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| 66 | 7.1 |
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| 90 | <p class="caption"><span class="caption-text">Table of Contents:</span></p> |
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| 91 | <ul class="current"> |
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| 92 | <li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul> |
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| 93 | <li class="toctree-l2"><a class="reference internal" href="#registration-at-ecmwf">Registration at ECMWF</a></li> |
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| 94 | <li class="toctree-l2"><a class="reference internal" href="#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> |
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| 95 | <li class="toctree-l2"><a class="reference internal" href="#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> |
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| 96 | <li class="toctree-l2"><a class="reference internal" href="#dependencies">Dependencies</a></li> |
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| 97 | <li class="toctree-l2"><a class="reference internal" href="#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul> |
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| 98 | <li class="toctree-l3"><a class="reference internal" href="Installation/remote.html">Remote mode installation</a></li> |
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| 99 | <li class="toctree-l3"><a class="reference internal" href="Installation/gateway.html">Gateway mode installation</a></li> |
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| 100 | <li class="toctree-l3"><a class="reference internal" href="Installation/local.html">Local mode installation</a></li> |
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| 101 | </ul> |
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| 102 | </li> |
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| 103 | <li class="toctree-l2"><a class="reference internal" href="#flex-extract-in-combination-with-flexpart"><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> in combination with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code></a></li> |
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| 104 | <li class="toctree-l2"><a class="reference internal" href="#test-installation">Test installation</a><ul> |
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| 105 | <li class="toctree-l3"><a class="reference internal" href="#fortran-program-test">Fortran program test</a></li> |
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| 106 | <li class="toctree-l3"><a class="reference internal" href="#full-test">Full test</a></li> |
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| 107 | </ul> |
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| 183 | |
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| 184 | <div class="section" id="installation"> |
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| 185 | <h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1> |
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| 186 | <div class="toctree-wrapper compound"> |
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| 187 | </div> |
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| 188 | <p>The <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> software package contains python and shell scripts as well as a Fortran program. These components rely on several libraries which need to be available before starting the installation process. Currently, the software is only tested for a GNU/Linux environment. Feel free to try it out on other platforms.</p> |
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| 189 | <p>At first, go to the <a class="reference external" href="Ecmwf/access.html">user group</a> section and decide which group you belong to and follow the instructions at <a class="reference internal" href="#ref-registration"><span class="std std-ref">Registration at ECMWF</span></a> to obtain an account at ECMWF (if you don’t have it already). Depending on the user group and the way to access the ECWMF MARS archive, there are four possible <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a>:</p> |
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| 190 | <ul class="simple"> |
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| 191 | <li>Remote (member-state users only) <a class="reference internal" href="Installation/remote.html#ref-remote-mode"><span class="std std-ref">[installation]</span></a></li> |
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| 192 | <li>Gateway (member-state users only) <a class="reference internal" href="Installation/gateway.html#ref-gateway-mode"><span class="std std-ref">[installation]</span></a></li> |
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| 193 | <li>Local, member-state user <a class="reference internal" href="Installation/local.html#ref-local-mode"><span class="std std-ref">[installation]</span></a></li> |
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| 194 | <li>Local, public user <a class="reference internal" href="Installation/local.html#ref-local-mode"><span class="std std-ref">[installation]</span></a></li> |
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| 195 | </ul> |
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| 196 | <p>Please follow the link <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> to get a description of the modes.</p> |
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| 197 | <div class="admonition note"> |
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| 198 | <p class="first admonition-title">Note</p> |
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| 199 | <p class="last">If you encounter any problems in the installation process, you can ask for <a class="reference internal" href="support.html"><span class="doc">Support</span></a>.</p> |
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| 200 | </div> |
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| 201 | <div class="section" id="registration-at-ecmwf"> |
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| 202 | <span id="ref-registration"></span><h2>Registration at ECMWF<a class="headerlink" href="#registration-at-ecmwf" title="Permalink to this headline">¶</a></h2> |
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| 203 | <p>The registration depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> and in case of the local mode also on the data set you’d like to retrieve. The following table gives an overview where you need to register.</p> |
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| 204 | <table border="1" class="docutils"> |
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| 205 | <colgroup> |
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| 206 | <col width="23%" /> |
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| 207 | <col width="15%" /> |
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| 208 | <col width="16%" /> |
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| 209 | <col width="24%" /> |
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| 210 | <col width="23%" /> |
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| 211 | </colgroup> |
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| 212 | <tbody valign="top"> |
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| 213 | <tr class="row-odd"><td rowspan="2">Data sets</td> |
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| 214 | <td colspan="3">Member-state user</td> |
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| 215 | <td>Public user</td> |
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| 216 | </tr> |
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| 217 | <tr class="row-even"><td>Remote</td> |
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| 218 | <td>Gateway</td> |
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| 219 | <td>Local</td> |
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| 220 | <td>Local</td> |
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| 221 | </tr> |
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| 222 | <tr class="row-odd"><td>Operational</td> |
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| 223 | <td>1</td> |
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| 224 | <td>1</td> |
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| 225 | <td>1,2</td> |
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| 226 | <td><ul class="first last simple"> |
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| 227 | <li></li> |
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| 228 | </ul> |
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| 229 | </td> |
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| 230 | </tr> |
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| 231 | <tr class="row-even"><td>ERA-Interim</td> |
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| 232 | <td>1</td> |
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| 233 | <td>1</td> |
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| 234 | <td>1,2</td> |
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| 235 | <td>2</td> |
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| 236 | </tr> |
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| 237 | <tr class="row-odd"><td>CERA-20C</td> |
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| 238 | <td>1</td> |
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| 239 | <td>1</td> |
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| 240 | <td>1,2</td> |
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| 241 | <td>2</td> |
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| 242 | </tr> |
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| 243 | <tr class="row-even"><td>ERA5</td> |
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| 244 | <td>1</td> |
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| 245 | <td>1</td> |
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| 246 | <td>3</td> |
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| 247 | <td><ul class="first last simple"> |
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| 248 | <li></li> |
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| 249 | </ul> |
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| 250 | </td> |
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| 251 | </tr> |
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| 252 | </tbody> |
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| 253 | </table> |
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| 254 | <p>Registration options:</p> |
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| 255 | <blockquote> |
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| 256 | <div><p>1.) Access through a member-state user account granted by the <a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Computing Representative</a>. The credentials have to be provided during installation.</p> |
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| 257 | <p>2.) Access through the ECMWF Web API. Need to sign in at <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ECMWF Web API</a> and configure the ECMWF key as described. Member-state users can sign in with their credentials from the <a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Computing Representative</a> and public users have to fill out the <a class="reference external" href="https://apps.ecmwf.int/registration/">registration form</a> to get an account.</p> |
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| 258 | <p>3.) Access through the <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">CDS API</a>. Extra registration for member-state users is required at <a class="reference external" href="https://cds.climate.copernicus.eu/user/register">Copernicus Climate Data Store</a> including the configurations of the CDS key as described. This mode is currently not available for public users. See the note at <a class="reference external" href="Ecmwf/access.html">user group</a> for information.</p> |
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| 259 | </div></blockquote> |
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| 260 | </div> |
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| 261 | <div class="section" id="licence-agreement-for-public-datasets"> |
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| 262 | <span id="ref-licence"></span><h2>Licence agreement for public datasets<a class="headerlink" href="#licence-agreement-for-public-datasets" title="Permalink to this headline">¶</a></h2> |
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| 263 | <p>Each ECMWF public dataset has its own licence which has to be accepted, regardless of the user group.</p> |
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| 264 | <p>For the <em>ERA-Interim</em> and <em>CERA-20C</em> datasets this can be done at the ECMWF website <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">Available ECMWF Public Datasets</a>. Log in and follow the licence links on the right side for each dataset and accept it.</p> |
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| 265 | <p>For the <em>ERA5</em> dataset this has to be done at the <a class="reference external" href="https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset">Climate Data Store (CDS) website</a>. Log in and select, on the left panel, product type “Reanalysis” for finding <em>ERA5</em> datasets. Then follow any link with <em>ERA5</em> to the full dataset record, click on tab “Download data” and scroll down. There is a section “Terms of use” where you have to click the <span class="underline">Accept terms</span> button.</p> |
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| 266 | </div> |
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| 267 | <div class="section" id="download-flex-extract"> |
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| 268 | <span id="ref-download"></span><h2>Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code><a class="headerlink" href="#download-flex-extract" title="Permalink to this headline">¶</a></h2> |
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| 269 | <p>There are two options to download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>:</p> |
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| 270 | <dl class="docutils"> |
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| 271 | <dt>tar ball</dt> |
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| 272 | <dd><p class="first">You can download a tar ball with the latest release from the <a class="reference external" href="https://www.flexpart.eu/wiki/FpInputMetEcmwf">flex_extract page</a> from our <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> community website and then untar the file.</p> |
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| 273 | <div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>tar -xvf <flex_extract_vX.X.tar> |
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| 274 | </pre></div> |
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| 275 | </div> |
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| 276 | </dd> |
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| 277 | <dt>git repo</dt> |
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| 278 | <dd><p class="first">Alternatively, if you have <code class="docutils literal notranslate"><span class="pre">git</span></code> installed on your machine, and if you are interested to keep the code in a version control system, you may clone the latest version from our git repository master branch.</p> |
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| 279 | <div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>$ git clone --single-branch --branch master https://www.flexpart.eu/gitmob/flexpart |
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| 280 | </pre></div> |
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| 281 | </div> |
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| 282 | </dd> |
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| 283 | </dl> |
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| 284 | </div> |
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| 285 | <div class="section" id="dependencies"> |
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| 286 | <span id="ref-requirements"></span><h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2> |
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| 287 | <p>The software required for running <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> and therefore is described in the respective specific installation sections.</p> |
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| 288 | <p>Generally speaking, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> requires <a class="reference external" href="https://docs.python.org/3/">Python 3</a> and Fortran together with certain modules / libraries. |
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| 289 | We tested <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the python3 package from the the GNU/Linux distribution and Anaconda Python. The required python3 modules should prefarably be installed as distribution packages, or alternatively using Python’s own package manager <code class="docutils literal notranslate"><span class="pre">pip</span></code> (this may mess up some aspects of your python installation, especially if you use <code class="docutils literal notranslate"><span class="pre">pip</span></code> as root. Think about using virtual environments.).</p> |
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| 290 | <p>Before installing the system packages check the availability with <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or <code class="docutils literal notranslate"><span class="pre">rpm</span> <span class="pre">-q</span> <span class="pre"><package_name></span></code>, depending on your system. For example:</p> |
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| 291 | <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>$ dpkg -s libeccodes-dev <span class="p">|</span> grep Status |
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| 292 | <span class="c1"># or</span> |
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| 293 | $ rpm -q libeccodes-dev |
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| 294 | </pre></div> |
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| 295 | </div> |
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| 296 | </div> |
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| 297 | <div class="section" id="installation-of-flex-extract"> |
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| 298 | <span id="ref-install-fe"></span><h2>Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code><a class="headerlink" href="#installation-of-flex-extract" title="Permalink to this headline">¶</a></h2> |
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| 299 | <p>The actual installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is done by executing a shell script called <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>. |
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| 300 | It defines some parameters and calls a Python script passing the parameters as command line arguments. For details, see <a class="reference internal" href="Documentation/Input/setup.html"><span class="doc">The Installation Script - setup.sh</span></a>.</p> |
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| 301 | <p>For each application mode installation section we describe the requirements for the explicit |
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| 302 | environment and how it is installed, test if it works and how the actual <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> |
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| 303 | installation has to be done. At the users local side not all software has to be present for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p> |
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| 304 | <p>Select one of the following modes to install:</p> |
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| 305 | <blockquote> |
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| 306 | <div><p><a class="reference internal" href="Installation/remote.html"><span class="doc">Remote mode installation</span></a></p> |
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| 307 | <p><a class="reference internal" href="Installation/gateway.html"><span class="doc">Gateway mode installation</span></a></p> |
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| 308 | <p><a class="reference internal" href="Installation/local.html"><span class="doc">Local mode installation</span></a></p> |
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| 309 | </div></blockquote> |
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| 310 | <div class="toctree-wrapper compound"> |
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| 311 | </div> |
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| 312 | </div> |
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| 313 | <div class="section" id="flex-extract-in-combination-with-flexpart"> |
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| 314 | <h2><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> in combination with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code><a class="headerlink" href="#flex-extract-in-combination-with-flexpart" title="Permalink to this headline">¶</a></h2> |
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| 315 | <p>Some users might wish to incorporate <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly into the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> distribution. Then the installation path has to be changed by setting the parameter <cite>installdir</cite> in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file to the <code class="docutils literal notranslate"><span class="pre">script</span></code> directory in the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> root directoy.</p> |
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| 316 | </div> |
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| 317 | <div class="section" id="test-installation"> |
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| 318 | <span id="ref-testinstallfe"></span><h2>Test installation<a class="headerlink" href="#test-installation" title="Permalink to this headline">¶</a></h2> |
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| 319 | <div class="section" id="fortran-program-test"> |
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| 320 | <h3>Fortran program test<a class="headerlink" href="#fortran-program-test" title="Permalink to this headline">¶</a></h3> |
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| 321 | <p>To check whether the Fortran program <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> has been compiled and runs properly, it can be applied to a prepared minimal dataset.</p> |
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| 322 | <p>For this, go from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory to the <code class="docutils literal notranslate"><span class="pre">Testing/Installation/Convert/</span></code> directory and execute the Fortran program.</p> |
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| 323 | <div class="admonition note"> |
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| 324 | <p class="first admonition-title">Note</p> |
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| 325 | <p class="last">Remember that you might have to log in at the ECMWF server if you used the installation for the <strong>remote</strong> or <strong>gateway</strong> mode. There you find the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory in your <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory.</p> |
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| 326 | </div> |
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| 327 | <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> Testing/Installation/Convert |
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| 328 | <span class="c1"># execute the Fortran progam without arguments</span> |
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| 329 | ../../../Source/Fortran/CONVERT2 |
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| 330 | </pre></div> |
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| 331 | </div> |
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| 332 | <p>The installation was successfull if you obtain on standard output:</p> |
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| 333 | <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> readspectral: <span class="m">1</span> records <span class="nb">read</span> |
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| 334 | readlatlon: <span class="m">8</span> records <span class="nb">read</span> |
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| 335 | STATISTICS: <span class="m">98842</span>.4598 <span class="m">98709</span>.7359 <span class="m">5120</span>.5385 |
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| 336 | readlatlon: <span class="m">4</span> records <span class="nb">read</span> |
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| 337 | readlatlon: <span class="m">4</span> records <span class="nb">read</span> |
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| 338 | readlatlon: <span class="m">4</span> records <span class="nb">read</span> |
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| 339 | SUCCESSFULLY FINISHED CONVERT_PRE: CONGRATULATIONS |
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| 340 | </pre></div> |
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| 341 | </div> |
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| 342 | <p>Now go back to the root directory:</p> |
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| 343 | <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> ../../../ |
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| 344 | </pre></div> |
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| 345 | </div> |
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| 346 | </div> |
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| 347 | <div class="section" id="full-test"> |
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| 348 | <h3>Full test<a class="headerlink" href="#full-test" title="Permalink to this headline">¶</a></h3> |
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| 349 | <blockquote> |
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| 350 | <div>see <a class="reference internal" href="quick_start.html"><span class="doc">Quick Start</span></a></div></blockquote> |
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| 351 | </div> |
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| 352 | </div> |
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| 364 | |
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| 366 | <a href="index.html" class="btn btn-neutral float-left" title="Welcome to flex_extract’s user documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a> |
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| 367 | |
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| 374 | <p> |
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| 375 | © Copyright 2019, Anne Philipp and Leopold Haimberger |
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| 376 | |
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| 377 | </p> |
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