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Documentation/html/Documentation/Api/api_python.html
r47be2684 r08c9091 2494 2494 <p>This module contains a collection of diverse tasks within flex_extract.</p> 2495 2495 <dl class="function"> 2496 <dt id="tools.check_for_string_in_file">2497 <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">check_for_string_in_file</code><span class="sig-paren">(</span><em class="sig-param">filepath</em>, <em class="sig-param">search_string</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#check_for_string_in_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.check_for_string_in_file" title="Permalink to this definition">¶</a></dt>2498 <dd><p>Search for a specific string in a file and return True if2499 the string was found.</p>2500 <dl class="field-list simple">2501 <dt class="field-odd">Parameters</dt>2502 <dd class="field-odd"><ul class="simple">2503 <li><p><strong>filepath</strong> (<em>str</em>) – The full file path which is to be examined.</p></li>2504 <li><p><strong>search_string</strong> (<em>str</em>) – The string which is looked up for in the file.</p></li>2505 </ul>2506 </dd>2507 <dt class="field-even">Returns</dt>2508 <dd class="field-even"><p>True : String was found2509 False : String was not found</p>2510 </dd>2511 <dt class="field-odd">Return type</dt>2512 <dd class="field-odd"><p>Boolean</p>2513 </dd>2514 </dl>2515 </dd></dl>2516 2517 <dl class="function">2518 2496 <dt id="tools.clean_up"> 2519 2497 <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">clean_up</code><span class="sig-paren">(</span><em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#clean_up"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.clean_up" title="Permalink to this definition">¶</a></dt> … … 2754 2732 <dt class="field-odd">Parameters</dt> 2755 2733 <dd class="field-odd"><p><strong>message</strong> (<em>str</em><em>, </em><em>optional</em>) – Message for exiting program. Default value is “Done!”.</p> 2756 </dd>2757 </dl>2758 </dd></dl>2759 2760 <dl class="function">2761 <dt id="tools.overwrite_lines_in_file">2762 <code class="sig-prename descclassname">tools.</code><code class="sig-name descname">overwrite_lines_in_file</code><span class="sig-paren">(</span><em class="sig-param">filepath</em>, <em class="sig-param">search_string</em>, <em class="sig-param">sub_string</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#overwrite_lines_in_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.overwrite_lines_in_file" title="Permalink to this definition">¶</a></dt>2763 <dd><p>Overwrites lines which contain the given search string with the2764 substitution string.</p>2765 <dl class="field-list simple">2766 <dt class="field-odd">Parameters</dt>2767 <dd class="field-odd"><ul class="simple">2768 <li><p><strong>search_string</strong> (<em>str</em>) – The string which is looked up for in the file.</p></li>2769 <li><p><strong>sub_string</strong> (<em>str</em>) – The string which overwrites the search string.</p></li>2770 </ul>2771 2734 </dd> 2772 2735 </dl> -
Documentation/html/Documentation/Input/setup.html
r47be2684 r08c9091 235 235 <tr class="row-even"><td><p>TARGET</p></td> 236 236 <td><p>String</p></td> 237 <td><p>local, syslocal,ecgate, cca, ccb</p></td>238 <td><p>None</p></td> 239 <td><p>Defines the flex_extract application mode to be used. Local = local mode; ecgate = Remote or Gateway mode, cca or ccb = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here. Syslocal = seperates the executables and user application files during installation. Paths are selectable through INSTALLDIR and SYSINSTALLDIR</p></td>237 <td><p>local, ecgate, cca, ccb</p></td> 238 <td><p>None</p></td> 239 <td><p>Defines the flex_extract application mode to be used. Local = local mode; ecgate = Remote or Gateway mode, cca or ccb = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here.</p></td> 240 240 </tr> 241 241 <tr class="row-odd"><td><p>MAKEFILE</p></td> … … 275 275 <td><p>Root path where flex_extract should be installed. It will always be $HOME on ECMWF servers and if not set for the local mode, it will be the current flex_extract root path on local servers. </p></td> 276 276 </tr> 277 <tr class="row-odd"><td><p>SYSINSTALLDIR</p></td> 278 <td><p>String</p></td> 279 <td><p>a full path </p></td> 280 <td><p>None</p></td> 281 <td><p>This will be the same as INSTALLDIR if TARGET=local. Otherwise, the executable files are stored in this path. If it is choosen to be in a system path, don’t forget to start the script with admin rights. </p></td> 282 </tr> 283 <tr class="row-even"><td><p>JOB_TEMPLATE</p></td> 277 <tr class="row-odd"><td><p>JOB_TEMPLATE</p></td> 284 278 <td><p>String</p></td> 285 279 <td><p>installscript.template</p></td> … … 287 281 <td><p>The rudimentary template file to create a batch job template for submission to ECMWF servers. Should not be changed because it is already optimised for ECMWF servers. (Remote and Gateway mode)</p></td> 288 282 </tr> 289 <tr class="row- odd"><td><p>CONTROLFILE</p></td>283 <tr class="row-even"><td><p>CONTROLFILE</p></td> 290 284 <td><p>String</p></td> 291 285 <td><p>any CONTROL file</p></td> … … 408 402 <span class="o">[</span>--ecuid ECUID<span class="o">]</span> <span class="o">[</span>--ecgid ECGID<span class="o">]</span> <span class="o">[</span>--gateway GATEWAY<span class="o">]</span> 409 403 <span class="o">[</span>--destination DESTINATION<span class="o">]</span> <span class="o">[</span>--installdir INSTALLDIR<span class="o">]</span> 410 <span class="o">[</span>--sysinstalldir SYSINSTALLDIR<span class="o">]</span>411 404 <span class="o">[</span>--job_template JOB_TEMPLATE<span class="o">]</span> <span class="o">[</span>--controlfile CONTROLFILE<span class="o">]</span> 412 405 … … 416 409 -h, --help show this <span class="nb">help</span> message and <span class="nb">exit</span> 417 410 --target INSTALL_TARGET 418 Valid targets: syslocal <span class="p">|</span><span class="nb">local</span> <span class="p">|</span> ecgate <span class="p">|</span> cca , the latter two411 Valid targets: <span class="nb">local</span> <span class="p">|</span> ecgate <span class="p">|</span> cca , the latter two 419 412 are at ECMWF <span class="o">(</span>default: None<span class="o">)</span> 420 413 --makefile MAKEFILE Name of makefile to compile the Fortran … … 430 423 Root directory where flex_extract will be installed 431 424 to. <span class="o">(</span>default: None<span class="o">)</span> 432 --sysinstalldir SYSINSTALLDIR433 System installation path<span class="p">;</span> where executables are434 stored. <span class="o">(</span>default: None<span class="o">)</span>435 425 --job_template JOB_TEMPLATE 436 426 The rudimentary template file to create a batch job -
Documentation/html/Installation/local.html
r903ed4f r73308e0 104 104 <li class="toctree-l4"><a class="reference internal" href="#testing-the-local-environment">Testing the local environment</a></li> 105 105 <li class="toctree-l4"><a class="reference internal" href="#local-installation">Local installation</a></li> 106 <li class="toctree-l4"><a class="reference internal" href="#local-system-installation">Local system installation</a></li>107 106 </ul> 108 107 </li> … … 396 395 <p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> will be compiled during the 397 396 installation process. A suitable makefile (<code class="docutils literal notranslate"><span class="pre">makefile_local_gfortran</span></code>) for the compilation is set by default. 398 This may be overwritten by the <code class="docutils literal notranslate"><span class="pre">MAKEFILE</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">setup _local.sh</span></code>.</p>399 <p>However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into <code class="docutils literal notranslate"><span class="pre">setup _local.sh</span></code>397 This may be overwritten by the <code class="docutils literal notranslate"><span class="pre">MAKEFILE</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.</p> 398 <p>However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> 400 399 For details on the makefile and how to adapt them, see <a class="reference internal" href="../Documentation/Input/fortran_makefile.html#ref-convert"><span class="std std-ref">Fortran Makefile</span></a>.</p> 401 <p>In the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, open the <code class="docutils literal notranslate"><span class="pre">setup _local.sh</span></code> script400 <p>In the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, open the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script 402 401 with an editor and adapt the installation parameters in the section labelled with 403 402 “AVAILABLE COMMANDLINE ARGUMENTS TO SET” as shown below:</p> 404 <div class="literal-block-wrapper docutils container" id="setup- local-sh">405 <div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#setup- local-sh" title="Permalink to this code">¶</a></div>403 <div class="literal-block-wrapper docutils container" id="setup-sh"> 404 <div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#setup-sh" title="Permalink to this code">¶</a></div> 406 405 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>... 407 406 <span class="c1"># -----------------------------------------------------------------</span> … … 417 416 <span class="nv">DESTINATION</span><span class="o">=</span>None 418 417 <span class="nv">INSTALLDIR</span><span class="o">=</span>None 419 <span class="nv">SYSINSTALLDIR</span><span class="o">=</span>None420 418 <span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">''</span> 421 419 <span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span> … … 425 423 </div> 426 424 <p>Afterwards, type:</p> 427 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup _local.sh425 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup.sh 428 426 </pre></div> 429 427 </div> 430 428 <p>to start the installation. You should see the following standard output.</p> 431 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup _local.sh</span>429 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span> 432 430 WARNING: installdir has not been specified 433 431 flex_extract will be installed in here by compiling the Fortran <span class="nb">source</span> in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran … … 448 446 </div> 449 447 </div> 450 <div class="section" id="local-system-installation">451 <h2>Local system installation<a class="headerlink" href="#local-system-installation" title="Permalink to this headline">¶</a></h2>452 <p>There is also the possibility to separate the software executables from the user application files. For doing so, the <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> parameter can be set to “syslocal” and the additional parameter <code class="docutils literal notranslate"><span class="pre">SYSINSTALLDIR</span></code> in the <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code> has to be specified. This new path will contain the Fortran and Python executables of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. If you chose to set a system path for this, please start the script as root.453 The user directory for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, which basically consists of everything except the <code class="docutils literal notranslate"><span class="pre">Source</span></code> directory, will be installed into <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code>.454 In this installation mode, an extra (hidden) <code class="docutils literal notranslate"><span class="pre">.setup.rc</span></code> file will be generated in the <code class="docutils literal notranslate"><span class="pre">Run</span></code> directory. It contains the necessary settings for running the local system mode.</p>455 <p>Despite the change in the <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> parameter, the meaning of <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code> and the additional <code class="docutils literal notranslate"><span class="pre">SYSINSTALLDIR</span></code>, the steps for installation are the same as in the local installation mentioned above. For example, modify the <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code> file as follows:</p>456 <div class="literal-block-wrapper docutils container" id="id1">457 <div class="code-block-caption"><span class="caption-text">‘Example settings for a local system installation.’</span><a class="headerlink" href="#id1" title="Permalink to this code">¶</a></div>458 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...459 <span class="c1"># -----------------------------------------------------------------</span>460 <span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>461 <span class="c1">#</span>462 <span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>463 <span class="c1">#</span>464 <span class="nv">TARGET</span><span class="o">=</span><span class="s1">'syslocal'</span>465 <span class="nv">MAKEFILE</span><span class="o">=</span><name_of_your_makefile>466 <span class="nv">ECUID</span><span class="o">=</span>None467 <span class="nv">ECGID</span><span class="o">=</span>None468 <span class="nv">GATEWAY</span><span class="o">=</span>None469 <span class="nv">DESTINATION</span><span class="o">=</span>None470 <span class="nv">INSTALLDIR</span><span class="o">=</span><span class="nv">$HOME</span>471 <span class="nv">SYSINSTALLDIR</span><span class="o">=</span>/usr/bin/472 <span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">''</span>473 <span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>474 ...475 </pre></div>476 </div>477 </div>478 <p>Afterwards, type:</p>479 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ sudo ./setup_local.sh480 </pre></div>481 </div>482 <p>to start the installation. You should see the following standard output.</p>483 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>Flex_extract will be installed in <<span class="nv">$HOME</span>>484 Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2485 486 Using makefile: makefile_local_gfortran487 /usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./rwgrib2.f90488 /usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./phgrreal.f90489 /usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./grphreal.f90490 /usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./ftrafo.f90491 /usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./calc_etadot.f90492 /usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./posnam.f90493 /usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp494 ln -sf calc_etadot_fast.out calc_etadot495 496 lrwxrwxrwx. <span class="m">1</span> <username> tmc <span class="m">20</span> <span class="m">27</span>. Okt <span class="m">23</span>:25 ./calc_etadot -> calc_etadot_fast.out497 SUCCESS: INSTALLATION FINISHED!498 </pre></div>499 </div>500 <p>You can now change into the user directory specified in <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code> and find a <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X</span></code> directory there.</p>501 </div>502 448 </div> 503 449 -
Documentation/html/_modules/ControlFile.html
r903ed4f r08c9091 183 183 <span class="c1"># June 2020 - Anne Philipp</span> 184 184 <span class="c1"># - update default makefile to None</span> 185 <span class="c1"># August 2020 - Leopold Haimberger</span>186 <span class="c1"># - added a class parameter for system installation path</span>187 185 <span class="c1">#</span> 188 186 <span class="c1"># @License:</span> … … 568 566 <span class="bp">self</span><span class="o">.</span><span class="n">exedir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span> 569 567 <span class="bp">self</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="kc">None</span> 570 <span class="bp">self</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="o">=</span> <span class="kc">None</span>571 568 <span class="bp">self</span><span class="o">.</span><span class="n">makefile</span> <span class="o">=</span> <span class="kc">None</span> 572 569 <span class="bp">self</span><span class="o">.</span><span class="n">destination</span> <span class="o">=</span> <span class="kc">None</span> -
Documentation/html/_modules/install.html
r903ed4f r08c9091 181 181 <span class="c1"># June 2020 - Anne Philipp</span> 182 182 <span class="c1"># - renamed "convert" functions to "fortran" functions</span> 183 <span class="c1"># - reconfigured mk_tarball to select *.template files instead </span>183 <span class="c1"># - reconfigured mk_tarball to select *.template files instead </span> 184 184 <span class="c1"># of *.nl and *.temp</span> 185 185 <span class="c1"># - added check for makefile settings</span> 186 <span class="c1"># August 2020 - Leopold Haimberger</span>187 <span class="c1"># - added a new installation section for system installation (if-else block)</span>188 <span class="c1"># - read new argument from command line</span>189 <span class="c1"># - write .setup.rc for a system installation into Run directory</span>190 <span class="c1"># - copy executables to system path and user files to user path</span>191 186 <span class="c1">#</span> 192 187 <span class="c1"># @License:</span> … … 242 237 <span class="kn">import</span> <span class="nn">subprocess</span> 243 238 <span class="kn">import</span> <span class="nn">tarfile</span> 244 <span class="kn">import</span> <span class="nn">shutil</span>245 239 <span class="kn">from</span> <span class="nn">argparse</span> <span class="kn">import</span> <span class="n">ArgumentParser</span><span class="p">,</span> <span class="n">ArgumentDefaultsHelpFormatter</span> 246 240 … … 250 244 <span class="kn">from</span> <span class="nn">Classes.UioFiles</span> <span class="kn">import</span> <span class="n">UioFiles</span> 251 245 <span class="kn">from</span> <span class="nn">Mods.tools</span> <span class="kn">import</span> <span class="p">(</span><span class="n">make_dir</span><span class="p">,</span> <span class="n">put_file_to_ecserver</span><span class="p">,</span> <span class="n">submit_job_to_ecserver</span><span class="p">,</span> 252 <span class="n">silent_remove</span><span class="p">,</span> <span class="n">execute_subprocess</span><span class="p">,</span> <span class="n">none_or_str</span><span class="p">,</span> 253 <span class="n">overwrite_lines_in_file</span><span class="p">,</span> <span class="n">check_for_string_in_file</span><span class="p">)</span> 246 <span class="n">silent_remove</span><span class="p">,</span> <span class="n">execute_subprocess</span><span class="p">,</span> <span class="n">none_or_str</span><span class="p">)</span> 254 247 255 248 <span class="c1"># ------------------------------------------------------------------------------</span> … … 272 265 <span class="n">check_install_conditions</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> 273 266 274 <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o w">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'local'</span><span class="p">,</span> <span class="s1">'syslocal'</span><span class="p">]:</span> <span class="c1"># ecgate or cca</span>267 <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">'local'</span><span class="p">:</span> <span class="c1"># ecgate or cca</span> 275 268 <span class="n">install_via_gateway</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> 276 269 <span class="k">else</span><span class="p">:</span> <span class="c1"># local</span> 277 270 <span class="n">install_local</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> 278 271 279 <span class="nb">print</span><span class="p">(</span><span class="s2">"SUCCESS: INSTALLATION FINISHED!"</span><span class="p">)</span>280 281 272 <span class="k">return</span></div> 282 273 … … 299 290 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--target'</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">'install_target'</span><span class="p">,</span> 300 291 <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> 301 <span class="n">help</span><span class="o">=</span><span class="s2">"Valid targets: syslocal |local | ecgate | cca , </span><span class="se">\</span>292 <span class="n">help</span><span class="o">=</span><span class="s2">"Valid targets: local | ecgate | cca , </span><span class="se">\</span> 302 293 <span class="s2"> the latter two are at ECMWF"</span><span class="p">)</span> 303 294 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--makefile"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"makefile"</span><span class="p">,</span> … … 321 312 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--installdir"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"installdir"</span><span class="p">,</span> 322 313 <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> 323 <span class="n">help</span><span class="o">=</span><span class="s1">'Root (user)directory of the '</span>314 <span class="n">help</span><span class="o">=</span><span class="s1">'Root directory of the '</span> 324 315 <span class="s1">'flex_extract installation'</span><span class="p">)</span> 325 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--sysinstalldir"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"sysinstalldir"</span><span class="p">,</span>326 <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>327 <span class="n">help</span><span class="o">=</span><span class="s1">'System installation path; where '</span>328 <span class="s1">'executables are stored.'</span><span class="p">)</span>329 316 330 317 <span class="c1"># arguments for job submission to ECMWF, only needed by submit.py</span> … … 403 390 <span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">'.tar'</span><span class="p">)</span> 404 391 405 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expandvars</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span> 406 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)))</span> 407 <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expandvars</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span> 408 <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)))</span> 409 410 <span class="c1"># this is standard installation into a single directory</span> 411 <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">==</span> <span class="s1">'local'</span><span class="p">:</span> 412 413 <span class="c1"># installation into the current directory</span> 414 <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">==</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">:</span> 415 <span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: installdir has not been specified'</span><span class="p">)</span> 416 <span class="nb">print</span><span class="p">(</span><span class="s1">'flex_extract will be installed in current dir by compiling the '</span> <span class="o">+</span> 417 <span class="s1">'Fortran source in '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span><span class="p">)</span> 418 <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span><span class="p">)</span> 419 <span class="c1"># installation into a different path</span> 420 <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">!=</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="p">:</span> 421 422 <span class="c1"># creates the target working directory for flex_extract</span> 392 <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">==</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">:</span> 393 <span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: installdir has not been specified'</span><span class="p">)</span> 394 <span class="nb">print</span><span class="p">(</span><span class="s1">'flex_extract will be installed in here by compiling the '</span> <span class="o">+</span> 395 <span class="s1">'Fortran source in '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span><span class="p">)</span> 396 <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span><span class="p">)</span> 397 <span class="k">else</span><span class="p">:</span> <span class="c1"># creates the target working directory for flex_extract</span> 398 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expandvars</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span> 399 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">))</span> 400 <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">!=</span> \ 401 <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">):</span> 423 402 <span class="n">mk_tarball</span><span class="p">(</span><span class="n">tar_file</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span><span class="p">)</span> 424 403 <span class="n">make_dir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span> … … 431 410 <span class="n">_config</span><span class="o">.</span><span class="n">PATH_REL_FORTRAN_SRC</span><span class="p">))</span> 432 411 433 <span class="c1"># Create Fortran executable</span> 434 <span class="nb">print</span><span class="p">(</span><span class="s1">'Install '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">' software at '</span> <span class="o">+</span> 435 <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">+</span> <span class="s1">' in directory '</span> <span class="o">+</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 436 437 <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)</span> 438 <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span> 439 <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s1">'../../'</span><span class="p">)</span> 440 <span class="c1"># make sure that the correct calling of submit.py script is in run_local.sh</span> 441 <span class="n">overwrite_lines_in_file</span><span class="p">(</span><span class="s1">'Run/run_local.sh'</span><span class="p">,</span> 442 <span class="s1">'pyscript='</span><span class="p">,</span> <span class="s1">'pyscript=../Source/Python/submit.py</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 443 444 <span class="c1"># this is system installation were executables and user files are separated</span> 445 <span class="k">elif</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">==</span> <span class="s1">'syslocal'</span><span class="p">:</span> 446 <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">==</span> <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="p">:</span> 447 <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'ERROR: System installation path is equal to user '</span> 448 <span class="s1">'installation path.</span><span class="se">\n</span><span class="s1"> Please change either the system '</span> 449 <span class="s1">'installation path or use installation target "local".'</span><span class="p">)</span> 450 <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">==</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="p">:</span> 451 <span class="nb">print</span><span class="p">(</span><span class="s1">'Flex_extract will be installed in current directory!'</span><span class="p">)</span> 452 <span class="k">else</span><span class="p">:</span> <span class="c1"># install user part in different dir</span> 453 <span class="nb">print</span><span class="p">(</span><span class="s1">'Flex_extract will be installed in '</span> <span class="o">+</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="p">)</span> 454 455 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span><span class="p">)</span> 456 <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">):</span> 457 <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)</span> 458 459 <span class="c1"># copy all files except Python and Fortranfiles to this dir</span> 460 <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">,</span> 461 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span> <span class="n">symlinks</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> 462 <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'Source'</span><span class="p">))</span> 463 <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'.git'</span><span class="p">))</span> 464 <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">UioFiles</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span> <span class="s1">'*~'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">:</span> 465 <span class="n">silent_remove</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> 466 467 <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'setup.sh'</span><span class="p">))</span> 468 <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'setup_local.sh'</span><span class="p">))</span> 469 470 <span class="c1"># configure run_local script correctly</span> 471 <span class="c1"># check if source of system config file is already in run_local.sh,</span> 472 <span class="c1"># if not, add it</span> 473 <span class="k">if</span> <span class="ow">not</span> <span class="n">check_for_string_in_file</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'Run/run_local.sh'</span><span class="p">),</span> 474 <span class="s1">'source .setup.rc'</span><span class="p">):</span> 475 <span class="n">overwrite_lines_in_file</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'Run/run_local.sh'</span><span class="p">),</span> 476 <span class="s1">'# PATH TO SUBMISSION SCRIPT'</span><span class="p">,</span> 477 <span class="s1">'# PATH TO SUBMISSION SCRIPT</span><span class="se">\n</span><span class="s1">source '</span><span class="o">+</span><span class="n">_config</span><span class="o">.</span><span class="n">FILE_SYS_CONFIG</span><span class="o">+</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 478 <span class="c1"># make sure that the correct calling of submit.py script is in run_local.sh</span> 479 <span class="n">overwrite_lines_in_file</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'Run/run_local.sh'</span><span class="p">),</span> 480 <span class="s1">'pyscript='</span><span class="p">,</span> <span class="s1">'pyscript=submit.py</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 481 482 <span class="c1"># change permission for file to executable</span> 483 <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">'chmod'</span><span class="p">,</span> <span class="s1">'0775'</span><span class="p">,</span> 484 <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">),</span><span class="s1">'Run/run_local.sh'</span><span class="p">)])</span> 485 486 487 <span class="c1"># create systemdir</span> 488 <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span><span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span><span class="p">)</span> 489 <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">):</span> 490 <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span> 491 492 <span class="c1"># create setup file for running flex_extract with system installation</span> 493 <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">),</span><span class="s1">'Run/.setup.rc'</span><span class="p">),</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span> 494 <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'#!/bin/bash </span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 495 <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'export FLEXEXTRACT_USER_DIR='</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)</span><span class="o">+</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 496 <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'export PATH='</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span><span class="o">+</span><span class="s1">'/Python:$</span><span class="si">{PATH}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 497 <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'export PATH='</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span><span class="o">+</span><span class="s1">':$</span><span class="si">{PATH}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 498 499 <span class="c1"># copy all Python and Fortranfiles to this dir</span> 500 <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_SOURCES</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span> <span class="n">symlinks</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> 501 502 <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span><span class="s1">'Fortran'</span><span class="p">))</span> 503 <span class="c1"># Create Fortran executable</span> 504 <span class="nb">print</span><span class="p">(</span><span class="s1">'Install '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">' software as '</span> <span class="o">+</span> 505 <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">+</span> <span class="s1">' in directory '</span> <span class="o">+</span> 506 <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 507 508 <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)</span> 509 <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span> 510 511 <span class="n">outfile</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">UioFiles</span><span class="p">(</span><span class="s1">'.'</span><span class="p">,</span><span class="s1">'*.out'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span> 512 <span class="n">test</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span><span class="s1">'calc_etadot'</span><span class="p">)</span> 513 <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">outfile</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span> 514 <span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: Multiple executables for Fortran code are available!'</span><span class="p">)</span> 515 <span class="c1"># move executable one dir up and delete Fortran dir</span> 516 <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s1">'..'</span><span class="p">)</span> 517 <span class="n">shutil</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="n">outfile</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span><span class="s1">'calc_etadot'</span><span class="p">))</span> 518 <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">),</span><span class="s1">'Fortran'</span><span class="p">))</span> 412 <span class="c1"># Create Fortran executable</span> 413 <span class="nb">print</span><span class="p">(</span><span class="s1">'Install '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">' software at '</span> <span class="o">+</span> 414 <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">+</span> <span class="s1">' in directory '</span> <span class="o">+</span> 415 <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> 416 417 <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)</span> 418 <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span> 519 419 520 420 <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> … … 551 451 <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> 552 452 553 <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="ow">and</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o w">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'local'</span><span class="p">,</span> <span class="s1">'syslocal'</span><span class="p">]:</span>453 <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="ow">and</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">!=</span> <span class="s1">'local'</span><span class="p">:</span> 554 454 <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">ecgid</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">ecuid</span><span class="p">:</span> 555 455 <span class="nb">print</span><span class="p">(</span><span class="s1">'Please enter your ECMWF user id and group id '</span> … … 567 467 <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">:</span> 568 468 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="s1">'$</span><span class="si">{HOME}</span><span class="s1">'</span> 569 <span class="k">el if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">==</span> <span class="s1">'local'</span><span class="p">:</span>469 <span class="k">else</span><span class="p">:</span> <span class="c1"># local</span> 570 470 <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">:</span> 571 471 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span> 572 <span class="k">elif</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">==</span> <span class="s1">'syslocal'</span><span class="p">:</span>573 <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">:</span>574 <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span>575 <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">:</span>576 <span class="nb">print</span><span class="p">(</span><span class="s1">'ERROR: System installation was selected but '</span>577 <span class="s1">'no system installation path was defined.'</span><span class="p">)</span>578 <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>579 472 580 473 <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">:</span> … … 592 485 <span class="k">else</span><span class="p">:</span> 593 486 <span class="k">pass</span> 594 487 595 488 <span class="k">return</span></div> 596 489 … … 984 877 <span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="p">)</span> 985 878 <span class="k">else</span><span class="p">:</span> 986 <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">'ls'</span><span class="p">,</span> <span class="s1">'-l'</span><span class="p">,</span> 879 <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">'ls'</span><span class="p">,</span> <span class="s1">'-l'</span><span class="p">,</span> 987 880 <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">src_path</span><span class="p">,</span> <span class="n">_config</span><span class="o">.</span><span class="n">FORTRAN_EXECUTABLE</span><span class="p">)],</span> 988 881 <span class="n">error_msg</span><span class="o">=</span><span class="s1">'FORTRAN EXECUTABLE COULD NOT BE FOUND!'</span><span class="p">)</span> -
Documentation/html/_modules/submit.html
r47be2684 r08c9091 276 276 <span class="k">else</span><span class="p">:</span> 277 277 <span class="n">submit</span><span class="p">(</span><span class="n">job_template</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">queue</span><span class="p">)</span> 278 <span class="n">exit_message</span> <span class="o">=</span> <span class="s1">'FLEX_EXTRACT JOB SCRIPT IS SUBMIT TED!'</span>278 <span class="n">exit_message</span> <span class="o">=</span> <span class="s1">'FLEX_EXTRACT JOB SCRIPT IS SUBMITED!'</span> 279 279 280 280 <span class="n">normal_exit</span><span class="p">(</span><span class="n">exit_message</span><span class="p">)</span> -
Documentation/html/_modules/tools.html
r903ed4f r08c9091 184 184 <span class="c1"># put_file_to_ecserver, submit_job_to_ecserver, get_informations,</span> 185 185 <span class="c1"># get_dimensions, execute_subprocess, none_or_int, none_or_str</span> 186 <span class="c1">#</span>187 <span class="c1"># August 2020 - Leopold Haimberger (University of Vienna)</span>188 <span class="c1"># - added function to check if a specific string is in a file</span>189 <span class="c1"># - added function to overwrite lines in a file which contain specific string</span>190 186 <span class="c1">#</span> 191 187 <span class="c1"># @License:</span> … … 415 411 <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> 416 412 <span class="n">help</span><span class="o">=</span><span class="s1">'The name of the ECMWF server name where the'</span> 417 <span class="s1">'job script is to be submitted '</span> 413 <span class="s1">'job script is to be submitted '</span> 418 414 <span class="s1">'(e.g. ecgate | cca | ccb)'</span><span class="p">)</span> 419 415 … … 790 786 <span class="sd">'''Creates a directory.</span> 791 787 792 <span class="sd"> If the directory already exists, an information is printed and the creation </span>788 <span class="sd"> If the directory already exists, an information is printed and the creation </span> 793 789 <span class="sd"> skipped. The program stops only if there is another problem.</span> 794 790 … … 1022 1018 <span class="sd"> ----------</span> 1023 1019 <span class="sd"> cmd_list : list of str</span> 1024 <span class="sd"> A list of the components for the command line execution. </span>1025 <span class="sd"> They will be concatenated with blank space for the command </span>1020 <span class="sd"> A list of the components for the command line execution. </span> 1021 <span class="sd"> They will be concatenated with blank space for the command </span> 1026 1022 <span class="sd"> to be submitted, like ['mv', file1, file2] for mv file1 file2.</span> 1027 1023 … … 1076 1072 1077 1073 <span class="k">return</span> <span class="n">start_period</span><span class="p">,</span> <span class="n">end_period</span></div> 1078 1079 1080 <div class="viewcode-block" id="check_for_string_in_file"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.check_for_string_in_file">[docs]</a><span class="k">def</span> <span class="nf">check_for_string_in_file</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">search_string</span><span class="p">):</span>1081 <span class="sd">"""</span>1082 <span class="sd"> Search for a specific string in a file and return True if</span>1083 <span class="sd"> the string was found.</span>1084 1085 <span class="sd"> Parameters</span>1086 <span class="sd"> ----------</span>1087 <span class="sd"> filepath : str</span>1088 <span class="sd"> The full file path which is to be examined.</span>1089 1090 <span class="sd"> search_string : str</span>1091 <span class="sd"> The string which is looked up for in the file.</span>1092 1093 <span class="sd"> Return</span>1094 <span class="sd"> ------</span>1095 <span class="sd"> Boolean :</span>1096 <span class="sd"> True : String was found</span>1097 <span class="sd"> False : String was not found</span>1098 <span class="sd"> """</span>1099 <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>1100 <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fio</span><span class="p">:</span>1101 <span class="k">if</span> <span class="n">search_string</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>1102 <span class="k">return</span> <span class="kc">True</span>1103 <span class="k">return</span> <span class="kc">False</span></div>1104 1105 1106 <div class="viewcode-block" id="overwrite_lines_in_file"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.overwrite_lines_in_file">[docs]</a><span class="k">def</span> <span class="nf">overwrite_lines_in_file</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">search_string</span><span class="p">,</span> <span class="n">sub_string</span><span class="p">):</span>1107 <span class="sd">"""</span>1108 <span class="sd"> Overwrites lines which contain the given search string with the</span>1109 <span class="sd"> substitution string.</span>1110 1111 <span class="sd"> Parameters</span>1112 <span class="sd"> ----------</span>1113 <span class="sd"> search_string : str</span>1114 <span class="sd"> The string which is looked up for in the file.</span>1115 1116 <span class="sd"> sub_string : str</span>1117 <span class="sd"> The string which overwrites the search string.</span>1118 1119 <span class="sd"> Return</span>1120 <span class="sd"> ------</span>1121 <span class="sd"> """</span>1122 <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>1123 <span class="n">data</span> <span class="o">=</span> <span class="n">fio</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>1124 1125 <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>1126 <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>1127 <span class="k">if</span> <span class="n">search_string</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>1128 <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">sub_string</span><span class="p">)</span>1129 <span class="k">else</span><span class="p">:</span>1130 <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>1131 1132 <span class="k">return</span></div>1133 1134 1074 </pre></div> 1135 1075 -
Documentation/html/_sources/Documentation/Input/setup.rst.txt
r47be2684 r5bee29a 165 165 [--ecuid ECUID] [--ecgid ECGID] [--gateway GATEWAY] 166 166 [--destination DESTINATION] [--installdir INSTALLDIR] 167 [--sysinstalldir SYSINSTALLDIR]168 167 [--job_template JOB_TEMPLATE] [--controlfile CONTROLFILE] 169 168 … … 173 172 -h, --help show this help message and exit 174 173 --target INSTALL_TARGET 175 Valid targets: syslocal |local | ecgate | cca , the latter two174 Valid targets: local | ecgate | cca , the latter two 176 175 are at ECMWF (default: None) 177 176 --makefile MAKEFILE Name of makefile to compile the Fortran … … 187 186 Root directory where flex_extract will be installed 188 187 to. (default: None) 189 --sysinstalldir SYSINSTALLDIR190 System installation path; where executables are191 stored. (default: None)192 188 --job_template JOB_TEMPLATE 193 189 The rudimentary template file to create a batch job … … 202 198 203 199 204 205 200 .. toctree:: 206 201 :hidden: -
Documentation/html/_sources/Installation/local.rst.txt
r903ed4f r73308e0 266 266 The Fortran program called ``calc_etadot`` will be compiled during the 267 267 installation process. A suitable makefile (``makefile_local_gfortran``) for the compilation is set by default. 268 This may be overwritten by the ``MAKEFILE`` parameter in ``setup _local.sh``.269 270 However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup _local.sh``268 This may be overwritten by the ``MAKEFILE`` parameter in ``setup.sh``. 269 270 However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup.sh`` 271 271 For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`. 272 272 273 273 274 In the root directory of ``flex_extract``, open the ``setup _local.sh`` script274 In the root directory of ``flex_extract``, open the ``setup.sh`` script 275 275 with an editor and adapt the installation parameters in the section labelled with 276 276 "AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below: … … 279 279 .. code-block:: bash 280 280 :caption: 'Example settings for a local installation.' 281 :name: setup _local.sh281 :name: setup.sh 282 282 283 283 ... … … 294 294 DESTINATION=None 295 295 INSTALLDIR=None 296 SYSINSTALLDIR=None297 296 JOB_TEMPLATE='' 298 297 CONTROLFILE='CONTROL_EA5' … … 304 303 .. code-block:: bash 305 304 306 $ ./setup _local.sh305 $ ./setup.sh 307 306 308 307 to start the installation. You should see the following standard output. … … 311 310 .. code-block:: bash 312 311 313 # Output of setup _local.sh312 # Output of setup.sh 314 313 WARNING: installdir has not been specified 315 314 flex_extract will be installed in here by compiling the Fortran source in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran … … 328 327 lrwxrwxrwx. 1 <username> tmc 20 Aug 12 10:59 ./calc_etadot -> calc_etadot_fast.out 329 328 330 331 Local system installation332 =========================333 334 There is also the possibility to separate the software executables from the user application files. For doing so, the ``TARGET`` parameter can be set to "syslocal" and the additional parameter ``SYSINSTALLDIR`` in the ``setup_local.sh`` has to be specified. This new path will contain the Fortran and Python executables of ``flex_extract``. If you chose to set a system path for this, please start the script as root.335 The user directory for ``flex_extract``, which basically consists of everything except the ``Source`` directory, will be installed into ``INSTALLDIR``.336 In this installation mode, an extra (hidden) ``.setup.rc`` file will be generated in the ``Run`` directory. It contains the necessary settings for running the local system mode.337 338 Despite the change in the ``TARGET`` parameter, the meaning of ``INSTALLDIR`` and the additional ``SYSINSTALLDIR``, the steps for installation are the same as in the local installation mentioned above. For example, modify the ``setup_local.sh`` file as follows:339 340 341 .. code-block:: bash342 :caption: 'Example settings for a local system installation.'343 :name: setup_local.sh344 345 ...346 # -----------------------------------------------------------------347 # AVAILABLE COMMANDLINE ARGUMENTS TO SET348 #349 # THE USER HAS TO SPECIFY THESE PARAMETER350 #351 TARGET='syslocal'352 MAKEFILE=<name_of_your_makefile>353 ECUID=None354 ECGID=None355 GATEWAY=None356 DESTINATION=None357 INSTALLDIR=$HOME358 SYSINSTALLDIR=/usr/bin/359 JOB_TEMPLATE=''360 CONTROLFILE='CONTROL_EA5'361 ...362 363 364 Afterwards, type:365 366 .. code-block:: bash367 368 $ sudo ./setup_local.sh369 370 to start the installation. You should see the following standard output.371 372 .. code-block:: bash373 374 Flex_extract will be installed in <$HOME>375 Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2376 377 Using makefile: makefile_local_gfortran378 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./rwgrib2.f90379 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./phgrreal.f90380 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./grphreal.f90381 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./ftrafo.f90382 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./calc_etadot.f90383 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./posnam.f90384 /usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp385 ln -sf calc_etadot_fast.out calc_etadot386 387 lrwxrwxrwx. 1 <username> tmc 20 27. Okt 23:25 ./calc_etadot -> calc_etadot_fast.out388 SUCCESS: INSTALLATION FINISHED!389 390 391 You can now change into the user directory specified in ``INSTALLDIR`` and find a ``flex_extract_vX.X`` directory there. -
Documentation/html/genindex.html
r47be2684 r08c9091 274 274 <li><a href="Documentation/Api/api_python.html#get_mars_data.check_dates_for_nonflux_fc_times">check_dates_for_nonflux_fc_times() (in module get_mars_data)</a> 275 275 </li> 276 <li><a href="Documentation/Api/api_python.html#tools.check_for_string_in_file">check_for_string_in_file() (in module tools)</a>277 </li>278 276 <li><a href="Documentation/Api/api_python.html#checks.check_grid">check_grid() (in module checks)</a> 279 277 </li> … … 652 650 <li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.omegadiff">omegadiff (ControlFile.ControlFile attribute)</a> 653 651 </li> 652 </ul></td> 653 <td style="width: 33%; vertical-align: top;"><ul> 654 654 <li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.oper">oper (ControlFile.ControlFile attribute)</a> 655 655 </li> 656 </ul></td>657 <td style="width: 33%; vertical-align: top;"><ul>658 656 <li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.outputdir">outputdir (ControlFile.ControlFile attribute)</a> 659 657 </li> 660 658 <li><a href="Documentation/Api/api_python.html#EcFlexpart.EcFlexpart.outputfilelist">outputfilelist (EcFlexpart.EcFlexpart attribute)</a> 661 </li>662 <li><a href="Documentation/Api/api_python.html#tools.overwrite_lines_in_file">overwrite_lines_in_file() (in module tools)</a>663 659 </li> 664 660 </ul></td> -
Documentation/html/searchindex.js
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the documentation","Auto-generated documentation for the Fortran programme","Auto-generated documentation for the Python scripts","CONTROL file changes","The compilation job script <code class=\"docutils literal notranslate\"><span class=\"pre\">compilejob.ksh</span></code>","The CONTROL file","The CONTROL parameters","ECMWF user credential file <code class=\"docutils literal notranslate\"><span class=\"pre\">ECMWF_ENV</span></code>","CONTROL file examples","The Fortran makefile for <code class=\"docutils literal notranslate\"><span class=\"pre\">calc_etadot</span></code>","The job script <code class=\"docutils literal notranslate\"><span class=\"pre\">job.ksh</span></code>","The executable script - <code class=\"docutils literal notranslate\"><span class=\"pre\">run.sh</span></code>","The installation script - <code class=\"docutils literal notranslate\"><span class=\"pre\">setup.sh</span></code>","Templates","Application modes","Program flow","Auto-generated documentation","Disaggregation of flux data","Control & input data","Output data","Overview","Vertical wind","Access modes","Link collection","Hints for data set selection","Available data sets for member-state users","Available data sets for public users","Metrics","Static code analysis","Test cases","Gateway mode installation","Local mode installation","Remote mode installation","FAQ - Frequently asked questions","Known Bugs and Issues","Developer Team","Changelog","Developer Guide","Code-Level Documentation","ECMWF Data","Evaluation","Welcome to the <code class=\"docutils literal notranslate\"><span class=\"pre\">flex_extract</span></code> Documentation!","Installation","Usage","Support","ToDos"],titleterms:{"case":29,"class":2,"long":19,"new":[19,36],"public":[26,42,43],"static":28,CDS:[31,34],The:[4,5,6,9,10,11,12],accept:42,access:22,addit:[0,6,19],adjust:43,agreement:[],analysi:28,api:[31,34],applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calc_etadot:[9,19,34],calc_etadot_nml:13,calcul:21,can:[24,33],cera:43,certain:43,chang:[3,36],changelog:36,check:2,code:[28,34,38],collect:23,combin:[42,43],comparison:29,compil:4,compilejob:4,content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert:[],coordin:[],credenti:7,data:[6,17,18,19,24,25,26,34,39,43],dataset:[42,43],definit:43,depend:[30,31,32,42],destin:34,develop:[35,37],diagramm:0,differ:15,disaggreg:[2,17,19],distribut:33,document:[0,1,2,16,38,41],doe:[4,10],domain:6,download:42,eccod:34,ecflexpart:2,ecmwf:[7,31,39,42],ecmwf_env:[7,13],ensembl:19,environ:[30,31,32],equat:21,era5:34,era:43,error:34,evalu:40,exampl:[4,5,8,10,15],execut:11,faq:[33,44],featur:[36,43],field:[6,17,19],file:[3,5,6,7,8,19,21,29,43],find:24,finder:[],fix:36,flex_extract:[41,42],flexpart:[19,42],flow:15,flux:[6,17,19],forecast:19,format:5,fort:19,fortran:[1,9,19,34,42],frequent:33,from:[21,33],full:42,gatewai:[30,34,43],gener:[1,2,6,15,16],get_mars_data:2,grib:[19,29],gributil:2,guid:37,hint:[24,43],horizont:21,how:24,index:19,input:[18,19],instal:[2,12,30,31,32,33,34,42],installscript:13,interim:43,issu:[34,44],job:[4,10,43],jobscript:13,known:[34,44],ksh:[4,10],level:[25,38],librari:33,licenc:42,line:0,link:23,list:44,local:[15,31,43],mail:44,makefil:9,mar:[19,21,29],marsretriev:2,member:[15,25],metric:27,mode:[14,15,22,30,31,32,43],model:25,modul:2,older:17,onlin:[],oper:43,option:[11,12],other:17,out:24,output:[19,21],overview:20,packag:33,paramet:[6,11,12,21,34,43],parti:33,pre:21,precipit:[17,19],predict:19,prepar:[21,30,31,32,43],prepare_flexpart:2,problem:34,program:[2,15,19,34,42],programm:1,proper:43,pure:[],python:2,question:33,quick:[],registr:42,releas:[34,36],remot:[32,43],report:44,request:[19,29],rest:[],retriev:[],run:11,script:[2,4,10,11,12],section:6,select:[24,43],sequenc:0,set:[15,24,25,26],setup:12,softwar:0,some:[],specif:43,specifi:[],sphinx:0,standard:19,start:[],state:25,submiss:11,submit:[2,11],submitscript:13,support:44,surfac:25,system:44,team:35,temp:[],templat:13,temporari:19,test:[29,30,31,42],testcas:[],third:33,ticket:44,time:6,todo:45,tool:2,uiofil:2,updat:0,usag:[11,12,43],user:[6,7,15,25,26],using:21,veloc:21,version:17,vertic:[6,21],web:31,welcom:41,what:[4,10,24,33],wind:[6,21],workflow:15}}) -
For_developers/Sphinx/Source/Documentation/Input/setup.rst
r47be2684 r7271b6f 165 165 [--ecuid ECUID] [--ecgid ECGID] [--gateway GATEWAY] 166 166 [--destination DESTINATION] [--installdir INSTALLDIR] 167 [--sysinstalldir SYSINSTALLDIR]168 167 [--job_template JOB_TEMPLATE] [--controlfile CONTROLFILE] 169 168 … … 173 172 -h, --help show this help message and exit 174 173 --target INSTALL_TARGET 175 Valid targets: syslocal |local | ecgate | cca , the latter two174 Valid targets: local | ecgate | cca , the latter two 176 175 are at ECMWF (default: None) 177 176 --makefile MAKEFILE Name of makefile to compile the Fortran … … 187 186 Root directory where flex_extract will be installed 188 187 to. (default: None) 189 --sysinstalldir SYSINSTALLDIR190 System installation path; where executables are191 stored. (default: None)192 188 --job_template JOB_TEMPLATE 193 189 The rudimentary template file to create a batch job … … 202 198 203 199 204 205 200 .. toctree:: 206 201 :hidden: -
For_developers/Sphinx/Source/Installation/local.rst
r903ed4f r73308e0 266 266 The Fortran program called ``calc_etadot`` will be compiled during the 267 267 installation process. A suitable makefile (``makefile_local_gfortran``) for the compilation is set by default. 268 This may be overwritten by the ``MAKEFILE`` parameter in ``setup _local.sh``.269 270 However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup _local.sh``268 This may be overwritten by the ``MAKEFILE`` parameter in ``setup.sh``. 269 270 However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup.sh`` 271 271 For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`. 272 272 273 273 274 In the root directory of ``flex_extract``, open the ``setup _local.sh`` script274 In the root directory of ``flex_extract``, open the ``setup.sh`` script 275 275 with an editor and adapt the installation parameters in the section labelled with 276 276 "AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below: … … 279 279 .. code-block:: bash 280 280 :caption: 'Example settings for a local installation.' 281 :name: setup _local.sh281 :name: setup.sh 282 282 283 283 ... … … 294 294 DESTINATION=None 295 295 INSTALLDIR=None 296 SYSINSTALLDIR=None297 296 JOB_TEMPLATE='' 298 297 CONTROLFILE='CONTROL_EA5' … … 304 303 .. code-block:: bash 305 304 306 $ ./setup _local.sh305 $ ./setup.sh 307 306 308 307 to start the installation. You should see the following standard output. … … 311 310 .. code-block:: bash 312 311 313 # Output of setup _local.sh312 # Output of setup.sh 314 313 WARNING: installdir has not been specified 315 314 flex_extract will be installed in here by compiling the Fortran source in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran … … 328 327 lrwxrwxrwx. 1 <username> tmc 20 Aug 12 10:59 ./calc_etadot -> calc_etadot_fast.out 329 328 330 331 Local system installation332 =========================333 334 There is also the possibility to separate the software executables from the user application files. For doing so, the ``TARGET`` parameter can be set to "syslocal" and the additional parameter ``SYSINSTALLDIR`` in the ``setup_local.sh`` has to be specified. This new path will contain the Fortran and Python executables of ``flex_extract``. If you chose to set a system path for this, please start the script as root.335 The user directory for ``flex_extract``, which basically consists of everything except the ``Source`` directory, will be installed into ``INSTALLDIR``.336 In this installation mode, an extra (hidden) ``.setup.rc`` file will be generated in the ``Run`` directory. It contains the necessary settings for running the local system mode.337 338 Despite the change in the ``TARGET`` parameter, the meaning of ``INSTALLDIR`` and the additional ``SYSINSTALLDIR``, the steps for installation are the same as in the local installation mentioned above. For example, modify the ``setup_local.sh`` file as follows:339 340 341 .. code-block:: bash342 :caption: 'Example settings for a local system installation.'343 :name: setup_local.sh344 345 ...346 # -----------------------------------------------------------------347 # AVAILABLE COMMANDLINE ARGUMENTS TO SET348 #349 # THE USER HAS TO SPECIFY THESE PARAMETER350 #351 TARGET='syslocal'352 MAKEFILE=<name_of_your_makefile>353 ECUID=None354 ECGID=None355 GATEWAY=None356 DESTINATION=None357 INSTALLDIR=$HOME358 SYSINSTALLDIR=/usr/bin/359 JOB_TEMPLATE=''360 CONTROLFILE='CONTROL_EA5'361 ...362 363 364 Afterwards, type:365 366 .. code-block:: bash367 368 $ sudo ./setup_local.sh369 370 to start the installation. You should see the following standard output.371 372 .. code-block:: bash373 374 Flex_extract will be installed in <$HOME>375 Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2376 377 Using makefile: makefile_local_gfortran378 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./rwgrib2.f90379 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./phgrreal.f90380 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./grphreal.f90381 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./ftrafo.f90382 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./calc_etadot.f90383 /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./posnam.f90384 /usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp385 ln -sf calc_etadot_fast.out calc_etadot386 387 lrwxrwxrwx. 1 <username> tmc 20 27. Okt 23:25 ./calc_etadot -> calc_etadot_fast.out388 SUCCESS: INSTALLATION FINISHED!389 390 391 You can now change into the user directory specified in ``INSTALLDIR`` and find a ``flex_extract_vX.X`` directory there. -
README.md
r037f7bb re70c85f 3 3 `flex_extract` is a software package to support retrieving meteorological fields from the European Centre for Medium-Range Weather Forecasts' (ECMWF) Meteorological Archival and Retrieval System (MARS) as input for the `FLEXTRA`/`FLEXPART` Atmospheric Transport Modelling system. 4 4 5 `FLEXPART` ( "FLEXible PARTicle dispersion model", http://flexpart.eu) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes.5 `FLEXPART` (“FLEXible PARTicle dispersion model”, http://flexpart.eu) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes. 6 6 7 7 … … 17 17 ## Authors 18 18 19 Anne Tipka (formerly Philipp), Leopold Haimberger and Petra Seibert19 Anne Philipp, Leopold Haimberger and Petra Seibert 20 20 21 21 ## License 22 (C) Copyright 2014-20 20.22 (C) Copyright 2014-2019. 23 23 24 24 SPDX-License-Identifier: CC-BY-4.0 … … 28 28 http://creativecommons.org/licenses/by/4.0/ or send a letter to 29 29 Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. 30 -
Run/run_local.sh
r47be2684 r98f09d2 12 12 # 13 13 # @Licence: 14 # (C) Copyright 2014-20 20.14 # (C) Copyright 2014-2019. 15 15 # 16 16 # SPDX-License-Identifier: CC-BY-4.0 -
Source/Python/Classes/ControlFile.py
r75db9b0 r0a75335 21 21 # June 2020 - Anne Philipp 22 22 # - update default makefile to None 23 # August 2020 - Leopold Haimberger24 # - added a class parameter for system installation path25 23 # 26 24 # @License: … … 406 404 self.exedir = _config.PATH_FORTRAN_SRC 407 405 self.installdir = None 408 self.sysinstalldir = None409 406 self.makefile = None 410 407 self.destination = None -
Source/Python/Mods/tools.py
r75db9b0 r026b359 22 22 # put_file_to_ecserver, submit_job_to_ecserver, get_informations, 23 23 # get_dimensions, execute_subprocess, none_or_int, none_or_str 24 #25 # August 2020 - Leopold Haimberger (University of Vienna)26 # - added function to check if a specific string is in a file27 # - added function to overwrite lines in a file which contain specific string28 24 # 29 25 # @License: … … 253 249 type=none_or_str, default=None, 254 250 help='The name of the ECMWF server name where the' 255 'job script is to be submitted ' 251 'job script is to be submitted ' 256 252 '(e.g. ecgate | cca | ccb)') 257 253 … … 628 624 '''Creates a directory. 629 625 630 If the directory already exists, an information is printed and the creation 626 If the directory already exists, an information is printed and the creation 631 627 skipped. The program stops only if there is another problem. 632 628 … … 860 856 ---------- 861 857 cmd_list : list of str 862 A list of the components for the command line execution. 863 They will be concatenated with blank space for the command 858 A list of the components for the command line execution. 859 They will be concatenated with blank space for the command 864 860 to be submitted, like ['mv', file1, file2] for mv file1 file2. 865 861 … … 914 910 915 911 return start_period, end_period 916 917 918 def check_for_string_in_file(filepath, search_string):919 """920 Search for a specific string in a file and return True if921 the string was found.922 923 Parameters924 ----------925 filepath : str926 The full file path which is to be examined.927 928 search_string : str929 The string which is looked up for in the file.930 931 Return932 ------933 Boolean :934 True : String was found935 False : String was not found936 """937 with open(filepath, 'r') as fio:938 for line in fio:939 if search_string in line:940 return True941 return False942 943 944 def overwrite_lines_in_file(filepath, search_string, sub_string):945 """946 Overwrites lines which contain the given search string with the947 substitution string.948 949 Parameters950 ----------951 search_string : str952 The string which is looked up for in the file.953 954 sub_string : str955 The string which overwrites the search string.956 957 Return958 ------959 """960 with open(filepath, 'r') as fio:961 data = fio.readlines()962 963 with open(filepath, 'w') as fio:964 for line in data:965 if search_string in line:966 fio.write(sub_string)967 else:968 fio.write(line)969 970 return971 -
Source/Python/_config.py
r75db9b0 r0a75335 9 9 # June 2020 - Anne Philipp 10 10 # - changed template filenames to .template 11 # August 2020 - Leopold Haimberger12 # - added another target for installation13 # - added filename which will contain paths for system version14 # - checks if software runs in normal local mode or system local mode15 # and defines paths to user directory and executable paths16 11 # 17 12 # @License: … … 43 38 # ------------------------------------------------------------------------------ 44 39 45 _VERSION_STR = '7.1.2 _ctbto'40 _VERSION_STR = '7.1.2' 46 41 47 42 FLAG_ON_ECMWFSERVER = 'ecgb' in platform.node() … … 49 44 QUEUES_LIST = ['ecgate', 'cca', 'ccb'] 50 45 51 INSTALL_TARGETS = ['local', ' syslocal', 'ecgate', 'cca', 'ccb']46 INSTALL_TARGETS = ['local', 'ecgate', 'cca', 'ccb'] 52 47 53 48 CDS_DATASET_ML = 'reanalysis-era5-complete' … … 75 70 FILE_GRIB_INDEX = 'date_time_stepRange.idx' 76 71 FILE_GRIBTABLE = 'ecmwf_grib1_table_128' 77 FILE_SYS_CONFIG = '.setup.rc'78 72 79 73 # ------------------------------------------------------------------------------ … … 85 79 86 80 # ------------------------------------------------------------------------------ 87 # LOAD ENVIRONMENT VARIABLES FOR SYS VERSION; IF NECESSARRY81 # PATHES 88 82 # ------------------------------------------------------------------------------ 89 83 … … 95 89 if PATH_LOCAL_PYTHON not in sys.path: 96 90 sys.path.append(PATH_LOCAL_PYTHON) 97 98 # ------------------------------------------------------------------------------99 # PATHES100 # ------------------------------------------------------------------------------101 102 91 PATH_FLEXEXTRACT_DIR = os.path.normpath(os.path.dirname(os.path.abspath( 103 92 inspect.getfile(inspect.currentframe()))) + '/../../') 104 if not os.path.isdir(os.path.join(PATH_FLEXEXTRACT_DIR,'Run')):105 # if it does not exist, we have a system installation in place106 # we need to have a sys and user path107 # configure correct system path108 PATH_SYSTEM_DIR = os.path.join(PATH_FLEXEXTRACT_DIR, FLEXEXTRACT_DIRNAME)109 # configure correct user path110 PATH_FLEXEXTRACT_DIR = os.environ.get('FLEXEXTRACT_USER_DIR')111 else:112 PATH_SYSTEM_DIR = PATH_FLEXEXTRACT_DIR113 114 93 PATH_RUN_DIR = os.path.join(PATH_FLEXEXTRACT_DIR, 'Run') 115 PATH_SOURCES = os.path.join(PATH_ SYSTEM_DIR, 'Source')94 PATH_SOURCES = os.path.join(PATH_FLEXEXTRACT_DIR, 'Source') 116 95 PATH_TEMPLATES = os.path.join(PATH_FLEXEXTRACT_DIR, 'Templates') 117 96 PATH_ECMWF_ENV = os.path.join(PATH_RUN_DIR, FILE_USER_ENVVARS) 118 97 PATH_GRIBTABLE = os.path.join(PATH_TEMPLATES, FILE_GRIBTABLE) 119 98 PATH_JOBSCRIPTS = os.path.join(PATH_RUN_DIR, 'Jobscripts') 120 if os.path.isdir(os.path.join(PATH_SYSTEM_DIR,'Fortran')): 121 PATH_FORTRAN_SRC = PATH_SYSTEM_DIR 122 else: 123 PATH_FORTRAN_SRC = os.path.join(PATH_SOURCES, 'Fortran') 99 PATH_FORTRAN_SRC = os.path.join(PATH_SOURCES, 'Fortran') 124 100 PATH_PYTHONTEST_SRC = os.path.join(PATH_SOURCES, 'Pythontest') 125 101 PATH_INPUT_DIR = os.path.join(PATH_RUN_DIR, INPUT_DIRNAME_DEFAULT) -
Source/Python/install.py
r75db9b0 r8028176 19 19 # June 2020 - Anne Philipp 20 20 # - renamed "convert" functions to "fortran" functions 21 # - reconfigured mk_tarball to select *.template files instead 21 # - reconfigured mk_tarball to select *.template files instead 22 22 # of *.nl and *.temp 23 23 # - added check for makefile settings 24 # August 2020 - Leopold Haimberger25 # - added a new installation section for system installation (if-else block)26 # - read new argument from command line27 # - write .setup.rc for a system installation into Run directory28 # - copy executables to system path and user files to user path29 24 # 30 25 # @License: … … 80 75 import subprocess 81 76 import tarfile 82 import shutil83 77 from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter 84 78 … … 88 82 from Classes.UioFiles import UioFiles 89 83 from Mods.tools import (make_dir, put_file_to_ecserver, submit_job_to_ecserver, 90 silent_remove, execute_subprocess, none_or_str, 91 overwrite_lines_in_file, check_for_string_in_file) 84 silent_remove, execute_subprocess, none_or_str) 92 85 93 86 # ------------------------------------------------------------------------------ … … 110 103 check_install_conditions(c) 111 104 112 if c.install_target.lower() not in ['local', 'syslocal']: # ecgate or cca105 if c.install_target.lower() != 'local': # ecgate or cca 113 106 install_via_gateway(c) 114 107 else: # local 115 108 install_local(c) 116 109 117 print("SUCCESS: INSTALLATION FINISHED!")118 119 110 return 120 111 … … 137 128 parser.add_argument('--target', dest='install_target', 138 129 type=none_or_str, default=None, 139 help="Valid targets: syslocal |local | ecgate | cca , \130 help="Valid targets: local | ecgate | cca , \ 140 131 the latter two are at ECMWF") 141 132 parser.add_argument("--makefile", dest="makefile", … … 159 150 parser.add_argument("--installdir", dest="installdir", 160 151 type=none_or_str, default=None, 161 help='Root (user)directory of the '152 help='Root directory of the ' 162 153 'flex_extract installation') 163 parser.add_argument("--sysinstalldir", dest="sysinstalldir",164 type=none_or_str, default=None,165 help='System installation path; where '166 'executables are stored.')167 154 168 155 # arguments for job submission to ECMWF, only needed by submit.py … … 241 228 _config.FLEXEXTRACT_DIRNAME + '.tar') 242 229 243 c.installdir = os.path.abspath(os.path.expandvars(os.path.expanduser( 244 c.installdir))) 245 c.sysinstalldir = os.path.abspath(os.path.expandvars(os.path.expanduser( 246 c.sysinstalldir))) 247 248 # this is standard installation into a single directory 249 if c.install_target == 'local': 250 251 # installation into the current directory 252 if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.installdir: 253 print('WARNING: installdir has not been specified') 254 print('flex_extract will be installed in current dir by compiling the ' + 255 'Fortran source in ' + _config.PATH_FORTRAN_SRC) 256 os.chdir(_config.PATH_FORTRAN_SRC) 257 # installation into a different path 258 elif os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) != c.installdir : 259 260 # creates the target working directory for flex_extract 230 if c.installdir == _config.PATH_FLEXEXTRACT_DIR: 231 print('WARNING: installdir has not been specified') 232 print('flex_extract will be installed in here by compiling the ' + 233 'Fortran source in ' + _config.PATH_FORTRAN_SRC) 234 os.chdir(_config.PATH_FORTRAN_SRC) 235 else: # creates the target working directory for flex_extract 236 c.installdir = os.path.expandvars(os.path.expanduser( 237 c.installdir)) 238 if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) != \ 239 os.path.abspath(c.installdir): 261 240 mk_tarball(tar_file, c.install_target) 262 241 make_dir(os.path.join(c.installdir, … … 269 248 _config.PATH_REL_FORTRAN_SRC)) 270 249 271 # Create Fortran executable 272 print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software at ' + 273 c.install_target + ' in directory ' + c.installdir + '\n') 274 275 del_fortran_build('.') 276 mk_fortran_build('.', c.makefile) 277 os.chdir('../../') 278 # make sure that the correct calling of submit.py script is in run_local.sh 279 overwrite_lines_in_file('Run/run_local.sh', 280 'pyscript=', 'pyscript=../Source/Python/submit.py\n') 281 282 # this is system installation were executables and user files are separated 283 elif c.install_target == 'syslocal': 284 if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.sysinstalldir : 285 sys.exit('ERROR: System installation path is equal to user ' 286 'installation path.\n Please change either the system ' 287 'installation path or use installation target "local".') 288 if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.installdir : 289 print('Flex_extract will be installed in current directory!') 290 else: # install user part in different dir 291 print('Flex_extract will be installed in ' + c.installdir ) 292 293 c.installdir = os.path.join(c.installdir,_config.FLEXEXTRACT_DIRNAME) 294 if os.path.isdir(c.installdir): 295 shutil.rmtree(c.installdir) 296 297 # copy all files except Python and Fortranfiles to this dir 298 shutil.copytree(_config.PATH_FLEXEXTRACT_DIR, 299 c.installdir, symlinks=True) 300 shutil.rmtree(os.path.join(c.installdir,'Source')) 301 shutil.rmtree(os.path.join(c.installdir,'.git')) 302 for x in UioFiles(c.installdir, '*~').files: 303 silent_remove(x) 304 305 os.remove(os.path.join(c.installdir,'setup.sh')) 306 os.remove(os.path.join(c.installdir,'setup_local.sh')) 307 308 # configure run_local script correctly 309 # check if source of system config file is already in run_local.sh, 310 # if not, add it 311 if not check_for_string_in_file(os.path.join(c.installdir,'Run/run_local.sh'), 312 'source .setup.rc'): 313 overwrite_lines_in_file(os.path.join(c.installdir,'Run/run_local.sh'), 314 '# PATH TO SUBMISSION SCRIPT', 315 '# PATH TO SUBMISSION SCRIPT\nsource '+_config.FILE_SYS_CONFIG+'\n') 316 # make sure that the correct calling of submit.py script is in run_local.sh 317 overwrite_lines_in_file(os.path.join(c.installdir,'Run/run_local.sh'), 318 'pyscript=', 'pyscript=submit.py\n') 319 320 # change permission for file to executable 321 execute_subprocess(['chmod', '0775', 322 os.path.join(os.path.abspath(c.installdir),'Run/run_local.sh')]) 323 324 325 # create systemdir 326 c.sysinstalldir = os.path.join(c.sysinstalldir,_config.FLEXEXTRACT_DIRNAME) 327 if os.path.isdir(c.sysinstalldir): 328 shutil.rmtree(c.sysinstalldir) 329 330 # create setup file for running flex_extract with system installation 331 with open(os.path.join(os.path.abspath(c.installdir),'Run/.setup.rc'),'w') as fio: 332 fio.write('#!/bin/bash \n') 333 fio.write('export FLEXEXTRACT_USER_DIR='+os.path.abspath(c.installdir)+'\n') 334 fio.write('export PATH='+os.path.abspath(c.sysinstalldir)+'/Python:${PATH}\n') 335 fio.write('export PATH='+os.path.abspath(c.sysinstalldir)+':${PATH}\n') 336 337 # copy all Python and Fortranfiles to this dir 338 shutil.copytree(_config.PATH_SOURCES, c.sysinstalldir, symlinks=True) 339 340 os.chdir(os.path.join(c.sysinstalldir,'Fortran')) 341 # Create Fortran executable 342 print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software as ' + 343 c.install_target + ' in directory ' + 344 os.path.abspath(c.sysinstalldir) + '\n') 345 346 del_fortran_build('.') 347 mk_fortran_build('.', c.makefile) 348 349 outfile = [x for x in UioFiles('.','*.out').files] 350 test=os.path.join(c.sysinstalldir,'calc_etadot') 351 if len(outfile) != 1: 352 print('WARNING: Multiple executables for Fortran code are available!') 353 # move executable one dir up and delete Fortran dir 354 os.chdir('..') 355 shutil.move(outfile[0], os.path.join(c.sysinstalldir,'calc_etadot')) 356 shutil.rmtree(os.path.join(os.path.abspath(c.sysinstalldir),'Fortran')) 250 # Create Fortran executable 251 print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software at ' + 252 c.install_target + ' in directory ' + 253 os.path.abspath(c.installdir) + '\n') 254 255 del_fortran_build('.') 256 mk_fortran_build('.', c.makefile) 357 257 358 258 os.chdir(_config.PATH_FLEXEXTRACT_DIR) … … 389 289 sys.exit(1) 390 290 391 if c.install_target and c.install_target not in ['local', 'syslocal']:291 if c.install_target and c.install_target != 'local': 392 292 if not c.ecgid or not c.ecuid: 393 293 print('Please enter your ECMWF user id and group id ' … … 405 305 if not c.installdir: 406 306 c.installdir = '${HOME}' 407 el if c.install_target == 'local':307 else: # local 408 308 if not c.installdir: 409 309 c.installdir = _config.PATH_FLEXEXTRACT_DIR 410 elif c.install_target == 'syslocal':411 if not c.installdir:412 c.installdir = _config.PATH_FLEXEXTRACT_DIR413 if not c.sysinstalldir:414 print('ERROR: System installation was selected but '415 'no system installation path was defined.')416 sys.exit()417 310 418 311 if not c.makefile: … … 430 323 else: 431 324 pass 432 325 433 326 return 434 327 … … 822 715 print(e) 823 716 else: 824 execute_subprocess(['ls', '-l', 717 execute_subprocess(['ls', '-l', 825 718 os.path.join(src_path, _config.FORTRAN_EXECUTABLE)], 826 719 error_msg='FORTRAN EXECUTABLE COULD NOT BE FOUND!') -
Source/Python/submit.py
r47be2684 ra916e8f 114 114 else: 115 115 submit(job_template, c, queue) 116 exit_message = 'FLEX_EXTRACT JOB SCRIPT IS SUBMIT TED!'116 exit_message = 'FLEX_EXTRACT JOB SCRIPT IS SUBMITED!' 117 117 118 118 normal_exit(exit_message) -
setup_local.sh
r75db9b0 r98f09d2 10 10 # python installation script. It also does some checks to 11 11 # guarantee necessary parameters were set. 12 #13 # @History:14 # Leopold Haimberger; Aug 202015 # added new parameter for a system installation16 # (seperate executable and user directories)17 12 # 18 13 # @Licence: … … 38 33 DESTINATION='<name>@genericSftp' 39 34 INSTALLDIR=None 40 SYSINSTALLDIR=None41 35 JOB_TEMPLATE='' 42 36 CONTROLFILE='CONTROL_CERA' … … 82 76 parameterlist+=" --makefile=$MAKEFILE" 83 77 fi 84 if [ -n "$INSTALLDIR" ]; then 85 parameterlist+=" --installdir=$INSTALLDIR" 86 fi 87 if [ -n "$SYSINSTALLDIR" ]; then 88 parameterlist+=" --sysinstalldir=$SYSINSTALLDIR" 78 if [ -n "$FLEXPARTDIR" ]; then # not empty 79 parameterlist+=" --flexpartdir=$FLEXPARTDIR" 89 80 fi 90 81 if [ -n "$JOB_TEMPLATE" ]; then … … 100 91 $script $parameterlist 101 92 102 103
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