1 | #!/usr/bin/env python |
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2 | # -*- coding: utf-8 -*- |
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3 | #******************************************************************************* |
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4 | # @Author: Leopold Haimberger (University of Vienna) |
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5 | # |
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6 | # @Date: November 2015 |
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7 | # |
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8 | # @Change History: |
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9 | # |
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10 | # February 2018 - Anne Philipp (University of Vienna): |
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11 | # - applied PEP8 style guide |
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12 | # - added documentation |
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13 | # - moved install_args_and_control in here |
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14 | # - splitted code in smaller functions |
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15 | # - delete convert build files in here instead of compile job script |
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16 | # - changed static path names to Variables from config file |
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17 | # |
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18 | # @License: |
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19 | # (C) Copyright 2015-2018. |
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20 | # |
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21 | # This software is licensed under the terms of the Apache Licence Version 2.0 |
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22 | # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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23 | # |
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24 | # @Program Functionality: |
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25 | # Depending on the selected installation environment (locally or on the |
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26 | # ECMWF server ecgate or cca) the program extracts the commandline |
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27 | # arguments and the CONTROL file parameter and prepares the corresponding |
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28 | # environment. The necessary files are collected in a tar-ball and placed |
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29 | # at the target location. There its untared, the environment variables will |
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30 | # be set and the Fortran code will be compiled. If the ECMWF environment is |
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31 | # selected a job script is prepared and submitted for the remaining |
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32 | # configurations after putting the tar-ball to the target ECMWF server. |
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33 | # |
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34 | # @Program Content: |
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35 | # - main |
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36 | # - get_install_cmdline_arguments |
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37 | # - install_via_gateway |
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38 | # - mk_tarball |
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39 | # - un_tarball |
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40 | # - mk_env_vars |
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41 | # - mk_compilejob |
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42 | # - mk_job_template |
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43 | # - delete_convert_build |
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44 | # - make_convert_build |
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45 | # |
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46 | #******************************************************************************* |
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47 | |
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48 | # ------------------------------------------------------------------------------ |
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49 | # MODULES |
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50 | # ------------------------------------------------------------------------------ |
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51 | import os |
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52 | import sys |
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53 | import glob |
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54 | import subprocess |
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55 | import inspect |
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56 | from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter |
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57 | |
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58 | # software specific classes and modules from flex_extract |
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59 | import _config |
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60 | from classes.ControlFile import ControlFile |
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61 | from classes.UioFiles import UioFiles |
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62 | from mods.tools import make_dir, put_file_to_ecserver, submit_job_to_ecserver |
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63 | |
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64 | # ------------------------------------------------------------------------------ |
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65 | # FUNCTIONS |
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66 | # ------------------------------------------------------------------------------ |
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67 | def main(): |
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68 | ''' |
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69 | @Description: |
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70 | Controls the installation process. Calls the installation function |
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71 | if target is specified. |
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72 | |
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73 | @Intput: |
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74 | <nothing> |
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75 | |
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76 | @Return: |
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77 | <nothing> |
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78 | ''' |
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79 | |
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80 | args = get_install_cmdline_arguments() |
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81 | c = ControlFile(args.controlfile) |
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82 | c.assign_args_to_control(args) |
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83 | c.check_install_conditions() |
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84 | |
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85 | install_via_gateway(c) |
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86 | |
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87 | return |
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88 | |
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89 | def get_install_cmdline_arguments(): |
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90 | ''' |
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91 | @Description: |
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92 | Decomposes the command line arguments and assigns them to variables. |
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93 | Apply default values for non mentioned arguments. |
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94 | |
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95 | @Input: |
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96 | <nothing> |
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97 | |
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98 | @Return: |
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99 | args: instance of ArgumentParser |
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100 | Contains the commandline arguments from script/program call. |
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101 | ''' |
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102 | parser = ArgumentParser(description='Install flex_extract software locally or \ |
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103 | on ECMWF machines', |
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104 | formatter_class=ArgumentDefaultsHelpFormatter) |
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105 | |
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106 | parser.add_argument('--target', dest='install_target', default=None, |
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107 | help="Valid targets: local | ecgate | cca , \ |
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108 | the latter two are at ECMWF") |
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109 | parser.add_argument("--makefile", dest="makefile", default=None, |
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110 | help='Name of Makefile to use for compiling CONVERT2') |
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111 | parser.add_argument("--ecuid", dest="ecuid", default=None, |
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112 | help='user id at ECMWF') |
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113 | parser.add_argument("--ecgid", dest="ecgid", default=None, |
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114 | help='group id at ECMWF') |
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115 | parser.add_argument("--gateway", dest="gateway", default=None, |
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116 | help='name of local gateway server') |
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117 | parser.add_argument("--destination", dest="destination", default=None, |
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118 | help='ecaccess destination, e.g. leo@genericSftp') |
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119 | |
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120 | parser.add_argument("--flexpart_root_scripts", dest="flexpart_root_scripts", |
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121 | default=None, help="FLEXPART root directory on ECMWF \ |
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122 | servers (to find grib2flexpart and COMMAND file)\n\ |
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123 | Normally flex_extract resides in the scripts directory \ |
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124 | of the FLEXPART distribution.") |
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125 | |
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126 | # arguments for job submission to ECMWF, only needed by submit.py |
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127 | parser.add_argument("--job_template", dest='job_template', |
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128 | default="job.temp.o", |
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129 | help="job template file for submission to ECMWF") |
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130 | |
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131 | parser.add_argument("--controlfile", dest="controlfile", |
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132 | default='CONTROL.temp', |
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133 | help="file with CONTROL parameters") |
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134 | |
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135 | args = parser.parse_args() |
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136 | |
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137 | return args |
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138 | |
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139 | |
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140 | def install_via_gateway(c): |
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141 | ''' |
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142 | @Description: |
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143 | Perform the actual installation on local machine or prepare data |
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144 | transfer to remote gate and submit a job script which will |
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145 | install everything on the remote gate. |
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146 | |
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147 | @Input: |
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148 | c: instance of class ControlFile |
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149 | Contains all the parameters of CONTROL file and |
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150 | command line. |
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151 | For more information about format and content of the parameter |
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152 | see documentation. |
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153 | |
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154 | @Return: |
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155 | <nothing> |
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156 | ''' |
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157 | import tarfile |
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158 | |
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159 | ecd = _config.PATH_FLEXEXTRACT_DIR |
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160 | tarball_name = _config.FLEXEXTRACT_DIRNAME + '.tar' |
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161 | tar_file = os.path.join(ecd, tarball_name) |
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162 | |
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163 | target_dirname = _config.FLEXEXTRACT_DIRNAME |
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164 | fortran_executable = _config.FORTRAN_EXECUTABLE |
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165 | |
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166 | if c.install_target.lower() != 'local': # ecgate or cca |
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167 | |
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168 | mk_compilejob(c.makefile, c.install_target, c.ecuid, c.ecgid, |
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169 | c.flexpart_root_scripts) |
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170 | |
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171 | mk_job_template(c.ecuid, c.ecgid, c.gateway, |
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172 | c.destination, c.flexpart_root_scripts) |
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173 | |
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174 | mk_env_vars(c.ecuid, c.ecgid, c.gateway, c.destination) |
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175 | |
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176 | mk_tarball(tar_file, c.install_target) |
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177 | |
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178 | put_file_to_ecserver(ecd, tarball_name, c.install_target, |
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179 | c.ecuid, c.ecgid) |
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180 | |
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181 | submit_job_to_ecserver(c.install_target, |
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182 | os.path.join(_config.PATH_REL_JOBSCRIPTS, |
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183 | _config.FILE_INSTALL_COMPILEJOB)) |
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184 | |
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185 | print('job compilation script has been submitted to ecgate for ' + |
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186 | 'installation in ' + c.flexpart_root_scripts + |
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187 | '/' + target_dirname) |
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188 | print('You should get an email with subject "flexcompile" within ' + |
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189 | 'the next few minutes!') |
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190 | |
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191 | else: #local |
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192 | if c.flexpart_root_scripts == _config.PATH_FLEXEXTRACT_DIR : |
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193 | print('WARNING: FLEXPART_ROOT_SCRIPTS has not been specified') |
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194 | print('flex_extract will be installed in here by compiling the ' + |
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195 | 'Fortran source in ' + _config.PATH_FORTRAN_SRC) |
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196 | os.chdir(_config.PATH_FORTRAN_SRC) |
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197 | else: # creates the target working directory for flex_extract |
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198 | c.flexpart_root_scripts = os.path.expandvars(os.path.expanduser( |
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199 | c.flexpart_root_scripts)) |
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200 | if os.path.abspath(ecd) != os.path.abspath(c.flexpart_root_scripts): |
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201 | mk_tarball(tar_file, c.install_target) |
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202 | make_dir(os.path.join(c.flexpart_root_scripts, |
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203 | target_dirname)) |
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204 | os.chdir(os.path.join(c.flexpart_root_scripts, |
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205 | target_dirname)) |
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206 | un_tarball(tar_file) |
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207 | os.chdir(os.path.join(c.flexpart_root_scripts, |
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208 | target_dirname, |
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209 | _config.PATH_REL_FORTRAN_SRC)) |
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210 | |
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211 | # Create Fortran executable - CONVERT2 |
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212 | print('Install ' + target_dirname + ' software at ' + |
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213 | c.install_target + ' in directory ' + |
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214 | os.path.abspath(c.flexpart_root_scripts) + '\n') |
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215 | |
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216 | delete_convert_build('.') |
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217 | make_convert_build('.', c.makefile) |
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218 | |
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219 | os.chdir(ecd) |
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220 | if os.path.isfile(tar_file): |
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221 | os.remove(tar_file) |
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222 | |
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223 | return |
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224 | |
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225 | def mk_tarball(tarball_path, target): |
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226 | ''' |
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227 | @Description: |
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228 | Creates a tarball with all necessary files which need to be sent to the |
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229 | installation directory. |
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230 | It does not matter if this is local or remote. |
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231 | Collects all python files, the Fortran source and makefiles, |
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232 | the ECMWF_ENV file, the CONTROL files as well as the |
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233 | template files. |
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234 | |
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235 | @Input: |
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236 | tarball_path: string |
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237 | The complete path to the tar file which will contain all |
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238 | relevant data for flex_extract. |
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239 | |
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240 | target: string |
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241 | The queue where the job is submitted to. |
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242 | |
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243 | @Return: |
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244 | <nothing> |
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245 | ''' |
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246 | import tarfile |
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247 | from glob import glob |
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248 | |
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249 | print('Create tarball ...') |
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250 | |
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251 | # change to FLEXEXTRACT directory so that the tar can contain |
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252 | # relative pathes to the files and directories |
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253 | ecd = _config.PATH_FLEXEXTRACT_DIR + '/' |
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254 | os.chdir(ecd) |
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255 | |
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256 | # get lists of the files to be added to the tar file |
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257 | if target == 'local': |
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258 | ECMWF_ENV_FILE = [] |
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259 | else: |
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260 | ECMWF_ENV_FILE = [_config.PATH_REL_ECMWF_ENV] |
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261 | |
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262 | pyfiles = [os.path.relpath(x, ecd) |
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263 | for x in UioFiles(_config.PATH_LOCAL_PYTHON, '*py').files] |
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264 | controlfiles = [os.path.relpath(x, ecd) |
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265 | for x in UioFiles(_config.PATH_CONTROLFILES, |
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266 | 'CONTROL*').files] |
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267 | tempfiles = [os.path.relpath(x, ecd) |
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268 | for x in UioFiles(_config.PATH_TEMPLATES , '*').files] |
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269 | ffiles = [os.path.relpath(x, ecd) |
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270 | for x in UioFiles(_config.PATH_FORTRAN_SRC, '*.f*').files] |
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271 | hfiles = [os.path.relpath(x, ecd) |
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272 | for x in UioFiles(_config.PATH_FORTRAN_SRC, '*.h').files] |
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273 | makefiles = [os.path.relpath(x, ecd) |
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274 | for x in UioFiles(_config.PATH_FORTRAN_SRC, 'Makefile*').files] |
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275 | |
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276 | # concatenate single lists to one for a better looping |
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277 | filelist = pyfiles + controlfiles + tempfiles + ffiles + hfiles + \ |
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278 | makefiles + ECMWF_ENV_FILE |
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279 | |
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280 | # create installation tar-file |
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281 | try: |
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282 | with tarfile.open(tarball_path, "w:gz") as tar_handle: |
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283 | for file in filelist: |
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284 | tar_handle.add(file) |
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285 | |
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286 | except subprocess.CalledProcessError as e: |
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287 | print('... ERROR CODE:\n ... ' + str(e.returncode)) |
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288 | print('... ERROR MESSAGE:\n ... ' + str(e)) |
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289 | |
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290 | sys.exit('... could not make installation tar ball!') |
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291 | |
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292 | return |
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293 | |
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294 | |
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295 | def un_tarball(tarball_path): |
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296 | ''' |
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297 | @Description: |
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298 | Extracts the given tarball into current directory. |
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299 | |
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300 | @Input: |
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301 | tarball_path: string |
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302 | The complete path to the tar file which will contain all |
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303 | relevant data for flex_extract. |
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304 | |
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305 | @Return: |
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306 | <nothing> |
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307 | ''' |
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308 | import tarfile |
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309 | |
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310 | print('Untar ...') |
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311 | |
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312 | with tarfile.open(tarball_path) as tar_handle: |
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313 | tar_handle.extractall() |
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314 | |
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315 | return |
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316 | |
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317 | def mk_env_vars(ecuid, ecgid, gateway, destination): |
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318 | ''' |
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319 | @Description: |
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320 | Creates a file named ECMWF_ENV which contains the |
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321 | necessary environmental variables at ECMWF servers. |
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322 | It is based on the template ECMWF_ENV.template. |
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323 | |
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324 | @Input: |
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325 | ecuid: string |
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326 | The user id on ECMWF server. |
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327 | |
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328 | ecgid: string |
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329 | The group id on ECMWF server. |
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330 | |
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331 | gateway: string |
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332 | The gateway server the user is using. |
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333 | |
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334 | destination: string |
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335 | The remote destination which is used to transfer files |
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336 | from ECMWF server to local gateway server. |
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337 | |
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338 | @Return: |
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339 | <nothing> |
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340 | ''' |
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341 | from genshi.template.text import NewTextTemplate |
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342 | from genshi.template import TemplateLoader |
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343 | |
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344 | loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False) |
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345 | ecmwfvars_template = loader.load(_config.TEMPFILE_USER_ENVVARS, |
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346 | cls=NewTextTemplate) |
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347 | |
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348 | stream = ecmwfvars_template.generate(user_name = ecuid, |
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349 | user_group = ecgid, |
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350 | gateway_name = gateway, |
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351 | destination_name = destination |
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352 | ) |
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353 | |
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354 | with open(_config.PATH_ECMWF_ENV, 'w') as f: |
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355 | f.write(stream.render('text')) |
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356 | |
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357 | return |
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358 | |
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359 | def mk_compilejob(makefile, target, ecuid, ecgid, fp_root): |
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360 | ''' |
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361 | @Description: |
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362 | Modifies the original job template file so that it is specified |
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363 | for the user and the environment were it will be applied. Result |
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364 | is stored in a new file "job.temp" in the python directory. |
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365 | |
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366 | @Input: |
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367 | makefile: string |
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368 | Name of the makefile which should be used to compile FORTRAN |
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369 | CONVERT2 program. |
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370 | |
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371 | target: string |
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372 | The target where the installation should be done, e.g. the queue. |
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373 | |
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374 | ecuid: string |
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375 | The user id on ECMWF server. |
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376 | |
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377 | ecgid: string |
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378 | The group id on ECMWF server. |
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379 | |
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380 | fp_root: string |
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381 | Path to the root directory of FLEXPART environment or flex_extract |
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382 | environment. |
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383 | |
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384 | @Return: |
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385 | <nothing> |
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386 | ''' |
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387 | from genshi.template.text import NewTextTemplate |
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388 | from genshi.template import TemplateLoader |
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389 | |
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390 | loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False) |
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391 | compile_template = loader.load(_config.TEMPFILE_INSTALL_COMPILEJOB, |
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392 | cls=NewTextTemplate) |
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393 | |
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394 | if fp_root == '../': |
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395 | fp_root = '$HOME' |
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396 | |
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397 | stream = compile_template.generate( |
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398 | username = ecuid, |
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399 | usergroup = ecgid, |
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400 | version_number = _config._VERSION_STR, |
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401 | fp_root_scripts = fp_root, |
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402 | makefile = makefile, |
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403 | fortran_program = _config.FORTRAN_EXECUTABLE |
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404 | ) |
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405 | |
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406 | compilejob = os.path.join(_config.PATH_JOBSCRIPTS, |
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407 | _config.FILE_INSTALL_COMPILEJOB) |
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408 | |
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409 | with open(compilejob, 'w') as f: |
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410 | f.write(stream.render('text')) |
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411 | |
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412 | |
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413 | # template = os.path.join(_config.PATH_REL_TEMPLATES, |
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414 | # _config.TEMPFILE_INSTALL_COMPILEJOB) |
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415 | # with open(template) as f: |
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416 | # fdata = f.read().split('\n') |
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417 | |
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418 | |
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419 | # with open(compilejob, 'w') as fo: |
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420 | # for data in fdata: |
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421 | # if 'MAKEFILE=' in data: |
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422 | # data = 'export MAKEFILE=' + makefile |
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423 | # elif 'FLEXPART_ROOT_SCRIPTS=' in data: |
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424 | # if fp_root != '../': |
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425 | # data = 'export FLEXPART_ROOT_SCRIPTS=' + fp_root |
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426 | # else: |
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427 | # data = 'export FLEXPART_ROOT_SCRIPTS=$HOME' |
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428 | # elif target.lower() != 'local': |
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429 | # if '--workdir' in data: |
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430 | # data = '#SBATCH --workdir=/scratch/ms/' + \ |
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431 | # ecgid + '/' + ecuid |
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432 | # elif '##PBS -o' in data: |
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433 | # data = '##PBS -o /scratch/ms/' + ecgid + '/' + ecuid + \ |
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434 | # 'flex_ecmwf.$Jobname.$Job_ID.out' |
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435 | # elif 'FLEXPART_ROOT_SCRIPTS=' in data: |
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436 | # if fp_root != '../': |
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437 | # data = 'export FLEXPART_ROOT_SCRIPTS=' + fp_root |
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438 | # else: |
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439 | # data = 'export FLEXPART_ROOT_SCRIPTS=$HOME' |
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440 | # fo.write(data + '\n') |
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441 | |
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442 | return |
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443 | |
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444 | def mk_job_template(ecuid, ecgid, gateway, destination, fp_root): |
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445 | ''' |
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446 | @Description: |
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447 | Modifies the original job template file so that it is specified |
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448 | for the user and the environment were it will be applied. Result |
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449 | is stored in a new file. |
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450 | |
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451 | @Input: |
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452 | ecuid: string |
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453 | The user id on ECMWF server. |
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454 | |
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455 | ecgid: string |
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456 | The group id on ECMWF server. |
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457 | |
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458 | gateway: string |
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459 | The gateway server the user is using. |
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460 | |
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461 | destination: string |
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462 | The remote destination which is used to transfer files |
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463 | from ECMWF server to local gateway server. |
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464 | |
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465 | fp_root: string |
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466 | Path to the root directory of FLEXPART environment or flex_extract |
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467 | environment. |
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468 | |
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469 | @Return: |
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470 | <nothing> |
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471 | ''' |
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472 | fp_root_path_to_python = os.path.join(fp_root, _config.FLEXEXTRACT_DIRNAME, |
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473 | _config.PATH_REL_PYTHON) |
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474 | |
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475 | template = os.path.join(_config.PATH_REL_TEMPLATES, |
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476 | _config.TEMPFILE_INSTALL_JOB) |
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477 | with open(template) as f: |
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478 | fdata = f.read().split('\n') |
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479 | |
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480 | jobfile_temp = os.path.join(_config.PATH_REL_TEMPLATES, |
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481 | _config.TEMPFILE_JOB) |
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482 | with open(jobfile_temp, 'w') as fo: |
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483 | for data in fdata: |
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484 | if '--workdir' in data: |
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485 | data = '#SBATCH --workdir=/scratch/ms/' + ecgid + '/' + ecuid |
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486 | elif '##PBS -o' in data: |
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487 | data = '##PBS -o /scratch/ms/' + ecgid + '/' + \ |
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488 | ecuid + 'flex_ecmwf.$Jobname.$Job_ID.out' |
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489 | elif 'export PATH=${PATH}:' in data: |
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490 | data += fp_root_path_to_python |
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491 | |
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492 | fo.write(data + '\n') |
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493 | return |
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494 | |
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495 | def delete_convert_build(src_path): |
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496 | ''' |
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497 | @Description: |
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498 | Clean up the Fortran source directory and remove all |
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499 | build files (e.g. *.o, *.mod and CONVERT2) |
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500 | |
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501 | @Input: |
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502 | src_path: string |
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503 | Path to the fortran source directory. |
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504 | |
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505 | @Return: |
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506 | <nothing> |
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507 | ''' |
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508 | |
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509 | modfiles = UioFiles(src_path, '*.mod') |
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510 | objfiles = UioFiles(src_path, '*.o') |
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511 | exefile = UioFiles(src_path, _config.FORTRAN_EXECUTABLE) |
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512 | |
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513 | modfiles.delete_files() |
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514 | objfiles.delete_files() |
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515 | exefile.delete_files() |
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516 | |
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517 | return |
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518 | |
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519 | def make_convert_build(src_path, makefile): |
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520 | ''' |
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521 | @Description: |
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522 | Compiles the Fortran code and generates the executable. |
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523 | |
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524 | @Input: |
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525 | src_path: string |
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526 | Path to the fortran source directory. |
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527 | |
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528 | makefile: string |
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529 | The name of the makefile which should be used. |
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530 | |
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531 | @Return: |
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532 | <nothing> |
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533 | ''' |
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534 | |
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535 | try: |
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536 | print('Using makefile: ' + makefile) |
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537 | p = subprocess.Popen(['make', '-f', |
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538 | os.path.join(src_path, makefile)], |
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539 | stdin=subprocess.PIPE, |
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540 | stdout=subprocess.PIPE, |
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541 | stderr=subprocess.PIPE, |
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542 | bufsize=1) |
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543 | pout, perr = p.communicate() |
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544 | print(pout) |
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545 | if p.returncode != 0: |
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546 | print(perr) |
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547 | print('Please edit ' + makefile + |
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548 | ' or try another Makefile in the src directory.') |
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549 | print('Most likely GRIB_API_INCLUDE_DIR, GRIB_API_LIB ' |
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550 | 'and EMOSLIB must be adapted.') |
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551 | print('Available Makefiles:') |
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552 | print(UioFiles(src_path, 'Makefile*')) |
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553 | sys.exit('Compilation failed!') |
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554 | except ValueError as e: |
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555 | print('ERROR: Makefile call failed:') |
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556 | print(e) |
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557 | else: |
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558 | subprocess.check_call(['ls', '-l', |
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559 | os.path.join(src_path, |
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560 | _config.FORTRAN_EXECUTABLE)]) |
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561 | |
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562 | return |
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563 | |
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564 | |
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565 | if __name__ == "__main__": |
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566 | main() |
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