Changeset 47be2684 in flex_extract.git for Documentation


Ignore:
Timestamp:
Oct 28, 2020, 10:28:24 AM (4 years ago)
Author:
Leopold Haimberger <leopold.haimberger@…>
Branches:
ctbto, dev
Children:
75db9b0
Parents:
697b8d0
Message:

Adaptations to allow for a system installation with separate user and system path. Updated documentation

Location:
Documentation/html
Files:
12 edited

Legend:

Unmodified
Added
Removed

  • Documentation/html/Documentation/Api/api_python.html

    r08c9091 r47be2684  
    24942494<p>This module contains a collection of diverse tasks within flex_extract.</p>
    24952495<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 if
     2499the 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 found
     2509False : 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">
    24962518<dt id="tools.clean_up">
    24972519<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>
    … …  
    27322754<dt class="field-odd">Parameters</dt>
    27332755<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 the
     2764substitution 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>
    27342771</dd>
    27352772</dl>

  • Documentation/html/Documentation/Input/setup.html

    r08c9091 r47be2684  
    235235<tr class="row-even"><td><p>TARGET</p></td>
    236236<td><p>String</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>
     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>
    240240</tr>
    241241<tr class="row-odd"><td><p>MAKEFILE</p></td>
    … …  
    275275<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>
    276276</tr>
    277 <tr class="row-odd"><td><p>JOB_TEMPLATE</p></td>
     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>
    278284<td><p>String</p></td>
    279285<td><p>installscript.template</p></td>
    … …  
    281287<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>
    282288</tr>
    283 <tr class="row-even"><td><p>CONTROLFILE</p></td>
     289<tr class="row-odd"><td><p>CONTROLFILE</p></td>
    284290<td><p>String</p></td>
    285291<td><p>any CONTROL file</p></td>
    … …  
    402408              <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>
    403409              <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>
    404411              <span class="o">[</span>--job_template JOB_TEMPLATE<span class="o">]</span> <span class="o">[</span>--controlfile CONTROLFILE<span class="o">]</span>
    405412
    … …  
    409416  -h, --help            show this <span class="nb">help</span> message and <span class="nb">exit</span>
    410417  --target INSTALL_TARGET
    411                         Valid targets: <span class="nb">local</span> <span class="p">|</span> ecgate <span class="p">|</span> cca , the latter two
     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 two
    412419                        are at ECMWF <span class="o">(</span>default: None<span class="o">)</span>
    413420  --makefile MAKEFILE   Name of makefile to compile the Fortran
    … …  
    423430                        Root directory where flex_extract will be installed
    424431                        to. <span class="o">(</span>default: None<span class="o">)</span>
     432  --sysinstalldir SYSINSTALLDIR
     433                        System installation path<span class="p">;</span> where executables are
     434                        stored. <span class="o">(</span>default: None<span class="o">)</span>
    425435  --job_template JOB_TEMPLATE
    426436                        The rudimentary template file to create a batch job

  • Documentation/html/Installation/local.html

    r73308e0 r47be2684  
    104104<li class="toctree-l4"><a class="reference internal" href="#testing-the-local-environment">Testing the local environment</a></li>
    105105<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>
    106107</ul>
    107108</li>
    … …  
    395396<p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> will be compiled during the
    396397installation process. A suitable makefile (<code class="docutils literal notranslate"><span class="pre">makefile_local_gfortran</span></code>) for the compilation is set by default.
    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>
     398This 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>
    399400For 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>
    400 <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
     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> script
    401402with an editor and adapt the installation parameters in the section labelled with
    402403“AVAILABLE COMMANDLINE ARGUMENTS TO SET” as shown below:</p>
    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>
     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>
    405406<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...
    406407<span class="c1"># -----------------------------------------------------------------</span>
    … …  
    416417<span class="nv">DESTINATION</span><span class="o">=</span>None
    417418<span class="nv">INSTALLDIR</span><span class="o">=</span>None
     419<span class="nv">SYSINSTALLDIR</span><span class="o">=</span>None
    418420<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">&#39;&#39;</span>
    419421<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">&#39;CONTROL_EA5&#39;</span>
    … …  
    423425</div>
    424426<p>Afterwards, type:</p>
    425 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup.sh
     427<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup_local.sh
    426428</pre></div>
    427429</div>
    428430<p>to start the installation. You should see the following standard output.</p>
    429 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
     431<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup_local.sh</span>
    430432WARNING: installdir has not been specified
    431433flex_extract will be installed in here by compiling the Fortran <span class="nb">source</span> in &lt;path-to-flex_extract&gt;/flex_extract_v7.1/Source/Fortran
    … …  
    446448</div>
    447449</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 seperate 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.
     453The 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>.
     454In 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">&#39;syslocal&#39;</span>
     465<span class="nv">MAKEFILE</span><span class="o">=</span>&lt;name_of_your_makefile&gt;
     466<span class="nv">ECUID</span><span class="o">=</span>None
     467<span class="nv">ECGID</span><span class="o">=</span>None
     468<span class="nv">GATEWAY</span><span class="o">=</span>None
     469<span class="nv">DESTINATION</span><span class="o">=</span>None
     470<span class="nv">INSTALLDIR</span><span class="o">=</span><span class="nv">$HOME</span>
     471<span class="nv">SYSINSTALLDIR</span><span class="o">=</span>/usr/bin/
     472<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">&#39;&#39;</span>
     473<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">&#39;CONTROL_EA5&#39;</span>
     474...
     475</pre></div>
     476</div>
     477</div>
     478<p>Afterwards, type:</p>
     479<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ sudo ./setup_local.sh
     480</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 &lt;<span class="nv">$HOME</span>&gt;
     484Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2
     485
     486Using makefile: makefile_local_gfortran
     487/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.f90
     488/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.f90
     489/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.f90
     490/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.f90
     491/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.f90
     492/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.f90
     493/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 -fopenmp
     494ln -sf calc_etadot_fast.out calc_etadot
     495
     496lrwxrwxrwx. <span class="m">1</span> &lt;username&gt; tmc <span class="m">20</span> <span class="m">27</span>. Okt <span class="m">23</span>:25 ./calc_etadot -&gt; calc_etadot_fast.out
     497SUCCESS: 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 flex_extract_vX.X directory there.</p>
     501</div>
    448502</div>
    449503

  • Documentation/html/_modules/ControlFile.html

    r08c9091 r47be2684  
    566566        <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>
    567567        <span class="bp">self</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="kc">None</span>
     568        <span class="bp">self</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="o">=</span> <span class="kc">None</span>
    568569        <span class="bp">self</span><span class="o">.</span><span class="n">makefile</span> <span class="o">=</span> <span class="kc">None</span>
    569570        <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

    r08c9091 r47be2684  
    181181<span class="c1">#    June 2020 - Anne Philipp</span>
    182182<span class="c1">#        - renamed &quot;convert&quot; functions to &quot;fortran&quot; 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>
    184184<span class="c1">#          of *.nl and *.temp</span>
    185185<span class="c1">#        - added check for makefile settings</span>
    … …  
    237237<span class="kn">import</span> <span class="nn">subprocess</span>
    238238<span class="kn">import</span> <span class="nn">tarfile</span>
     239<span class="kn">import</span> <span class="nn">shutil</span>
    239240<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>
    240241
    … …  
    244245<span class="kn">from</span> <span class="nn">Classes.UioFiles</span> <span class="kn">import</span> <span class="n">UioFiles</span>
    245246<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>
    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>
     247                        <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>
     248                        <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>
    247249
    248250<span class="c1"># ------------------------------------------------------------------------------</span>
    … …  
    265267    <span class="n">check_install_conditions</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
    266268
    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">&#39;local&#39;</span><span class="p">:</span> <span class="c1"># ecgate or cca</span>
     269    <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="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;local&#39;</span><span class="p">,</span> <span class="s1">&#39;syslocal&#39;</span><span class="p">]:</span> <span class="c1"># ecgate or cca</span>
    268270        <span class="n">install_via_gateway</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
    269271    <span class="k">else</span><span class="p">:</span> <span class="c1"># local</span>
    270272        <span class="n">install_local</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
    271273
     274    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;SUCCESS: INSTALLATION FINISHED!&quot;</span><span class="p">)</span>
     275
    272276    <span class="k">return</span></div>
    273277
    … …  
    290294    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--target&#39;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">&#39;install_target&#39;</span><span class="p">,</span>
    291295                        <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>
    292                         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Valid targets: local | ecgate | cca , </span><span class="se">\</span>
     296                        <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Valid targets: syslocal | local | ecgate | cca , </span><span class="se">\</span>
    293297<span class="s2">                        the latter two are at ECMWF&quot;</span><span class="p">)</span>
    294298    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--makefile&quot;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">&quot;makefile&quot;</span><span class="p">,</span>
    … …  
    312316    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--installdir&quot;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">&quot;installdir&quot;</span><span class="p">,</span>
    313317                        <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>
    314                         <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Root directory of the &#39;</span>
     318                        <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Root (user) directory of the &#39;</span>
    315319                        <span class="s1">&#39;flex_extract installation&#39;</span><span class="p">)</span>
     320    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--sysinstalldir&quot;</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">&quot;sysinstalldir&quot;</span><span class="p">,</span>
     321                        <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>
     322                        <span class="n">help</span><span class="o">=</span><span class="s1">&#39;System installation path; where &#39;</span>
     323                        <span class="s1">&#39;executables are stored.&#39;</span><span class="p">)</span>
    316324
    317325    <span class="c1"># arguments for job submission to ECMWF, only needed by submit.py</span>
    … …  
    390398                            <span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">&#39;.tar&#39;</span><span class="p">)</span>
    391399
    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">&#39;WARNING: installdir has not been specified&#39;</span><span class="p">)</span>
    394         <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;flex_extract will be installed in here by compiling the &#39;</span> <span class="o">+</span>
    395               <span class="s1">&#39;Fortran source in &#39;</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>
     400    <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>
     401                <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)))</span>
     402    <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>
     403        <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)))</span>
     404
     405    <span class="c1"># this is standard installation into a single directory</span>
     406    <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">&#39;local&#39;</span><span class="p">:</span>
     407
     408        <span class="c1"># installation into the current directory</span>
     409        <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>
     410            <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;WARNING: installdir has not been specified&#39;</span><span class="p">)</span>
     411            <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;flex_extract will be installed in current dir by compiling the &#39;</span> <span class="o">+</span>
     412                  <span class="s1">&#39;Fortran source in &#39;</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>
     413            <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>
     414        <span class="c1"># installation into a different path</span>
     415        <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>
     416
     417            <span class="c1"># creates the target working directory for flex_extract</span>
    402418            <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>
    403419            <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>
    … …  
    410426                                  <span class="n">_config</span><span class="o">.</span><span class="n">PATH_REL_FORTRAN_SRC</span><span class="p">))</span>
    411427
    412     <span class="c1"># Create Fortran executable</span>
    413     <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Install &#39;</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">&#39; software at &#39;</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">&#39; in directory &#39;</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">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
    416 
    417     <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)</span>
    418     <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span>
     428        <span class="c1"># Create Fortran executable</span>
     429        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Install &#39;</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">&#39; software at &#39;</span> <span class="o">+</span>
     430              <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">+</span> <span class="s1">&#39; in directory &#39;</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">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     431
     432        <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)</span>
     433        <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span>
     434        <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s1">&#39;../../&#39;</span><span class="p">)</span>
     435        <span class="c1"># make sure that the correct calling of submit.py script is in run_local.sh</span>
     436        <span class="n">overwrite_lines_in_file</span><span class="p">(</span><span class="s1">&#39;Run/run_local.sh&#39;</span><span class="p">,</span>
     437                                <span class="s1">&#39;pyscript=&#39;</span><span class="p">,</span> <span class="s1">&#39;pyscript=../Source/Python/submit.py</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     438
     439    <span class="c1"># this is system installation were executables and user files are separated</span>
     440    <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">&#39;syslocal&#39;</span><span class="p">:</span>
     441        <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>
     442            <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">&#39;ERROR: System installation path is equal to user &#39;</span>
     443                     <span class="s1">&#39;installation path.</span><span class="se">\n</span><span class="s1"> Please change either the system &#39;</span>
     444                     <span class="s1">&#39;installation path or use installation target &quot;local&quot;.&#39;</span><span class="p">)</span>
     445        <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>
     446            <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Flex_extract will be installed in current directory!&#39;</span><span class="p">)</span>
     447        <span class="k">else</span><span class="p">:</span> <span class="c1"># install user part in different dir</span>
     448            <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Flex_extract will be installed in &#39;</span> <span class="o">+</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="p">)</span>
     449
     450            <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>
     451            <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>
     452                <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>
     453
     454            <span class="c1"># copy all files except Python and Fortranfiles to this dir</span>
     455            <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>
     456                            <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>
     457            <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">&#39;Source&#39;</span><span class="p">))</span>
     458            <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">&#39;.git&#39;</span><span class="p">))</span>
     459            <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">&#39;*~&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">:</span>
     460                <span class="n">silent_remove</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
     461
     462            <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">&#39;setup.sh&#39;</span><span class="p">))</span>
     463            <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">&#39;setup_local.sh&#39;</span><span class="p">))</span>
     464
     465        <span class="c1"># configure run_local script correctly</span>
     466        <span class="c1"># check if source of system config file is already in run_local.sh,</span>
     467        <span class="c1"># if not, add it</span>
     468        <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">&#39;Run/run_local.sh&#39;</span><span class="p">),</span>
     469                                 <span class="s1">&#39;source .setup.rc&#39;</span><span class="p">):</span>
     470            <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">&#39;Run/run_local.sh&#39;</span><span class="p">),</span>
     471                                    <span class="s1">&#39;# PATH TO SUBMISSION SCRIPT&#39;</span><span class="p">,</span>
     472                                    <span class="s1">&#39;# PATH TO SUBMISSION SCRIPT</span><span class="se">\n</span><span class="s1">source &#39;</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">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     473        <span class="c1"># make sure that the correct calling of submit.py script is in run_local.sh</span>
     474        <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">&#39;Run/run_local.sh&#39;</span><span class="p">),</span>
     475                                <span class="s1">&#39;pyscript=&#39;</span><span class="p">,</span> <span class="s1">&#39;pyscript=submit.py</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     476
     477        <span class="c1"># change permission for file to executable</span>
     478        <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">&#39;chmod&#39;</span><span class="p">,</span> <span class="s1">&#39;0775&#39;</span><span class="p">,</span>
     479                            <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">&#39;Run/run_local.sh&#39;</span><span class="p">)])</span>
     480
     481
     482        <span class="c1"># create systemdir</span>
     483        <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>
     484        <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>
     485            <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>
     486
     487        <span class="c1"># create setup file for running flex_extract with system installation</span>
     488        <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">&#39;Run/.setup.rc&#39;</span><span class="p">),</span><span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
     489            <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;#!/bin/bash </span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     490            <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;export FLEXEXTRACT_USER_DIR=&#39;</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">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     491            <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;export PATH=&#39;</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">&#39;/Python:$</span><span class="si">{PATH}</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     492            <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;export PATH=&#39;</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span><span class="o">+</span><span class="s1">&#39;:$</span><span class="si">{PATH}</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     493
     494        <span class="c1"># copy all Python and Fortranfiles to this dir</span>
     495        <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>
     496
     497        <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">&#39;Fortran&#39;</span><span class="p">))</span>
     498        <span class="c1"># Create Fortran executable</span>
     499        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Install &#39;</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">&#39; software as &#39;</span> <span class="o">+</span>
     500              <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">+</span> <span class="s1">&#39; in directory &#39;</span> <span class="o">+</span>
     501              <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">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
     502
     503        <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)</span>
     504        <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span>
     505
     506        <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">&#39;.&#39;</span><span class="p">,</span><span class="s1">&#39;*.out&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span>
     507        <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">&#39;calc_etadot&#39;</span><span class="p">)</span>
     508        <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>
     509            <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;WARNING: Multiple executables for Fortran code are available!&#39;</span><span class="p">)</span>
     510        <span class="c1"># move executable one dir up and delete Fortran dir</span>
     511        <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s1">&#39;..&#39;</span><span class="p">)</span>
     512        <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">&#39;calc_etadot&#39;</span><span class="p">))</span>
     513        <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">&#39;Fortran&#39;</span><span class="p">))</span>
    419514
    420515    <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>
    … …  
    451546        <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>
    452547
    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">&#39;local&#39;</span><span class="p">:</span>
     548    <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="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;local&#39;</span><span class="p">,</span> <span class="s1">&#39;syslocal&#39;</span><span class="p">]:</span>
    454549        <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>
    455550            <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Please enter your ECMWF user id and group id &#39;</span>
    … …  
    467562        <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>
    468563            <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="s1">&#39;$</span><span class="si">{HOME}</span><span class="s1">&#39;</span>
    469     <span class="k">else</span><span class="p">:</span> <span class="c1"># local</span>
     564    <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">&#39;local&#39;</span><span class="p">:</span>
    470565        <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>
    471566            <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>
     567    <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">&#39;syslocal&#39;</span><span class="p">:</span>
     568        <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>
     569            <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>
     570        <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>
     571            <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ERROR: System installation was selected but &#39;</span>
     572                  <span class="s1">&#39;no system installation path was defined.&#39;</span><span class="p">)</span>
     573            <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
    472574
    473575    <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>
    … …  
    485587        <span class="k">else</span><span class="p">:</span>
    486588            <span class="k">pass</span>
    487        
     589
    488590    <span class="k">return</span></div>
    489591
    … …  
    877979        <span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
    878980    <span class="k">else</span><span class="p">:</span>
    879         <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">&#39;ls&#39;</span><span class="p">,</span> <span class="s1">&#39;-l&#39;</span><span class="p">,</span> 
     981        <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">&#39;ls&#39;</span><span class="p">,</span> <span class="s1">&#39;-l&#39;</span><span class="p">,</span>
    880982                            <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>
    881983                           <span class="n">error_msg</span><span class="o">=</span><span class="s1">&#39;FORTRAN EXECUTABLE COULD NOT BE FOUND!&#39;</span><span class="p">)</span>

  • Documentation/html/_modules/submit.html

    r08c9091 r47be2684  
    276276    <span class="k">else</span><span class="p">:</span>
    277277        <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">&#39;FLEX_EXTRACT JOB SCRIPT IS SUBMITED!&#39;</span>
     278        <span class="n">exit_message</span> <span class="o">=</span> <span class="s1">&#39;FLEX_EXTRACT JOB SCRIPT IS SUBMITTED!&#39;</span>
    279279
    280280    <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

    r08c9091 r47be2684  
    411411                        <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>
    412412                        <span class="n">help</span><span class="o">=</span><span class="s1">&#39;The name of the ECMWF server name where the&#39;</span>
    413                         <span class="s1">&#39;job script is to be submitted &#39;</span> 
     413                        <span class="s1">&#39;job script is to be submitted &#39;</span>
    414414                        <span class="s1">&#39;(e.g. ecgate | cca | ccb)&#39;</span><span class="p">)</span>
    415415
    … …  
    786786    <span class="sd">&#39;&#39;&#39;Creates a directory.</span>
    787787
    788 <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>
    789789<span class="sd">    skipped. The program stops only if there is another problem.</span>
    790790
    … …  
    10181018<span class="sd">    ----------</span>
    10191019<span class="sd">    cmd_list : list of str</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>
     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>
    10221022<span class="sd">        to be submitted, like [&#39;mv&#39;, file1, file2] for mv file1 file2.</span>
    10231023
    … …  
    10721072
    10731073    <span class="k">return</span> <span class="n">start_period</span><span class="p">,</span> <span class="n">end_period</span></div>
     1074
     1075
     1076<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>
     1077    <span class="sd">&quot;&quot;&quot;</span>
     1078<span class="sd">    Search for a specific string in a file and return True if</span>
     1079<span class="sd">    the string was found.</span>
     1080
     1081<span class="sd">    Parameters</span>
     1082<span class="sd">    ----------</span>
     1083<span class="sd">    filepath : str</span>
     1084<span class="sd">        The full file path which is to be examined.</span>
     1085
     1086<span class="sd">    search_string : str</span>
     1087<span class="sd">        The string which is looked up for in the file.</span>
     1088
     1089<span class="sd">    Return</span>
     1090<span class="sd">    ------</span>
     1091<span class="sd">    Boolean :</span>
     1092<span class="sd">        True : String was found</span>
     1093<span class="sd">        False : String was not found</span>
     1094<span class="sd">    &quot;&quot;&quot;</span>
     1095    <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">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
     1096        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fio</span><span class="p">:</span>
     1097            <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>
     1098                <span class="k">return</span> <span class="kc">True</span>
     1099    <span class="k">return</span> <span class="kc">False</span></div>
     1100
     1101
     1102<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>
     1103    <span class="sd">&quot;&quot;&quot;</span>
     1104<span class="sd">    Overwrites lines which contain the given search string with the</span>
     1105<span class="sd">    substitution string.</span>
     1106
     1107<span class="sd">    Parameters</span>
     1108<span class="sd">    ----------</span>
     1109<span class="sd">    search_string : str</span>
     1110<span class="sd">        The string which is looked up for in the file.</span>
     1111
     1112<span class="sd">    sub_string : str</span>
     1113<span class="sd">        The string which overwrites the search string.</span>
     1114
     1115<span class="sd">    Return</span>
     1116<span class="sd">    ------</span>
     1117<span class="sd">    &quot;&quot;&quot;</span>
     1118    <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">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
     1119        <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>
     1120
     1121    <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">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
     1122        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
     1123            <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>
     1124                <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>
     1125            <span class="k">else</span><span class="p">:</span>
     1126                <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>
     1127
     1128    <span class="k">return</span></div>
     1129
    10741130</pre></div>
    10751131

  • Documentation/html/_sources/Documentation/Input/setup.rst.txt

    r5bee29a r47be2684  
    165165                  [--ecuid ECUID] [--ecgid ECGID] [--gateway GATEWAY]
    166166                  [--destination DESTINATION] [--installdir INSTALLDIR]
     167                  [--sysinstalldir SYSINSTALLDIR]
    167168                  [--job_template JOB_TEMPLATE] [--controlfile CONTROLFILE]
    168169
    … …  
    172173      -h, --help            show this help message and exit
    173174      --target INSTALL_TARGET
    174                             Valid targets: local | ecgate | cca , the latter two
     175                            Valid targets: syslocal | local | ecgate | cca , the latter two
    175176                            are at ECMWF (default: None)
    176177      --makefile MAKEFILE   Name of makefile to compile the Fortran
    … …  
    186187                            Root directory where flex_extract will be installed
    187188                            to. (default: None)
     189      --sysinstalldir SYSINSTALLDIR
     190                            System installation path; where executables are
     191                            stored. (default: None)
    188192      --job_template JOB_TEMPLATE
    189193                            The rudimentary template file to create a batch job
    … …  
    198202
    199203
     204
    200205.. toctree::
    201206    :hidden:

  • Documentation/html/_sources/Installation/local.rst.txt

    r73308e0 r47be2684  
    266266The Fortran program called ``calc_etadot`` will be compiled during the
    267267installation 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.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``
     268This may be overwritten by the ``MAKEFILE`` parameter in ``setup_local.sh``.
     269
     270However, 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``
    271271For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`.
    272272
    273273 
    274 In the root directory of ``flex_extract``, open the ``setup.sh`` script
     274In the root directory of ``flex_extract``, open the ``setup_local.sh`` script
    275275with an editor and adapt the installation parameters in the section labelled with
    276276"AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below:
    … …  
    279279.. code-block:: bash
    280280   :caption: 'Example settings for a local installation.'
    281    :name: setup.sh
     281   :name: setup_local.sh
    282282   
    283283   ...
    … …  
    294294   DESTINATION=None
    295295   INSTALLDIR=None
     296   SYSINSTALLDIR=None
    296297   JOB_TEMPLATE=''
    297298   CONTROLFILE='CONTROL_EA5'
    … …  
    303304.. code-block:: bash
    304305
    305    $ ./setup.sh
     306   $ ./setup_local.sh
    306307   
    307308to start the installation. You should see the following standard output.
    … …  
    310311.. code-block:: bash
    311312
    312     # Output of setup.sh   
     313    # Output of setup_local.sh   
    313314    WARNING: installdir has not been specified
    314315    flex_extract will be installed in here by compiling the Fortran source in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran
    … …  
    327328    lrwxrwxrwx. 1 <username> tmc 20 Aug 12  10:59 ./calc_etadot -> calc_etadot_fast.out
    328329
     330
     331Local system installation
     332=========================
     333
     334There is also the possibility to seperate 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.
     335The user directory for ``flex_extract``, which basically consists of everything except the ``Source`` directory, will be installed into ``INSTALLDIR``.
     336In 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
     338Despite 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:: bash
     342   :caption: 'Example settings for a local system installation.'
     343   :name: setup_local.sh
     344   
     345   ...
     346   # -----------------------------------------------------------------
     347   # AVAILABLE COMMANDLINE ARGUMENTS TO SET
     348   #
     349   # THE USER HAS TO SPECIFY THESE PARAMETER
     350   #
     351   TARGET='syslocal'
     352   MAKEFILE=<name_of_your_makefile>
     353   ECUID=None
     354   ECGID=None
     355   GATEWAY=None
     356   DESTINATION=None
     357   INSTALLDIR=$HOME
     358   SYSINSTALLDIR=/usr/bin/
     359   JOB_TEMPLATE=''
     360   CONTROLFILE='CONTROL_EA5'
     361   ...
     362
     363
     364Afterwards, type:
     365
     366.. code-block:: bash
     367
     368   $ sudo ./setup_local.sh
     369   
     370to start the installation. You should see the following standard output.
     371
     372.. code-block:: bash
     373
     374        Flex_extract will be installed in <$HOME>
     375        Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2
     376
     377        Using makefile: makefile_local_gfortran
     378        /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.f90
     379        /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.f90
     380        /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.f90
     381        /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.f90
     382        /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.f90
     383        /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.f90
     384        /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 -fopenmp
     385        ln -sf calc_etadot_fast.out calc_etadot
     386
     387        lrwxrwxrwx. 1 <username> tmc 20 27. Okt 23:25 ./calc_etadot -> calc_etadot_fast.out
     388        SUCCESS: INSTALLATION FINISHED!
     389
     390
     391You can now change into the user directory specified in ``INSTALLDIR`` and find a flex_extract_vX.X directory there.

  • Documentation/html/genindex.html

    r08c9091 r47be2684  
    274274      <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>
    275275</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>
    276278      <li><a href="Documentation/Api/api_python.html#checks.check_grid">check_grid() (in module checks)</a>
    277279</li>
    … …  
    650652      <li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.omegadiff">omegadiff (ControlFile.ControlFile attribute)</a>
    651653</li>
    652   </ul></td>
    653   <td style="width: 33%; vertical-align: top;"><ul>
    654654      <li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.oper">oper (ControlFile.ControlFile attribute)</a>
    655655</li>
     656  </ul></td>
     657  <td style="width: 33%; vertical-align: top;"><ul>
    656658      <li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.outputdir">outputdir (ControlFile.ControlFile attribute)</a>
    657659</li>
    658660      <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>
    659663</li>
    660664  </ul></td>

  • Documentation/html/searchindex.js

    r73308e0 r47be2684  
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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 &amp; 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> 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