after the last "/") |
---|
| 1352 | basefilename=$(basename ${line}) |
---|
| 1353 | |
---|
| 1354 | # check if there is an extension |
---|
| 1355 | extension=${basefilename##*.} |
---|
| 1356 | if [[ "$extension" = "${extin[$nr_of_input_files]}" ]] |
---|
| 1357 | then |
---|
| 1358 | basefilename=${basefilename%.*} |
---|
| 1359 | fi |
---|
| 1360 | |
---|
| 1361 | # check for an existing cycle number |
---|
| 1362 | cycle=${basefilename##*.} |
---|
| 1363 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
| 1364 | then |
---|
[2669] | 1365 | # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS |
---|
| 1366 | # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 |
---|
| 1367 | (( icycle = $((10#$cycle)) )) |
---|
[2610] | 1368 | else |
---|
| 1369 | (( icycle = 0 )) |
---|
| 1370 | fi |
---|
| 1371 | |
---|
| 1372 | if (( icycle > maxcycle )) |
---|
| 1373 | then |
---|
| 1374 | (( maxcycle = icycle )) |
---|
| 1375 | |
---|
| 1376 | # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS |
---|
| 1377 | # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS |
---|
| 1378 | if [[ $(echo $cycle | cut -c1) = 0 ]] |
---|
| 1379 | then |
---|
| 1380 | leading_zero=true |
---|
| 1381 | else |
---|
| 1382 | leading_zero=false |
---|
| 1383 | fi |
---|
| 1384 | fi |
---|
| 1385 | |
---|
| 1386 | done <filelist |
---|
| 1387 | rm filelist |
---|
| 1388 | |
---|
| 1389 | # MAKE CYCLE NUMBER THREE DIGITS WIDE |
---|
| 1390 | if [[ $leading_zero = true ]] |
---|
[2380] | 1391 | then |
---|
[2610] | 1392 | cyclestring=`printf "%03d" $maxcycle` |
---|
| 1393 | else |
---|
| 1394 | cyclestring=$maxcycle |
---|
[2380] | 1395 | fi |
---|
[2610] | 1396 | |
---|
| 1397 | # APPEND CYCLE NUMBER TO FILENAME |
---|
| 1398 | if (( maxcycle > 0 )) |
---|
[2380] | 1399 | then |
---|
[2610] | 1400 | if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]] |
---|
| 1401 | then |
---|
| 1402 | filename=${filename}.$cyclestring.${extin[$nr_of_input_files]} |
---|
| 1403 | else |
---|
| 1404 | filename=${filename}.$cyclestring |
---|
| 1405 | fi |
---|
[2380] | 1406 | else |
---|
[2610] | 1407 | if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]] |
---|
| 1408 | then |
---|
| 1409 | filename=${filename}.${extin[$nr_of_input_files]} |
---|
| 1410 | fi |
---|
[2380] | 1411 | fi |
---|
[2610] | 1412 | |
---|
| 1413 | # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER, |
---|
| 1414 | # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE) |
---|
| 1415 | absnamein[$nr_of_input_files]=$filename |
---|
| 1416 | if (( maxcycle > 0 )) |
---|
[2380] | 1417 | then |
---|
[2610] | 1418 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
| 1419 | then |
---|
| 1420 | frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring |
---|
| 1421 | else |
---|
[3236] | 1422 | frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring |
---|
[2610] | 1423 | fi |
---|
[2380] | 1424 | else |
---|
[2610] | 1425 | if [[ "${actionin[$nr_of_input_files]}" = di ]] |
---|
| 1426 | then |
---|
| 1427 | frelin[$nr_of_input_files]=${endin[$nr_of_input_files]} |
---|
| 1428 | else |
---|
[3236] | 1429 | frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]} |
---|
[2610] | 1430 | fi |
---|
[2380] | 1431 | fi |
---|
| 1432 | |
---|
[2610] | 1433 | done |
---|
| 1434 | |
---|
[2380] | 1435 | fi |
---|
[2610] | 1436 | |
---|
[2380] | 1437 | done |
---|
| 1438 | |
---|
[2610] | 1439 | |
---|
[2380] | 1440 | # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~), |
---|
| 1441 | # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST), |
---|
| 1442 | # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED |
---|
[2610] | 1443 | # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO |
---|
[2380] | 1444 | # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE |
---|
| 1445 | # REMOTE HOST) |
---|
| 1446 | (( i = 0 )) |
---|
| 1447 | while (( i < iout )) |
---|
| 1448 | do |
---|
| 1449 | (( i = i + 1 )) |
---|
[2610] | 1450 | if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]] |
---|
[2380] | 1451 | then |
---|
[2610] | 1452 | if [[ "${actionout_pre[$i]}" = tr ]] |
---|
[2380] | 1453 | then |
---|
[2610] | 1454 | actionout_pre[$i]="" |
---|
| 1455 | elif [[ "${actionout_pre[$i]}" = trpe ]] |
---|
[2380] | 1456 | then |
---|
[2610] | 1457 | actionout_pre[$i]=pe |
---|
| 1458 | elif [[ "${actionout_pre[$i]}" = tra ]] |
---|
[2380] | 1459 | then |
---|
[2610] | 1460 | actionout_pre[$i]=a |
---|
[2380] | 1461 | fi |
---|
| 1462 | (( maxcycle = 0 )) |
---|
[3236] | 1463 | eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]} |
---|
[2610] | 1464 | eval catalogname=${pathout_pre[$i]} |
---|
[2380] | 1465 | if ! ls $filename* 1>/dev/null 2>&1 |
---|
| 1466 | then |
---|
| 1467 | |
---|
| 1468 | # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED |
---|
| 1469 | if cat /dev/null > $filename |
---|
| 1470 | then |
---|
| 1471 | rm $filename |
---|
| 1472 | else |
---|
| 1473 | |
---|
| 1474 | # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS |
---|
| 1475 | # IF IT DOES NOT EXIST, TRY TO CREATE IT |
---|
| 1476 | if [[ ! -d $catalogname ]] |
---|
| 1477 | then |
---|
| 1478 | if mkdir -p $catalogname |
---|
| 1479 | then |
---|
| 1480 | printf "\n\n *** directory:" |
---|
| 1481 | printf "\n $catalogname" |
---|
| 1482 | printf "\n was created\n" |
---|
| 1483 | else |
---|
| 1484 | printf "\n\n +++ OUTPUT-file:" |
---|
| 1485 | printf "\n $filename" |
---|
| 1486 | printf "\n cannot be created, because directory does not exist" |
---|
| 1487 | printf "\n and cannot be created either" |
---|
| 1488 | printf "\n" |
---|
| 1489 | locat=output ; exit |
---|
| 1490 | fi 2>/dev/null |
---|
| 1491 | else |
---|
| 1492 | printf "\n\n +++ OUTPUT-file:" |
---|
| 1493 | printf "\n $filename" |
---|
| 1494 | printf "\n cannot be created, although directory exists" |
---|
| 1495 | printf "\n" |
---|
| 1496 | locat=output ; exit |
---|
| 1497 | fi |
---|
| 1498 | fi 2>/dev/null |
---|
| 1499 | |
---|
| 1500 | fi |
---|
| 1501 | |
---|
| 1502 | fi |
---|
| 1503 | done |
---|
| 1504 | |
---|
| 1505 | |
---|
| 1506 | # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY |
---|
| 1507 | if [[ $running_in_batch_mode = false ]] |
---|
| 1508 | then |
---|
[3236] | 1509 | run_id_number=$RANDOM |
---|
| 1510 | run_id=${run_identifier}.$run_id_number |
---|
[2380] | 1511 | |
---|
[3236] | 1512 | tempdir=$fast_io_catalog/$run_id |
---|
[3346] | 1513 | |
---|
| 1514 | # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID |
---|
| 1515 | export job_id=$run_id |
---|
| 1516 | |
---|
[2380] | 1517 | fi |
---|
| 1518 | |
---|
| 1519 | |
---|
| 1520 | # CHECK SETTINGS REQUIRED FOR BATCH JOBS |
---|
| 1521 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1522 | then |
---|
| 1523 | |
---|
| 1524 | # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE |
---|
| 1525 | if [[ $ibd = 0 ]] |
---|
| 1526 | then |
---|
| 1527 | printf "\n" |
---|
| 1528 | printf "\n +++ no batch directives found in configuration file" |
---|
| 1529 | locat=config_file_batch_directives; (( iec = 0 )); exit |
---|
| 1530 | fi |
---|
| 1531 | |
---|
| 1532 | # CHECK IF CPUTIME IS GIVEN FOR JOB |
---|
| 1533 | done=false |
---|
[2384] | 1534 | cputime=$cpumax |
---|
[2380] | 1535 | while [[ $done = false ]] |
---|
| 1536 | do |
---|
[2384] | 1537 | if (( cputime == 0 )) |
---|
[2380] | 1538 | then |
---|
| 1539 | printf "\n +++ cpu-time is undefined" |
---|
| 1540 | printf "\n >>> Please type CPU-time in seconds as INTEGER:" |
---|
| 1541 | printf "\n >>> " |
---|
[2384] | 1542 | read cputime 1>/dev/null 2>&1 |
---|
[2380] | 1543 | else |
---|
| 1544 | done=true |
---|
| 1545 | fi |
---|
| 1546 | done |
---|
[2420] | 1547 | cpumax=$cputime |
---|
[2380] | 1548 | |
---|
| 1549 | # CHECK THE MEMORY DEMAND |
---|
| 1550 | done=false |
---|
| 1551 | while [[ $done = false ]] |
---|
| 1552 | do |
---|
| 1553 | if (( memory == 0 )) |
---|
| 1554 | then |
---|
| 1555 | printf "\n +++ memory demand is undefined" |
---|
| 1556 | printf "\n >>> Please type memory in MByte per process as INTEGER:" |
---|
| 1557 | printf "\n >>> " |
---|
| 1558 | read memory 1>/dev/null 2>&1 |
---|
| 1559 | else |
---|
| 1560 | done=true |
---|
| 1561 | fi |
---|
| 1562 | done |
---|
| 1563 | |
---|
| 1564 | # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN |
---|
| 1565 | if [[ $create_remote_batch_job = true && -z $remote_username ]] |
---|
| 1566 | then |
---|
| 1567 | while [[ -z $remote_username ]] |
---|
| 1568 | do |
---|
[2420] | 1569 | printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined" |
---|
[2380] | 1570 | printf "\n >>> Please type username:" |
---|
| 1571 | printf "\n >>> " |
---|
| 1572 | read remote_username |
---|
| 1573 | done |
---|
| 1574 | fi |
---|
| 1575 | |
---|
| 1576 | else |
---|
| 1577 | |
---|
[2420] | 1578 | if [[ $running_in_batch_mode = false ]] |
---|
| 1579 | then |
---|
| 1580 | cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS |
---|
| 1581 | cpumax=$cputime |
---|
| 1582 | else |
---|
| 1583 | cputime=$cpumax |
---|
| 1584 | fi |
---|
[2380] | 1585 | |
---|
| 1586 | fi |
---|
| 1587 | |
---|
| 1588 | |
---|
| 1589 | # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES |
---|
| 1590 | (( cpu_hours = cputime / 3600 )) |
---|
| 1591 | (( resttime = cputime - cpu_hours * 3600 )) |
---|
| 1592 | (( cpu_minutes = resttime / 60 )) |
---|
| 1593 | (( cpu_seconds = resttime - cpu_minutes * 60 )) |
---|
| 1594 | timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds} |
---|
| 1595 | |
---|
| 1596 | |
---|
| 1597 | # OUTPUT OF THE PALMRUN-HEADER |
---|
| 1598 | calltime=$(date) |
---|
| 1599 | printf "\n" |
---|
| 1600 | printf "#------------------------------------------------------------------------# \n" |
---|
| 1601 | printf "| %-35s%35s | \n" "$version" "$calltime" |
---|
[3151] | 1602 | printf "| %-35s%35s | \n" "PALM code $global_revision" " " |
---|
[2380] | 1603 | printf "| | \n" |
---|
| 1604 | column1="called on:"; column2=$(hostname) |
---|
| 1605 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1606 | if [[ $create_remote_batch_job = true ]] |
---|
| 1607 | then |
---|
[3236] | 1608 | column1="execution on:"; column2="$configuration_identifier (username: $remote_username)" |
---|
[2380] | 1609 | else |
---|
| 1610 | if [[ $running_on_remote = true ]] |
---|
| 1611 | then |
---|
[3236] | 1612 | column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)" |
---|
[2380] | 1613 | else |
---|
[3236] | 1614 | column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)" |
---|
[2380] | 1615 | fi |
---|
| 1616 | fi |
---|
| 1617 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1618 | |
---|
| 1619 | column1="running in:" |
---|
| 1620 | if [[ $running_in_batch_mode = true ]] |
---|
| 1621 | then |
---|
| 1622 | column2="batch job mode" |
---|
| 1623 | else |
---|
| 1624 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1625 | then |
---|
| 1626 | column2="job creation mode" |
---|
| 1627 | else |
---|
| 1628 | column2="interactive run mode" |
---|
| 1629 | fi |
---|
| 1630 | fi |
---|
| 1631 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1632 | |
---|
[2479] | 1633 | if [[ $running_in_batch_mode = true || $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1634 | then |
---|
[2480] | 1635 | if [[ "$project_account" != "" ]] |
---|
[2479] | 1636 | then |
---|
| 1637 | column1="project account number:" |
---|
| 1638 | column2="$project_account" |
---|
| 1639 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1640 | fi |
---|
| 1641 | fi |
---|
| 1642 | |
---|
[2380] | 1643 | if [[ -n $cores ]] |
---|
| 1644 | then |
---|
| 1645 | if [[ $run_coupled_model = false ]] |
---|
| 1646 | then |
---|
| 1647 | column1="number of cores:"; column2=$cores |
---|
| 1648 | else |
---|
| 1649 | column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)" |
---|
| 1650 | fi |
---|
| 1651 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1652 | fi |
---|
| 1653 | if [[ -n $tasks_per_node ]] |
---|
| 1654 | then |
---|
| 1655 | column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)" |
---|
| 1656 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1657 | if (( remaining_cores > 0 )) |
---|
| 1658 | then |
---|
| 1659 | column1=" "; column2="one of the nodes only filled with $remaining_cores tasks" |
---|
| 1660 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1661 | fi |
---|
| 1662 | fi |
---|
| 1663 | if [[ $maximum_parallel_io_streams != $cores ]] |
---|
| 1664 | then |
---|
| 1665 | column1="max par io streams:"; column2="$maximum_parallel_io_streams" |
---|
| 1666 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1667 | fi |
---|
| 1668 | if [[ $use_openmp = true ]] |
---|
| 1669 | then |
---|
| 1670 | column1="threads per task:"; column2="$threads_per_task" |
---|
| 1671 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1672 | fi |
---|
[2384] | 1673 | if [[ $create_batch_job = true || $create_remote_batch_job = true || $running_in_batch_mode = true ]] |
---|
| 1674 | then |
---|
[2506] | 1675 | column1="memory demand / PE":; column2="$memory MB" |
---|
| 1676 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
[2384] | 1677 | column1="job cpu time (h:m:s):"; column2="$timestring" |
---|
| 1678 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1679 | fi |
---|
[2380] | 1680 | printf "| | \n" |
---|
| 1681 | if [[ "$source_list" != "" ]] |
---|
| 1682 | then |
---|
| 1683 | if [[ "$make_options" != "" ]] |
---|
| 1684 | then |
---|
| 1685 | column1="make options:"; column2=$(echo "$make_options" | cut -c-45) |
---|
| 1686 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1687 | line=$(echo "$make_options" | cut -c46-) |
---|
| 1688 | while [[ "$line" != "" ]] |
---|
| 1689 | do |
---|
| 1690 | column1="" |
---|
| 1691 | column2=$(echo "$line" | cut -c-45) |
---|
| 1692 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1693 | line=$(echo "$line" | cut -c46-) |
---|
| 1694 | done |
---|
| 1695 | fi |
---|
| 1696 | fi |
---|
| 1697 | |
---|
| 1698 | column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45) |
---|
| 1699 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1700 | line=$(echo "$cpp_options" | cut -c46-) |
---|
| 1701 | while [[ "$line" != "" ]] |
---|
| 1702 | do |
---|
| 1703 | column1="" |
---|
| 1704 | column2=$(echo "$line" | cut -c-45) |
---|
| 1705 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1706 | line=$(echo "$line" | cut -c46-) |
---|
| 1707 | done |
---|
| 1708 | |
---|
| 1709 | column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45) |
---|
| 1710 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1711 | line=$(echo "$compiler_options" | cut -c46-) |
---|
| 1712 | while [[ "$line" != "" ]] |
---|
| 1713 | do |
---|
| 1714 | column1="" |
---|
| 1715 | column2=$(echo "$line" | cut -c-45) |
---|
| 1716 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1717 | line=$(echo "$line" | cut -c46-) |
---|
| 1718 | done |
---|
| 1719 | |
---|
[2388] | 1720 | column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45) |
---|
[2380] | 1721 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
[2388] | 1722 | line=$(echo "$linker_options" | cut -c46-) |
---|
[2380] | 1723 | while [[ "$line" != "" ]] |
---|
| 1724 | do |
---|
| 1725 | column1="" |
---|
| 1726 | column2=$(echo "$line" | cut -c-45) |
---|
| 1727 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1728 | line=$(echo "$line" | cut -c46-) |
---|
| 1729 | done |
---|
| 1730 | |
---|
| 1731 | if [[ "$login_init_cmd" != "" ]] |
---|
| 1732 | then |
---|
| 1733 | column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45) |
---|
| 1734 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1735 | line=$(echo "$login_init_cmd" | cut -c46-) |
---|
| 1736 | while [[ "$line" != "" ]] |
---|
| 1737 | do |
---|
| 1738 | column1="" |
---|
| 1739 | column2=$(echo "$line" | cut -c-45) |
---|
| 1740 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1741 | line=$(echo "$line" | cut -c46-) |
---|
| 1742 | done |
---|
| 1743 | fi |
---|
| 1744 | |
---|
| 1745 | if [[ "$module_commands" != "" ]] |
---|
| 1746 | then |
---|
| 1747 | column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45) |
---|
| 1748 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1749 | line=$(echo "$module_commands" | cut -c46-) |
---|
| 1750 | while [[ "$line" != "" ]] |
---|
| 1751 | do |
---|
| 1752 | column1="" |
---|
| 1753 | column2=$(echo "$line" | cut -c-45) |
---|
| 1754 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1755 | line=$(echo "$line" | cut -c46-) |
---|
| 1756 | done |
---|
| 1757 | fi |
---|
| 1758 | printf "| | \n" |
---|
[3236] | 1759 | column1="run identifier:"; column2=$run_identifier |
---|
[2380] | 1760 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1761 | column1="activation string list:"; column2=$(echo $activation_string_list) |
---|
| 1762 | printf "| %-25s%-45s | \n" "$column1" "$column2" |
---|
| 1763 | |
---|
| 1764 | if [[ "$ocean_file_appendix" = true ]] |
---|
| 1765 | then |
---|
| 1766 | printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " " |
---|
| 1767 | fi |
---|
| 1768 | |
---|
| 1769 | if [[ "$source_list" != "" ]] |
---|
| 1770 | then |
---|
| 1771 | printf "| | \n" |
---|
| 1772 | printf "| Files to be compiled: | \n" |
---|
| 1773 | line=$source_list |
---|
| 1774 | while [[ "$line" != "" ]] |
---|
| 1775 | do |
---|
| 1776 | linestart=$(echo $line | cut -c-70) |
---|
| 1777 | printf "| %-70s | \n" "$linestart" |
---|
| 1778 | line=$(echo "$line" | cut -c71-) |
---|
| 1779 | done |
---|
| 1780 | fi |
---|
| 1781 | printf "#------------------------------------------------------------------------#" |
---|
| 1782 | |
---|
| 1783 | |
---|
| 1784 | |
---|
| 1785 | # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK |
---|
| 1786 | if [[ $do_trace = true ]] |
---|
| 1787 | then |
---|
| 1788 | (( i = 0 )) |
---|
[2610] | 1789 | while (( i < nr_of_input_files )) |
---|
[2380] | 1790 | do |
---|
| 1791 | (( i = i + 1 )) |
---|
| 1792 | if (( i == 1 )) |
---|
| 1793 | then |
---|
| 1794 | printf "\n\n >>> INPUT-file assignments:\n" |
---|
| 1795 | fi |
---|
| 1796 | printf "\n ${localin[$i]} : ${absnamein[$i]}" |
---|
| 1797 | done |
---|
| 1798 | (( i = 0 )) |
---|
| 1799 | while (( i < iout )) |
---|
| 1800 | do |
---|
| 1801 | (( i = i + 1 )) |
---|
| 1802 | if (( i == 1 )) |
---|
| 1803 | then |
---|
| 1804 | printf "\n\n >>> OUTPUT-file assignments:\n" |
---|
| 1805 | fi |
---|
| 1806 | printf "\n ${localout[$i]} : ${pathout[$i]}" |
---|
| 1807 | done |
---|
| 1808 | (( i = 0 )) |
---|
| 1809 | while (( i < iic )) |
---|
| 1810 | do |
---|
| 1811 | (( i = i + 1 )) |
---|
| 1812 | if (( i == 1 )) |
---|
| 1813 | then |
---|
| 1814 | printf "\n\n >>> INPUT-commands:\n" |
---|
| 1815 | fi |
---|
| 1816 | printf "\n ${in_command[$i]}" |
---|
| 1817 | done |
---|
| 1818 | (( i = 0 )) |
---|
| 1819 | while (( i < ioc )) |
---|
| 1820 | do |
---|
| 1821 | (( i = i + 1 )) |
---|
| 1822 | if (( i == 1 )) |
---|
| 1823 | then |
---|
| 1824 | printf "\n\n >>> OUTPUT-commands:\n" |
---|
| 1825 | fi |
---|
| 1826 | printf "\n ${out_command[$i]}" |
---|
| 1827 | done |
---|
| 1828 | fi |
---|
| 1829 | |
---|
| 1830 | # QUERY FOR CONTINUE |
---|
| 1831 | if [[ $silent = false && $running_in_batch_mode = false ]] |
---|
| 1832 | then |
---|
| 1833 | antwort=dummy |
---|
| 1834 | printf "\n\n" |
---|
| 1835 | printf " >>> everything o.k. (y/n) ? " |
---|
| 1836 | while read antwort |
---|
| 1837 | do |
---|
| 1838 | if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]] |
---|
| 1839 | then |
---|
| 1840 | printf " >>> everything o.k. (y/n) ? " |
---|
| 1841 | else |
---|
| 1842 | break |
---|
| 1843 | fi |
---|
| 1844 | done |
---|
| 1845 | if [[ $antwort = n || $antwort = N ]] |
---|
| 1846 | then |
---|
| 1847 | locat=user_abort; (( iec = 0 )); exit |
---|
| 1848 | fi |
---|
| 1849 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1850 | then |
---|
[2566] | 1851 | printf "\n *** batch-job will be created and submitted" |
---|
[2380] | 1852 | else |
---|
[2566] | 1853 | printf "\n *** PALMRUN will now continue to execute on this machine" |
---|
[2380] | 1854 | fi |
---|
| 1855 | fi |
---|
| 1856 | |
---|
| 1857 | |
---|
| 1858 | |
---|
| 1859 | # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE |
---|
| 1860 | if [[ $restart_run = false && $running_in_batch_mode = false ]] |
---|
| 1861 | then |
---|
| 1862 | |
---|
| 1863 | if [[ $create_batch_job = true || $create_remote_batch_job = true ]] |
---|
| 1864 | then |
---|
[2566] | 1865 | printf "\n\n *** creating executable and other sources for the remote host\n" |
---|
[2380] | 1866 | else |
---|
[2566] | 1867 | printf "\n\n *** creating executable and other sources for the local host\n" |
---|
[2380] | 1868 | fi |
---|
| 1869 | |
---|
[2422] | 1870 | # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF |
---|
| 1871 | # IT SHALL BE CREATED |
---|
| 1872 | ask_for_make_depository=false |
---|
| 1873 | if [[ $create_remote_batch_job = true ]] |
---|
| 1874 | then |
---|
| 1875 | |
---|
| 1876 | line=`grep %base_directory $config_file` |
---|
[3236] | 1877 | make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier} |
---|
[3534] | 1878 | ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 | tee ${configuration_identifier}_last_make_protokoll |
---|
[2422] | 1879 | |
---|
[3236] | 1880 | if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]] |
---|
[2422] | 1881 | then |
---|
| 1882 | printf "\n\n +++ make depository \"${make_depository}\"" |
---|
| 1883 | printf "\n on remote host not found!" |
---|
| 1884 | ask_for_make_depository=true |
---|
| 1885 | fi |
---|
[3236] | 1886 | rm ${configuration_identifier}_last_make_protokoll |
---|
[2422] | 1887 | |
---|
| 1888 | else |
---|
| 1889 | |
---|
| 1890 | # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST |
---|
[3236] | 1891 | make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier} |
---|
[2422] | 1892 | if [[ ! -d ${make_depository} ]] |
---|
| 1893 | then |
---|
| 1894 | printf "\n\n +++ make depository \"${make_depository}\"" |
---|
| 1895 | printf "\n on local host not found!" |
---|
| 1896 | ask_for_make_depository=true |
---|
| 1897 | fi |
---|
| 1898 | |
---|
| 1899 | fi |
---|
| 1900 | |
---|
| 1901 | if [[ $ask_for_make_depository = true ]] |
---|
| 1902 | then |
---|
| 1903 | |
---|
| 1904 | antwort=dummy |
---|
| 1905 | printf "\n\n" |
---|
| 1906 | printf " >>> Create a new one (y/n) ? " |
---|
| 1907 | while read antwort |
---|
| 1908 | do |
---|
| 1909 | if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]] |
---|
| 1910 | then |
---|
| 1911 | printf " >>> Create a new one (y/n) ? " |
---|
| 1912 | else |
---|
| 1913 | break |
---|
| 1914 | fi |
---|
| 1915 | done |
---|
| 1916 | if [[ $antwort = n || $antwort = N ]] |
---|
| 1917 | then |
---|
| 1918 | locat=user_abort; (( iec = 0 )); exit |
---|
| 1919 | fi |
---|
| 1920 | |
---|
[2566] | 1921 | if [[ $do_trace = true ]] |
---|
| 1922 | then |
---|
[3455] | 1923 | palmbuild -c $configuration_identifier |
---|
[2566] | 1924 | else |
---|
[3455] | 1925 | palmbuild -v -c $configuration_identifier |
---|
[2566] | 1926 | fi |
---|
[2422] | 1927 | |
---|
[3312] | 1928 | if [[ ${PIPESTATUS[0]} != 0 ]] |
---|
[2422] | 1929 | then |
---|
| 1930 | |
---|
| 1931 | # ABORT IN CASE OF COMPILATION PROBLEMS |
---|
| 1932 | printf "\n +++ error while compiling for the MAKE_DEPOSITORY" |
---|
| 1933 | locat=make_depository |
---|
| 1934 | exit |
---|
| 1935 | else |
---|
| 1936 | echo " *** now continue with creating executable and other sources" |
---|
| 1937 | fi |
---|
| 1938 | |
---|
| 1939 | fi |
---|
| 1940 | |
---|
[2566] | 1941 | # NOW CREATE THE SOURCES_FOR_RUN FOLDER |
---|
[3455] | 1942 | palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier |
---|
[2380] | 1943 | |
---|
[3312] | 1944 | if [[ ${PIPESTATUS[0]} != 0 ]] |
---|
[2380] | 1945 | then |
---|
| 1946 | |
---|
| 1947 | # ABORT IN CASE OF COMPILATION PROBLEMS |
---|
| 1948 | printf "\n +++ error while creating executable and/or other sources" |
---|
| 1949 | locat=execution |
---|
[2990] | 1950 | rm -rf ${base_directory}/${sources_for_run_catalog} |
---|
[2380] | 1951 | exit |
---|
| 1952 | |
---|
| 1953 | else |
---|
| 1954 | |
---|
[2566] | 1955 | printf " *** executable and other sources created\n" |
---|
[2990] | 1956 | rm -rf ${base_directory}/${sources_for_run_catalog} |
---|
[2380] | 1957 | |
---|
| 1958 | fi |
---|
| 1959 | |
---|
| 1960 | fi |
---|
| 1961 | |
---|
| 1962 | |
---|
[2669] | 1963 | # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT |
---|
| 1964 | # WILL BE COPIED TO THE REMOTE HOST |
---|
[2605] | 1965 | if [[ $create_remote_batch_job = true ]] |
---|
| 1966 | then |
---|
| 1967 | (( i = 0 )) |
---|
[2610] | 1968 | while (( i < nr_of_input_files )) |
---|
[2605] | 1969 | do |
---|
| 1970 | (( i = i + 1 )) |
---|
[2669] | 1971 | if [[ "${actionin[$i]}" = tr ]] |
---|
[2605] | 1972 | then |
---|
| 1973 | eval inputfile=${pathin[$i]}/${frelin[$i]} |
---|
| 1974 | scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]} |
---|
| 1975 | fi |
---|
| 1976 | done |
---|
| 1977 | if (( i > 0 )) |
---|
| 1978 | then |
---|
[3025] | 1979 | printf "\n\n *** input files have been copied to the remote host\n" |
---|
[2605] | 1980 | fi |
---|
| 1981 | fi |
---|
| 1982 | |
---|
| 1983 | |
---|
[2380] | 1984 | # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE |
---|
| 1985 | # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES) |
---|
| 1986 | if [[ $create_batch_job = false && $create_remote_batch_job = false ]] |
---|
| 1987 | then |
---|
| 1988 | |
---|
| 1989 | # CHANGE TO THE TEMPORARY WORKING DIRECTORY |
---|
| 1990 | if [[ $running_in_batch_mode = false ]] |
---|
| 1991 | then |
---|
[3917] | 1992 | # CREATE THE DIRECTORY |
---|
[2566] | 1993 | mkdir -p $tempdir |
---|
[4303] | 1994 | if [[ $? != 0 ]] |
---|
| 1995 | then |
---|
| 1996 | printf "\n +++ temporary working directory cannot be created." |
---|
| 1997 | printf "\n Check setting of variable fast_io_catalog in your config file." |
---|
| 1998 | locat=execution |
---|
| 1999 | exit |
---|
| 2000 | fi |
---|
[2566] | 2001 | chmod go+rx $tempdir |
---|
| 2002 | cd $tempdir |
---|
| 2003 | printf "\n *** changed to temporary directory: $tempdir" |
---|
[2380] | 2004 | |
---|
| 2005 | else |
---|
| 2006 | |
---|
| 2007 | # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR |
---|
[2566] | 2008 | printf "\n *** running in temporary directory: $tempdir" |
---|
[2380] | 2009 | |
---|
| 2010 | fi |
---|
| 2011 | |
---|
| 2012 | |
---|
| 2013 | # PROVIDE THE INPUT FILES |
---|
| 2014 | # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE) |
---|
[2669] | 2015 | optional_files_missing=false |
---|
[2380] | 2016 | (( i = 0 )) |
---|
[2610] | 2017 | while (( i < nr_of_input_files )) |
---|
[2380] | 2018 | do |
---|
| 2019 | (( i = i + 1 )) |
---|
| 2020 | if (( i == 1 )) |
---|
| 2021 | then |
---|
| 2022 | printf "\n\n *** providing INPUT-files:\n$dashes" |
---|
| 2023 | fi |
---|
| 2024 | |
---|
| 2025 | |
---|
| 2026 | # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST |
---|
[2669] | 2027 | if [[ "${actionin[$i]}" = unavailable ]] |
---|
[2380] | 2028 | then |
---|
[2669] | 2029 | optional_files_missing=true |
---|
[2380] | 2030 | continue |
---|
| 2031 | fi |
---|
| 2032 | |
---|
| 2033 | # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION) |
---|
| 2034 | files_for_cores=false; filetype=file |
---|
| 2035 | if [[ "${actionin[$i]}" = pe && -n $cores ]] |
---|
| 2036 | then |
---|
| 2037 | files_for_cores=true; filetype=files |
---|
| 2038 | actionin[$i]="" |
---|
| 2039 | elif [[ "${actionin[$i]}" = pe && ! -n $cores ]] |
---|
| 2040 | then |
---|
| 2041 | actionin[$i]="" |
---|
| 2042 | elif [[ "${actionin[$i]}" = lnpe && -n $cores ]] |
---|
| 2043 | then |
---|
| 2044 | files_for_cores=true; filetype=files |
---|
| 2045 | actionin[$i]="ln" |
---|
| 2046 | elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]] |
---|
| 2047 | then |
---|
| 2048 | actionin[$i]="ln" |
---|
| 2049 | fi |
---|
| 2050 | |
---|
| 2051 | if [[ $files_for_cores = true ]] |
---|
| 2052 | then |
---|
| 2053 | printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}" |
---|
| 2054 | else |
---|
| 2055 | printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}" |
---|
| 2056 | fi |
---|
| 2057 | |
---|
| 2058 | # INPUT-FILES TO BE LINKED |
---|
| 2059 | if [[ "${actionin[$i]}" = ln ]] |
---|
| 2060 | then |
---|
| 2061 | |
---|
| 2062 | printf "\n $filetype will be linked" |
---|
| 2063 | if [[ $files_for_cores = false ]] |
---|
| 2064 | then |
---|
| 2065 | if [[ -f "${absnamein[$i]}" ]] |
---|
| 2066 | then |
---|
| 2067 | ln ${absnamein[$i]} ${localin[$i]} |
---|
| 2068 | got_tmp[$i]=true |
---|
| 2069 | fi |
---|
| 2070 | else |
---|
| 2071 | if [[ -d "${absnamein[$i]}" ]] |
---|
| 2072 | then |
---|
[2396] | 2073 | mkdir -p ${localin[$i]} |
---|
[2380] | 2074 | cd ${absnamein[$i]} |
---|
| 2075 | for file in $(ls *) |
---|
| 2076 | do |
---|
[2566] | 2077 | ln $file $tempdir/${localin[$i]} |
---|
[2380] | 2078 | done >|/dev/null 2>&1 |
---|
[2566] | 2079 | cd $tempdir |
---|
[2380] | 2080 | fi |
---|
| 2081 | |
---|
| 2082 | # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r" |
---|
| 2083 | if [[ ! -f "${localin[$i]}/_000000" ]] |
---|
| 2084 | then |
---|
| 2085 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
| 2086 | cp -r ${absnamein[$i]}/* ${localin[$i]} |
---|
| 2087 | fi |
---|
| 2088 | |
---|
| 2089 | got_tmp[$i]=true |
---|
| 2090 | fi |
---|
| 2091 | fi |
---|
| 2092 | |
---|
| 2093 | # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE |
---|
[2669] | 2094 | if [[ "${actionin[$i]}" = "" || "${actionin[$i]}" = "di" || "${actionin[$i]}" = "tr" || "${actionin[$i]}" = "npe" ]] |
---|
[2380] | 2095 | then |
---|
| 2096 | |
---|
| 2097 | if [[ "${actionin[$i]}" = "npe" && -n $cores ]] |
---|
| 2098 | then |
---|
| 2099 | |
---|
| 2100 | # FILE COPIES ARE PROVIDED FOR ALL CORES |
---|
| 2101 | # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER |
---|
| 2102 | printf "\n file will be provided for $cores processors" |
---|
[2396] | 2103 | mkdir -p ${localin[$i]} |
---|
[2380] | 2104 | ival=$cores |
---|
| 2105 | (( ii = 0 )) |
---|
| 2106 | while (( ii <= ival-1 )) |
---|
| 2107 | do |
---|
| 2108 | if (( ii < 10 )) |
---|
| 2109 | then |
---|
| 2110 | cp ${absnamein[$i]} ${localin[$i]}/_000$ii |
---|
| 2111 | elif (( ii < 100 )) |
---|
| 2112 | then |
---|
| 2113 | cp ${absnamein[$i]} ${localin[$i]}/_00$ii |
---|
| 2114 | elif (( ii < 1000 )) |
---|
| 2115 | then |
---|
| 2116 | cp ${absnamein[$i]} ${localin[$i]}/_0$ii |
---|
| 2117 | else |
---|
| 2118 | cp ${absnamein[$i]} ${localin[$i]}/_$ii |
---|
| 2119 | fi |
---|
| 2120 | (( ii = ii + 1 )) |
---|
| 2121 | done |
---|
| 2122 | |
---|
| 2123 | else |
---|
| 2124 | |
---|
| 2125 | if [[ $files_for_cores = true ]] |
---|
| 2126 | then |
---|
| 2127 | |
---|
| 2128 | # PROVIDE FILES FOR EACH CORE |
---|
| 2129 | # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES |
---|
| 2130 | # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE |
---|
| 2131 | printf "\n providing $cores files for the respective cores" |
---|
[2396] | 2132 | mkdir -p ${localin[$i]} |
---|
[2380] | 2133 | if [[ $link_local_input = true ]] |
---|
| 2134 | then |
---|
| 2135 | printf " files will be linked\n" |
---|
| 2136 | cd ${absnamein[$i]} |
---|
| 2137 | for file in $(ls *) |
---|
| 2138 | do |
---|
| 2139 | ln -f $file ${localin[$i]} |
---|
| 2140 | done |
---|
[2566] | 2141 | cd $tempdir |
---|
[2380] | 2142 | fi |
---|
| 2143 | |
---|
| 2144 | # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r" |
---|
| 2145 | if [[ ! -f "${localin[$i]}/_000000" ]] |
---|
| 2146 | then |
---|
| 2147 | if [[ $link_local_input = true ]] |
---|
| 2148 | then |
---|
| 2149 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
| 2150 | fi |
---|
| 2151 | cp -r ${absnamein[$i]}/* ${localin[$i]} |
---|
| 2152 | fi |
---|
| 2153 | |
---|
| 2154 | else |
---|
| 2155 | |
---|
| 2156 | # PROVIDE FILE FOR RUNS ON A SINGLE CORE |
---|
| 2157 | if [[ $link_local_input = true ]] |
---|
| 2158 | then |
---|
| 2159 | printf " file will be linked\n" |
---|
| 2160 | ln -f ${absnamein[$i]} ${localin[$i]} |
---|
| 2161 | fi |
---|
[2605] | 2162 | # If "ln -f" fails or if "$link_local_input = false" do a normal "cp" |
---|
[2380] | 2163 | if [[ ! -f "${localin[$i]}" ]] |
---|
| 2164 | then |
---|
| 2165 | if [[ $link_local_input = true ]] |
---|
| 2166 | then |
---|
| 2167 | printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" |
---|
| 2168 | fi |
---|
[2669] | 2169 | if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]] |
---|
[2605] | 2170 | then |
---|
| 2171 | mv ${absnamein[$i]} ${localin[$i]} |
---|
| 2172 | else |
---|
| 2173 | cp ${absnamein[$i]} ${localin[$i]} |
---|
| 2174 | fi |
---|
[2380] | 2175 | fi |
---|
| 2176 | fi |
---|
| 2177 | fi |
---|
| 2178 | fi |
---|
| 2179 | |
---|
| 2180 | done |
---|
| 2181 | if (( i != 0 )) |
---|
| 2182 | then |
---|
[2669] | 2183 | if [[ $optional_files_missing = true ]] |
---|
| 2184 | then |
---|
| 2185 | printf "\n *** INFORMATIVE: some optional INPUT-files are not present" |
---|
| 2186 | fi |
---|
[2380] | 2187 | printf "\n$dashes\n *** all INPUT-files provided \n" |
---|
| 2188 | fi |
---|
| 2189 | |
---|
[3917] | 2190 | # NOW COPY FILES (*.f90, *.o, config files, etc.) FROM SOURCES_FOR_RUN_... TO THE TEMPORARY |
---|
| 2191 | # WORKING DIRECTORY |
---|
| 2192 | cp ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*} $tempdir |
---|
[2380] | 2193 | |
---|
[3917] | 2194 | |
---|
[2380] | 2195 | # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE |
---|
| 2196 | (( i = 0 )) |
---|
| 2197 | while (( i < iic )) |
---|
| 2198 | do |
---|
| 2199 | (( i = i + 1 )) |
---|
| 2200 | if (( i == 1 )) |
---|
| 2201 | then |
---|
| 2202 | printf "\n\n *** execution of INPUT-commands:\n$dashes" |
---|
| 2203 | fi |
---|
| 2204 | printf "\n >>> ${in_command[$i]}" |
---|
| 2205 | eval ${in_command[$i]} |
---|
| 2206 | if (( i == iic )) |
---|
| 2207 | then |
---|
| 2208 | printf "\n$dashes\n" |
---|
| 2209 | fi |
---|
| 2210 | done |
---|
| 2211 | |
---|
| 2212 | |
---|
[3313] | 2213 | # CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED |
---|
| 2214 | if [[ $running_in_batch_mode = true || $running_in_test_mode = true ]] |
---|
| 2215 | then |
---|
| 2216 | progress_bar_disabled=true |
---|
| 2217 | else |
---|
| 2218 | progress_bar_disabled=false |
---|
| 2219 | fi |
---|
| 2220 | |
---|
| 2221 | |
---|
[2380] | 2222 | # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM |
---|
| 2223 | # (FILE ENVPAR WILL BE READ BY PALM) |
---|
| 2224 | cat > ENVPAR << EOF |
---|
[3236] | 2225 | &envpar run_identifier = '$run_identifier', host = '$configuration_identifier', |
---|
[2906] | 2226 | write_svf = .${write_svf}., write_binary = .${write_binary}., |
---|
| 2227 | read_svf = .${read_svf}., tasks_per_node = $tasks_per_node, |
---|
[2380] | 2228 | maximum_parallel_io_streams = $maximum_parallel_io_streams, |
---|
| 2229 | maximum_cpu_time_allowed = ${cpumax}., |
---|
| 2230 | revision = '$global_revision', |
---|
[3313] | 2231 | progress_bar_disabled = .${progress_bar_disabled}. / |
---|
[2380] | 2232 | |
---|
| 2233 | EOF |
---|
| 2234 | |
---|
| 2235 | |
---|
| 2236 | # STARTING THE EXECUTABLE |
---|
| 2237 | printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n" |
---|
[2566] | 2238 | PATH=$PATH:$tempdir |
---|
[2380] | 2239 | |
---|
| 2240 | |
---|
| 2241 | # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES |
---|
[2693] | 2242 | line=`echo "${execute_command}" | sed 's/{{/$/g' | sed 's/}}//g'` |
---|
| 2243 | line2=`echo "${execute_command}" | sed 's/{{mpi_tasks}}/1/g' | sed 's/{{tasks_per_node}}/1/g' | sed 's/palm/combine_plot_fields.x/g'` |
---|
[2380] | 2244 | eval line=\"$line\" |
---|
| 2245 | execute_command="$line" |
---|
| 2246 | |
---|
| 2247 | |
---|
| 2248 | # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS |
---|
[2566] | 2249 | if [[ "$execute_command_for_combine" = "" ]] |
---|
| 2250 | then |
---|
| 2251 | eval line2=\"$line2\" |
---|
| 2252 | execute_command_for_combine="$line2" |
---|
| 2253 | fi |
---|
| 2254 | |
---|
[2380] | 2255 | |
---|
| 2256 | |
---|
| 2257 | # PROVIDE A HOSTFILE, IF REQUIRED |
---|
| 2258 | if [[ "$hostfile" != "" ]] |
---|
| 2259 | then |
---|
| 2260 | |
---|
| 2261 | if [[ $hostfile = auto ]] |
---|
| 2262 | then |
---|
| 2263 | # CREATE A NEW HOSTFILE |
---|
| 2264 | (( ii = 1 )) |
---|
| 2265 | while (( ii <= cores / threads_per_task )) |
---|
| 2266 | do |
---|
| 2267 | echo $(hostname) >> hostfile |
---|
| 2268 | (( ii = ii + 1 )) |
---|
| 2269 | done |
---|
| 2270 | if (( cores / threads_per_task == 0 )) |
---|
| 2271 | then |
---|
| 2272 | echo $(hostname) >> hostfile |
---|
| 2273 | fi |
---|
| 2274 | |
---|
| 2275 | else |
---|
| 2276 | cp $hostfile hostfile |
---|
| 2277 | fi |
---|
| 2278 | eval line=\"`head -n $ii hostfile`\" |
---|
| 2279 | printf "\n *** running on: $line" |
---|
| 2280 | fi |
---|
| 2281 | |
---|
| 2282 | |
---|
| 2283 | |
---|
| 2284 | # SET THE NUMBER OF OPENMP-THREADS |
---|
| 2285 | if [[ $use_openmp = true ]] |
---|
| 2286 | then |
---|
| 2287 | export OMP_NUM_THREADS=$threads_per_task |
---|
| 2288 | printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS" |
---|
| 2289 | else |
---|
| 2290 | export OMP_NUM_THREADS=1 |
---|
| 2291 | fi |
---|
| 2292 | |
---|
| 2293 | |
---|
[2610] | 2294 | # PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING |
---|
[2380] | 2295 | if [[ $run_coupled_model = false ]] |
---|
| 2296 | then |
---|
| 2297 | if [[ "$ocean_file_appendix" = true ]] |
---|
| 2298 | then |
---|
| 2299 | echo "precursor_ocean" > coupling_steering |
---|
| 2300 | else |
---|
| 2301 | echo "precursor_atmos" > coupling_steering |
---|
| 2302 | fi |
---|
| 2303 | else |
---|
| 2304 | (( iia = $cores_atmos / $threads_per_task )) |
---|
| 2305 | (( iio = $cores_ocean / $threads_per_task )) |
---|
| 2306 | printf "\n coupled run ($iia atmosphere, $iio ocean)" |
---|
| 2307 | printf "\n\n" |
---|
| 2308 | echo "coupled_run $iia $iio" > coupling_steering |
---|
| 2309 | fi |
---|
| 2310 | |
---|
| 2311 | printf "\n *** execute command:" |
---|
| 2312 | printf "\n \"$execute_command\" \n\n" |
---|
| 2313 | |
---|
| 2314 | |
---|
[3393] | 2315 | if [[ $progress_bar_disabled = true ]] |
---|
[2380] | 2316 | then |
---|
[3402] | 2317 | $execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) ) |
---|
[3393] | 2318 | exit_code=${PIPESTATUS[0]} |
---|
| 2319 | else |
---|
| 2320 | $execute_command < coupling_steering &> >(tee STDOUT) |
---|
| 2321 | exit_code=${PIPESTATUS[0]} |
---|
| 2322 | fi |
---|
[2380] | 2323 | |
---|
[3393] | 2324 | if [[ ${exit_code} != 0 ]] |
---|
| 2325 | then |
---|
| 2326 | |
---|
[2380] | 2327 | # ABORT IN CASE OF RUNTIME ERRORS |
---|
| 2328 | printf "\n +++ runtime error occured" |
---|
| 2329 | locat=execution |
---|
| 2330 | exit |
---|
| 2331 | |
---|
| 2332 | else |
---|
| 2333 | |
---|
| 2334 | printf "\n$dashes\n *** execution finished \n" |
---|
| 2335 | |
---|
| 2336 | fi |
---|
| 2337 | |
---|
| 2338 | |
---|
| 2339 | # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN |
---|
| 2340 | # BY EACH CORE INTO ONE FILE |
---|
| 2341 | if [[ ! -f combine_plot_fields.x ]] |
---|
| 2342 | then |
---|
| 2343 | |
---|
| 2344 | printf "\n\n\n +++ WARNING: no combine_plot_fields found" |
---|
| 2345 | printf "\n 2d- and/or 3d-data may be incomplete!" |
---|
| 2346 | printf "\n Your previous palmbuild may have failed. Please check.\n" |
---|
| 2347 | |
---|
| 2348 | elif [[ "$combine_plot_fields" == true ]] |
---|
| 2349 | then |
---|
| 2350 | |
---|
| 2351 | printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..." |
---|
| 2352 | $execute_command_for_combine |
---|
| 2353 | |
---|
| 2354 | else |
---|
| 2355 | |
---|
| 2356 | # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF |
---|
[2605] | 2357 | # DATA OUTPUT |
---|
[2380] | 2358 | printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..." |
---|
| 2359 | fi |
---|
| 2360 | |
---|
| 2361 | |
---|
| 2362 | |
---|
| 2363 | # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE |
---|
| 2364 | (( i = 0 )) |
---|
| 2365 | while (( i < ioc )) |
---|
| 2366 | do |
---|
| 2367 | (( i = i + 1 )) |
---|
| 2368 | if (( i == 1 )) |
---|
| 2369 | then |
---|
| 2370 | printf "\n\n *** execution of OUTPUT-commands:\n$dashes" |
---|
| 2371 | fi |
---|
[2799] | 2372 | |
---|
| 2373 | # REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES |
---|
| 2374 | out_command[$i]=`echo "${out_command[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'` |
---|
| 2375 | |
---|
[2380] | 2376 | printf "\n >>> ${out_command[$i]}" |
---|
| 2377 | eval ${out_command[$i]} |
---|
| 2378 | if (( i == ioc )) |
---|
| 2379 | then |
---|
| 2380 | printf "\n$dashes\n" |
---|
| 2381 | fi |
---|
| 2382 | done |
---|
| 2383 | |
---|
| 2384 | |
---|
[2610] | 2385 | # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF |
---|
| 2386 | # WILDCARDS |
---|
[2380] | 2387 | (( i = 0 )) |
---|
[2610] | 2388 | (( nr_of_output_files = 0 )) |
---|
| 2389 | |
---|
[2380] | 2390 | while (( i < iout )) |
---|
| 2391 | do |
---|
[2610] | 2392 | |
---|
[2380] | 2393 | (( i = i + 1 )) |
---|
[2610] | 2394 | |
---|
| 2395 | # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND |
---|
| 2396 | # CREATE A LIST FOR THE DETECTED ENDINGS |
---|
| 2397 | if [[ "${multout[$i]}" = true ]] |
---|
| 2398 | then |
---|
| 2399 | # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES |
---|
| 2400 | ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null |
---|
| 2401 | ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null |
---|
| 2402 | |
---|
| 2403 | endings="DEFAULT" |
---|
| 2404 | while read line |
---|
| 2405 | do |
---|
| 2406 | # remove the local name from the beginning |
---|
| 2407 | localnamestring="${localout_pre[$i]}" |
---|
| 2408 | length_localname=${#localnamestring} |
---|
| 2409 | ending=${line:${length_localname}} |
---|
| 2410 | |
---|
| 2411 | if [[ "$ending" != "" ]] |
---|
| 2412 | then |
---|
| 2413 | endings="$endings $ending" |
---|
| 2414 | fi |
---|
| 2415 | |
---|
| 2416 | done <filelist |
---|
| 2417 | |
---|
| 2418 | rm filelist |
---|
| 2419 | |
---|
| 2420 | else |
---|
| 2421 | |
---|
| 2422 | # SINGLE NAME |
---|
| 2423 | endings=DEFAULT |
---|
| 2424 | |
---|
| 2425 | fi |
---|
| 2426 | |
---|
| 2427 | # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST |
---|
| 2428 | for ending in $endings |
---|
| 2429 | do |
---|
| 2430 | |
---|
| 2431 | # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED |
---|
| 2432 | if [[ $ending = DEFAULT ]] |
---|
| 2433 | then |
---|
| 2434 | ending="" |
---|
| 2435 | fi |
---|
| 2436 | |
---|
| 2437 | # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!) |
---|
| 2438 | (( nr_of_output_files = nr_of_output_files + 1 )) |
---|
| 2439 | localout[$nr_of_output_files]="${localout_pre[$i]}"$ending |
---|
| 2440 | transout[$nr_of_output_files]="${transout_pre[$i]}" |
---|
| 2441 | actionout[$nr_of_output_files]="${actionout_pre[$i]}" |
---|
| 2442 | pathout[$nr_of_output_files]="${pathout_pre[$i]}" |
---|
| 2443 | endout[$nr_of_output_files]="${endout_pre[$i]}"$ending |
---|
| 2444 | extout[$nr_of_output_files]="${extout_pre[$i]}" |
---|
[2669] | 2445 | warnout[$nr_of_output_files]="${warnout_pre[$i]}" |
---|
[2610] | 2446 | |
---|
| 2447 | done |
---|
| 2448 | |
---|
| 2449 | done |
---|
| 2450 | |
---|
| 2451 | |
---|
| 2452 | |
---|
| 2453 | |
---|
| 2454 | # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS |
---|
| 2455 | (( i = 0 )) |
---|
| 2456 | while (( i < nr_of_output_files )) |
---|
| 2457 | do |
---|
| 2458 | (( i = i + 1 )) |
---|
[2380] | 2459 | if (( i == 1 )) |
---|
| 2460 | then |
---|
[3860] | 2461 | timestring=`date +%H:%M:%S` |
---|
| 2462 | printf "\n\n *** saving OUTPUT-files: local time: $timestring" |
---|
[2380] | 2463 | |
---|
| 2464 | # GET RUN NUMBER ASSIGNED BY PALM |
---|
| 2465 | if [[ -f RUN_NUMBER ]] |
---|
| 2466 | then |
---|
| 2467 | read run_number < RUN_NUMBER |
---|
| 2468 | printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files" |
---|
| 2469 | usecycle_option="-U $run_number" |
---|
| 2470 | else |
---|
| 2471 | run_number=0 |
---|
| 2472 | usecycle_option="" |
---|
| 2473 | fi |
---|
| 2474 | if [[ $running_on_remote = true && "$remote_loginnode" != "" ]] |
---|
| 2475 | then |
---|
[2404] | 2476 | printf "\n *** in case of SCP transfers to local host" |
---|
| 2477 | printf "\n they will be done via remote login-node \"$remote_loginnode\" " |
---|
[2380] | 2478 | fi |
---|
| 2479 | printf "\n$dashes" |
---|
| 2480 | fi |
---|
| 2481 | |
---|
| 2482 | if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]] |
---|
| 2483 | then |
---|
| 2484 | |
---|
[3236] | 2485 | eval filename=${pathout[$i]}/${run_identifier}${endout[$i]} |
---|
[2610] | 2486 | |
---|
| 2487 | # DETERMINE THE CYCLE NUMBER |
---|
| 2488 | ls -1 -d $filename > filelist 2>/dev/null |
---|
| 2489 | ls -1 -d $filename.* >> filelist 2>/dev/null |
---|
| 2490 | while read line |
---|
| 2491 | do |
---|
| 2492 | |
---|
| 2493 | # filename without path (i.e. after the last "/") |
---|
| 2494 | basefilename=$(basename ${line}) |
---|
| 2495 | |
---|
| 2496 | # check if there is an extension |
---|
| 2497 | extension=${basefilename##*.} |
---|
| 2498 | if [[ "$extension" = "${extout[$i]}" ]] |
---|
| 2499 | then |
---|
| 2500 | basefilename=${basefilename%.*} |
---|
| 2501 | fi |
---|
| 2502 | |
---|
| 2503 | # check for an existing cycle number |
---|
| 2504 | cycle=${basefilename##*.} |
---|
| 2505 | if [[ $cycle =~ ^-?[0-9]+$ ]] |
---|
| 2506 | then |
---|
[2669] | 2507 | # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS |
---|
| 2508 | # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 |
---|
| 2509 | (( icycle = $((10#$cycle)) + 1 )) |
---|
[2610] | 2510 | else |
---|
| 2511 | (( icycle = 1 )) |
---|
| 2512 | fi |
---|
| 2513 | |
---|
| 2514 | if (( icycle > maxcycle )) |
---|
| 2515 | then |
---|
| 2516 | (( maxcycle = icycle )) |
---|
| 2517 | fi |
---|
| 2518 | |
---|
| 2519 | done <filelist |
---|
| 2520 | rm filelist |
---|
| 2521 | |
---|
| 2522 | |
---|
| 2523 | # SET THE CYCLE NUMBER |
---|
| 2524 | # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER |
---|
| 2525 | if [[ "${actionout[$i]}" = a ]] |
---|
| 2526 | then |
---|
| 2527 | (( maxcycle = maxcycle - 1 )) |
---|
| 2528 | fi |
---|
| 2529 | |
---|
| 2530 | (( cycnum[$i] = maxcycle )) |
---|
| 2531 | pathout[$i]=$filename |
---|
| 2532 | |
---|
| 2533 | |
---|
| 2534 | # ADD CYCLE NUMBER TO FILENAME |
---|
| 2535 | # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER |
---|
[2380] | 2536 | if [[ "${actionout[$i]}" != "a" ]] |
---|
| 2537 | then |
---|
| 2538 | # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT |
---|
| 2539 | # WITH AN EXISTING CYCLE NUMBER |
---|
| 2540 | if (( run_number >= cycnum[$i] )) |
---|
| 2541 | then |
---|
| 2542 | (( cycnum[$i] = run_number )) |
---|
| 2543 | else |
---|
| 2544 | if (( run_number > 0 )) |
---|
| 2545 | then |
---|
| 2546 | printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number" |
---|
| 2547 | fi |
---|
| 2548 | fi |
---|
| 2549 | fi |
---|
| 2550 | if (( cycnum[$i] > 0 )) |
---|
| 2551 | then |
---|
[2600] | 2552 | cyclestring=`printf "%03d" ${cycnum[$i]}` |
---|
| 2553 | pathout[$i]=${pathout[$i]}.$cyclestring |
---|
[2380] | 2554 | fi |
---|
| 2555 | fi |
---|
| 2556 | |
---|
| 2557 | # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION) |
---|
| 2558 | files_for_cores=false; filetype=file |
---|
| 2559 | link_local_output=false |
---|
| 2560 | if [[ "${actionout[$i]}" = pe && -n $cores ]] |
---|
| 2561 | then |
---|
| 2562 | files_for_cores=true; filetype=directory |
---|
| 2563 | actionout[$i]="" |
---|
| 2564 | elif [[ "${actionout[$i]}" = pe && ! -n $cores ]] |
---|
| 2565 | then |
---|
| 2566 | actionout[$i]="" |
---|
| 2567 | elif [[ "${actionout[$i]}" = lnpe && -n $cores ]] |
---|
| 2568 | then |
---|
| 2569 | files_for_cores=true; filetype=directory |
---|
| 2570 | link_local_output=true |
---|
| 2571 | actionout[$i]="" |
---|
| 2572 | elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]] |
---|
| 2573 | then |
---|
| 2574 | link_local_output |
---|
| 2575 | actionout[$i]="" |
---|
| 2576 | elif [[ "${actionout[$i]}" = trpe && -n $cores ]] |
---|
| 2577 | then |
---|
| 2578 | files_for_cores=true; filetype=directory |
---|
| 2579 | actionout[$i]="tr" |
---|
| 2580 | elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]] |
---|
| 2581 | then |
---|
| 2582 | actionout[$i]="tr" |
---|
| 2583 | fi |
---|
| 2584 | |
---|
| 2585 | if [[ ! -f ${localout[$i]} && $files_for_cores = false ]] |
---|
| 2586 | then |
---|
[2669] | 2587 | if [[ ${warnout[$i]} = true ]] |
---|
| 2588 | then |
---|
| 2589 | printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n" |
---|
| 2590 | fi |
---|
[2380] | 2591 | elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]] |
---|
| 2592 | then |
---|
[2669] | 2593 | if [[ ${warnout[$i]} = true ]] |
---|
| 2594 | then |
---|
| 2595 | printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n" |
---|
| 2596 | fi |
---|
[2380] | 2597 | else |
---|
| 2598 | |
---|
| 2599 | |
---|
| 2600 | # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m) |
---|
| 2601 | # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT |
---|
| 2602 | if [[ "${actionout[$i]}" = tr || "${actionout[$i]}" = tra ]] |
---|
| 2603 | then |
---|
| 2604 | if [[ $running_on_remote = true ]] |
---|
| 2605 | then |
---|
| 2606 | |
---|
| 2607 | # SET OPTIONS FOR TRANSFER |
---|
| 2608 | if [[ "${actionout[$i]}" = tr ]] |
---|
| 2609 | then |
---|
| 2610 | if [[ $files_for_cores = false ]] |
---|
| 2611 | then |
---|
| 2612 | catalog_option="" |
---|
| 2613 | catalog_string="" |
---|
| 2614 | else |
---|
| 2615 | catalog_option="-c" |
---|
| 2616 | catalog_string="/" |
---|
| 2617 | fi |
---|
| 2618 | append_option="" |
---|
| 2619 | append_string="" |
---|
| 2620 | else |
---|
| 2621 | append_option="-A" |
---|
| 2622 | append_string="append" |
---|
| 2623 | fi |
---|
| 2624 | |
---|
| 2625 | transfer_failed=false |
---|
| 2626 | printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to" |
---|
[3236] | 2627 | printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n" |
---|
[2380] | 2628 | |
---|
| 2629 | # TRANSFER VIA SCP |
---|
| 2630 | if [[ "$remote_loginnode" != "" ]] |
---|
| 2631 | then |
---|
[3534] | 2632 | ssh -q $remote_username@$remote_loginnode "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" |
---|
[2380] | 2633 | else |
---|
[3236] | 2634 | batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]} |
---|
[2380] | 2635 | fi |
---|
[3312] | 2636 | [[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true |
---|
[2380] | 2637 | |
---|
| 2638 | |
---|
| 2639 | # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE |
---|
| 2640 | if [[ $transfer_failed = true ]] |
---|
| 2641 | then |
---|
| 2642 | printf " +++ transfer failed. Trying to save a copy on this host under:\n" |
---|
[3236] | 2643 | printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n" |
---|
[2380] | 2644 | |
---|
| 2645 | # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY |
---|
| 2646 | eval local_catalog=${pathout[$i]} |
---|
| 2647 | if [[ ! -d $local_catalog ]] |
---|
| 2648 | then |
---|
| 2649 | printf " *** local directory does not exist. Trying to create:\n" |
---|
| 2650 | printf " $local_catalog \n" |
---|
| 2651 | mkdir -p $local_catalog |
---|
| 2652 | fi |
---|
[3236] | 2653 | eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number |
---|
[2380] | 2654 | transfer_problems=true |
---|
| 2655 | fi |
---|
| 2656 | |
---|
| 2657 | else |
---|
| 2658 | |
---|
| 2659 | # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST |
---|
| 2660 | # BE COPIED OR APPENDED ON THIS MACHINE |
---|
| 2661 | if [[ "${actionout[$i]}" = tr ]] |
---|
| 2662 | then |
---|
| 2663 | actionout[$i]="" |
---|
| 2664 | else |
---|
| 2665 | actionout[$i]="a" |
---|
| 2666 | fi |
---|
| 2667 | fi |
---|
| 2668 | fi |
---|
| 2669 | |
---|
| 2670 | |
---|
| 2671 | # APPEND ON THIS MACHINE |
---|
| 2672 | if [[ "${actionout[$i]}" = "a" ]] |
---|
| 2673 | then |
---|
| 2674 | if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] |
---|
| 2675 | then |
---|
| 2676 | printf "\n >>> OUTPUT: ${localout[$i]} append to" |
---|
| 2677 | printf "\n ${pathout[$i]}.${extout[$i]}\n" |
---|
| 2678 | cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]} |
---|
| 2679 | else |
---|
| 2680 | printf "\n >>> OUTPUT: ${localout[$i]} append to" |
---|
| 2681 | printf "\n ${pathout[$i]}\n" |
---|
| 2682 | cat ${localout[$i]} >> ${pathout[$i]} |
---|
| 2683 | fi |
---|
| 2684 | fi |
---|
| 2685 | |
---|
| 2686 | # COPY ON THIS MACHINE |
---|
| 2687 | # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE |
---|
| 2688 | # ON DIFFERENT FILE-SYSTEMS |
---|
| 2689 | if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]] |
---|
| 2690 | then |
---|
| 2691 | |
---|
| 2692 | # COPY IN CASE OF RUNS ON SINGLE CORES |
---|
| 2693 | if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] |
---|
| 2694 | then |
---|
| 2695 | printf "\n >>> OUTPUT: ${localout[$i]} to" |
---|
| 2696 | printf "\n ${pathout[$i]}.${extout[$i]}\n" |
---|
| 2697 | if [[ $link_local_output = true ]] |
---|
| 2698 | then |
---|
| 2699 | printf " file will be linked\n" |
---|
| 2700 | ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]} |
---|
| 2701 | fi |
---|
| 2702 | # If "ln -f" fails of if "$link_local_output = false" do a normal "cp" |
---|
| 2703 | if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]] |
---|
| 2704 | then |
---|
| 2705 | if [[ $link_local_output = true ]] |
---|
| 2706 | then |
---|
| 2707 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
| 2708 | fi |
---|
| 2709 | cp ${localout[$i]} ${pathout[$i]}.${extout[$i]} |
---|
| 2710 | else |
---|
| 2711 | printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n" |
---|
| 2712 | fi |
---|
| 2713 | else |
---|
| 2714 | printf "\n >>> OUTPUT: ${localout[$i]} to" |
---|
| 2715 | printf "\n ${pathout[$i]}\n" |
---|
| 2716 | if [[ $link_local_output = true ]] |
---|
| 2717 | then |
---|
| 2718 | printf " file will be linked\n" |
---|
| 2719 | ln -f ${localout[$i]} ${pathout[$i]} |
---|
| 2720 | fi |
---|
| 2721 | # If "ln -f" fails of if "$link_local_output = false" do a normal "cp" |
---|
| 2722 | if [[ ! -f "${pathout[$i]}" ]] |
---|
| 2723 | then |
---|
| 2724 | if [[ $link_local_output = true ]] |
---|
| 2725 | then |
---|
| 2726 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
| 2727 | fi |
---|
| 2728 | cp ${localout[$i]} ${pathout[$i]} |
---|
| 2729 | else |
---|
| 2730 | printf "+++ no copy because file ${pathout[$i]} exists\n" |
---|
| 2731 | fi |
---|
| 2732 | fi |
---|
| 2733 | |
---|
| 2734 | elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]] |
---|
| 2735 | then |
---|
| 2736 | |
---|
| 2737 | # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY |
---|
| 2738 | # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED |
---|
| 2739 | printf "\n >>> OUTPUT: ${localout[$i]}/_.... to" |
---|
| 2740 | printf "\n ${pathout[$i]}\n" |
---|
| 2741 | if [[ $link_local_output = true ]] |
---|
| 2742 | then |
---|
| 2743 | printf " files will be linked\n" |
---|
[2396] | 2744 | mkdir -p ${pathout[$i]} |
---|
[2380] | 2745 | cd ${localout[$i]} |
---|
| 2746 | for file in $(ls *) |
---|
| 2747 | do |
---|
| 2748 | ln -f $file ${pathout[$i]} |
---|
| 2749 | done >|/dev/null 2>&1 |
---|
[2566] | 2750 | cd $tempdir |
---|
[2380] | 2751 | fi |
---|
| 2752 | |
---|
| 2753 | # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r" |
---|
| 2754 | if [[ ! -f "${pathout[$i]}/_000000" ]] |
---|
| 2755 | then |
---|
| 2756 | if [[ $link_local_output = true ]] |
---|
| 2757 | then |
---|
| 2758 | printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" |
---|
| 2759 | fi |
---|
[3025] | 2760 | [[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]} |
---|
[2380] | 2761 | cp -r ${localout[$i]}/* ${pathout[$i]} |
---|
| 2762 | fi |
---|
| 2763 | |
---|
| 2764 | fi |
---|
| 2765 | fi |
---|
| 2766 | done |
---|
| 2767 | |
---|
| 2768 | if (( i != 0 )) |
---|
| 2769 | then |
---|
[3860] | 2770 | timestring=`date +%H:%M:%S` |
---|
[2380] | 2771 | if [[ $transfer_problems = true ]] |
---|
| 2772 | then |
---|
[3860] | 2773 | printf "\n$dashes\n *** OUTPUT-files saved local time: $timestring" |
---|
[2380] | 2774 | printf "\n +++ WARNING: some data transfers failed! \n" |
---|
| 2775 | else |
---|
[3860] | 2776 | printf "\n$dashes\n *** all OUTPUT-files saved local time: $timestring \n" |
---|
[2380] | 2777 | fi |
---|
| 2778 | fi |
---|
| 2779 | |
---|
| 2780 | |
---|
| 2781 | # IF REQUIRED, START A RESTART-JOB |
---|
| 2782 | # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM) |
---|
| 2783 | if [[ -f CONTINUE_RUN ]] |
---|
| 2784 | then |
---|
| 2785 | |
---|
| 2786 | # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY): |
---|
| 2787 | # -C TELLS PALMRUN THAT IT IS A RESTART-RUN |
---|
| 2788 | # -v SILENT MODE WITHOUT INTERACTIVE QUERIES |
---|
| 2789 | # -b START A BATCH JOB |
---|
| 2790 | [[ $(echo $prc | grep -c "\-C") = 0 ]] && prc="$prc -C" |
---|
| 2791 | [[ $(echo $prc | grep -c "\-v") = 0 ]] && prc="$prc -v" |
---|
[3982] | 2792 | [[ $(echo $prc | grep -c "\-b") = 0 && $running_on_remote = false ]] && prc="$prc -b" |
---|
[2380] | 2793 | |
---|
[2957] | 2794 | # REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a) |
---|
| 2795 | # SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN |
---|
| 2796 | if [[ $(echo $prc | grep -c "svfout") != 0 ]] |
---|
| 2797 | then |
---|
| 2798 | prc=`echo $prc | sed 's/svfout/svfin/g'` |
---|
| 2799 | fi |
---|
[2380] | 2800 | |
---|
| 2801 | # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a) |
---|
| 2802 | # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN |
---|
| 2803 | if [[ $(echo $prc | grep -c "#") != 0 ]] |
---|
| 2804 | then |
---|
[2381] | 2805 | prc=`echo $prc | sed 's/#/r/g'` |
---|
[2380] | 2806 | fi |
---|
| 2807 | |
---|
| 2808 | |
---|
| 2809 | # START THE RESTART-JOB |
---|
| 2810 | printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n" |
---|
| 2811 | echo " $prc" |
---|
| 2812 | printf "\n$dashes\n" |
---|
| 2813 | if [[ $running_on_remote = true ]] |
---|
| 2814 | then |
---|
| 2815 | |
---|
| 2816 | echo "*** ssh will be used to initiate restart-runs!" |
---|
| 2817 | echo " return_address=\"$return_address\" " |
---|
| 2818 | echo " return_username=\"$local_username\" " |
---|
| 2819 | |
---|
| 2820 | if [[ "$remote_loginnode" != "" ]] |
---|
| 2821 | then |
---|
[3534] | 2822 | ssh -q $remote_username@$remote_loginnode "ssh -q $SSH_PORTOPT $local_username@$return_address \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" " | tee palmrun_restart.log |
---|
[2380] | 2823 | else |
---|
[3534] | 2824 | ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" | tee palmrun_restart.log |
---|
[2380] | 2825 | fi |
---|
| 2826 | |
---|
| 2827 | # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED |
---|
| 2828 | sleep 30 |
---|
| 2829 | |
---|
| 2830 | else |
---|
| 2831 | |
---|
| 2832 | # START THE RESTART JOB ON THE LOCAL HOST |
---|
[3132] | 2833 | eval $prc | tee palmrun_restart.log # THE ' MUST BE EVALUATED |
---|
[2380] | 2834 | |
---|
| 2835 | fi |
---|
| 2836 | |
---|
[3132] | 2837 | # CHECK, IF RESTART JOB HAS BEEN STARTED |
---|
[3725] | 2838 | if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]] |
---|
[3132] | 2839 | then |
---|
| 2840 | printf "\n$dashes\n +++ creating restart run failed \n" |
---|
| 2841 | locat=create_restart |
---|
[3455] | 2842 | rm palmrun_restart.log |
---|
[3132] | 2843 | exit |
---|
[3725] | 2844 | elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]] |
---|
| 2845 | then |
---|
| 2846 | printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n" |
---|
| 2847 | locat=create_restart |
---|
| 2848 | rm palmrun_restart.log |
---|
| 2849 | exit |
---|
[3132] | 2850 | else |
---|
| 2851 | printf "\n$dashes\n *** restart run initiated \n" |
---|
| 2852 | rm palmrun_restart.log |
---|
| 2853 | fi |
---|
[2380] | 2854 | |
---|
[3132] | 2855 | |
---|
[2380] | 2856 | # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA |
---|
| 2857 | # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB. |
---|
| 2858 | # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES |
---|
| 2859 | # MAY BE VERY HUGE) |
---|
| 2860 | (( i = 0 )) |
---|
[2610] | 2861 | while (( i < nr_of_input_files )) |
---|
[2380] | 2862 | do |
---|
| 2863 | (( i = i + 1 )) |
---|
| 2864 | if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]] |
---|
| 2865 | then |
---|
| 2866 | rm -r ${absnamein[$i]} |
---|
| 2867 | fi |
---|
| 2868 | done |
---|
| 2869 | |
---|
| 2870 | fi |
---|
| 2871 | |
---|
| 2872 | |
---|
| 2873 | # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED |
---|
| 2874 | cd $HOME |
---|
[2566] | 2875 | [[ $delete_temporary_catalog = true ]] && rm -rf $tempdir |
---|
[2380] | 2876 | |
---|
| 2877 | |
---|
| 2878 | else |
---|
| 2879 | |
---|
| 2880 | |
---|
| 2881 | # PREPARING ACTIONS, |
---|
| 2882 | # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE |
---|
| 2883 | |
---|
| 2884 | # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB |
---|
[3455] | 2885 | palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username" |
---|
[2380] | 2886 | [[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\"" |
---|
| 2887 | [[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\"" |
---|
| 2888 | [[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k" |
---|
| 2889 | [[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x" |
---|
| 2890 | [[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores" |
---|
| 2891 | [[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task" |
---|
[2501] | 2892 | [[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node" |
---|
[2380] | 2893 | [[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B" |
---|
| 2894 | [[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y" |
---|
| 2895 | [[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\"" |
---|
| 2896 | [[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z" |
---|
| 2897 | [[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str" |
---|
[2479] | 2898 | [[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account" |
---|
[2380] | 2899 | if [[ $create_remote_batch_job = true ]] |
---|
| 2900 | then |
---|
| 2901 | palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip" |
---|
[2420] | 2902 | if [[ $do_trace = true ]] |
---|
| 2903 | then |
---|
| 2904 | printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n" |
---|
| 2905 | fi |
---|
[2380] | 2906 | elif [[ $create_batch_job = true ]] |
---|
| 2907 | then |
---|
| 2908 | palmrun_com=${palmrun_com}" -j" |
---|
[2420] | 2909 | if [[ $do_trace = true ]] |
---|
| 2910 | then |
---|
| 2911 | printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n" |
---|
| 2912 | fi |
---|
[2380] | 2913 | fi |
---|
| 2914 | |
---|
| 2915 | |
---|
| 2916 | # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND |
---|
| 2917 | # REMOTE HOST |
---|
[3236] | 2918 | job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id} |
---|
[2380] | 2919 | job_protocol_file=$job_protocol_file_local |
---|
| 2920 | if [[ $create_remote_batch_job = true ]] |
---|
| 2921 | then |
---|
[3236] | 2922 | job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id} |
---|
[2380] | 2923 | job_protocol_file=$job_protocol_file_remote |
---|
| 2924 | job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol |
---|
[3236] | 2925 | scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number |
---|
[2380] | 2926 | fi |
---|
| 2927 | |
---|
| 2928 | |
---|
| 2929 | # BUILD THE JOB-SCRIPTS ON FILE jobfile |
---|
[3236] | 2930 | jobfile=jobfile.$run_id_number |
---|
[2380] | 2931 | |
---|
| 2932 | |
---|
| 2933 | # FIRST CREATE THE BATCH DIRECTIVES |
---|
| 2934 | (( i = 0 )) |
---|
| 2935 | while (( i < ibd )) |
---|
| 2936 | do |
---|
| 2937 | (( i = i + 1 )) |
---|
[2693] | 2938 | line=`echo "${batch_directive[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'` |
---|
[2380] | 2939 | eval line=\"$line\" |
---|
| 2940 | echo "$line" >> $jobfile |
---|
| 2941 | done |
---|
| 2942 | echo " " >> $jobfile |
---|
| 2943 | |
---|
| 2944 | |
---|
| 2945 | # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB |
---|
| 2946 | # PROTOCOL |
---|
| 2947 | if [[ $create_remote_batch_job = true ]] |
---|
| 2948 | then |
---|
[3236] | 2949 | echo "set +vx" >> $jobfile |
---|
| 2950 | echo "trap '" >> $jobfile |
---|
| 2951 | echo "set +vx" >> $jobfile |
---|
| 2952 | echo "cd ${remote_jobcatalog}" >> $jobfile |
---|
| 2953 | echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile |
---|
[2380] | 2954 | |
---|
| 2955 | # ADD THE BATCH DIRECTIVES |
---|
| 2956 | (( i = 0 )) |
---|
| 2957 | while (( i < ibdt )) |
---|
| 2958 | do |
---|
| 2959 | (( i = i + 1 )) |
---|
[2693] | 2960 | line=`echo "${batch_directive_transfer[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'` |
---|
[2380] | 2961 | eval line=\"$line\" |
---|
| 2962 | echo "$line" >> $jobfile |
---|
| 2963 | done |
---|
| 2964 | echo " " >> $jobfile |
---|
| 2965 | |
---|
| 2966 | echo "set -x" >> $jobfile |
---|
[3534] | 2967 | if [[ "$remote_loginnode" != "" ]] |
---|
| 2968 | then |
---|
| 2969 | echo "ssh -q $remote_username@$remote_loginnode \"cd ${remote_jobcatalog}; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \\\"$local_jobcatalog\\\" ${configuration_identifier}_${run_identifier}\" " >> $jobfile |
---|
| 2970 | else |
---|
| 2971 | echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile |
---|
| 2972 | fi |
---|
[2380] | 2973 | echo "%%END%%" >> $jobfile |
---|
| 2974 | echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile |
---|
[3534] | 2975 | echo "$submit_command $scpjob_file" >> $jobfile |
---|
[2380] | 2976 | echo "rm $scpjob_file" >> $jobfile |
---|
[2404] | 2977 | echo "rm -rf $job_transfer_protocol_file" >> $jobfile |
---|
[2380] | 2978 | echo "set -x" >> $jobfile |
---|
| 2979 | echo " ' exit" >> $jobfile |
---|
| 2980 | fi |
---|
| 2981 | |
---|
| 2982 | |
---|
| 2983 | # ACTIVATE ERROR-TRACEBACK |
---|
| 2984 | if [[ $do_trace = true ]] |
---|
| 2985 | then |
---|
| 2986 | echo "set -x" >> $jobfile |
---|
| 2987 | else |
---|
| 2988 | echo "set +vx" >> $jobfile |
---|
| 2989 | fi |
---|
| 2990 | |
---|
| 2991 | |
---|
| 2992 | # INITIALIZE THE ENVIRONMENT AND LOAD MODULES |
---|
| 2993 | if [[ "$login_init_cmd" != "" ]] |
---|
| 2994 | then |
---|
| 2995 | echo "$login_init_cmd" >> $jobfile |
---|
| 2996 | fi |
---|
| 2997 | if [[ "$module_commands" != "" ]] |
---|
| 2998 | then |
---|
| 2999 | echo "$module_commands" >> $jobfile |
---|
| 3000 | fi |
---|
| 3001 | |
---|
| 3002 | |
---|
| 3003 | # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT |
---|
[2566] | 3004 | if [[ $create_remote_batch_job = true ]] |
---|
| 3005 | then |
---|
| 3006 | echo "mkdir $tempdir" >> $jobfile |
---|
[4303] | 3007 | echo "if [[ \$? != 0 ]]" >> $jobfile |
---|
| 3008 | echo "then" >> $jobfile |
---|
| 3009 | echo " echo \"+++ temporary working directory cannot be created.\" " >> $jobfile |
---|
| 3010 | echo " echo \" Check setting of variable fast_io_catalog in your config file.\" " >> $jobfile |
---|
| 3011 | echo " exit" >> $jobfile |
---|
| 3012 | echo "fi" >> $jobfile |
---|
[2566] | 3013 | echo "chmod go+rx $tempdir" >> $jobfile |
---|
| 3014 | else |
---|
| 3015 | # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A |
---|
| 3016 | # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN |
---|
| 3017 | # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED) |
---|
| 3018 | mkdir $tempdir |
---|
[4303] | 3019 | if [[ $? != 0 ]] |
---|
| 3020 | then |
---|
| 3021 | printf "\n +++ temporary working directory cannot be created." |
---|
| 3022 | printf "\n Check setting of variable fast_io_catalog in your config file." |
---|
| 3023 | locat=execution |
---|
| 3024 | exit |
---|
| 3025 | fi |
---|
[2566] | 3026 | chmod go+rx $tempdir |
---|
| 3027 | fi |
---|
| 3028 | echo "cd $tempdir" >> $jobfile |
---|
| 3029 | echo "export tempdir=$tempdir" >> $jobfile |
---|
[3917] | 3030 | echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/.[!.]* ." >> $jobfile |
---|
| 3031 | echo "export PATH=.:${fast_io_catalog}/${sources_for_run_catalog}:\$PATH" >> $jobfile |
---|
[2380] | 3032 | echo "export execute_palmrun=true" >> $jobfile |
---|
| 3033 | |
---|
| 3034 | |
---|
| 3035 | # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS |
---|
| 3036 | # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN |
---|
| 3037 | # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED |
---|
| 3038 | echo "LOCAL_PWD=$working_directory" >> $jobfile |
---|
| 3039 | echo "export LOCAL_PWD" >> $jobfile |
---|
| 3040 | |
---|
| 3041 | |
---|
| 3042 | # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON |
---|
[2420] | 3043 | echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile |
---|
[2380] | 3044 | echo "export LOCAL_PALMRUN_PATH" >> $jobfile |
---|
| 3045 | |
---|
| 3046 | |
---|
| 3047 | # CALL PALMRUN WITHIN THE JOB |
---|
| 3048 | # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB |
---|
| 3049 | echo "set -x" >> $jobfile |
---|
| 3050 | echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile |
---|
| 3051 | |
---|
| 3052 | |
---|
| 3053 | # TRANSFER JOBFILE TO THE TARGET HOST |
---|
| 3054 | if [[ $create_jobfile_only = false ]] |
---|
| 3055 | then |
---|
| 3056 | |
---|
[3505] | 3057 | # CREATE LOCAL JOB FOLDER |
---|
| 3058 | eval local_jobcatalog=$local_jobcatalog |
---|
| 3059 | if [[ ! -d $local_jobcatalog ]] |
---|
| 3060 | then |
---|
| 3061 | echo " " |
---|
| 3062 | echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now" |
---|
| 3063 | mkdir $local_jobcatalog |
---|
| 3064 | fi |
---|
| 3065 | |
---|
[2380] | 3066 | if [[ $create_remote_batch_job = true ]] |
---|
| 3067 | then |
---|
| 3068 | |
---|
[2420] | 3069 | echo " " |
---|
[2566] | 3070 | echo " *** transfer of job to remote host via scp" |
---|
[3505] | 3071 | |
---|
| 3072 | # CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST |
---|
[3534] | 3073 | ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1 |
---|
[3505] | 3074 | |
---|
| 3075 | # COPY THE JOB FILE |
---|
[2420] | 3076 | if [[ $do_trace = true ]] |
---|
| 3077 | then |
---|
[3236] | 3078 | echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}" |
---|
[2420] | 3079 | fi |
---|
[3236] | 3080 | scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null |
---|
[2380] | 3081 | |
---|
[3505] | 3082 | # SUBMIT THE JOB |
---|
[3574] | 3083 | printf " *** submit the job (output of submit command, \n" |
---|
[3573] | 3084 | printf " e.g. the job-id given by the batch-system, may follow) \n" |
---|
[2420] | 3085 | if [[ $do_trace = true ]] |
---|
| 3086 | then |
---|
[3665] | 3087 | echo " ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" " |
---|
[2420] | 3088 | fi |
---|
[3665] | 3089 | ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" |
---|
[2380] | 3090 | |
---|
| 3091 | elif [[ $create_batch_job = true ]] |
---|
| 3092 | then |
---|
| 3093 | |
---|
[2385] | 3094 | eval local_jobcatalog=$local_jobcatalog |
---|
[3236] | 3095 | cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id} |
---|
[2385] | 3096 | cd $local_jobcatalog |
---|
[2380] | 3097 | echo " " |
---|
[2420] | 3098 | echo " *** submit the job" |
---|
| 3099 | if [[ $do_trace = true ]] |
---|
| 3100 | then |
---|
[3236] | 3101 | echo "$submit_command ${configuration_identifier}_${run_id}" |
---|
[2420] | 3102 | fi |
---|
[3236] | 3103 | $submit_command ${configuration_identifier}_${run_id} |
---|
| 3104 | rm ${configuration_identifier}_${run_id} |
---|
[2380] | 3105 | cd - > /dev/null |
---|
| 3106 | |
---|
| 3107 | fi |
---|
| 3108 | |
---|
| 3109 | rm -rf $jobfile |
---|
| 3110 | |
---|
| 3111 | else |
---|
| 3112 | |
---|
| 3113 | printf "\n *** jobfile created under name \"$jobfile\" " |
---|
| 3114 | printf "\n no batch-job has been sent!" |
---|
| 3115 | |
---|
| 3116 | fi |
---|
| 3117 | |
---|
| 3118 | fi # END OF REMOTE-PART |
---|