| 1 | #!/usr/bin/env python |
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| 2 | # -*- coding: utf-8 -*- |
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| 3 | #******************************************************************************* |
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| 4 | # @Author: Leopold Haimberger (University of Vienna) |
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| 5 | # |
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| 6 | # @Date: November 2015 |
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| 7 | # |
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| 8 | # @Change History: |
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| 9 | # |
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| 10 | # February 2018 - Anne Philipp (University of Vienna): |
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| 11 | # - applied PEP8 style guide |
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| 12 | # - added documentation |
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| 13 | # - moved install_args_and_control in here |
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| 14 | # - splitted code in smaller functions |
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| 15 | # - delete convert build files in here instead of compile job script |
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| 16 | # - changed static path names to Variables from config file |
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| 17 | # |
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| 18 | # @License: |
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| 19 | # (C) Copyright 2015-2018. |
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| 20 | # |
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| 21 | # This software is licensed under the terms of the Apache Licence Version 2.0 |
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| 22 | # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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| 23 | # |
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| 24 | # @Program Functionality: |
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| 25 | # Depending on the selected installation environment (locally or on the |
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| 26 | # ECMWF server ecgate or cca) the program extracts the commandline |
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| 27 | # arguments and the CONTROL file parameter and prepares the corresponding |
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| 28 | # environment. The necessary files are collected in a tar-ball and placed |
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| 29 | # at the target location. There its untared, the environment variables will |
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| 30 | # be set and the Fortran code will be compiled. If the ECMWF environment is |
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| 31 | # selected a job script is prepared and submitted for the remaining |
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| 32 | # configurations after putting the tar-ball to the target ECMWF server. |
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| 33 | # |
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| 34 | # @Program Content: |
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| 35 | # - main |
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| 36 | # - get_install_cmdline_arguments |
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| 37 | # - install_via_gateway |
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| 38 | # - mk_tarball |
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| 39 | # - un_tarball |
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| 40 | # - mk_env_vars |
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| 41 | # - mk_compilejob |
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| 42 | # - mk_job_template |
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| 43 | # - delete_convert_build |
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| 44 | # - make_convert_build |
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| 45 | # |
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| 46 | #******************************************************************************* |
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| 47 | |
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| 48 | # ------------------------------------------------------------------------------ |
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| 49 | # MODULES |
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| 50 | # ------------------------------------------------------------------------------ |
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| 51 | import os |
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| 52 | import sys |
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| 53 | import glob |
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| 54 | import subprocess |
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| 55 | import inspect |
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| 56 | from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter |
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| 57 | |
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| 58 | # software specific classes and modules from flex_extract |
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| 59 | import _config |
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| 60 | from classes.ControlFile import ControlFile |
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| 61 | from classes.UioFiles import UioFiles |
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| 62 | from mods.tools import make_dir, put_file_to_ecserver, submit_job_to_ecserver |
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| 63 | |
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| 64 | # ------------------------------------------------------------------------------ |
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| 65 | # FUNCTIONS |
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| 66 | # ------------------------------------------------------------------------------ |
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| 67 | def main(): |
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| 68 | ''' |
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| 69 | @Description: |
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| 70 | Controls the installation process. Calls the installation function |
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| 71 | if target is specified. |
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| 72 | |
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| 73 | @Intput: |
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| 74 | <nothing> |
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| 75 | |
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| 76 | @Return: |
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| 77 | <nothing> |
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| 78 | ''' |
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| 79 | |
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| 80 | args = get_install_cmdline_arguments() |
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| 81 | c = ControlFile(args.controlfile) |
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| 82 | c.assign_args_to_control(args) |
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| 83 | c.check_install_conditions() |
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| 84 | |
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| 85 | install_via_gateway(c) |
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| 86 | |
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| 87 | return |
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| 88 | |
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| 89 | def get_install_cmdline_arguments(): |
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| 90 | ''' |
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| 91 | @Description: |
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| 92 | Decomposes the command line arguments and assigns them to variables. |
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| 93 | Apply default values for non mentioned arguments. |
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| 94 | |
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| 95 | @Input: |
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| 96 | <nothing> |
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| 97 | |
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| 98 | @Return: |
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| 99 | args: instance of ArgumentParser |
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| 100 | Contains the commandline arguments from script/program call. |
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| 101 | ''' |
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| 102 | parser = ArgumentParser(description='Install flex_extract software locally or \ |
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| 103 | on ECMWF machines', |
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| 104 | formatter_class=ArgumentDefaultsHelpFormatter) |
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| 105 | |
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| 106 | parser.add_argument('--target', dest='install_target', default=None, |
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| 107 | help="Valid targets: local | ecgate | cca , \ |
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| 108 | the latter two are at ECMWF") |
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| 109 | parser.add_argument("--makefile", dest="makefile", default=None, |
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| 110 | help='Name of Makefile to use for compiling CONVERT2') |
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| 111 | parser.add_argument("--ecuid", dest="ecuid", default=None, |
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| 112 | help='user id at ECMWF') |
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| 113 | parser.add_argument("--ecgid", dest="ecgid", default=None, |
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| 114 | help='group id at ECMWF') |
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| 115 | parser.add_argument("--gateway", dest="gateway", default=None, |
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| 116 | help='name of local gateway server') |
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| 117 | parser.add_argument("--destination", dest="destination", default=None, |
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| 118 | help='ecaccess destination, e.g. leo@genericSftp') |
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| 119 | |
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| 120 | parser.add_argument("--flexpart_root_scripts", dest="flexpart_root_scripts", |
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| 121 | default=None, help="FLEXPART root directory on ECMWF \ |
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| 122 | servers (to find grib2flexpart and COMMAND file)\n\ |
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| 123 | Normally flex_extract resides in the scripts directory \ |
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| 124 | of the FLEXPART distribution.") |
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| 125 | |
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| 126 | # arguments for job submission to ECMWF, only needed by submit.py |
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| 127 | parser.add_argument("--job_template", dest='job_template', |
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| 128 | default="job.temp.o", |
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| 129 | help="job template file for submission to ECMWF") |
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| 130 | |
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| 131 | parser.add_argument("--controlfile", dest="controlfile", |
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| 132 | default='CONTROL.temp', |
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| 133 | help="file with CONTROL parameters") |
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| 134 | |
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| 135 | args = parser.parse_args() |
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| 136 | |
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| 137 | return args |
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| 138 | |
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| 139 | |
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| 140 | def install_via_gateway(c): |
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| 141 | ''' |
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| 142 | @Description: |
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| 143 | Perform the actual installation on local machine or prepare data |
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| 144 | transfer to remote gate and submit a job script which will |
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| 145 | install everything on the remote gate. |
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| 146 | |
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| 147 | @Input: |
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| 148 | c: instance of class ControlFile |
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| 149 | Contains all the parameters of CONTROL file and |
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| 150 | command line. |
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| 151 | For more information about format and content of the parameter |
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| 152 | see documentation. |
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| 153 | |
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| 154 | @Return: |
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| 155 | <nothing> |
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| 156 | ''' |
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| 157 | import tarfile |
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| 158 | |
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| 159 | ecd = _config.PATH_FLEXEXTRACT_DIR |
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| 160 | tarball_name = _config.FLEXEXTRACT_DIRNAME + '.tar' |
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| 161 | tar_file = os.path.join(ecd, tarball_name) |
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| 162 | |
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| 163 | target_dirname = _config.FLEXEXTRACT_DIRNAME |
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| 164 | fortran_executable = _config.FORTRAN_EXECUTABLE |
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| 165 | |
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| 166 | if c.install_target.lower() != 'local': # ecgate or cca |
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| 167 | |
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| 168 | mk_compilejob(c.makefile, c.install_target, c.ecuid, c.ecgid, |
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| 169 | c.flexpart_root_scripts) |
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| 170 | |
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| 171 | mk_job_template(c.ecuid, c.ecgid, c.gateway, |
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| 172 | c.destination, c.flexpart_root_scripts) |
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| 173 | |
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| 174 | mk_env_vars(c.ecuid, c.ecgid, c.gateway, c.destination) |
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| 175 | |
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| 176 | mk_tarball(tar_file, c.install_target) |
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| 177 | |
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| 178 | put_file_to_ecserver(ecd, tarball_name, c.install_target, |
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| 179 | c.ecuid, c.ecgid) |
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| 180 | |
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| 181 | submit_job_to_ecserver(c.install_target, |
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| 182 | os.path.join(_config.PATH_REL_JOBSCRIPTS, |
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| 183 | _config.FILE_INSTALL_COMPILEJOB)) |
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| 184 | |
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| 185 | print('job compilation script has been submitted to ecgate for ' + |
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| 186 | 'installation in ' + c.flexpart_root_scripts + |
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| 187 | '/' + target_dirname) |
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| 188 | print('You should get an email with subject "flexcompile" within ' + |
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| 189 | 'the next few minutes!') |
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| 190 | |
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| 191 | else: #local |
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| 192 | if c.flexpart_root_scripts == _config.PATH_FLEXEXTRACT_DIR : |
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| 193 | print('WARNING: FLEXPART_ROOT_SCRIPTS has not been specified') |
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| 194 | print('flex_extract will be installed in here by compiling the ' + |
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| 195 | 'Fortran source in ' + _config.PATH_FORTRAN_SRC) |
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| 196 | os.chdir(_config.PATH_FORTRAN_SRC) |
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| 197 | else: # creates the target working directory for flex_extract |
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| 198 | c.flexpart_root_scripts = os.path.expandvars(os.path.expanduser( |
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| 199 | c.flexpart_root_scripts)) |
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| 200 | if os.path.abspath(ecd) != os.path.abspath(c.flexpart_root_scripts): |
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| 201 | mk_tarball(tar_file, c.install_target) |
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| 202 | make_dir(os.path.join(c.flexpart_root_scripts, |
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| 203 | target_dirname)) |
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| 204 | os.chdir(os.path.join(c.flexpart_root_scripts, |
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| 205 | target_dirname)) |
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| 206 | un_tarball(tar_file) |
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| 207 | os.chdir(os.path.join(c.flexpart_root_scripts, |
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| 208 | target_dirname, |
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| 209 | _config.PATH_REL_FORTRAN_SRC)) |
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| 210 | |
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| 211 | # Create Fortran executable - CONVERT2 |
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| 212 | print('Install ' + target_dirname + ' software at ' + |
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| 213 | c.install_target + ' in directory ' + |
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| 214 | os.path.abspath(c.flexpart_root_scripts) + '\n') |
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| 215 | |
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| 216 | delete_convert_build('.') |
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| 217 | make_convert_build('.', c.makefile) |
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| 218 | |
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| 219 | os.chdir(ecd) |
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| 220 | if os.path.isfile(tar_file): |
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| 221 | os.remove(tar_file) |
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| 222 | |
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| 223 | return |
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| 224 | |
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| 225 | def mk_tarball(tarball_path, target): |
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| 226 | ''' |
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| 227 | @Description: |
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| 228 | Creates a tarball with all necessary files which need to be sent to the |
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| 229 | installation directory. |
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| 230 | It does not matter if this is local or remote. |
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| 231 | Collects all python files, the Fortran source and makefiles, |
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| 232 | the ECMWF_ENV file, the CONTROL files as well as the |
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| 233 | template files. |
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| 234 | |
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| 235 | @Input: |
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| 236 | tarball_path: string |
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| 237 | The complete path to the tar file which will contain all |
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| 238 | relevant data for flex_extract. |
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| 239 | |
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| 240 | target: string |
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| 241 | The queue where the job is submitted to. |
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| 242 | |
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| 243 | @Return: |
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| 244 | <nothing> |
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| 245 | ''' |
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| 246 | import tarfile |
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| 247 | from glob import glob |
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| 248 | |
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| 249 | print('Create tarball ...') |
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| 250 | |
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| 251 | # change to FLEXEXTRACT directory so that the tar can contain |
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| 252 | # relative pathes to the files and directories |
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| 253 | ecd = _config.PATH_FLEXEXTRACT_DIR + '/' |
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| 254 | os.chdir(ecd) |
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| 255 | |
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| 256 | # get lists of the files to be added to the tar file |
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| 257 | if target == 'local': |
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| 258 | ECMWF_ENV_FILE = [] |
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| 259 | else: |
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| 260 | ECMWF_ENV_FILE = [_config.PATH_REL_ECMWF_ENV] |
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| 261 | |
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| 262 | pyfiles = [os.path.relpath(x, ecd) |
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| 263 | for x in UioFiles(_config.PATH_LOCAL_PYTHON, '*py').files] |
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| 264 | controlfiles = [os.path.relpath(x, ecd) |
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| 265 | for x in UioFiles(_config.PATH_CONTROLFILES, |
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| 266 | 'CONTROL*').files] |
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| 267 | tempfiles = [os.path.relpath(x, ecd) |
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| 268 | for x in UioFiles(_config.PATH_TEMPLATES , '*').files] |
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| 269 | ffiles = [os.path.relpath(x, ecd) |
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| 270 | for x in UioFiles(_config.PATH_FORTRAN_SRC, '*.f*').files] |
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| 271 | hfiles = [os.path.relpath(x, ecd) |
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| 272 | for x in UioFiles(_config.PATH_FORTRAN_SRC, '*.h').files] |
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| 273 | makefiles = [os.path.relpath(x, ecd) |
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| 274 | for x in UioFiles(_config.PATH_FORTRAN_SRC, 'Makefile*').files] |
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| 275 | |
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| 276 | # concatenate single lists to one for a better looping |
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| 277 | filelist = pyfiles + controlfiles + tempfiles + ffiles + hfiles + \ |
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| 278 | makefiles + ECMWF_ENV_FILE |
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| 279 | |
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| 280 | # create installation tar-file |
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| 281 | try: |
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| 282 | with tarfile.open(tarball_path, "w:gz") as tar_handle: |
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| 283 | for file in filelist: |
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| 284 | tar_handle.add(file) |
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| 285 | |
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| 286 | except subprocess.CalledProcessError as e: |
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| 287 | print('... ERROR CODE:\n ... ' + str(e.returncode)) |
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| 288 | print('... ERROR MESSAGE:\n ... ' + str(e)) |
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| 289 | |
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| 290 | sys.exit('... could not make installation tar ball!') |
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| 291 | |
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| 292 | return |
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| 293 | |
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| 294 | |
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| 295 | def un_tarball(tarball_path): |
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| 296 | ''' |
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| 297 | @Description: |
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| 298 | Extracts the given tarball into current directory. |
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| 299 | |
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| 300 | @Input: |
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| 301 | tarball_path: string |
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| 302 | The complete path to the tar file which will contain all |
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| 303 | relevant data for flex_extract. |
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| 304 | |
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| 305 | @Return: |
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| 306 | <nothing> |
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| 307 | ''' |
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| 308 | import tarfile |
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| 309 | |
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| 310 | print('Untar ...') |
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| 311 | |
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| 312 | with tarfile.open(tarball_path) as tar_handle: |
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| 313 | tar_handle.extractall() |
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| 314 | |
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| 315 | return |
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| 316 | |
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| 317 | def mk_env_vars(ecuid, ecgid, gateway, destination): |
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| 318 | ''' |
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| 319 | @Description: |
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| 320 | Creates a file named ECMWF_ENV which contains the |
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| 321 | necessary environmental variables at ECMWF servers. |
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| 322 | |
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| 323 | @Input: |
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| 324 | ecuid: string |
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| 325 | The user id on ECMWF server. |
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| 326 | |
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| 327 | ecgid: string |
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| 328 | The group id on ECMWF server. |
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| 329 | |
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| 330 | gateway: string |
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| 331 | The gateway server the user is using. |
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| 332 | |
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| 333 | destination: string |
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| 334 | The remote destination which is used to transfer files |
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| 335 | from ECMWF server to local gateway server. |
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| 336 | |
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| 337 | @Return: |
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| 338 | <nothing> |
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| 339 | ''' |
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| 340 | |
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| 341 | with open(_config.PATH_REL_ECMWF_ENV, 'w') as fo: |
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| 342 | fo.write('ECUID ' + ecuid + '\n') |
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| 343 | fo.write('ECGID ' + ecgid + '\n') |
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| 344 | fo.write('GATEWAY ' + gateway + '\n') |
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| 345 | fo.write('DESTINATION ' + destination + '\n') |
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| 346 | |
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| 347 | return |
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| 348 | |
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| 349 | def mk_compilejob(makefile, target, ecuid, ecgid, fp_root): |
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| 350 | ''' |
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| 351 | @Description: |
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| 352 | Modifies the original job template file so that it is specified |
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| 353 | for the user and the environment were it will be applied. Result |
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| 354 | is stored in a new file "job.temp" in the python directory. |
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| 355 | |
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| 356 | @Input: |
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| 357 | makefile: string |
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| 358 | Name of the makefile which should be used to compile FORTRAN |
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| 359 | CONVERT2 program. |
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| 360 | |
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| 361 | target: string |
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| 362 | The target where the installation should be done, e.g. the queue. |
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| 363 | |
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| 364 | ecuid: string |
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| 365 | The user id on ECMWF server. |
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| 366 | |
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| 367 | ecgid: string |
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| 368 | The group id on ECMWF server. |
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| 369 | |
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| 370 | fp_root: string |
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| 371 | Path to the root directory of FLEXPART environment or flex_extract |
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| 372 | environment. |
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| 373 | |
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| 374 | @Return: |
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| 375 | <nothing> |
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| 376 | ''' |
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| 377 | |
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| 378 | template = os.path.join(_config.PATH_REL_TEMPLATES, |
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| 379 | _config.TEMPFILE_INSTALL_COMPILEJOB) |
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| 380 | with open(template) as f: |
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| 381 | fdata = f.read().split('\n') |
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| 382 | |
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| 383 | compilejob = os.path.join(_config.PATH_REL_JOBSCRIPTS, |
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| 384 | _config.FILE_INSTALL_COMPILEJOB) |
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| 385 | with open(compilejob, 'w') as fo: |
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| 386 | for data in fdata: |
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| 387 | if 'MAKEFILE=' in data: |
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| 388 | data = 'export MAKEFILE=' + makefile |
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| 389 | elif 'FLEXPART_ROOT_SCRIPTS=' in data: |
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| 390 | if fp_root != '../': |
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| 391 | data = 'export FLEXPART_ROOT_SCRIPTS=' + fp_root |
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| 392 | else: |
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| 393 | data = 'export FLEXPART_ROOT_SCRIPTS=$HOME' |
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| 394 | elif target.lower() != 'local': |
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| 395 | if '--workdir' in data: |
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| 396 | data = '#SBATCH --workdir=/scratch/ms/' + \ |
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| 397 | ecgid + '/' + ecuid |
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| 398 | elif '##PBS -o' in data: |
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| 399 | data = '##PBS -o /scratch/ms/' + ecgid + '/' + ecuid + \ |
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| 400 | 'flex_ecmwf.$Jobname.$Job_ID.out' |
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| 401 | elif 'FLEXPART_ROOT_SCRIPTS=' in data: |
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| 402 | if fp_root != '../': |
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| 403 | data = 'export FLEXPART_ROOT_SCRIPTS=' + fp_root |
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| 404 | else: |
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| 405 | data = 'export FLEXPART_ROOT_SCRIPTS=$HOME' |
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| 406 | fo.write(data + '\n') |
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| 407 | |
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| 408 | return |
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| 409 | |
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| 410 | def mk_job_template(ecuid, ecgid, gateway, destination, fp_root): |
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| 411 | ''' |
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| 412 | @Description: |
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| 413 | Modifies the original job template file so that it is specified |
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| 414 | for the user and the environment were it will be applied. Result |
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| 415 | is stored in a new file. |
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| 416 | |
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| 417 | @Input: |
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| 418 | ecuid: string |
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| 419 | The user id on ECMWF server. |
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| 420 | |
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| 421 | ecgid: string |
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| 422 | The group id on ECMWF server. |
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| 423 | |
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| 424 | gateway: string |
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| 425 | The gateway server the user is using. |
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| 426 | |
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| 427 | destination: string |
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| 428 | The remote destination which is used to transfer files |
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| 429 | from ECMWF server to local gateway server. |
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| 430 | |
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| 431 | fp_root: string |
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| 432 | Path to the root directory of FLEXPART environment or flex_extract |
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| 433 | environment. |
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| 434 | |
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| 435 | @Return: |
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| 436 | <nothing> |
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| 437 | ''' |
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| 438 | fp_root_path_to_python = os.path.join(fp_root, _config.FLEXEXTRACT_DIRNAME, |
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| 439 | _config.PATH_REL_PYTHON) |
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| 440 | |
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| 441 | template = os.path.join(_config.PATH_REL_TEMPLATES, |
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| 442 | _config.TEMPFILE_INSTALL_JOB) |
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| 443 | with open(template) as f: |
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| 444 | fdata = f.read().split('\n') |
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| 445 | |
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| 446 | jobfile_temp = os.path.join(_config.PATH_REL_TEMPLATES, |
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| 447 | _config.TEMPFILE_JOB) |
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| 448 | with open(jobfile_temp, 'w') as fo: |
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| 449 | for data in fdata: |
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| 450 | if '--workdir' in data: |
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| 451 | data = '#SBATCH --workdir=/scratch/ms/' + ecgid + '/' + ecuid |
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| 452 | elif '##PBS -o' in data: |
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| 453 | data = '##PBS -o /scratch/ms/' + ecgid + '/' + \ |
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| 454 | ecuid + 'flex_ecmwf.$Jobname.$Job_ID.out' |
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| 455 | elif 'export PATH=${PATH}:' in data: |
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| 456 | data += fp_root_path_to_python |
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| 457 | |
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| 458 | fo.write(data + '\n') |
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| 459 | return |
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| 460 | |
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| 461 | def delete_convert_build(src_path): |
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| 462 | ''' |
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| 463 | @Description: |
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| 464 | Clean up the Fortran source directory and remove all |
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| 465 | build files (e.g. *.o, *.mod and CONVERT2) |
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| 466 | |
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| 467 | @Input: |
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| 468 | src_path: string |
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| 469 | Path to the fortran source directory. |
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| 470 | |
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| 471 | @Return: |
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| 472 | <nothing> |
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| 473 | ''' |
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| 474 | |
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| 475 | modfiles = UioFiles(src_path, '*.mod') |
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| 476 | objfiles = UioFiles(src_path, '*.o') |
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| 477 | exefile = UioFiles(src_path, _config.FORTRAN_EXECUTABLE) |
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| 478 | |
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| 479 | modfiles.delete_files() |
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| 480 | objfiles.delete_files() |
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| 481 | exefile.delete_files() |
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| 482 | |
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| 483 | return |
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| 484 | |
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| 485 | def make_convert_build(src_path, makefile): |
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| 486 | ''' |
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| 487 | @Description: |
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| 488 | Compiles the Fortran code and generates the executable. |
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| 489 | |
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| 490 | @Input: |
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| 491 | src_path: string |
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| 492 | Path to the fortran source directory. |
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| 493 | |
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| 494 | makefile: string |
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| 495 | The name of the makefile which should be used. |
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| 496 | |
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| 497 | @Return: |
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| 498 | <nothing> |
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| 499 | ''' |
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| 500 | |
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| 501 | try: |
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| 502 | print('Using makefile: ' + makefile) |
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| 503 | p = subprocess.Popen(['make', '-f', |
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| 504 | os.path.join(src_path, makefile)], |
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| 505 | stdin=subprocess.PIPE, |
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| 506 | stdout=subprocess.PIPE, |
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| 507 | stderr=subprocess.PIPE, |
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| 508 | bufsize=1) |
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| 509 | pout, perr = p.communicate() |
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| 510 | print(pout) |
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| 511 | if p.returncode != 0: |
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| 512 | print(perr) |
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| 513 | print('Please edit ' + makefile + |
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| 514 | ' or try another Makefile in the src directory.') |
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| 515 | print('Most likely GRIB_API_INCLUDE_DIR, GRIB_API_LIB ' |
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| 516 | 'and EMOSLIB must be adapted.') |
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| 517 | print('Available Makefiles:') |
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| 518 | print(UioFiles(src_path, 'Makefile*')) |
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| 519 | sys.exit('Compilation failed!') |
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| 520 | except ValueError as e: |
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| 521 | print('ERROR: Makefile call failed:') |
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| 522 | print(e) |
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| 523 | else: |
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| 524 | subprocess.check_call(['ls', '-l', |
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| 525 | os.path.join(src_path, |
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| 526 | _config.FORTRAN_EXECUTABLE)]) |
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| 527 | |
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| 528 | return |
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| 529 | |
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| 530 | |
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| 531 | if __name__ == "__main__": |
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| 532 | main() |
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