[8463d78] | 1 | #!/usr/bin/env python3 |
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[64cf353] | 2 | # -*- coding: utf-8 -*- |
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[991df6a] | 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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[ff99eae] | 13 | # - moved install_args_and_control in here |
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[2fb99de] | 14 | # - splitted code in smaller functions |
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[5f67883] | 15 | # - delete fortran build files in here instead of compile job script |
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[6f951ca] | 16 | # - changed static path names to variables from config file |
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| 17 | # - splitted install function into several smaller pieces |
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| 18 | # - use of tarfile package in python |
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[a916e8f] | 19 | # June 2020 - Anne Philipp |
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| 20 | # - renamed "convert" functions to "fortran" functions |
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[47be2684] | 21 | # - reconfigured mk_tarball to select *.template files instead |
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[a916e8f] | 22 | # of *.nl and *.temp |
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| 23 | # - added check for makefile settings |
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[75db9b0] | 24 | # August 2020 - Leopold Haimberger |
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| 25 | # - added a new installation section for system installation (if-else block) |
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| 26 | # - read new argument from command line |
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| 27 | # - write .setup.rc for a system installation into Run directory |
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| 28 | # - copy executables to system path and user files to user path |
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[01bd8aa] | 29 | # July 2022 - Anne Tipka (formerly Philipp) |
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| 30 | # - BugFix: sysinstalldir must be defined in related else path |
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| 31 | # - template files are now using $HOME and $SCRATCH and hence don't |
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| 32 | # need ecmwf user group id. Eliminated from function mk_compile_job |
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| 33 | # and mk_job_template |
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[991df6a] | 34 | # |
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| 35 | # @License: |
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[026b359] | 36 | # (C) Copyright 2014-2020. |
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[6f951ca] | 37 | # Anne Philipp, Leopold Haimberger |
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[991df6a] | 38 | # |
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[44174de] | 39 | # SPDX-License-Identifier: CC-BY-4.0 |
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| 40 | # |
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[6f951ca] | 41 | # This work is licensed under the Creative Commons Attribution 4.0 |
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| 42 | # International License. To view a copy of this license, visit |
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| 43 | # http://creativecommons.org/licenses/by/4.0/ or send a letter to |
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| 44 | # Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. |
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[991df6a] | 45 | # |
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[6f951ca] | 46 | # @Methods: |
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| 47 | # main |
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| 48 | # get_install_cmdline_args |
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| 49 | # install_via_gateway |
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| 50 | # check_install_conditions |
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| 51 | # mk_tarball |
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| 52 | # un_tarball |
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| 53 | # mk_env_vars |
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| 54 | # mk_compilejob |
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| 55 | # mk_job_template |
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[5f67883] | 56 | # del_fortran_build |
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| 57 | # mk_fortran_build |
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[991df6a] | 58 | # |
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| 59 | #******************************************************************************* |
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[6f951ca] | 60 | '''This script installs the flex_extract program. |
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| 61 | |
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| 62 | Depending on the selected installation environment (locally or on the |
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[8209738] | 63 | ECMWF server ecgate or cca) the program extracts the command line |
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[6f951ca] | 64 | arguments and the CONTROL file parameter and prepares the corresponding |
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| 65 | environment. |
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[8209738] | 66 | The necessary files are collected in a tar ball and placed |
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| 67 | at the target location. There, is is untared, the environment variables are |
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| 68 | set, and the Fortran code is compiled. |
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| 69 | If the ECMWF environment is selected, a job script is prepared and submitted |
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| 70 | for the remaining configurations after putting the tar ball on the |
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[6f951ca] | 71 | target ECMWF server. |
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| 72 | |
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| 73 | Type: install.py --help |
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| 74 | to get information about command line parameters. |
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| 75 | Read the documentation for usage instructions. |
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| 76 | ''' |
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[991df6a] | 77 | |
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[64cf353] | 78 | # ------------------------------------------------------------------------------ |
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| 79 | # MODULES |
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| 80 | # ------------------------------------------------------------------------------ |
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[8ce3be6] | 81 | from __future__ import print_function |
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| 82 | |
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[991df6a] | 83 | import os |
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| 84 | import sys |
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[d69b677] | 85 | import subprocess |
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[3946de5] | 86 | import tarfile |
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[47be2684] | 87 | import shutil |
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[ff99eae] | 88 | from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter |
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[991df6a] | 89 | |
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| 90 | # software specific classes and modules from flex_extract |
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[2fb99de] | 91 | import _config |
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[ba99230] | 92 | from Classes.ControlFile import ControlFile |
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| 93 | from Classes.UioFiles import UioFiles |
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| 94 | from Mods.tools import (make_dir, put_file_to_ecserver, submit_job_to_ecserver, |
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[47be2684] | 95 | silent_remove, execute_subprocess, none_or_str, |
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| 96 | overwrite_lines_in_file, check_for_string_in_file) |
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[d69b677] | 97 | |
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[64cf353] | 98 | # ------------------------------------------------------------------------------ |
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| 99 | # FUNCTIONS |
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| 100 | # ------------------------------------------------------------------------------ |
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[991df6a] | 101 | def main(): |
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[274f9ef] | 102 | '''Controls the installation process. Calls the installation function |
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| 103 | if target is specified. |
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[991df6a] | 104 | |
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[274f9ef] | 105 | Parameters |
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| 106 | ---------- |
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[991df6a] | 107 | |
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[274f9ef] | 108 | Return |
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| 109 | ------ |
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[991df6a] | 110 | ''' |
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| 111 | |
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[8652e7e] | 112 | args = get_install_cmdline_args() |
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[4971f63] | 113 | c = ControlFile(args.controlfile) |
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[54a8a01] | 114 | c.assign_args_to_control(args) |
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[6cda7c1] | 115 | check_install_conditions(c) |
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[991df6a] | 116 | |
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[b6ea29e] | 117 | if c.install_target.lower() not in ['local', 'syslocal']: # ecmwf servers e.g. ecgate (ecs) and hpc |
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[8ce3be6] | 118 | install_via_gateway(c) |
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| 119 | else: # local |
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| 120 | install_local(c) |
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[991df6a] | 121 | |
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[47be2684] | 122 | print("SUCCESS: INSTALLATION FINISHED!") |
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| 123 | |
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[54a8a01] | 124 | return |
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[991df6a] | 125 | |
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[8652e7e] | 126 | def get_install_cmdline_args(): |
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[274f9ef] | 127 | '''Decomposes the command line arguments and assigns them to variables. |
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[8209738] | 128 | Apply default values for arguments not present. |
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[efdb01a] | 129 | |
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[274f9ef] | 130 | Parameters |
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| 131 | ---------- |
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[efdb01a] | 132 | |
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[274f9ef] | 133 | Return |
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| 134 | ------ |
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[6f951ca] | 135 | args : Namespace |
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[274f9ef] | 136 | Contains the commandline arguments from script/program call. |
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[efdb01a] | 137 | ''' |
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[8ce3be6] | 138 | parser = ArgumentParser(description='Install flex_extract software ' |
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| 139 | 'locally or on ECMWF machines', |
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[efdb01a] | 140 | formatter_class=ArgumentDefaultsHelpFormatter) |
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| 141 | |
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[8ce3be6] | 142 | parser.add_argument('--target', dest='install_target', |
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| 143 | type=none_or_str, default=None, |
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[b6ea29e] | 144 | help="Valid targets: syslocal | local | ecgate | cca | \ |
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| 145 | ccb | ecs | hpc , the latter 5 are at ECMWF servers") |
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[8ce3be6] | 146 | parser.add_argument("--makefile", dest="makefile", |
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| 147 | type=none_or_str, default=None, |
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[8209738] | 148 | help='Name of makefile for compiling the ' |
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[8ce3be6] | 149 | 'Fortran program') |
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| 150 | parser.add_argument("--ecuid", dest="ecuid", |
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| 151 | type=none_or_str, default=None, |
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[8209738] | 152 | help='User id at ECMWF') |
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[8ce3be6] | 153 | parser.add_argument("--ecgid", dest="ecgid", |
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| 154 | type=none_or_str, default=None, |
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[8209738] | 155 | help='Group id at ECMWF') |
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[8ce3be6] | 156 | parser.add_argument("--gateway", dest="gateway", |
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| 157 | type=none_or_str, default=None, |
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[8209738] | 158 | help='Name of the local gateway server') |
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[8ce3be6] | 159 | parser.add_argument("--destination", dest="destination", |
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| 160 | type=none_or_str, default=None, |
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[8209738] | 161 | help='ecaccess association, e.g. ' |
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[8ce3be6] | 162 | 'myUser@genericSftp') |
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| 163 | |
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| 164 | parser.add_argument("--installdir", dest="installdir", |
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| 165 | type=none_or_str, default=None, |
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[47be2684] | 166 | help='Root (user) directory of the ' |
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[8209738] | 167 | 'flex_extract installation') |
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[47be2684] | 168 | parser.add_argument("--sysinstalldir", dest="sysinstalldir", |
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| 169 | type=none_or_str, default=None, |
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| 170 | help='System installation path; where ' |
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| 171 | 'executables are stored.') |
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[efdb01a] | 172 | |
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[54a8a01] | 173 | # arguments for job submission to ECMWF, only needed by submit.py |
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[efdb01a] | 174 | parser.add_argument("--job_template", dest='job_template', |
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[8ce3be6] | 175 | type=none_or_str, default="job.template", |
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[8209738] | 176 | help='Rudimentary template file to create a batch ' |
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| 177 | 'job template for submission to ECMWF servers') |
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[efdb01a] | 178 | |
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| 179 | parser.add_argument("--controlfile", dest="controlfile", |
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[8ce3be6] | 180 | type=none_or_str, default='CONTROL_EA5', |
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[8209738] | 181 | help="A file that contains all CONTROL parameters.") |
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[efdb01a] | 182 | |
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| 183 | args = parser.parse_args() |
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| 184 | |
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[54a8a01] | 185 | return args |
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| 186 | |
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[efdb01a] | 187 | |
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[54a8a01] | 188 | def install_via_gateway(c): |
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[8209738] | 189 | '''Prepare data transfer to remote gateway and submit a job script which will |
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| 190 | install everything on the remote gateway. |
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[274f9ef] | 191 | |
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| 192 | Parameters |
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| 193 | ---------- |
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[6f951ca] | 194 | c : ControlFile |
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[274f9ef] | 195 | Contains all the parameters of CONTROL file and |
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| 196 | command line. |
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| 197 | |
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| 198 | Return |
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| 199 | ------ |
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| 200 | |
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[54a8a01] | 201 | ''' |
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[2fb99de] | 202 | |
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| 203 | tarball_name = _config.FLEXEXTRACT_DIRNAME + '.tar' |
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[8ce3be6] | 204 | tar_file = os.path.join(_config.PATH_FLEXEXTRACT_DIR, tarball_name) |
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[54a8a01] | 205 | |
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[b6ea29e] | 206 | mk_compilejob(c.makefile, c.ecuid, c.installdir) |
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[54a8a01] | 207 | |
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[0f89116] | 208 | mk_job_template(c.ecuid, c.ecgid, c.installdir) |
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[8ce3be6] | 209 | |
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| 210 | mk_env_vars(c.ecuid, c.ecgid, c.gateway, c.destination) |
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| 211 | |
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| 212 | mk_tarball(tar_file, c.install_target) |
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| 213 | |
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[b6ea29e] | 214 | put_file_to_ecserver(_config.PATH_FLEXEXTRACT_DIR, tarball_name) |
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[8ce3be6] | 215 | |
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| 216 | submit_job_to_ecserver(c.install_target, |
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| 217 | os.path.join(_config.PATH_REL_JOBSCRIPTS, |
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| 218 | _config.FILE_INSTALL_COMPILEJOB)) |
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| 219 | |
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| 220 | silent_remove(tar_file) |
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| 221 | |
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| 222 | print('Job compilation script has been submitted to ecgate for ' + |
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| 223 | 'installation in ' + c.installdir + |
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[0f89116] | 224 | '/' + _config.FLEXEXTRACT_DIRNAME) |
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[8ce3be6] | 225 | print('You should get an email with subject "flexcompile" within ' + |
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| 226 | 'the next few minutes!') |
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| 227 | |
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| 228 | return |
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| 229 | |
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| 230 | def install_local(c): |
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| 231 | '''Perform the actual installation on a local machine. |
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[54a8a01] | 232 | |
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[8ce3be6] | 233 | Parameters |
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| 234 | ---------- |
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| 235 | c : ControlFile |
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| 236 | Contains all the parameters of CONTROL file and |
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| 237 | command line. |
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| 238 | |
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| 239 | Return |
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| 240 | ------ |
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| 241 | |
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| 242 | ''' |
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| 243 | |
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| 244 | tar_file = os.path.join(_config.PATH_FLEXEXTRACT_DIR, |
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| 245 | _config.FLEXEXTRACT_DIRNAME + '.tar') |
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| 246 | |
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[47be2684] | 247 | # this is standard installation into a single directory |
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| 248 | if c.install_target == 'local': |
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[5adaf8a] | 249 | c.installdir = os.path.abspath(os.path.expandvars(os.path.expanduser( |
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| 250 | c.installdir))) |
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[47be2684] | 251 | |
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| 252 | # installation into the current directory |
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| 253 | if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.installdir: |
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| 254 | print('WARNING: installdir has not been specified') |
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| 255 | print('flex_extract will be installed in current dir by compiling the ' + |
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| 256 | 'Fortran source in ' + _config.PATH_FORTRAN_SRC) |
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| 257 | os.chdir(_config.PATH_FORTRAN_SRC) |
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| 258 | # installation into a different path |
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| 259 | elif os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) != c.installdir : |
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| 260 | |
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| 261 | # creates the target working directory for flex_extract |
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[8ce3be6] | 262 | mk_tarball(tar_file, c.install_target) |
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| 263 | make_dir(os.path.join(c.installdir, |
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[0f89116] | 264 | _config.FLEXEXTRACT_DIRNAME)) |
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[8ce3be6] | 265 | os.chdir(os.path.join(c.installdir, |
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[0f89116] | 266 | _config.FLEXEXTRACT_DIRNAME)) |
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[8ce3be6] | 267 | un_tarball(tar_file) |
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| 268 | os.chdir(os.path.join(c.installdir, |
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[0f89116] | 269 | _config.FLEXEXTRACT_DIRNAME, |
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[8ce3be6] | 270 | _config.PATH_REL_FORTRAN_SRC)) |
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| 271 | |
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[47be2684] | 272 | # Create Fortran executable |
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| 273 | print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software at ' + |
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| 274 | c.install_target + ' in directory ' + c.installdir + '\n') |
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| 275 | |
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| 276 | del_fortran_build('.') |
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| 277 | mk_fortran_build('.', c.makefile) |
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| 278 | os.chdir('../../') |
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| 279 | # make sure that the correct calling of submit.py script is in run_local.sh |
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| 280 | overwrite_lines_in_file('Run/run_local.sh', |
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| 281 | 'pyscript=', 'pyscript=../Source/Python/submit.py\n') |
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| 282 | |
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| 283 | # this is system installation were executables and user files are separated |
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| 284 | elif c.install_target == 'syslocal': |
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[5adaf8a] | 285 | c.sysinstalldir = os.path.abspath(os.path.expandvars(os.path.expanduser( |
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| 286 | c.sysinstalldir))) |
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[47be2684] | 287 | if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.sysinstalldir : |
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| 288 | sys.exit('ERROR: System installation path is equal to user ' |
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| 289 | 'installation path.\n Please change either the system ' |
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| 290 | 'installation path or use installation target "local".') |
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| 291 | if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.installdir : |
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| 292 | print('Flex_extract will be installed in current directory!') |
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| 293 | else: # install user part in different dir |
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| 294 | print('Flex_extract will be installed in ' + c.installdir ) |
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| 295 | |
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| 296 | c.installdir = os.path.join(c.installdir,_config.FLEXEXTRACT_DIRNAME) |
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| 297 | if os.path.isdir(c.installdir): |
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| 298 | shutil.rmtree(c.installdir) |
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| 299 | |
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| 300 | # copy all files except Python and Fortranfiles to this dir |
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| 301 | shutil.copytree(_config.PATH_FLEXEXTRACT_DIR, |
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| 302 | c.installdir, symlinks=True) |
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| 303 | shutil.rmtree(os.path.join(c.installdir,'Source')) |
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| 304 | shutil.rmtree(os.path.join(c.installdir,'.git')) |
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| 305 | for x in UioFiles(c.installdir, '*~').files: |
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| 306 | silent_remove(x) |
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| 307 | |
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| 308 | os.remove(os.path.join(c.installdir,'setup.sh')) |
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| 309 | os.remove(os.path.join(c.installdir,'setup_local.sh')) |
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| 310 | |
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| 311 | # configure run_local script correctly |
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| 312 | # check if source of system config file is already in run_local.sh, |
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| 313 | # if not, add it |
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| 314 | if not check_for_string_in_file(os.path.join(c.installdir,'Run/run_local.sh'), |
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| 315 | 'source .setup.rc'): |
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| 316 | overwrite_lines_in_file(os.path.join(c.installdir,'Run/run_local.sh'), |
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| 317 | '# PATH TO SUBMISSION SCRIPT', |
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| 318 | '# PATH TO SUBMISSION SCRIPT\nsource '+_config.FILE_SYS_CONFIG+'\n') |
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| 319 | # make sure that the correct calling of submit.py script is in run_local.sh |
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| 320 | overwrite_lines_in_file(os.path.join(c.installdir,'Run/run_local.sh'), |
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| 321 | 'pyscript=', 'pyscript=submit.py\n') |
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| 322 | |
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| 323 | # change permission for file to executable |
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| 324 | execute_subprocess(['chmod', '0775', |
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| 325 | os.path.join(os.path.abspath(c.installdir),'Run/run_local.sh')]) |
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| 326 | |
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| 327 | |
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| 328 | # create systemdir |
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| 329 | c.sysinstalldir = os.path.join(c.sysinstalldir,_config.FLEXEXTRACT_DIRNAME) |
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| 330 | if os.path.isdir(c.sysinstalldir): |
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| 331 | shutil.rmtree(c.sysinstalldir) |
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| 332 | |
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| 333 | # create setup file for running flex_extract with system installation |
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| 334 | with open(os.path.join(os.path.abspath(c.installdir),'Run/.setup.rc'),'w') as fio: |
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| 335 | fio.write('#!/bin/bash \n') |
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| 336 | fio.write('export FLEXEXTRACT_USER_DIR='+os.path.abspath(c.installdir)+'\n') |
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| 337 | fio.write('export PATH='+os.path.abspath(c.sysinstalldir)+'/Python:${PATH}\n') |
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| 338 | fio.write('export PATH='+os.path.abspath(c.sysinstalldir)+':${PATH}\n') |
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| 339 | |
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| 340 | # copy all Python and Fortranfiles to this dir |
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| 341 | shutil.copytree(_config.PATH_SOURCES, c.sysinstalldir, symlinks=True) |
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| 342 | |
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| 343 | os.chdir(os.path.join(c.sysinstalldir,'Fortran')) |
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| 344 | # Create Fortran executable |
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| 345 | print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software as ' + |
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| 346 | c.install_target + ' in directory ' + |
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| 347 | os.path.abspath(c.sysinstalldir) + '\n') |
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| 348 | |
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| 349 | del_fortran_build('.') |
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| 350 | mk_fortran_build('.', c.makefile) |
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| 351 | |
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| 352 | outfile = [x for x in UioFiles('.','*.out').files] |
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| 353 | test=os.path.join(c.sysinstalldir,'calc_etadot') |
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| 354 | if len(outfile) != 1: |
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| 355 | print('WARNING: Multiple executables for Fortran code are available!') |
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| 356 | # move executable one dir up and delete Fortran dir |
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| 357 | os.chdir('..') |
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| 358 | shutil.move(outfile[0], os.path.join(c.sysinstalldir,'calc_etadot')) |
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| 359 | shutil.rmtree(os.path.join(os.path.abspath(c.sysinstalldir),'Fortran')) |
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[8ce3be6] | 360 | |
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| 361 | os.chdir(_config.PATH_FLEXEXTRACT_DIR) |
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| 362 | if os.path.isfile(tar_file): |
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| 363 | os.remove(tar_file) |
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[54a8a01] | 364 | |
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| 365 | return |
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| 366 | |
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[8ce3be6] | 367 | |
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[6cda7c1] | 368 | def check_install_conditions(c): |
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[8209738] | 369 | '''Checks necessary attributes and conditions |
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| 370 | for the installation, e.g. whether they exist and contain values. |
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[6cda7c1] | 371 | Otherwise set default values. |
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| 372 | |
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| 373 | Parameters |
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| 374 | ---------- |
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[6f951ca] | 375 | c : ControlFile |
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[6cda7c1] | 376 | Contains all the parameters of CONTROL file and |
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| 377 | command line. |
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| 378 | |
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| 379 | |
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| 380 | Return |
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| 381 | ------ |
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| 382 | |
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| 383 | ''' |
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| 384 | |
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| 385 | if c.install_target and \ |
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| 386 | c.install_target not in _config.INSTALL_TARGETS: |
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| 387 | print('ERROR: unknown or missing installation target ') |
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| 388 | print('target: ', c.install_target) |
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| 389 | print('please specify correct installation target ' + |
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[0f89116] | 390 | str(_config.INSTALL_TARGETS)) |
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[6cda7c1] | 391 | print('use -h or --help for help') |
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| 392 | sys.exit(1) |
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| 393 | |
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[47be2684] | 394 | if c.install_target and c.install_target not in ['local', 'syslocal']: |
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[50f9ca6] | 395 | if not c.ecgid or not c.ecuid: |
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| 396 | print('Please enter your ECMWF user id and group id ' |
---|
| 397 | ' with command line options --ecuid --ecgid') |
---|
[6cda7c1] | 398 | print('Try "' + sys.argv[0].split('/')[-1] + \ |
---|
| 399 | ' -h" to print usage information') |
---|
[50f9ca6] | 400 | print('Please consult ecaccess documentation or ECMWF user ' |
---|
| 401 | 'support for further details.\n') |
---|
[6cda7c1] | 402 | sys.exit(1) |
---|
[50f9ca6] | 403 | if not c.gateway or not c.destination: |
---|
| 404 | print('WARNING: Parameters GATEWAY and DESTINATION were ' |
---|
| 405 | 'not properly set for working on ECMWF server. \n' |
---|
| 406 | 'There will be no transfer of output files to the ' |
---|
| 407 | 'local gateway server possible!') |
---|
[8ce3be6] | 408 | if not c.installdir: |
---|
| 409 | c.installdir = '${HOME}' |
---|
[47be2684] | 410 | elif c.install_target == 'local': |
---|
[8ce3be6] | 411 | if not c.installdir: |
---|
| 412 | c.installdir = _config.PATH_FLEXEXTRACT_DIR |
---|
[47be2684] | 413 | elif c.install_target == 'syslocal': |
---|
| 414 | if not c.installdir: |
---|
| 415 | c.installdir = _config.PATH_FLEXEXTRACT_DIR |
---|
| 416 | if not c.sysinstalldir: |
---|
| 417 | print('ERROR: System installation was selected but ' |
---|
| 418 | 'no system installation path was defined.') |
---|
| 419 | sys.exit() |
---|
[6cda7c1] | 420 | |
---|
[5f67883] | 421 | if not c.makefile: |
---|
| 422 | print('WARNING: no makefile was specified.') |
---|
| 423 | if c.install_target == 'local': |
---|
| 424 | c.makefile = 'makefile_local_gfortran' |
---|
| 425 | print('WARNING: default makefile selected: makefile_local_gfortan') |
---|
| 426 | elif c.install_target == 'ecgate': |
---|
| 427 | c.makefile = 'makefile_ecgate' |
---|
| 428 | print('WARNING: default makefile selected: makefile_ecgate') |
---|
| 429 | elif c.install_target == 'cca' or \ |
---|
| 430 | c.install_target == 'ccb': |
---|
| 431 | c.makefile = 'makefile_cray' |
---|
| 432 | print('WARNING: default makefile selected: makefile_cray') |
---|
| 433 | else: |
---|
| 434 | pass |
---|
[47be2684] | 435 | |
---|
[6cda7c1] | 436 | return |
---|
| 437 | |
---|
| 438 | |
---|
[25b14be] | 439 | def mk_tarball(tarball_path, target): |
---|
[274f9ef] | 440 | '''Creates a tarball with all necessary files which need to be sent to the |
---|
| 441 | installation directory. |
---|
[8209738] | 442 | It does not matter whether this is local or remote. |
---|
| 443 | Collects all Python files, the Fortran source and makefiles, |
---|
[274f9ef] | 444 | the ECMWF_ENV file, the CONTROL files as well as the |
---|
| 445 | template files. |
---|
| 446 | |
---|
| 447 | Parameters |
---|
| 448 | ---------- |
---|
[6f951ca] | 449 | tarball_path : str |
---|
[274f9ef] | 450 | The complete path to the tar file which will contain all |
---|
| 451 | relevant data for flex_extract. |
---|
| 452 | |
---|
[6f951ca] | 453 | target : str |
---|
[274f9ef] | 454 | The queue where the job is submitted to. |
---|
| 455 | |
---|
| 456 | Return |
---|
| 457 | ------ |
---|
| 458 | |
---|
[54a8a01] | 459 | ''' |
---|
[2fb99de] | 460 | |
---|
| 461 | print('Create tarball ...') |
---|
| 462 | |
---|
| 463 | # change to FLEXEXTRACT directory so that the tar can contain |
---|
| 464 | # relative pathes to the files and directories |
---|
| 465 | ecd = _config.PATH_FLEXEXTRACT_DIR + '/' |
---|
| 466 | os.chdir(ecd) |
---|
| 467 | |
---|
| 468 | # get lists of the files to be added to the tar file |
---|
[25b14be] | 469 | if target == 'local': |
---|
[0f89116] | 470 | ecmwf_env_file = [] |
---|
[3946de5] | 471 | runfile = [os.path.relpath(x, ecd) |
---|
| 472 | for x in UioFiles(_config.PATH_REL_RUN_DIR, |
---|
| 473 | 'run_local.sh').files] |
---|
[25b14be] | 474 | else: |
---|
[0f89116] | 475 | ecmwf_env_file = [_config.PATH_REL_ECMWF_ENV] |
---|
[3946de5] | 476 | runfile = [os.path.relpath(x, ecd) |
---|
[0f89116] | 477 | for x in UioFiles(_config.PATH_REL_RUN_DIR, |
---|
| 478 | 'run.sh').files] |
---|
[25b14be] | 479 | |
---|
[2fb99de] | 480 | pyfiles = [os.path.relpath(x, ecd) |
---|
[3946de5] | 481 | for x in UioFiles(_config.PATH_REL_PYTHON_SRC, '*py').files] |
---|
| 482 | pytestfiles = [os.path.relpath(x, ecd) |
---|
[0f89116] | 483 | for x in UioFiles(_config.PATH_REL_PYTHONTEST_SRC, '*py').files] |
---|
[2fb99de] | 484 | controlfiles = [os.path.relpath(x, ecd) |
---|
[3946de5] | 485 | for x in UioFiles(_config.PATH_REL_CONTROLFILES, |
---|
[25b14be] | 486 | 'CONTROL*').files] |
---|
[1eca806] | 487 | testfiles = [os.path.relpath(x, ecd) |
---|
[8028176] | 488 | for x in UioFiles(_config.PATH_REL_TEST+"/Installation", '*').files] |
---|
[2fb99de] | 489 | tempfiles = [os.path.relpath(x, ecd) |
---|
[a916e8f] | 490 | for x in UioFiles(_config.PATH_REL_TEMPLATES, '*.template').files] |
---|
[3946de5] | 491 | gribtable = [os.path.relpath(x, ecd) |
---|
[0f89116] | 492 | for x in UioFiles(_config.PATH_REL_TEMPLATES, '*grib*').files] |
---|
[2fb99de] | 493 | ffiles = [os.path.relpath(x, ecd) |
---|
[0f89116] | 494 | for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, '*.f90').files] |
---|
[2fb99de] | 495 | hfiles = [os.path.relpath(x, ecd) |
---|
[3946de5] | 496 | for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, '*.h').files] |
---|
[2fb99de] | 497 | makefiles = [os.path.relpath(x, ecd) |
---|
[3a41083] | 498 | for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, 'makefile*').files] |
---|
[8028176] | 499 | jobdir = [os.path.relpath(x, ecd) |
---|
| 500 | for x in UioFiles(_config.PATH_REL_JOBSCRIPTS, '*.md').files] |
---|
[2fb99de] | 501 | |
---|
| 502 | # concatenate single lists to one for a better looping |
---|
[a916e8f] | 503 | filelist = pyfiles + pytestfiles + controlfiles + tempfiles + \ |
---|
[0f89116] | 504 | ffiles + gribtable + hfiles + makefiles + ecmwf_env_file + \ |
---|
[1eca806] | 505 | runfile + jobdir + testfiles +\ |
---|
[3946de5] | 506 | ['CODE_OF_CONDUCT.md', 'LICENSE.md', 'README.md'] |
---|
[2fb99de] | 507 | |
---|
| 508 | # create installation tar-file |
---|
[0f89116] | 509 | exclude_files = [".ksh", ".tar"] |
---|
[54a8a01] | 510 | try: |
---|
[2fb99de] | 511 | with tarfile.open(tarball_path, "w:gz") as tar_handle: |
---|
[0f89116] | 512 | for filename in filelist: |
---|
| 513 | tar_handle.add(filename, recursive=False, |
---|
[3946de5] | 514 | filter=lambda tarinfo: None |
---|
[0f89116] | 515 | if os.path.splitext(tarinfo.name)[1] |
---|
| 516 | in exclude_files |
---|
| 517 | else tarinfo) |
---|
[79729d5] | 518 | except tarfile.TarError as e: |
---|
[0f89116] | 519 | print('... ERROR: ' + str(e)) |
---|
| 520 | |
---|
[79729d5] | 521 | sys.exit('\n... error occured while trying to create the tar-file ' + |
---|
[0f89116] | 522 | str(tarball_path)) |
---|
[54a8a01] | 523 | |
---|
| 524 | return |
---|
| 525 | |
---|
[2fb99de] | 526 | |
---|
| 527 | def un_tarball(tarball_path): |
---|
[274f9ef] | 528 | '''Extracts the given tarball into current directory. |
---|
[2fb99de] | 529 | |
---|
[274f9ef] | 530 | Parameters |
---|
| 531 | ---------- |
---|
[6f951ca] | 532 | tarball_path : str |
---|
[274f9ef] | 533 | The complete path to the tar file which will contain all |
---|
| 534 | relevant data for flex_extract. |
---|
| 535 | |
---|
| 536 | Return |
---|
| 537 | ------ |
---|
[2fb99de] | 538 | |
---|
| 539 | ''' |
---|
| 540 | |
---|
| 541 | print('Untar ...') |
---|
| 542 | |
---|
[3946de5] | 543 | try: |
---|
| 544 | with tarfile.open(tarball_path) as tar_handle: |
---|
| 545 | tar_handle.extractall() |
---|
| 546 | except tarfile.TarError as e: |
---|
| 547 | sys.exit('\n... error occured while trying to read tar-file ' + |
---|
[0f89116] | 548 | str(tarball_path)) |
---|
[3946de5] | 549 | except OSError as e: |
---|
| 550 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 551 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 552 | |
---|
| 553 | sys.exit('\n... error occured while trying to read tar-file ' + |
---|
| 554 | str(tarball_path)) |
---|
[2fb99de] | 555 | |
---|
| 556 | return |
---|
| 557 | |
---|
| 558 | def mk_env_vars(ecuid, ecgid, gateway, destination): |
---|
[274f9ef] | 559 | '''Creates a file named ECMWF_ENV which contains the |
---|
| 560 | necessary environmental variables at ECMWF servers. |
---|
| 561 | It is based on the template ECMWF_ENV.template. |
---|
| 562 | |
---|
| 563 | Parameters |
---|
| 564 | ---------- |
---|
[6f951ca] | 565 | ecuid : str |
---|
[274f9ef] | 566 | The user id on ECMWF server. |
---|
[54a8a01] | 567 | |
---|
[6f951ca] | 568 | ecgid : str |
---|
[274f9ef] | 569 | The group id on ECMWF server. |
---|
[54a8a01] | 570 | |
---|
[6f951ca] | 571 | gateway : str |
---|
[274f9ef] | 572 | The gateway server the user is using. |
---|
[54a8a01] | 573 | |
---|
[6f951ca] | 574 | destination : str |
---|
[274f9ef] | 575 | The remote destination which is used to transfer files |
---|
| 576 | from ECMWF server to local gateway server. |
---|
[54a8a01] | 577 | |
---|
[274f9ef] | 578 | Return |
---|
| 579 | ------ |
---|
[54a8a01] | 580 | |
---|
| 581 | ''' |
---|
[0aaeb04] | 582 | from genshi.template.text import NewTextTemplate |
---|
| 583 | from genshi.template import TemplateLoader |
---|
[3946de5] | 584 | from genshi.template.eval import UndefinedError |
---|
[54a8a01] | 585 | |
---|
[3946de5] | 586 | try: |
---|
| 587 | loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False) |
---|
| 588 | ecmwfvars_template = loader.load(_config.TEMPFILE_USER_ENVVARS, |
---|
| 589 | cls=NewTextTemplate) |
---|
| 590 | |
---|
[0f89116] | 591 | stream = ecmwfvars_template.generate(user_name=ecuid, |
---|
| 592 | user_group=ecgid, |
---|
| 593 | gateway_name=gateway, |
---|
| 594 | destination_name=destination |
---|
| 595 | ) |
---|
[3946de5] | 596 | except UndefinedError as e: |
---|
| 597 | print('... ERROR ' + str(e)) |
---|
| 598 | |
---|
| 599 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 600 | _config.PATH_ECMWF_ENV) |
---|
| 601 | except OSError as e: |
---|
| 602 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 603 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 604 | |
---|
| 605 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 606 | _config.PATH_ECMWF_ENV) |
---|
[0aaeb04] | 607 | |
---|
[3946de5] | 608 | try: |
---|
| 609 | with open(_config.PATH_ECMWF_ENV, 'w') as f: |
---|
| 610 | f.write(stream.render('text')) |
---|
| 611 | except OSError as e: |
---|
| 612 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 613 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
[0aaeb04] | 614 | |
---|
[3946de5] | 615 | sys.exit('\n... error occured while trying to write ' + |
---|
| 616 | _config.PATH_ECMWF_ENV) |
---|
[54a8a01] | 617 | |
---|
| 618 | return |
---|
| 619 | |
---|
[b6ea29e] | 620 | def mk_compilejob(makefile, ecuid, fp_root): |
---|
[274f9ef] | 621 | '''Modifies the original job template file so that it is specified |
---|
| 622 | for the user and the environment were it will be applied. Result |
---|
[b6ea29e] | 623 | is stored in a new file "compilejob.ksh" in the Jobscript directory. |
---|
[274f9ef] | 624 | |
---|
| 625 | Parameters |
---|
| 626 | ---------- |
---|
[6f951ca] | 627 | makefile : str |
---|
[8209738] | 628 | Name of the makefile which should be used to compile the Fortran |
---|
[5f67883] | 629 | program. |
---|
[54a8a01] | 630 | |
---|
[6f951ca] | 631 | ecuid : str |
---|
[274f9ef] | 632 | The user id on ECMWF server. |
---|
[54a8a01] | 633 | |
---|
[6f951ca] | 634 | fp_root : str |
---|
[274f9ef] | 635 | Path to the root directory of FLEXPART environment or flex_extract |
---|
| 636 | environment. |
---|
[54a8a01] | 637 | |
---|
[274f9ef] | 638 | Return |
---|
| 639 | ------ |
---|
[a4b6cef] | 640 | |
---|
[991df6a] | 641 | ''' |
---|
[0aaeb04] | 642 | from genshi.template.text import NewTextTemplate |
---|
| 643 | from genshi.template import TemplateLoader |
---|
[3946de5] | 644 | from genshi.template.eval import UndefinedError |
---|
[0aaeb04] | 645 | |
---|
| 646 | if fp_root == '../': |
---|
| 647 | fp_root = '$HOME' |
---|
| 648 | |
---|
[3946de5] | 649 | try: |
---|
| 650 | loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False) |
---|
| 651 | compile_template = loader.load(_config.TEMPFILE_INSTALL_COMPILEJOB, |
---|
| 652 | cls=NewTextTemplate) |
---|
| 653 | |
---|
| 654 | stream = compile_template.generate( |
---|
[0f89116] | 655 | username=ecuid, |
---|
| 656 | version_number=_config._VERSION_STR, |
---|
| 657 | fp_root_scripts=fp_root, |
---|
| 658 | makefile=makefile, |
---|
| 659 | fortran_program=_config.FORTRAN_EXECUTABLE |
---|
[3946de5] | 660 | ) |
---|
| 661 | except UndefinedError as e: |
---|
| 662 | print('... ERROR ' + str(e)) |
---|
| 663 | |
---|
| 664 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 665 | _config.TEMPFILE_INSTALL_COMPILEJOB) |
---|
| 666 | except OSError as e: |
---|
| 667 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 668 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 669 | |
---|
| 670 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 671 | _config.TEMPFILE_INSTALL_COMPILEJOB) |
---|
[0aaeb04] | 672 | |
---|
[3946de5] | 673 | try: |
---|
| 674 | compilejob = os.path.join(_config.PATH_JOBSCRIPTS, |
---|
| 675 | _config.FILE_INSTALL_COMPILEJOB) |
---|
[0aaeb04] | 676 | |
---|
[3946de5] | 677 | with open(compilejob, 'w') as f: |
---|
| 678 | f.write(stream.render('text')) |
---|
| 679 | except OSError as e: |
---|
| 680 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 681 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 682 | |
---|
| 683 | sys.exit('\n... error occured while trying to write ' + |
---|
| 684 | compilejob) |
---|
[0aaeb04] | 685 | |
---|
[54a8a01] | 686 | return |
---|
| 687 | |
---|
[01bd8aa] | 688 | def mk_job_template(ecuid, fp_root): |
---|
[274f9ef] | 689 | '''Modifies the original job template file so that it is specified |
---|
| 690 | for the user and the environment were it will be applied. Result |
---|
| 691 | is stored in a new file. |
---|
[54a8a01] | 692 | |
---|
[274f9ef] | 693 | Parameters |
---|
| 694 | ---------- |
---|
[6f951ca] | 695 | ecuid : str |
---|
[274f9ef] | 696 | The user id on ECMWF server. |
---|
[54a8a01] | 697 | |
---|
[6f951ca] | 698 | fp_root : str |
---|
[274f9ef] | 699 | Path to the root directory of FLEXPART environment or flex_extract |
---|
| 700 | environment. |
---|
| 701 | |
---|
| 702 | Return |
---|
| 703 | ------ |
---|
[54a8a01] | 704 | |
---|
| 705 | ''' |
---|
[c5074d2] | 706 | from genshi.template.text import NewTextTemplate |
---|
| 707 | from genshi.template import TemplateLoader |
---|
[3946de5] | 708 | from genshi.template.eval import UndefinedError |
---|
[c5074d2] | 709 | |
---|
| 710 | fp_root_path_to_python = os.path.join(fp_root, |
---|
| 711 | _config.FLEXEXTRACT_DIRNAME, |
---|
[3946de5] | 712 | _config.PATH_REL_PYTHON_SRC) |
---|
[ff2a11c] | 713 | if '$' in fp_root_path_to_python: |
---|
| 714 | ind = fp_root_path_to_python.index('$') |
---|
| 715 | fp_root_path_to_python = fp_root_path_to_python[0:ind] + '$' + \ |
---|
| 716 | fp_root_path_to_python[ind:] |
---|
[3946de5] | 717 | |
---|
| 718 | try: |
---|
| 719 | loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False) |
---|
| 720 | compile_template = loader.load(_config.TEMPFILE_INSTALL_JOB, |
---|
| 721 | cls=NewTextTemplate) |
---|
| 722 | |
---|
| 723 | stream = compile_template.generate( |
---|
[0f89116] | 724 | username=ecuid, |
---|
| 725 | version_number=_config._VERSION_STR, |
---|
| 726 | fp_root_path=fp_root_path_to_python, |
---|
[3946de5] | 727 | ) |
---|
| 728 | except UndefinedError as e: |
---|
| 729 | print('... ERROR ' + str(e)) |
---|
[c5074d2] | 730 | |
---|
[3946de5] | 731 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 732 | _config.TEMPFILE_INSTALL_JOB) |
---|
| 733 | except OSError as e: |
---|
| 734 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 735 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 736 | |
---|
| 737 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 738 | _config.TEMPFILE_INSTALL_JOB) |
---|
| 739 | |
---|
| 740 | |
---|
| 741 | try: |
---|
| 742 | tempjobfile = os.path.join(_config.PATH_TEMPLATES, |
---|
| 743 | _config.TEMPFILE_JOB) |
---|
[c5074d2] | 744 | |
---|
[3946de5] | 745 | with open(tempjobfile, 'w') as f: |
---|
| 746 | f.write(stream.render('text')) |
---|
| 747 | except OSError as e: |
---|
| 748 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 749 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
[c5074d2] | 750 | |
---|
[3946de5] | 751 | sys.exit('\n... error occured while trying to write ' + |
---|
| 752 | tempjobfile) |
---|
[c5074d2] | 753 | |
---|
[54a8a01] | 754 | return |
---|
| 755 | |
---|
[5f67883] | 756 | def del_fortran_build(src_path): |
---|
[274f9ef] | 757 | '''Clean up the Fortran source directory and remove all |
---|
[5f67883] | 758 | build files (e.g. \*.o, \*.mod and FORTRAN EXECUTABLE) |
---|
[274f9ef] | 759 | |
---|
| 760 | Parameters |
---|
| 761 | ---------- |
---|
[6f951ca] | 762 | src_path : str |
---|
[274f9ef] | 763 | Path to the fortran source directory. |
---|
[54a8a01] | 764 | |
---|
[274f9ef] | 765 | Return |
---|
| 766 | ------ |
---|
[54a8a01] | 767 | |
---|
| 768 | ''' |
---|
| 769 | |
---|
[2fb99de] | 770 | modfiles = UioFiles(src_path, '*.mod') |
---|
| 771 | objfiles = UioFiles(src_path, '*.o') |
---|
| 772 | exefile = UioFiles(src_path, _config.FORTRAN_EXECUTABLE) |
---|
[54a8a01] | 773 | |
---|
| 774 | modfiles.delete_files() |
---|
| 775 | objfiles.delete_files() |
---|
| 776 | exefile.delete_files() |
---|
| 777 | |
---|
| 778 | return |
---|
| 779 | |
---|
[5f67883] | 780 | def mk_fortran_build(src_path, makefile): |
---|
[274f9ef] | 781 | '''Compiles the Fortran code and generates the executable. |
---|
| 782 | |
---|
| 783 | Parameters |
---|
| 784 | ---------- |
---|
[6f951ca] | 785 | src_path : str |
---|
[274f9ef] | 786 | Path to the fortran source directory. |
---|
[54a8a01] | 787 | |
---|
[6f951ca] | 788 | makefile : str |
---|
[274f9ef] | 789 | The name of the makefile which should be used. |
---|
[54a8a01] | 790 | |
---|
[274f9ef] | 791 | Return |
---|
| 792 | ------ |
---|
[54a8a01] | 793 | |
---|
| 794 | ''' |
---|
| 795 | |
---|
| 796 | try: |
---|
[2fb99de] | 797 | print('Using makefile: ' + makefile) |
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| 798 | p = subprocess.Popen(['make', '-f', |
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| 799 | os.path.join(src_path, makefile)], |
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[54a8a01] | 800 | stdin=subprocess.PIPE, |
---|
| 801 | stdout=subprocess.PIPE, |
---|
| 802 | stderr=subprocess.PIPE, |
---|
| 803 | bufsize=1) |
---|
| 804 | pout, perr = p.communicate() |
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[79729d5] | 805 | print(pout.decode()) |
---|
[54a8a01] | 806 | if p.returncode != 0: |
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[79729d5] | 807 | print(perr.decode()) |
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[2fb99de] | 808 | print('Please edit ' + makefile + |
---|
[5f67883] | 809 | ' or try another makefile in the src directory.') |
---|
| 810 | print('Most likely ECCODES_INCLUDE_DIR, ECCODES_LIB ' |
---|
[2fb99de] | 811 | 'and EMOSLIB must be adapted.') |
---|
[5f67883] | 812 | print('Available makefiles:') |
---|
| 813 | print(UioFiles(src_path, 'makefile*')) |
---|
[54a8a01] | 814 | sys.exit('Compilation failed!') |
---|
| 815 | except ValueError as e: |
---|
[5f67883] | 816 | print('ERROR: makefile call failed:') |
---|
[2fb99de] | 817 | print(e) |
---|
[d69b677] | 818 | else: |
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[47be2684] | 819 | execute_subprocess(['ls', '-l', |
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[0f89116] | 820 | os.path.join(src_path, _config.FORTRAN_EXECUTABLE)], |
---|
| 821 | error_msg='FORTRAN EXECUTABLE COULD NOT BE FOUND!') |
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[a4b6cef] | 822 | |
---|
[d69b677] | 823 | return |
---|
| 824 | |
---|
[a4b6cef] | 825 | |
---|
[d69b677] | 826 | if __name__ == "__main__": |
---|
| 827 | main() |
---|