[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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[5cff464] | 96 | overwrite_lines_in_file, check_for_string_in_file, |
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| 97 | submit_sbatch_job) |
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[d69b677] | 98 | |
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[64cf353] | 99 | # ------------------------------------------------------------------------------ |
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| 100 | # FUNCTIONS |
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| 101 | # ------------------------------------------------------------------------------ |
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[991df6a] | 102 | def main(): |
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[274f9ef] | 103 | '''Controls the installation process. Calls the installation function |
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| 104 | if target is specified. |
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[991df6a] | 105 | |
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[274f9ef] | 106 | Parameters |
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| 107 | ---------- |
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[991df6a] | 108 | |
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[274f9ef] | 109 | Return |
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| 110 | ------ |
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[991df6a] | 111 | ''' |
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| 112 | |
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[8652e7e] | 113 | args = get_install_cmdline_args() |
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[4971f63] | 114 | c = ControlFile(args.controlfile) |
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[54a8a01] | 115 | c.assign_args_to_control(args) |
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[6cda7c1] | 116 | check_install_conditions(c) |
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[5cff464] | 117 | |
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[b6ea29e] | 118 | if c.install_target.lower() not in ['local', 'syslocal']: # ecmwf servers e.g. ecgate (ecs) and hpc |
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[8ce3be6] | 119 | install_via_gateway(c) |
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| 120 | else: # local |
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| 121 | install_local(c) |
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[991df6a] | 122 | |
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[47be2684] | 123 | print("SUCCESS: INSTALLATION FINISHED!") |
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| 124 | |
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[54a8a01] | 125 | return |
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[991df6a] | 126 | |
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[8652e7e] | 127 | def get_install_cmdline_args(): |
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[274f9ef] | 128 | '''Decomposes the command line arguments and assigns them to variables. |
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[8209738] | 129 | Apply default values for arguments not present. |
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[efdb01a] | 130 | |
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[274f9ef] | 131 | Parameters |
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| 132 | ---------- |
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[efdb01a] | 133 | |
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[274f9ef] | 134 | Return |
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| 135 | ------ |
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[6f951ca] | 136 | args : Namespace |
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[274f9ef] | 137 | Contains the commandline arguments from script/program call. |
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[efdb01a] | 138 | ''' |
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[8ce3be6] | 139 | parser = ArgumentParser(description='Install flex_extract software ' |
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| 140 | 'locally or on ECMWF machines', |
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[efdb01a] | 141 | formatter_class=ArgumentDefaultsHelpFormatter) |
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| 142 | |
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[8ce3be6] | 143 | parser.add_argument('--target', dest='install_target', |
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| 144 | type=none_or_str, default=None, |
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[b6ea29e] | 145 | help="Valid targets: syslocal | local | ecgate | cca | \ |
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| 146 | ccb | ecs | hpc , the latter 5 are at ECMWF servers") |
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[8ce3be6] | 147 | parser.add_argument("--makefile", dest="makefile", |
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| 148 | type=none_or_str, default=None, |
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[8209738] | 149 | help='Name of makefile for compiling the ' |
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[8ce3be6] | 150 | 'Fortran program') |
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| 151 | parser.add_argument("--ecuid", dest="ecuid", |
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| 152 | type=none_or_str, default=None, |
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[8209738] | 153 | help='User id at ECMWF') |
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[8ce3be6] | 154 | parser.add_argument("--ecgid", dest="ecgid", |
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| 155 | type=none_or_str, default=None, |
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[8209738] | 156 | help='Group id at ECMWF') |
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[8ce3be6] | 157 | parser.add_argument("--gateway", dest="gateway", |
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| 158 | type=none_or_str, default=None, |
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[8209738] | 159 | help='Name of the local gateway server') |
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[8ce3be6] | 160 | parser.add_argument("--destination", dest="destination", |
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| 161 | type=none_or_str, default=None, |
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[8209738] | 162 | help='ecaccess association, e.g. ' |
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[8ce3be6] | 163 | 'myUser@genericSftp') |
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| 164 | |
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| 165 | parser.add_argument("--installdir", dest="installdir", |
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| 166 | type=none_or_str, default=None, |
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[47be2684] | 167 | help='Root (user) directory of the ' |
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[8209738] | 168 | 'flex_extract installation') |
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[47be2684] | 169 | parser.add_argument("--sysinstalldir", dest="sysinstalldir", |
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| 170 | type=none_or_str, default=None, |
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| 171 | help='System installation path; where ' |
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| 172 | 'executables are stored.') |
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[efdb01a] | 173 | |
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[54a8a01] | 174 | # arguments for job submission to ECMWF, only needed by submit.py |
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[efdb01a] | 175 | parser.add_argument("--job_template", dest='job_template', |
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[8ce3be6] | 176 | type=none_or_str, default="job.template", |
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[8209738] | 177 | help='Rudimentary template file to create a batch ' |
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| 178 | 'job template for submission to ECMWF servers') |
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[efdb01a] | 179 | |
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| 180 | parser.add_argument("--controlfile", dest="controlfile", |
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[8ce3be6] | 181 | type=none_or_str, default='CONTROL_EA5', |
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[8209738] | 182 | help="A file that contains all CONTROL parameters.") |
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[efdb01a] | 183 | |
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| 184 | args = parser.parse_args() |
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| 185 | |
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[54a8a01] | 186 | return args |
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| 187 | |
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[efdb01a] | 188 | |
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[54a8a01] | 189 | def install_via_gateway(c): |
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[8209738] | 190 | '''Prepare data transfer to remote gateway and submit a job script which will |
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| 191 | install everything on the remote gateway. |
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[274f9ef] | 192 | |
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| 193 | Parameters |
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| 194 | ---------- |
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[6f951ca] | 195 | c : ControlFile |
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[274f9ef] | 196 | Contains all the parameters of CONTROL file and |
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| 197 | command line. |
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| 198 | |
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| 199 | Return |
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| 200 | ------ |
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| 201 | |
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[54a8a01] | 202 | ''' |
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[2fb99de] | 203 | |
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| 204 | tarball_name = _config.FLEXEXTRACT_DIRNAME + '.tar' |
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[8ce3be6] | 205 | tar_file = os.path.join(_config.PATH_FLEXEXTRACT_DIR, tarball_name) |
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[54a8a01] | 206 | |
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[b6ea29e] | 207 | mk_compilejob(c.makefile, c.ecuid, c.installdir) |
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[54a8a01] | 208 | |
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[5cff464] | 209 | mk_job_template(c.ecuid, c.installdir) |
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[8ce3be6] | 210 | |
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| 211 | mk_env_vars(c.ecuid, c.ecgid, c.gateway, c.destination) |
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| 212 | |
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| 213 | mk_tarball(tar_file, c.install_target) |
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| 214 | |
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[b6ea29e] | 215 | put_file_to_ecserver(_config.PATH_FLEXEXTRACT_DIR, tarball_name) |
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[8ce3be6] | 216 | |
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[94d3227] | 217 | # submit_sbatch_job(os.path.join(_config.PATH_REL_JOBSCRIPTS, |
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| 218 | # _config.FILE_INSTALL_COMPILEJOB)) |
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[5cff464] | 219 | |
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[94d3227] | 220 | submit_job_to_ecserver(c.install_target, |
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| 221 | os.path.join(_config.PATH_REL_JOBSCRIPTS, |
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| 222 | _config.FILE_INSTALL_COMPILEJOB)) |
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[8ce3be6] | 223 | |
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| 224 | silent_remove(tar_file) |
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| 225 | |
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| 226 | print('Job compilation script has been submitted to ecgate for ' + |
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| 227 | 'installation in ' + c.installdir + |
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[0f89116] | 228 | '/' + _config.FLEXEXTRACT_DIRNAME) |
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[8ce3be6] | 229 | print('You should get an email with subject "flexcompile" within ' + |
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| 230 | 'the next few minutes!') |
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| 231 | |
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| 232 | return |
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| 233 | |
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| 234 | def install_local(c): |
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| 235 | '''Perform the actual installation on a local machine. |
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[54a8a01] | 236 | |
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[8ce3be6] | 237 | Parameters |
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| 238 | ---------- |
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| 239 | c : ControlFile |
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| 240 | Contains all the parameters of CONTROL file and |
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| 241 | command line. |
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| 242 | |
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| 243 | Return |
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| 244 | ------ |
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| 245 | |
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| 246 | ''' |
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| 247 | |
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| 248 | tar_file = os.path.join(_config.PATH_FLEXEXTRACT_DIR, |
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| 249 | _config.FLEXEXTRACT_DIRNAME + '.tar') |
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| 250 | |
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[47be2684] | 251 | # this is standard installation into a single directory |
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| 252 | if c.install_target == 'local': |
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[5adaf8a] | 253 | c.installdir = os.path.abspath(os.path.expandvars(os.path.expanduser( |
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| 254 | c.installdir))) |
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[47be2684] | 255 | |
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| 256 | # installation into the current directory |
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| 257 | if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.installdir: |
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| 258 | print('WARNING: installdir has not been specified') |
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| 259 | print('flex_extract will be installed in current dir by compiling the ' + |
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| 260 | 'Fortran source in ' + _config.PATH_FORTRAN_SRC) |
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| 261 | os.chdir(_config.PATH_FORTRAN_SRC) |
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| 262 | # installation into a different path |
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| 263 | elif os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) != c.installdir : |
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| 264 | |
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| 265 | # creates the target working directory for flex_extract |
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[8ce3be6] | 266 | mk_tarball(tar_file, c.install_target) |
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| 267 | make_dir(os.path.join(c.installdir, |
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[0f89116] | 268 | _config.FLEXEXTRACT_DIRNAME)) |
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[8ce3be6] | 269 | os.chdir(os.path.join(c.installdir, |
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[0f89116] | 270 | _config.FLEXEXTRACT_DIRNAME)) |
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[8ce3be6] | 271 | un_tarball(tar_file) |
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| 272 | os.chdir(os.path.join(c.installdir, |
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[0f89116] | 273 | _config.FLEXEXTRACT_DIRNAME, |
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[8ce3be6] | 274 | _config.PATH_REL_FORTRAN_SRC)) |
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| 275 | |
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[47be2684] | 276 | # Create Fortran executable |
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| 277 | print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software at ' + |
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| 278 | c.install_target + ' in directory ' + c.installdir + '\n') |
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| 279 | |
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| 280 | del_fortran_build('.') |
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| 281 | mk_fortran_build('.', c.makefile) |
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| 282 | os.chdir('../../') |
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| 283 | # make sure that the correct calling of submit.py script is in run_local.sh |
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| 284 | overwrite_lines_in_file('Run/run_local.sh', |
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| 285 | 'pyscript=', 'pyscript=../Source/Python/submit.py\n') |
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| 286 | |
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| 287 | # this is system installation were executables and user files are separated |
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| 288 | elif c.install_target == 'syslocal': |
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[5adaf8a] | 289 | c.sysinstalldir = os.path.abspath(os.path.expandvars(os.path.expanduser( |
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| 290 | c.sysinstalldir))) |
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[47be2684] | 291 | if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.sysinstalldir : |
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| 292 | sys.exit('ERROR: System installation path is equal to user ' |
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| 293 | 'installation path.\n Please change either the system ' |
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| 294 | 'installation path or use installation target "local".') |
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| 295 | if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.installdir : |
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| 296 | print('Flex_extract will be installed in current directory!') |
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| 297 | else: # install user part in different dir |
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| 298 | print('Flex_extract will be installed in ' + c.installdir ) |
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| 299 | |
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| 300 | c.installdir = os.path.join(c.installdir,_config.FLEXEXTRACT_DIRNAME) |
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| 301 | if os.path.isdir(c.installdir): |
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| 302 | shutil.rmtree(c.installdir) |
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| 303 | |
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| 304 | # copy all files except Python and Fortranfiles to this dir |
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| 305 | shutil.copytree(_config.PATH_FLEXEXTRACT_DIR, |
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| 306 | c.installdir, symlinks=True) |
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| 307 | shutil.rmtree(os.path.join(c.installdir,'Source')) |
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| 308 | shutil.rmtree(os.path.join(c.installdir,'.git')) |
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| 309 | for x in UioFiles(c.installdir, '*~').files: |
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| 310 | silent_remove(x) |
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| 311 | |
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| 312 | os.remove(os.path.join(c.installdir,'setup.sh')) |
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| 313 | os.remove(os.path.join(c.installdir,'setup_local.sh')) |
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| 314 | |
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| 315 | # configure run_local script correctly |
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| 316 | # check if source of system config file is already in run_local.sh, |
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| 317 | # if not, add it |
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| 318 | if not check_for_string_in_file(os.path.join(c.installdir,'Run/run_local.sh'), |
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| 319 | 'source .setup.rc'): |
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| 320 | overwrite_lines_in_file(os.path.join(c.installdir,'Run/run_local.sh'), |
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| 321 | '# PATH TO SUBMISSION SCRIPT', |
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| 322 | '# PATH TO SUBMISSION SCRIPT\nsource '+_config.FILE_SYS_CONFIG+'\n') |
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| 323 | # make sure that the correct calling of submit.py script is in run_local.sh |
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| 324 | overwrite_lines_in_file(os.path.join(c.installdir,'Run/run_local.sh'), |
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| 325 | 'pyscript=', 'pyscript=submit.py\n') |
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| 326 | |
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| 327 | # change permission for file to executable |
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| 328 | execute_subprocess(['chmod', '0775', |
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| 329 | os.path.join(os.path.abspath(c.installdir),'Run/run_local.sh')]) |
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| 330 | |
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| 331 | |
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| 332 | # create systemdir |
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| 333 | c.sysinstalldir = os.path.join(c.sysinstalldir,_config.FLEXEXTRACT_DIRNAME) |
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| 334 | if os.path.isdir(c.sysinstalldir): |
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| 335 | shutil.rmtree(c.sysinstalldir) |
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| 336 | |
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| 337 | # create setup file for running flex_extract with system installation |
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| 338 | with open(os.path.join(os.path.abspath(c.installdir),'Run/.setup.rc'),'w') as fio: |
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| 339 | fio.write('#!/bin/bash \n') |
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| 340 | fio.write('export FLEXEXTRACT_USER_DIR='+os.path.abspath(c.installdir)+'\n') |
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| 341 | fio.write('export PATH='+os.path.abspath(c.sysinstalldir)+'/Python:${PATH}\n') |
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| 342 | fio.write('export PATH='+os.path.abspath(c.sysinstalldir)+':${PATH}\n') |
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| 343 | |
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| 344 | # copy all Python and Fortranfiles to this dir |
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| 345 | shutil.copytree(_config.PATH_SOURCES, c.sysinstalldir, symlinks=True) |
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| 346 | |
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| 347 | os.chdir(os.path.join(c.sysinstalldir,'Fortran')) |
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| 348 | # Create Fortran executable |
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| 349 | print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software as ' + |
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| 350 | c.install_target + ' in directory ' + |
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| 351 | os.path.abspath(c.sysinstalldir) + '\n') |
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| 352 | |
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| 353 | del_fortran_build('.') |
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| 354 | mk_fortran_build('.', c.makefile) |
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| 355 | |
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| 356 | outfile = [x for x in UioFiles('.','*.out').files] |
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| 357 | test=os.path.join(c.sysinstalldir,'calc_etadot') |
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| 358 | if len(outfile) != 1: |
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| 359 | print('WARNING: Multiple executables for Fortran code are available!') |
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| 360 | # move executable one dir up and delete Fortran dir |
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| 361 | os.chdir('..') |
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| 362 | shutil.move(outfile[0], os.path.join(c.sysinstalldir,'calc_etadot')) |
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| 363 | shutil.rmtree(os.path.join(os.path.abspath(c.sysinstalldir),'Fortran')) |
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[8ce3be6] | 364 | |
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| 365 | os.chdir(_config.PATH_FLEXEXTRACT_DIR) |
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| 366 | if os.path.isfile(tar_file): |
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| 367 | os.remove(tar_file) |
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[54a8a01] | 368 | |
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| 369 | return |
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| 370 | |
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[8ce3be6] | 371 | |
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[6cda7c1] | 372 | def check_install_conditions(c): |
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[8209738] | 373 | '''Checks necessary attributes and conditions |
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| 374 | for the installation, e.g. whether they exist and contain values. |
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[6cda7c1] | 375 | Otherwise set default values. |
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| 376 | |
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| 377 | Parameters |
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| 378 | ---------- |
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[6f951ca] | 379 | c : ControlFile |
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[6cda7c1] | 380 | Contains all the parameters of CONTROL file and |
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| 381 | command line. |
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| 382 | |
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| 383 | |
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| 384 | Return |
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| 385 | ------ |
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| 386 | |
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| 387 | ''' |
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| 388 | |
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| 389 | if c.install_target and \ |
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| 390 | c.install_target not in _config.INSTALL_TARGETS: |
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| 391 | print('ERROR: unknown or missing installation target ') |
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| 392 | print('target: ', c.install_target) |
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| 393 | print('please specify correct installation target ' + |
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[0f89116] | 394 | str(_config.INSTALL_TARGETS)) |
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[6cda7c1] | 395 | print('use -h or --help for help') |
---|
| 396 | sys.exit(1) |
---|
| 397 | |
---|
[47be2684] | 398 | if c.install_target and c.install_target not in ['local', 'syslocal']: |
---|
[50f9ca6] | 399 | if not c.ecgid or not c.ecuid: |
---|
| 400 | print('Please enter your ECMWF user id and group id ' |
---|
| 401 | ' with command line options --ecuid --ecgid') |
---|
[6cda7c1] | 402 | print('Try "' + sys.argv[0].split('/')[-1] + \ |
---|
| 403 | ' -h" to print usage information') |
---|
[50f9ca6] | 404 | print('Please consult ecaccess documentation or ECMWF user ' |
---|
| 405 | 'support for further details.\n') |
---|
[6cda7c1] | 406 | sys.exit(1) |
---|
[50f9ca6] | 407 | if not c.gateway or not c.destination: |
---|
| 408 | print('WARNING: Parameters GATEWAY and DESTINATION were ' |
---|
| 409 | 'not properly set for working on ECMWF server. \n' |
---|
| 410 | 'There will be no transfer of output files to the ' |
---|
| 411 | 'local gateway server possible!') |
---|
[8ce3be6] | 412 | if not c.installdir: |
---|
| 413 | c.installdir = '${HOME}' |
---|
[47be2684] | 414 | elif c.install_target == 'local': |
---|
[8ce3be6] | 415 | if not c.installdir: |
---|
| 416 | c.installdir = _config.PATH_FLEXEXTRACT_DIR |
---|
[47be2684] | 417 | elif c.install_target == 'syslocal': |
---|
| 418 | if not c.installdir: |
---|
| 419 | c.installdir = _config.PATH_FLEXEXTRACT_DIR |
---|
| 420 | if not c.sysinstalldir: |
---|
| 421 | print('ERROR: System installation was selected but ' |
---|
| 422 | 'no system installation path was defined.') |
---|
| 423 | sys.exit() |
---|
[6cda7c1] | 424 | |
---|
[5f67883] | 425 | if not c.makefile: |
---|
| 426 | print('WARNING: no makefile was specified.') |
---|
| 427 | if c.install_target == 'local': |
---|
| 428 | c.makefile = 'makefile_local_gfortran' |
---|
| 429 | print('WARNING: default makefile selected: makefile_local_gfortan') |
---|
| 430 | elif c.install_target == 'ecgate': |
---|
| 431 | c.makefile = 'makefile_ecgate' |
---|
| 432 | print('WARNING: default makefile selected: makefile_ecgate') |
---|
| 433 | elif c.install_target == 'cca' or \ |
---|
| 434 | c.install_target == 'ccb': |
---|
| 435 | c.makefile = 'makefile_cray' |
---|
| 436 | print('WARNING: default makefile selected: makefile_cray') |
---|
| 437 | else: |
---|
| 438 | pass |
---|
[47be2684] | 439 | |
---|
[6cda7c1] | 440 | return |
---|
| 441 | |
---|
| 442 | |
---|
[25b14be] | 443 | def mk_tarball(tarball_path, target): |
---|
[274f9ef] | 444 | '''Creates a tarball with all necessary files which need to be sent to the |
---|
| 445 | installation directory. |
---|
[8209738] | 446 | It does not matter whether this is local or remote. |
---|
| 447 | Collects all Python files, the Fortran source and makefiles, |
---|
[274f9ef] | 448 | the ECMWF_ENV file, the CONTROL files as well as the |
---|
| 449 | template files. |
---|
| 450 | |
---|
| 451 | Parameters |
---|
| 452 | ---------- |
---|
[6f951ca] | 453 | tarball_path : str |
---|
[274f9ef] | 454 | The complete path to the tar file which will contain all |
---|
| 455 | relevant data for flex_extract. |
---|
| 456 | |
---|
[6f951ca] | 457 | target : str |
---|
[274f9ef] | 458 | The queue where the job is submitted to. |
---|
| 459 | |
---|
| 460 | Return |
---|
| 461 | ------ |
---|
| 462 | |
---|
[54a8a01] | 463 | ''' |
---|
[2fb99de] | 464 | |
---|
| 465 | print('Create tarball ...') |
---|
| 466 | |
---|
| 467 | # change to FLEXEXTRACT directory so that the tar can contain |
---|
| 468 | # relative pathes to the files and directories |
---|
| 469 | ecd = _config.PATH_FLEXEXTRACT_DIR + '/' |
---|
| 470 | os.chdir(ecd) |
---|
| 471 | |
---|
| 472 | # get lists of the files to be added to the tar file |
---|
[25b14be] | 473 | if target == 'local': |
---|
[0f89116] | 474 | ecmwf_env_file = [] |
---|
[3946de5] | 475 | runfile = [os.path.relpath(x, ecd) |
---|
| 476 | for x in UioFiles(_config.PATH_REL_RUN_DIR, |
---|
| 477 | 'run_local.sh').files] |
---|
[25b14be] | 478 | else: |
---|
[0f89116] | 479 | ecmwf_env_file = [_config.PATH_REL_ECMWF_ENV] |
---|
[3946de5] | 480 | runfile = [os.path.relpath(x, ecd) |
---|
[0f89116] | 481 | for x in UioFiles(_config.PATH_REL_RUN_DIR, |
---|
| 482 | 'run.sh').files] |
---|
[25b14be] | 483 | |
---|
[2fb99de] | 484 | pyfiles = [os.path.relpath(x, ecd) |
---|
[3946de5] | 485 | for x in UioFiles(_config.PATH_REL_PYTHON_SRC, '*py').files] |
---|
| 486 | pytestfiles = [os.path.relpath(x, ecd) |
---|
[0f89116] | 487 | for x in UioFiles(_config.PATH_REL_PYTHONTEST_SRC, '*py').files] |
---|
[2fb99de] | 488 | controlfiles = [os.path.relpath(x, ecd) |
---|
[3946de5] | 489 | for x in UioFiles(_config.PATH_REL_CONTROLFILES, |
---|
[25b14be] | 490 | 'CONTROL*').files] |
---|
[1eca806] | 491 | testfiles = [os.path.relpath(x, ecd) |
---|
[8028176] | 492 | for x in UioFiles(_config.PATH_REL_TEST+"/Installation", '*').files] |
---|
[2fb99de] | 493 | tempfiles = [os.path.relpath(x, ecd) |
---|
[a916e8f] | 494 | for x in UioFiles(_config.PATH_REL_TEMPLATES, '*.template').files] |
---|
[3946de5] | 495 | gribtable = [os.path.relpath(x, ecd) |
---|
[0f89116] | 496 | for x in UioFiles(_config.PATH_REL_TEMPLATES, '*grib*').files] |
---|
[2fb99de] | 497 | ffiles = [os.path.relpath(x, ecd) |
---|
[0f89116] | 498 | for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, '*.f90').files] |
---|
[2fb99de] | 499 | hfiles = [os.path.relpath(x, ecd) |
---|
[3946de5] | 500 | for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, '*.h').files] |
---|
[2fb99de] | 501 | makefiles = [os.path.relpath(x, ecd) |
---|
[3a41083] | 502 | for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, 'makefile*').files] |
---|
[8028176] | 503 | jobdir = [os.path.relpath(x, ecd) |
---|
| 504 | for x in UioFiles(_config.PATH_REL_JOBSCRIPTS, '*.md').files] |
---|
[2fb99de] | 505 | |
---|
| 506 | # concatenate single lists to one for a better looping |
---|
[a916e8f] | 507 | filelist = pyfiles + pytestfiles + controlfiles + tempfiles + \ |
---|
[0f89116] | 508 | ffiles + gribtable + hfiles + makefiles + ecmwf_env_file + \ |
---|
[1eca806] | 509 | runfile + jobdir + testfiles +\ |
---|
[3946de5] | 510 | ['CODE_OF_CONDUCT.md', 'LICENSE.md', 'README.md'] |
---|
[2fb99de] | 511 | |
---|
| 512 | # create installation tar-file |
---|
[0f89116] | 513 | exclude_files = [".ksh", ".tar"] |
---|
[54a8a01] | 514 | try: |
---|
[2fb99de] | 515 | with tarfile.open(tarball_path, "w:gz") as tar_handle: |
---|
[0f89116] | 516 | for filename in filelist: |
---|
| 517 | tar_handle.add(filename, recursive=False, |
---|
[3946de5] | 518 | filter=lambda tarinfo: None |
---|
[0f89116] | 519 | if os.path.splitext(tarinfo.name)[1] |
---|
| 520 | in exclude_files |
---|
| 521 | else tarinfo) |
---|
[79729d5] | 522 | except tarfile.TarError as e: |
---|
[0f89116] | 523 | print('... ERROR: ' + str(e)) |
---|
| 524 | |
---|
[79729d5] | 525 | sys.exit('\n... error occured while trying to create the tar-file ' + |
---|
[0f89116] | 526 | str(tarball_path)) |
---|
[54a8a01] | 527 | |
---|
| 528 | return |
---|
| 529 | |
---|
[2fb99de] | 530 | |
---|
| 531 | def un_tarball(tarball_path): |
---|
[274f9ef] | 532 | '''Extracts the given tarball into current directory. |
---|
[2fb99de] | 533 | |
---|
[274f9ef] | 534 | Parameters |
---|
| 535 | ---------- |
---|
[6f951ca] | 536 | tarball_path : str |
---|
[274f9ef] | 537 | The complete path to the tar file which will contain all |
---|
| 538 | relevant data for flex_extract. |
---|
| 539 | |
---|
| 540 | Return |
---|
| 541 | ------ |
---|
[2fb99de] | 542 | |
---|
| 543 | ''' |
---|
| 544 | |
---|
| 545 | print('Untar ...') |
---|
| 546 | |
---|
[3946de5] | 547 | try: |
---|
| 548 | with tarfile.open(tarball_path) as tar_handle: |
---|
| 549 | tar_handle.extractall() |
---|
| 550 | except tarfile.TarError as e: |
---|
| 551 | sys.exit('\n... error occured while trying to read tar-file ' + |
---|
[0f89116] | 552 | str(tarball_path)) |
---|
[3946de5] | 553 | except OSError as e: |
---|
| 554 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 555 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 556 | |
---|
| 557 | sys.exit('\n... error occured while trying to read tar-file ' + |
---|
| 558 | str(tarball_path)) |
---|
[2fb99de] | 559 | |
---|
| 560 | return |
---|
| 561 | |
---|
| 562 | def mk_env_vars(ecuid, ecgid, gateway, destination): |
---|
[274f9ef] | 563 | '''Creates a file named ECMWF_ENV which contains the |
---|
| 564 | necessary environmental variables at ECMWF servers. |
---|
| 565 | It is based on the template ECMWF_ENV.template. |
---|
| 566 | |
---|
| 567 | Parameters |
---|
| 568 | ---------- |
---|
[6f951ca] | 569 | ecuid : str |
---|
[274f9ef] | 570 | The user id on ECMWF server. |
---|
[54a8a01] | 571 | |
---|
[6f951ca] | 572 | ecgid : str |
---|
[274f9ef] | 573 | The group id on ECMWF server. |
---|
[54a8a01] | 574 | |
---|
[6f951ca] | 575 | gateway : str |
---|
[274f9ef] | 576 | The gateway server the user is using. |
---|
[54a8a01] | 577 | |
---|
[6f951ca] | 578 | destination : str |
---|
[274f9ef] | 579 | The remote destination which is used to transfer files |
---|
| 580 | from ECMWF server to local gateway server. |
---|
[54a8a01] | 581 | |
---|
[274f9ef] | 582 | Return |
---|
| 583 | ------ |
---|
[54a8a01] | 584 | |
---|
| 585 | ''' |
---|
[0aaeb04] | 586 | from genshi.template.text import NewTextTemplate |
---|
| 587 | from genshi.template import TemplateLoader |
---|
[3946de5] | 588 | from genshi.template.eval import UndefinedError |
---|
[54a8a01] | 589 | |
---|
[3946de5] | 590 | try: |
---|
| 591 | loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False) |
---|
| 592 | ecmwfvars_template = loader.load(_config.TEMPFILE_USER_ENVVARS, |
---|
| 593 | cls=NewTextTemplate) |
---|
| 594 | |
---|
[0f89116] | 595 | stream = ecmwfvars_template.generate(user_name=ecuid, |
---|
| 596 | user_group=ecgid, |
---|
| 597 | gateway_name=gateway, |
---|
| 598 | destination_name=destination |
---|
| 599 | ) |
---|
[3946de5] | 600 | except UndefinedError as e: |
---|
| 601 | print('... ERROR ' + str(e)) |
---|
| 602 | |
---|
| 603 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 604 | _config.PATH_ECMWF_ENV) |
---|
| 605 | except OSError as e: |
---|
| 606 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 607 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 608 | |
---|
| 609 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 610 | _config.PATH_ECMWF_ENV) |
---|
[0aaeb04] | 611 | |
---|
[3946de5] | 612 | try: |
---|
| 613 | with open(_config.PATH_ECMWF_ENV, 'w') as f: |
---|
| 614 | f.write(stream.render('text')) |
---|
| 615 | except OSError as e: |
---|
| 616 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 617 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
[0aaeb04] | 618 | |
---|
[3946de5] | 619 | sys.exit('\n... error occured while trying to write ' + |
---|
| 620 | _config.PATH_ECMWF_ENV) |
---|
[54a8a01] | 621 | |
---|
| 622 | return |
---|
| 623 | |
---|
[b6ea29e] | 624 | def mk_compilejob(makefile, ecuid, fp_root): |
---|
[274f9ef] | 625 | '''Modifies the original job template file so that it is specified |
---|
| 626 | for the user and the environment were it will be applied. Result |
---|
[b6ea29e] | 627 | is stored in a new file "compilejob.ksh" in the Jobscript directory. |
---|
[274f9ef] | 628 | |
---|
| 629 | Parameters |
---|
| 630 | ---------- |
---|
[6f951ca] | 631 | makefile : str |
---|
[8209738] | 632 | Name of the makefile which should be used to compile the Fortran |
---|
[5f67883] | 633 | program. |
---|
[54a8a01] | 634 | |
---|
[6f951ca] | 635 | ecuid : str |
---|
[274f9ef] | 636 | The user id on ECMWF server. |
---|
[54a8a01] | 637 | |
---|
[6f951ca] | 638 | fp_root : str |
---|
[274f9ef] | 639 | Path to the root directory of FLEXPART environment or flex_extract |
---|
| 640 | environment. |
---|
[54a8a01] | 641 | |
---|
[274f9ef] | 642 | Return |
---|
| 643 | ------ |
---|
[a4b6cef] | 644 | |
---|
[991df6a] | 645 | ''' |
---|
[0aaeb04] | 646 | from genshi.template.text import NewTextTemplate |
---|
| 647 | from genshi.template import TemplateLoader |
---|
[3946de5] | 648 | from genshi.template.eval import UndefinedError |
---|
[0aaeb04] | 649 | |
---|
| 650 | if fp_root == '../': |
---|
| 651 | fp_root = '$HOME' |
---|
| 652 | |
---|
[3946de5] | 653 | try: |
---|
| 654 | loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False) |
---|
| 655 | compile_template = loader.load(_config.TEMPFILE_INSTALL_COMPILEJOB, |
---|
| 656 | cls=NewTextTemplate) |
---|
| 657 | |
---|
| 658 | stream = compile_template.generate( |
---|
[0f89116] | 659 | username=ecuid, |
---|
| 660 | version_number=_config._VERSION_STR, |
---|
| 661 | fp_root_scripts=fp_root, |
---|
| 662 | makefile=makefile, |
---|
| 663 | fortran_program=_config.FORTRAN_EXECUTABLE |
---|
[3946de5] | 664 | ) |
---|
| 665 | except UndefinedError as e: |
---|
| 666 | print('... ERROR ' + str(e)) |
---|
| 667 | |
---|
| 668 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 669 | _config.TEMPFILE_INSTALL_COMPILEJOB) |
---|
| 670 | except OSError as e: |
---|
| 671 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 672 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 673 | |
---|
| 674 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 675 | _config.TEMPFILE_INSTALL_COMPILEJOB) |
---|
[0aaeb04] | 676 | |
---|
[3946de5] | 677 | try: |
---|
| 678 | compilejob = os.path.join(_config.PATH_JOBSCRIPTS, |
---|
| 679 | _config.FILE_INSTALL_COMPILEJOB) |
---|
[0aaeb04] | 680 | |
---|
[3946de5] | 681 | with open(compilejob, 'w') as f: |
---|
| 682 | f.write(stream.render('text')) |
---|
| 683 | except OSError as e: |
---|
| 684 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 685 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 686 | |
---|
| 687 | sys.exit('\n... error occured while trying to write ' + |
---|
| 688 | compilejob) |
---|
[0aaeb04] | 689 | |
---|
[54a8a01] | 690 | return |
---|
| 691 | |
---|
[01bd8aa] | 692 | def mk_job_template(ecuid, fp_root): |
---|
[274f9ef] | 693 | '''Modifies the original job template file so that it is specified |
---|
| 694 | for the user and the environment were it will be applied. Result |
---|
| 695 | is stored in a new file. |
---|
[54a8a01] | 696 | |
---|
[274f9ef] | 697 | Parameters |
---|
| 698 | ---------- |
---|
[6f951ca] | 699 | ecuid : str |
---|
[274f9ef] | 700 | The user id on ECMWF server. |
---|
[54a8a01] | 701 | |
---|
[6f951ca] | 702 | fp_root : str |
---|
[274f9ef] | 703 | Path to the root directory of FLEXPART environment or flex_extract |
---|
| 704 | environment. |
---|
| 705 | |
---|
| 706 | Return |
---|
| 707 | ------ |
---|
[54a8a01] | 708 | |
---|
| 709 | ''' |
---|
[c5074d2] | 710 | from genshi.template.text import NewTextTemplate |
---|
| 711 | from genshi.template import TemplateLoader |
---|
[3946de5] | 712 | from genshi.template.eval import UndefinedError |
---|
[c5074d2] | 713 | |
---|
| 714 | fp_root_path_to_python = os.path.join(fp_root, |
---|
| 715 | _config.FLEXEXTRACT_DIRNAME, |
---|
[3946de5] | 716 | _config.PATH_REL_PYTHON_SRC) |
---|
[ff2a11c] | 717 | if '$' in fp_root_path_to_python: |
---|
| 718 | ind = fp_root_path_to_python.index('$') |
---|
| 719 | fp_root_path_to_python = fp_root_path_to_python[0:ind] + '$' + \ |
---|
| 720 | fp_root_path_to_python[ind:] |
---|
[3946de5] | 721 | |
---|
| 722 | try: |
---|
| 723 | loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False) |
---|
| 724 | compile_template = loader.load(_config.TEMPFILE_INSTALL_JOB, |
---|
| 725 | cls=NewTextTemplate) |
---|
| 726 | |
---|
| 727 | stream = compile_template.generate( |
---|
[0f89116] | 728 | username=ecuid, |
---|
| 729 | version_number=_config._VERSION_STR, |
---|
| 730 | fp_root_path=fp_root_path_to_python, |
---|
[3946de5] | 731 | ) |
---|
| 732 | except UndefinedError as e: |
---|
| 733 | print('... ERROR ' + str(e)) |
---|
[c5074d2] | 734 | |
---|
[3946de5] | 735 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 736 | _config.TEMPFILE_INSTALL_JOB) |
---|
| 737 | except OSError as e: |
---|
| 738 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 739 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
| 740 | |
---|
| 741 | sys.exit('\n... error occured while trying to generate template ' + |
---|
| 742 | _config.TEMPFILE_INSTALL_JOB) |
---|
| 743 | |
---|
| 744 | |
---|
| 745 | try: |
---|
| 746 | tempjobfile = os.path.join(_config.PATH_TEMPLATES, |
---|
| 747 | _config.TEMPFILE_JOB) |
---|
[c5074d2] | 748 | |
---|
[3946de5] | 749 | with open(tempjobfile, 'w') as f: |
---|
| 750 | f.write(stream.render('text')) |
---|
| 751 | except OSError as e: |
---|
| 752 | print('... ERROR CODE: ' + str(e.errno)) |
---|
| 753 | print('... ERROR MESSAGE:\n \t ' + str(e.strerror)) |
---|
[c5074d2] | 754 | |
---|
[3946de5] | 755 | sys.exit('\n... error occured while trying to write ' + |
---|
| 756 | tempjobfile) |
---|
[c5074d2] | 757 | |
---|
[54a8a01] | 758 | return |
---|
| 759 | |
---|
[5f67883] | 760 | def del_fortran_build(src_path): |
---|
[274f9ef] | 761 | '''Clean up the Fortran source directory and remove all |
---|
[5f67883] | 762 | build files (e.g. \*.o, \*.mod and FORTRAN EXECUTABLE) |
---|
[274f9ef] | 763 | |
---|
| 764 | Parameters |
---|
| 765 | ---------- |
---|
[6f951ca] | 766 | src_path : str |
---|
[274f9ef] | 767 | Path to the fortran source directory. |
---|
[54a8a01] | 768 | |
---|
[274f9ef] | 769 | Return |
---|
| 770 | ------ |
---|
[54a8a01] | 771 | |
---|
| 772 | ''' |
---|
| 773 | |
---|
[2fb99de] | 774 | modfiles = UioFiles(src_path, '*.mod') |
---|
| 775 | objfiles = UioFiles(src_path, '*.o') |
---|
| 776 | exefile = UioFiles(src_path, _config.FORTRAN_EXECUTABLE) |
---|
[54a8a01] | 777 | |
---|
| 778 | modfiles.delete_files() |
---|
| 779 | objfiles.delete_files() |
---|
| 780 | exefile.delete_files() |
---|
| 781 | |
---|
| 782 | return |
---|
| 783 | |
---|
[5f67883] | 784 | def mk_fortran_build(src_path, makefile): |
---|
[274f9ef] | 785 | '''Compiles the Fortran code and generates the executable. |
---|
| 786 | |
---|
| 787 | Parameters |
---|
| 788 | ---------- |
---|
[6f951ca] | 789 | src_path : str |
---|
[274f9ef] | 790 | Path to the fortran source directory. |
---|
[54a8a01] | 791 | |
---|
[6f951ca] | 792 | makefile : str |
---|
[274f9ef] | 793 | The name of the makefile which should be used. |
---|
[54a8a01] | 794 | |
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[274f9ef] | 795 | Return |
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| 796 | ------ |
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[54a8a01] | 797 | |
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| 798 | ''' |
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| 799 | |
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| 800 | try: |
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[2fb99de] | 801 | print('Using makefile: ' + makefile) |
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| 802 | p = subprocess.Popen(['make', '-f', |
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| 803 | os.path.join(src_path, makefile)], |
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[54a8a01] | 804 | stdin=subprocess.PIPE, |
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| 805 | stdout=subprocess.PIPE, |
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| 806 | stderr=subprocess.PIPE, |
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| 807 | bufsize=1) |
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| 808 | pout, perr = p.communicate() |
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[79729d5] | 809 | print(pout.decode()) |
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[54a8a01] | 810 | if p.returncode != 0: |
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[79729d5] | 811 | print(perr.decode()) |
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[2fb99de] | 812 | print('Please edit ' + makefile + |
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[5f67883] | 813 | ' or try another makefile in the src directory.') |
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| 814 | print('Most likely ECCODES_INCLUDE_DIR, ECCODES_LIB ' |
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[2fb99de] | 815 | 'and EMOSLIB must be adapted.') |
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[5f67883] | 816 | print('Available makefiles:') |
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| 817 | print(UioFiles(src_path, 'makefile*')) |
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[54a8a01] | 818 | sys.exit('Compilation failed!') |
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| 819 | except ValueError as e: |
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[5f67883] | 820 | print('ERROR: makefile call failed:') |
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[2fb99de] | 821 | print(e) |
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[d69b677] | 822 | else: |
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[47be2684] | 823 | execute_subprocess(['ls', '-l', |
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[0f89116] | 824 | os.path.join(src_path, _config.FORTRAN_EXECUTABLE)], |
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| 825 | error_msg='FORTRAN EXECUTABLE COULD NOT BE FOUND!') |
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[a4b6cef] | 826 | |
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[d69b677] | 827 | return |
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| 828 | |
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[a4b6cef] | 829 | |
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[d69b677] | 830 | if __name__ == "__main__": |
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| 831 | main() |
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