Changeset d720895 in flex_extract.git
- Timestamp:
- Dec 19, 2019, 8:12:11 PM (4 years ago)
- Branches:
- master, ctbto, dev
- Children:
- e70c85f
- Parents:
- 76c37a9
- Location:
- Documentation/html
- Files:
-
- 36 added
- 17 edited
Legend:
- Unmodified
- Added
- Removed
-
Documentation/html/Documentation/Input/run.html
r30f7911 rd720895 487 487 <span class="c1">#</span> 488 488 <span class="c1"># @Description: </span> 489 <span class="c1">#</span> 490 491 489 <span class="c1"># This script defines the available command-line parameters</span> 490 <span class="c1"># for running flex_extract and combines them for the execution </span> 491 <span class="c1"># of the Python program. It also does some checks to </span> 492 <span class="c1"># guarantee necessary parameters were set and consistent.</span> 493 <span class="c1">#</span> 494 <span class="c1"># @Licence:</span> 495 <span class="c1"># (C) Copyright 2014-2019.</span> 496 <span class="c1">#</span> 497 <span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span> 498 <span class="c1">#</span> 499 <span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span> 500 <span class="c1"># International License. To view a copy of this license, visit</span> 501 <span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span> 502 <span class="c1"># Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span> 503 <span class="c1">#</span> 492 504 <span class="c1"># -----------------------------------------------------------------</span> 493 505 <span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span> … … 508 520 <span class="nv">PP_ID</span><span class="o">=</span>None 509 521 <span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.temp'</span> 510 <span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_ OD.OPER.FC.gauss.global'</span>522 <span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span> 511 523 <span class="nv">DEBUG</span><span class="o">=</span><span class="m">0</span> 512 <span class="nv">REQUEST</span><span class="o">=</span><span class="m"> 2</span>524 <span class="nv">REQUEST</span><span class="o">=</span><span class="m">0</span> 513 525 <span class="nv">PUBLIC</span><span class="o">=</span><span class="m">0</span> 514 526 -
Documentation/html/Documentation/Input/setup.html
rba99230 rd720895 348 348 <span class="c1"># This file defines the flex_extract's available installation</span> 349 349 <span class="c1"># parameters and puts them together for the call of the actual </span> 350 <span class="c1"># python installation script. </span> 351 <span class="c1"># It also does some checks to guarantees necessary parameters </span> 352 <span class="c1"># were set.</span> 350 <span class="c1"># python installation script. It also does some checks to </span> 351 <span class="c1"># guarantee necessary parameters were set.</span> 352 <span class="c1">#</span> 353 <span class="c1"># @Licence:</span> 354 <span class="c1"># (C) Copyright 2014-2019.</span> 355 <span class="c1">#</span> 356 <span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span> 357 <span class="c1">#</span> 358 <span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span> 359 <span class="c1"># International License. To view a copy of this license, visit</span> 360 <span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span> 361 <span class="c1"># Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span> 353 362 <span class="c1">#</span> 354 363 <span class="c1"># -----------------------------------------------------------------</span> … … 358 367 <span class="c1">#</span> 359 368 <span class="nv">TARGET</span><span class="o">=</span><span class="s1">'ecgate'</span> 360 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">' Makefile.gfortran'</span>369 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'makefile.eccodes'</span> 361 370 <span class="nv">ECUID</span><span class="o">=</span><span class="s1">'km4a'</span> 362 371 <span class="nv">ECGID</span><span class="o">=</span><span class="s1">'at'</span> -
Documentation/html/Documentation/Input/templates.html
rba99230 rd720895 252 252 On the <strong>ecgate</strong> server the <code class="docutils literal notranslate"><span class="pre">SBATCH</span></code> comments are the directives for the SLURM workload manager. A description of the single lines can be found at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs">SLURM directives</a>. 253 253 For the high performance computers <strong>cca</strong> and <strong>ccb</strong> the <code class="docutils literal notranslate"><span class="pre">PBS</span></code> comments are necessary and can be view at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS">PBS directives</a>.</p> 254 <p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref"> Environment requirements</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>254 <p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p> 255 255 <p>Afterwards the installation steps as such are done. Including the generation of the root directory, putting files in place, compiling the Fortran program and sending a log file via email.</p> 256 256 <div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span> … … 336 336 On the <strong>ecgate</strong> server the <code class="docutils literal notranslate"><span class="pre">SBATCH</span></code> comments are the directives for the SLURM workload manager. A description of the single lines can be found at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs">SLURM directives</a>. 337 337 For the high performance computers <strong>cca</strong> and <strong>ccb</strong> the <code class="docutils literal notranslate"><span class="pre">PBS</span></code> comments are necessary and can be view at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS">PBS directives</a>.</p> 338 <p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref"> Environment requirements</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>338 <p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p> 339 339 <p>Afterwards the run directory and the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file are created and <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is executed. In the end a log file is send via email.</p> 340 340 <div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span> -
Documentation/html/Documentation/Overview/app_modes.html
r30f7911 rd720895 189 189 <li><dl class="first docutils"> 190 190 <dt>Remote (member)</dt> 191 <dd>In the <strong>Remote mode</strong> the user works directly on ECMWF Linux member state server, such as <code class="docutils literal notranslate"><span class="pre">ecgate</span></code> or <code class="docutils literal notranslate"><span class="pre">cca</span></code>. The software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory. The user does not need to install any of the additional third-party libraries mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref"> Environment requirements</span></a> as ECMWF provides everything with environment modules. The module selection will be done automatically in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</dd>191 <dd>In the <strong>Remote mode</strong> the user works directly on ECMWF Linux member state server, such as <code class="docutils literal notranslate"><span class="pre">ecgate</span></code> or <code class="docutils literal notranslate"><span class="pre">cca</span></code>. The software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory. The user does not need to install any of the additional third-party libraries mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> as ECMWF provides everything with environment modules. The module selection will be done automatically in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</dd> 192 192 </dl> 193 193 </li> … … 207 207 <li><dl class="first docutils"> 208 208 <dt>Local member</dt> 209 <dd>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API’s have to be installed to access ECMWF server. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode </span></a>.</dd>209 <dd>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API’s have to be installed to access ECMWF server. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode - dependencies</span></a>.</dd> 210 210 </dl> 211 211 </li> 212 212 <li><dl class="first docutils"> 213 213 <dt>Local public</dt> 214 <dd>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API’s have to be installed to access ECMWF server. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode </span></a>. In this case a direct registration at ECMWF is necessary and the user has to accept a specific license agreement for each dataset he/she intends to retrieve.</dd>214 <dd>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API’s have to be installed to access ECMWF server. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode - dependencies</span></a>. In this case a direct registration at ECMWF is necessary and the user has to accept a specific license agreement for each dataset he/she intends to retrieve.</dd> 215 215 </dl> 216 216 </li> -
Documentation/html/Documentation/overview.html
rba99230 rd720895 193 193 <p>Additionally, it has some Korn shell scripts which are used to set the environment and batch job features on ECMWF servers for the <em>gateway</em> and <em>remote</em> mode. See <a class="reference internal" href="Overview/app_modes.html"><span class="doc">Application Modes</span></a> for information of application modes.</p> 194 194 <p>A number of Shell scripts are wrapped around the software package for easy installation and fast job submission.</p> 195 <p>The software depends on a number of third-party libraries which can be found in <a class="reference internal" href="../installation.html#ref-requirements"><span class="std std-ref"> Environment requirements</span></a>.</p>195 <p>The software depends on a number of third-party libraries which can be found in <a class="reference internal" href="../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a>.</p> 196 196 <p>Some details on the tasks and program worksteps are described in <a class="reference internal" href="Overview/prog_flow.html"><span class="doc">Program Flow</span></a>.</p> 197 197 <div class="toctree-wrapper compound"> -
Documentation/html/Installation/gateway.html
r30f7911 rd720895 94 94 <li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> 95 95 <li class="toctree-l2"><a class="reference internal" href="../installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> 96 <li class="toctree-l2"><a class="reference internal" href="../installation.html# environment-requirements">Environment requirements</a></li>96 <li class="toctree-l2"><a class="reference internal" href="../installation.html#dependencies">Dependencies</a></li> 97 97 <li class="toctree-l2 current"><a class="reference internal" href="../installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul class="current"> 98 98 <li class="toctree-l3"><a class="reference internal" href="remote.html">Remote mode installation</a></li> 99 99 <li class="toctree-l3 current"><a class="current reference internal" href="#">Gateway mode installation</a><ul> 100 <li class="toctree-l4"><a class="reference internal" href="#gateway- environment-requirements">Gateway environment requirements</a></li>100 <li class="toctree-l4"><a class="reference internal" href="#gateway-mode-dependencies">Gateway mode - dependencies</a></li> 101 101 <li class="toctree-l4"><a class="reference internal" href="#prepare-gateway-environment">Prepare gateway environment</a></li> 102 102 <li class="toctree-l4"><a class="reference internal" href="#test-gateway-environment">Test gateway environment</a></li> … … 190 190 <div class="toctree-wrapper compound"> 191 191 </div> 192 <div class="section" id="gateway-environment-requirements"> 193 <span id="ref-req-gateway"></span><span id="ref-gateway-mode"></span><h2>Gateway environment requirements<a class="headerlink" href="#gateway-environment-requirements" title="Permalink to this headline">¶</a></h2> 194 <p>The environment on your local system has to provide these software packages 195 and libraries, since <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> does only prepare the job script and send 196 it to the ECMWF servers:</p> 192 <div class="section" id="gateway-mode-dependencies"> 193 <span id="ref-req-gateway"></span><span id="ref-gateway-mode"></span><h2>Gateway mode - dependencies<a class="headerlink" href="#gateway-mode-dependencies" title="Permalink to this headline">¶</a></h2> 197 194 <ul class="simple"> 198 <li><a class="reference external" href="https://www.python.org/downloads/">Python3</a> or <a class="reference external" href="https://www.anaconda.com/distribution/#download-section">Anaconda Python3</a></li>195 <li><a class="reference external" href="https://www.python.org/downloads/">Python3</a></li> 199 196 <li><a class="reference external" href="http://www.numpy.org/">numpy</a></li> 200 197 <li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li> … … 203 200 <div class="section" id="prepare-gateway-environment"> 204 201 <span id="ref-prep-gateway"></span><h2>Prepare gateway environment<a class="headerlink" href="#prepare-gateway-environment" title="Permalink to this headline">¶</a></h2> 205 <p>The easiest way to install all required packages is to use the package management system of your Linux distribution. To do so, it is necessary to use a user with admin rights. 206 The installation was tested on a <em>GNU/Linux Debian buster</em> and an <em>Ubuntu 18.04 Bionic Beaver</em> system.</p> 207 <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Linux Debian or Ubuntu system do</span> 202 <p>In this mode, access to the ECMWF computing and archiving facilities is enabled through an ECaccess gateway server on a local member state server. The ECaccess framework is necessary to interactively submit jobs to the ECMWF batch system and to transfer files between ECMWF and local gateway server.</p> 203 <p>Please see <a class="reference external" href="https://confluence.ecmwf.int/display/ECAC/ECaccess+Home">ECMWF’s instructions on gateway server</a> to establish the gateway server if not already in place. Additionally, to be able to use the ECaccess file transfer service <strong>ectrans</strong> it is necessary to create a so-called association. The easiest way is to visit the ECaccess Member State Gateway website (e.g. <a class="reference external" href="https://msgatway.ecmwf.int">https://msgatway.ecmwf.int</a>) and follow the instructions in the short <a class="reference external" href="https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf">ECaccess Presentation</a> (page 17 ff.). Additional documentation can be found on the <a class="reference external" href="https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans">ECMWF ectrans site</a>.</p> 204 <p>The next step is to create an <em>ecaccess certificate</em> to be able to send and receive files from and to the ECMWF server. You can do this by using the <code class="docutils literal notranslate"><span class="pre">ecaccess-certificate-create</span></code> command on the gateway server. You will be prompted for your ECMWF member state user name and a password (generated by a token). This certificate has to be renewed periodically (every 7 days).</p> 205 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ecaccess-certificate-create 206 Please enter your user-id: example_username 207 Your passcode: *** 208 </pre></div> 209 </div> 210 <p>The easiest way to install all required packages is to use the package management system of your Linux distribution which required admin rights. 211 The installation was tested under <em>GNU/Linux Debian buster</em> and <em>Ubuntu 18.04 Bionic Beaver</em>.</p> 212 <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Debian or Debian-derived sytem (e. g. Ubuntu) system you may use the following commands (or equivalent commands of your preferred package manager):</span> 208 213 <span class="c1"># (if not already available):</span> 209 214 apt-get install python3 210 apt-get install pip 211 apt-get install genshi 212 apt-get install numpy 215 apt-get install python3-genshi 216 apt-get install python3-numpy 213 217 </pre></div> 214 218 </div> … … 227 231 <div class="section" id="gateway-installation"> 228 232 <span id="ref-install-gateway"></span><h2>Gateway installation<a class="headerlink" href="#gateway-installation" title="Permalink to this headline">¶</a></h2> 229 <p>In this mode, access to the ECMWF computing and archiving facilities is enabled through an ECaccess gateway server on a local member state server. The ECaccess framework is necessary to interactively submit jobs to the ECMWF batch system and to transfer files between ECMWF and local gateway server.</p> 230 <p>Please see <a class="reference external" href="https://confluence.ecmwf.int/display/ECAC/ECaccess+Home">ECMWF’s instructions on gateway server</a> to establish the gateway server if not already in place. 231 Additionally, to be able to use the Ecaccess file transfer service <strong>ectrans</strong> please also create an association. 232 The easiest way is to visit the ECaccess Member State Gateway website (e.g. msgatway.ecmwf.int) and follow the instructions in the short <a class="reference external" href="https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf">ECaccess Presentation</a> (page 17 ff.). Additional documentation can be found on the <a class="reference external" href="https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans">ECMWF ectrans site</a>.</p> 233 <p>After everything is set up you have to create an <em>ecaccess certificate</em> to be able to send and receive files from and to the ECMWF server. You can do this by using the <code class="docutils literal notranslate"><span class="pre">ecaccess-certificate-create</span></code> command on the gateway server. You will be prompted for your ECMWF member state user name and a password (which will be usually generated by a Token). This certificate has to be re-newed periodically (every 7 days).</p> 234 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ecaccess-certificate-create 235 Please enter your user-id: example_username 236 Your passcode: *** 237 </pre></div> 238 </div> 239 <p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> will be run on an ECMWF server which makes the setup the same as for the <strong>remote mode</strong>. In the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script <a class="reference external" href="Documentation/Input/setup.html">[ref]</a>, select the <code class="docutils literal notranslate"><span class="pre">Makefile.gfortran</span></code> for the <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> Fortran program and the ECMWF server (<em>target</em>) you would like to use. 240 The job script, send to the job queue via the ECaccess software, selects again automatically the correct libraries from the module system. For enableing the file transfer you have to set the <em>ECUID</em>, <em>ECGID</em>, <em>GATEWAY</em> and <em>DESTINATION</em> parameter values.</p> 233 <p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> will be run on an ECMWF server which makes the setup the same as for the <strong>remote mode</strong>. In the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script <a class="reference external" href="Documentation/Input/setup.html">[ref]</a>, select the <code class="docutils literal notranslate"><span class="pre">makefile.gfortran</span></code> for the <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> Fortran program and the ECMWF server (<em>target</em>) you would like to use. 234 The job script, send to the job queue via the ECaccess software, loads the required modules from the module system. For enabling the file transfer via the gateway, you have to set the <em>ECUID</em>, <em>ECGID</em>, <em>GATEWAY</em> and <em>DESTINATION</em> parameter values.</p> 241 235 <div class="literal-block-wrapper docutils container" id="setup-sh"> 242 236 <div class="code-block-caption"><span class="caption-text">‘Example settings for a gateway installation.’</span><a class="headerlink" href="#setup-sh" title="Permalink to this code">¶</a></div> … … 247 241 <span class="c1">#</span> 248 242 <span class="nv">TARGET</span><span class="o">=</span><span class="s1">'ecgate'</span> 249 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">' Makefile.gfortran'</span>243 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'makefile.gfortran'</span> 250 244 <span class="nv">ECUID</span><span class="o">=</span><span class="s1">'uid'</span> 251 245 <span class="nv">ECGID</span><span class="o">=</span><span class="s1">'gid'</span> 252 <span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">' server.example.edu'</span>253 <span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">' example@genericSftp'</span>246 <span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'localserver.tld'</span> 247 <span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'association_name@genericSftp'</span> 254 248 <span class="nv">INSTALLDIR</span><span class="o">=</span>None 255 249 <span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span> … … 262 256 </pre></div> 263 257 </div> 264 <p>to start the installation. You should see the following o utput at the command line.</p>258 <p>to start the installation. You should see the following on standard output.</p> 265 259 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span> 266 260 Create tarball ... … … 269 263 </pre></div> 270 264 </div> 271 <p> The email content should look like this with a “SUCCESS” statement in the last line:</p>265 <p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the email address connectd to the user account on ECMWF servers. The email content should look like this with a “SUCCESS” statement in the last line:</p> 272 266 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp phgrreal.f 273 267 gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp grphreal.f -
Documentation/html/Installation/local.html
r30f7911 rd720895 94 94 <li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> 95 95 <li class="toctree-l2"><a class="reference internal" href="../installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> 96 <li class="toctree-l2"><a class="reference internal" href="../installation.html# environment-requirements">Environment requirements</a></li>96 <li class="toctree-l2"><a class="reference internal" href="../installation.html#dependencies">Dependencies</a></li> 97 97 <li class="toctree-l2 current"><a class="reference internal" href="../installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul class="current"> 98 98 <li class="toctree-l3"><a class="reference internal" href="remote.html">Remote mode installation</a></li> 99 99 <li class="toctree-l3"><a class="reference internal" href="gateway.html">Gateway mode installation</a></li> 100 100 <li class="toctree-l3 current"><a class="current reference internal" href="#">Local mode installation</a><ul> 101 <li class="toctree-l4"><a class="reference internal" href="#local- environment-requirements">Local environment requirements</a></li>101 <li class="toctree-l4"><a class="reference internal" href="#local-mode-dependencies">Local mode - dependencies</a></li> 102 102 <li class="toctree-l4"><a class="reference internal" href="#prepare-local-environment">Prepare local environment</a></li> 103 103 <li class="toctree-l4"><a class="reference internal" href="#test-local-environment">Test local environment</a></li> … … 190 190 <div class="toctree-wrapper compound"> 191 191 </div> 192 <div class="section" id="local-environment-requirements"> 193 <span id="ref-req-local"></span><span id="ref-local-mode"></span><h2>Local environment requirements<a class="headerlink" href="#local-environment-requirements" title="Permalink to this headline">¶</a></h2> 194 <p>For the local access modes <strong>member</strong> and <strong>public</strong> there is no difference in 195 the installation process.</p> 192 <div class="section" id="local-mode-dependencies"> 193 <span id="ref-req-local"></span><span id="ref-local-mode"></span><h2>Local mode - dependencies<a class="headerlink" href="#local-mode-dependencies" title="Permalink to this headline">¶</a></h2> 194 <p>The installation is the same for the access modes <strong>member</strong> and <strong>public</strong>.</p> 196 195 <p>The environment on your local system has to provide these software packages 197 and libraries, since all extraction and preparation is done at the local system:</p>196 and libraries, since the preparation of the extraction and the post-processing is done on the local machine:</p> 198 197 <table border="1" class="docutils"> 199 198 <colgroup> … … 227 226 <div class="section" id="prepare-local-environment"> 228 227 <span id="ref-prep-local"></span><h2>Prepare local environment<a class="headerlink" href="#prepare-local-environment" title="Permalink to this headline">¶</a></h2> 229 <p>The easiest way to install all required packages is to use the package management system of your Linux distribution . To do so, it is necessary to use a user withadmin rights.230 The installation was tested on a <em>Debian GNU/Linux buster /sid</em> and an <em>Ubuntu 18.04 Bionic Beaver</em> system.</p>231 <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Linux Debian or Ubuntu system do</span>228 <p>The easiest way to install all required packages is to use the package management system of your Linux distribution which requires admin rights. 229 The installation was tested on a <em>Debian GNU/Linux buster</em> and an <em>Ubuntu 18.04 Bionic Beaver</em> system.</p> 230 <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Debian or Debian-derived sytem (e. g. Ubuntu) system you may use the following commands (or equivalent commands of your preferred package manager):</span> 232 231 <span class="c1"># (if not already available):</span> 233 apt-get install python3 <span class="o">(</span>usually available on normal Linux systems<span class="o">)</span> 234 apt-get install pip 235 apt-get install gfortran 236 apt-get install fftw3-dev 237 apt-get install libeccodes-dev 238 apt-get install libemos-dev 239 apt-get install python3-eccodes 240 apt-get install genshi 241 apt-get install numpy 242 pip install cdsapi 243 pip install ecmwf-api-client 232 apt-get install python3 <span class="o">(</span>usually already available on GNU/Linux systems<span class="o">)</span> 233 apt-get install python3-eccodes 234 apt-get install python3-genshi 235 apt-get install python3-numpy 236 apt-get install gfortran 237 apt-get install fftw3-dev 238 apt-get install libeccodes-dev 239 apt-get install libemos-dev 240 <span class="c1"># Some of these packages will pull in further packages as dependencies. This is fine, and some are even needed by ``flex_extract''.</span> 241 242 243 <span class="c1"># As currently the CDS and ECMWF API packages are not available as Debian packages, they need to be installed outside of the Debian (Ubuntu etc.) package management system. The recommended way is:</span> 244 apt-get install pip 245 pip install cdsapi 246 pip install ecmwf-api-client 244 247 </pre></div> 245 248 </div> … … 253 256 </div> 254 257 </div> 255 <p>The CDS API (cdsapi) and the ECMWF Web API (ecmwf-api-client) have both to be installed since ERA5 can only be retrieved with the <code class="docutils literal notranslate"><span class="pre">CDS</span> <span class="pre">API</span></code> and all other datasets with the <code class="docutils literal notranslate"><span class="pre">ECMWF</span> <span class="pre">Web</span> <span class="pre">API</span></code>.</p>258 <p>The CDS API (cdsapi) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.</p> 256 259 <div class="admonition note"> 257 260 <p class="first admonition-title">Note</p> 258 261 <p class="last">Since <strong>public users</strong> currently don’t have access to the full <em>ERA5</em> dataset they can skip the installation of the <code class="docutils literal notranslate"><span class="pre">CDS</span> <span class="pre">API</span></code>.</p> 259 262 </div> 260 <p>Both user groups have to provide key ’s with their credentials for the Web API’s in their home directory. Therefore, follow these instructions:</p>263 <p>Both user groups have to provide keys with their credentials for the Web API’s in their home directory. Therefore, follow these instructions:</p> 261 264 <dl class="docutils"> 262 265 <dt>ECMWF Web API:</dt> 263 <dd>Go to <a class="reference external" href="https://confluence.ecmwf.int//display/WEBAPI/Access+MARS">MARS access</a> website and log in with your credentials. Afterwards, on this site in section “Install ECMWF KEY” the key for the ECMWF Web API should be listed. Please follow the instructions in this section under point1 (save the key in a file <cite>.ecmwfapirc</cite> in your home directory).</dd>266 <dd>Go to <a class="reference external" href="https://confluence.ecmwf.int//display/WEBAPI/Access+MARS">MARS access</a> website and log in with your credentials. Afterwards, on this site in section “Install ECMWF KEY” the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file <cite>.ecmwfapirc</cite> in your home directory).</dd> 264 267 <dt>CDS API:</dt> 265 268 <dd>Go to ‘CDS API registration’_ and register there too. Log in at the <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> website and follow the instructions at section “Install the CDS API key” to save your credentials in a <cite>.cdsapirc</cite> file.</dd> … … 268 271 <div class="section" id="test-local-environment"> 269 272 <span id="ref-test-local"></span><h2>Test local environment<a class="headerlink" href="#test-local-environment" title="Permalink to this headline">¶</a></h2> 270 <p>Check the availability of the system packages 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> 271 <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>$ dpkg -s libeccodes-dev <span class="p">|</span> grep Status 272 <span class="c1"># or</span> 273 $ rpm -q libeccodes-dev 274 </pre></div> 275 </div> 276 <p>Afterwards, check the availability of the python packages by typing <code class="docutils literal notranslate"><span class="pre">python3</span></code> in 277 a terminal window and run the <code class="docutils literal notranslate"><span class="pre">import</span></code> commands in the python shell. If there are no error messages, you succeeded in setting up the environment.</p> 273 <p>Check the availability of the python packages by typing <code class="docutils literal notranslate"><span class="pre">python3</span></code> in a terminal window and run the <code class="docutils literal notranslate"><span class="pre">import</span></code> commands in the python shell. If there are no error messages, you succeeded in setting up the environment.</p> 278 274 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span> 279 275 <span class="kn">import</span> <span class="nn">eccodes</span> … … 286 282 <div class="section" id="test-the-web-api-s"> 287 283 <h3>Test the Web API’s<a class="headerlink" href="#test-the-web-api-s" title="Permalink to this headline">¶</a></h3> 288 <p>You can start very simple test retrievals for both Web API ’s to be sure that everything works. This is recommended to minimize the range of possible errors using <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> later on.</p>284 <p>You can start very simple test retrievals for both Web APIs to be sure that everything works. This is recommended to minimise the range of possible errors using <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> later on.</p> 289 285 <div class="section" id="ecmwf-web-api"> 290 286 <h4>ECMWF Web API<a class="headerlink" href="#ecmwf-web-api" title="Permalink to this headline">¶</a></h4> … … 295 291 </colgroup> 296 292 <tbody valign="top"> 297 <tr class="row-odd"><td>Please use this piece of python code for <strong>Member user</strong>:</td>298 <td>Please use this piece of python code for <strong>Public user</strong>:</td>293 <tr class="row-odd"><td>Please use this piece of Python code for <strong>Member user</strong>:</td> 294 <td>Please use this piece of Python code for <strong>Public user</strong>:</td> 299 295 </tr> 300 296 <tr class="row-even"><td><div class="first last highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ecmwfapi</span> <span class="kn">import</span> <span class="n">ECMWFService</span> … … 344 340 <div class="section" id="cds-api"> 345 341 <h4>CDS API<a class="headerlink" href="#cds-api" title="Permalink to this headline">¶</a></h4> 346 <p> Since ERA5 extraction with CDS API might take some time due to the very high number of requests, you can start by retrieving some online stored pressure levels (not from MARS). This is usually much faster and gives a quick result to find out if the web API works:</p>347 <p>Please use this piece of python code to retrieve a small sample of <em>ERA5</em> pressure levels:</p>342 <p>Extraction of ERA5 data via CDS API might take time as currently there is a high demand for ERA5 data. Therefore, as a simple test for the API just retrieve pressure-level data (even if that is NOT what we need for FLEXPART), as they are stored on disk and don’t need to be retrieved from MARS (which is the time-consuming action):</p> 343 <p>Please use this piece of Python code to retrieve a small sample of <em>ERA5</em> pressure levels:</p> 348 344 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span> 349 345 … … 364 360 </pre></div> 365 361 </div> 366 <p>Afterwards, when you know that the CDS API generally works, you can try to extract some 367 data from the MARS archive. From the latest experience we know that this can take a while.</p> 368 <p>Please use this piece of python code to retrieve a small <em>ERA5</em> data sample as a <strong>member user</strong>! The <strong>public user</strong> doesn’t have access to the full <em>ERA5</em> dataset!</p> 362 <p>If you know that your CDS API works, you can try to extract some data from MARS.</p> 363 <p>Please use this piece of Python code to retrieve a small <em>ERA5</em> data sample as a <strong>member-state user</strong>! The <strong>Public user</strong> do not have access to the full <em>ERA5</em> dataset!</p> 369 364 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span> 370 365 … … 394 389 <div class="section" id="local-installation"> 395 390 <span id="ref-install-local"></span><h2>Local installation<a class="headerlink" href="#local-installation" title="Permalink to this headline">¶</a></h2> 396 <p>First prepare the Fortran <code class="docutils literal notranslate"><span class="pre">Makefile</span></code> for your environment and set it 397 in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script. (See section <span class="xref std std-ref">ref-convert</span> for information on 398 the Fortran program.) 399 <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> has already two <code class="docutils literal notranslate"><span class="pre">Makefiles</span></code> prepared for te <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> and 400 the <code class="docutils literal notranslate"><span class="pre">ifort</span></code> compiler:</p> 391 <p>First prepare the Fortran <code class="docutils literal notranslate"><span class="pre">makefile</span></code> for your environment and set it in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script. (See section <span class="xref std std-ref">ref-convert</span> for information on the Fortran program.) 392 <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> comes with two <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> prepared for the <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> and 393 the <code class="docutils literal notranslate"><span class="pre">ifort</span></code> compiler. The <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> version assumes that <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> and <code class="docutils literal notranslate"><span class="pre">emoslib</span></code> are installed as distribution packages.</p> 401 394 <blockquote> 402 395 <div><ul class="simple"> 403 <li> Makefile.local.gfortran</li>404 <li> Makefile.local.ifort</li>396 <li>makefile.local.gfortran</li> 397 <li>makefile.local.ifort</li> 405 398 </ul> 406 399 </div></blockquote> 407 <p>They can be found in the path <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/source/fortran</span></code>, where400 <p>They can be found at <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Fortran</span></code>, where 408 401 <code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted with the current version number.</p> 409 402 <div class="admonition caution"> 410 403 <p class="first admonition-title">Caution</p> 411 404 <p class="last">It is necessary to adapt <strong>ECCODES_INCLUDE_DIR</strong> and <strong>ECCODES_LIB</strong> in these 412 <code class="docutils literal notranslate"><span class="pre"> Makefiles</span></code>.</p>405 <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> if other than standard paths are used.</p> 413 406 </div> 414 407 <p>So starting from the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, 415 go to the <code class="docutils literal notranslate"><span class="pre">Fortran</span></code> source directory and open the <code class="docutils literal notranslate"><span class="pre"> Makefile</span></code> of your408 go to the <code class="docutils literal notranslate"><span class="pre">Fortran</span></code> source directory and open the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> of your 416 409 choice to modify with an editor of your choice. We use the <code class="docutils literal notranslate"><span class="pre">nedit</span></code> in this case.</p> 417 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> flex_extract_vX.X/ source/fortran418 nedit Makefile.local.gfortran419 </pre></div> 420 </div> 421 <p>Edit the path es to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library on your local machine.</p>410 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> flex_extract_vX.X/Source/Fortran 411 nedit makefile.local.gfortran 412 </pre></div> 413 </div> 414 <p>Edit the paths to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library on your local machine.</p> 422 415 <div class="admonition caution"> 423 416 <p class="first admonition-title">Caution</p> … … 432 425 <p class="last">to find out the path to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library.</p> 433 426 </div> 434 <p>Substitute these paths in the <code class="docutils literal notranslate"><span class="pre"> Makefile</span></code> for parameters <strong>ECCODES_INCLUDE_DIR</strong>427 <p>Substitute these paths in the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> for parameters <strong>ECCODES_INCLUDE_DIR</strong> 435 428 and <strong>ECCODES_LIB</strong> and save it.</p> 436 429 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># these are the paths on a current Debian 10 Testing system (May 2019)</span> … … 440 433 </div> 441 434 <p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> will be compiled during the 442 installation process to get an executable. Therefore the <code class="docutils literal notranslate"><span class="pre">Makefile</span></code> 443 has to be set in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script.</p> 435 installation process.Therefore the name of the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> to be used needs to be given in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.</p> 444 436 <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 445 437 and adapt the installation parameters in the section labelled with … … 454 446 <span class="c1">#</span> 455 447 <span class="nv">TARGET</span><span class="o">=</span><span class="s1">'local'</span> 456 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">' Makefile.local.gfortran'</span>448 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'makefile.local.gfortran'</span> 457 449 <span class="nv">ECUID</span><span class="o">=</span>None 458 450 <span class="nv">ECGID</span><span class="o">=</span>None … … 470 462 </pre></div> 471 463 </div> 472 <p>to start the installation. You should see the following output at the command line.</p>464 <p>to start the installation. You should see the following standard output.</p> 473 465 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span> 474 466 WARNING: installdir has not been specified -
Documentation/html/Installation/remote.html
r30f7911 rd720895 94 94 <li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> 95 95 <li class="toctree-l2"><a class="reference internal" href="../installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> 96 <li class="toctree-l2"><a class="reference internal" href="../installation.html# environment-requirements">Environment requirements</a></li>96 <li class="toctree-l2"><a class="reference internal" href="../installation.html#dependencies">Dependencies</a></li> 97 97 <li class="toctree-l2 current"><a class="reference internal" href="../installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul class="current"> 98 98 <li class="toctree-l3 current"><a class="current reference internal" href="#">Remote mode installation</a><ul> 99 <li class="toctree-l4"><a class="reference internal" href="#remote- environment-requirements">Remote environment requirements</a></li>99 <li class="toctree-l4"><a class="reference internal" href="#remote-mode-dependencies">Remote mode - dependencies</a></li> 100 100 <li class="toctree-l4"><a class="reference internal" href="#prepare-remote-environment">Prepare remote environment</a></li> 101 101 <li class="toctree-l4"><a class="reference internal" href="#remote-installation">Remote installation</a></li> … … 189 189 <div class="toctree-wrapper compound"> 190 190 </div> 191 <div class="section" id="remote-environment-requirements"> 192 <span id="ref-req-remote"></span><span id="ref-remote-mode"></span><h2>Remote environment requirements<a class="headerlink" href="#remote-environment-requirements" title="Permalink to this headline">¶</a></h2> 193 <p>The environment for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> on ECMWF servers has to provide these 194 software packages and libraries:</p> 191 <div class="section" id="remote-mode-dependencies"> 192 <span id="ref-req-remote"></span><span id="ref-remote-mode"></span><h2>Remote mode - dependencies<a class="headerlink" href="#remote-mode-dependencies" title="Permalink to this headline">¶</a></h2> 193 <p>The following software is required, and already available at the ECMWF servers:</p> 195 194 <table border="1" class="docutils"> 196 195 <colgroup> … … 222 221 <div class="section" id="prepare-remote-environment"> 223 222 <span id="ref-prep-remote"></span><h2>Prepare remote environment<a class="headerlink" href="#prepare-remote-environment" title="Permalink to this headline">¶</a></h2> 224 <p>The environment on the ECMWF server (such as <em>ecgate</em> or <em>cca</em>) is already 225 prepared. ECMWF server provide all libraries via a module system which is 226 going to be selected by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> automatically.</p> 223 <p>ECMWF servers provide all libraries via a module system. Loading the required modules is already built into <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> and no user action is needed.</p> 227 224 </div> 228 225 <div class="section" id="remote-installation"> 229 226 <span id="ref-install-remote"></span><h2>Remote installation<a class="headerlink" href="#remote-installation" title="Permalink to this headline">¶</a></h2> 230 <p>First, log in on one of the ECMWF Linux server, such as <em>ecgate</em> or <em>cca/ccb</em>.227 <p>First, log in on one of the ECMWF servers, such as <em>ecgate</em> or <em>cca/ccb</em>. 231 228 Substitute <em><ecuid></em> with your ECMWF user name:</p> 232 229 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ssh -X <ecuid>@ecaccess.ecmwf.int … … 251 248 *************************************************************** 252 249 253 <ecuid>@ 131.130.157.5's password: ***250 <ecuid>@<ipname/address>'s password: *** 254 251 Select hostname (ecgate, cca, ccb) [ecgate]: ecgate 255 252 … … 257 254 </pre></div> 258 255 </div> 259 <p>Then, copy the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> tar ball (from section <a class="reference internal" href="../installation.html#ref-download"><span class="std std-ref">Download flex_extract</span></a>) 260 to the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory of the ECMWF Linux server via <code class="docutils literal notranslate"><span class="pre">scp</span></code>. 261 Substitute the <em><localuser></em> and <em><server.edu></em> placeholders with your credentials. 256 <p>Substitute the <em><localuser></em> and <em><localmachine.tld></em> placeholders with your local user name and the IP name or address of your local machine. 262 257 Untar the file and change into the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory.</p> 263 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp <localuser>@< server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz <span class="nv">$HOME</span>/258 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp <localuser>@<localmachine.tld>:</path/to/tarfile/>flex_extract_vX.X.tar.gz <span class="nv">$HOME</span>/ 264 259 <span class="nb">cd</span> <span class="nv">$HOME</span> 265 260 tar xvf flex_extract_vX.X.tar.gz … … 267 262 </pre></div> 268 263 </div> 269 <p>On these ECMWF servers, it is not necessary to prepare the environment or the 270 <code class="docutils literal notranslate"><span class="pre">Makefile</span></code> for the Fortran program (<code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code>) as described above. 271 All third party libraries are available from a module system. The <code class="docutils literal notranslate"><span class="pre">Makefile</span></code> 272 is optimized for ECMWF servers and the compilation 273 script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code>, which will be submitted by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> to the 274 batch job queue at ECMWF, does load all relevant modules from the ECMWF’s module system.</p> 275 <p>So there is just the need to execute the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script from the 276 <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory for installation. 264 <p>Execute the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>’s root directory. 277 265 Before executing it, it is necessary to adapt some parameters from <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> 278 266 described in <span class="xref std std-doc">Documentation/Input/setup</span>.</p> 279 <p>Open <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> with your editorand adapt the values:</p>267 <p>Open <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> with your preferred editor (e.g., <a href="#id1"><span class="problematic" id="id2">``</span></a>nano’‘) and adapt the values:</p> 280 268 <table border="1" class="docutils"> 281 269 <colgroup> … … 284 272 </colgroup> 285 273 <tbody valign="top"> 286 <tr class="row-odd"><td> Take this for target = <strong>ectrans</strong></td>287 <td> Take this for target = <strong>cca</strong></td>274 <tr class="row-odd"><td>Use this for target = <strong>ectrans</strong></td> 275 <td>Use this for target = <strong>cca</strong></td> 288 276 </tr> 289 277 <tr class="row-even"><td><div class="first last highlight-bash notranslate"><div class="highlight"><pre><span></span>... … … 329 317 </table> 330 318 <p><span class="underline">Please substitute the values of ECUID and ECGID 331 with your own credentials and settings.</span></p>319 with your own ones (look at any of your files with ``ls -l’’ to see uid and gid).</span></p> 332 320 <div class="admonition note"> 333 321 <p class="first admonition-title">Note</p> 334 <p class="last">If a local gateway server is available the transfer of files could be done 335 via the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. Therefore a valid <em>GATEWAY</em> and <em>DESTINATION</em> 336 have to be present and should be set in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file.</p> 322 <p class="last">If a local gateway server is available, files can be transferred with <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. In that case, a valid <em>GATEWAY</em> and <em>DESTINATION</em> have to be present in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file (even if not used, the lines must not be deleted).</p> 337 323 </div> 338 324 <p>Afterwards, type:</p> … … 341 327 </pre></div> 342 328 </div> 343 <p>to start the installation. You should see the following o utput at the command line.</p>329 <p>to start the installation. You should see the following on standard output.</p> 344 330 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span> 345 331 Create tarball ... … … 348 334 </pre></div> 349 335 </div> 350 <p> The email content should look like this with a “SUCCESS” statement in the last line:</p>336 <p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the email address connectd to the user account on ECMWF servers. The email content should look like this with a “SUCCESS” statement in the last line:</p> 351 337 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp phgrreal.f 352 338 gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp grphreal.f -
Documentation/html/_modules/install.html
r30f7911 rd720895 537 537 <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">_config</span><span class="o">.</span><span class="n">PATH_REL_FORTRAN_SRC</span><span class="p">,</span> <span class="s1">'*.h'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span> 538 538 <span class="n">makefiles</span> <span class="o">=</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">relpath</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">ecd</span><span class="p">)</span> 539 <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">_config</span><span class="o">.</span><span class="n">PATH_REL_FORTRAN_SRC</span><span class="p">,</span> <span class="s1">' Makefile*'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span>539 <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">_config</span><span class="o">.</span><span class="n">PATH_REL_FORTRAN_SRC</span><span class="p">,</span> <span class="s1">'makefile*'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span> 540 540 <span class="n">jobdir</span> <span class="o">=</span> <span class="p">[</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_REL_JOBSCRIPTS</span><span class="p">]</span> 541 541 -
Documentation/html/_sources/Installation/gateway.rst.txt
r30f7911 rd720895 8 8 .. toctree:: 9 9 :hidden: 10 :maxdepth: 310 :maxdepth: 2 11 11 12 12 .. _Python 3: https://docs.python.org/3/ … … 43 43 .. _ref-req-gateway: 44 44 45 Gateway environment requirements46 =========================== =====45 Gateway mode - dependencies 46 =========================== 47 47 48 The environment on your local system has to provide these software packages 49 and libraries, since ``flex_extract`` does only prepare the job script and send 50 it to the ECMWF servers: 51 52 * `Python3`_ or `Anaconda Python3`_ 48 * `Python3`_ 53 49 * `numpy`_ 54 50 * `genshi`_ … … 60 56 =========================== 61 57 62 The easiest way to install all required packages is to use the package management system of your Linux distribution. To do so, it is necessary to use a user with admin rights. 63 The installation was tested on a *GNU/Linux Debian buster* and an *Ubuntu 18.04 Bionic Beaver* system. 58 In this mode, access to the ECMWF computing and archiving facilities is enabled through an ECaccess gateway server on a local member state server. The ECaccess framework is necessary to interactively submit jobs to the ECMWF batch system and to transfer files between ECMWF and local gateway server. 59 60 Please see `ECMWF's instructions on gateway server`_ to establish the gateway server if not already in place. Additionally, to be able to use the ECaccess file transfer service **ectrans** it is necessary to create a so-called association. The easiest way is to visit the ECaccess Member State Gateway website (e.g. https://msgatway.ecmwf.int) and follow the instructions in the short `ECaccess Presentation`_ (page 17 ff.). Additional documentation can be found on the `ECMWF ectrans site`_. 61 62 The next step is to create an *ecaccess certificate* to be able to send and receive files from and to the ECMWF server. You can do this by using the ``ecaccess-certificate-create`` command on the gateway server. You will be prompted for your ECMWF member state user name and a password (generated by a token). This certificate has to be renewed periodically (every 7 days). 63 64 65 .. code-block:: bash 66 67 $ ecaccess-certificate-create 68 Please enter your user-id: example_username 69 Your passcode: *** 70 71 72 73 The easiest way to install all required packages is to use the package management system of your Linux distribution which required admin rights. 74 The installation was tested under *GNU/Linux Debian buster* and *Ubuntu 18.04 Bionic Beaver*. 64 75 65 76 .. code-block:: sh 66 77 67 # On a Linux Debian or Ubuntu system do 78 79 # On a Debian or Debian-derived sytem (e. g. Ubuntu) system you may use the following commands (or equivalent commands of your preferred package manager): 68 80 # (if not already available): 69 81 apt-get install python3 70 apt-get install pip 71 apt-get install genshi 72 apt-get install numpy 73 82 apt-get install python3-genshi 83 apt-get install python3-numpy 84 74 85 75 86 .. _ref-test-gateway: … … 77 88 Test gateway environment 78 89 ======================== 79 90 80 91 Check the availability of the python packages by typing ``python3`` in 81 92 a terminal window and run the ``import`` commands in the python shell. 82 93 If there are no error messages, you succeeded in setting up the environment. 83 94 84 95 .. code-block:: python 85 96 … … 95 106 ==================== 96 107 97 In this mode, access to the ECMWF computing and archiving facilities is enabled through an ECaccess gateway server on a local member state server. The ECaccess framework is necessary to interactively submit jobs to the ECMWF batch system and to transfer files between ECMWF and local gateway server. 98 99 Please see `ECMWF's instructions on gateway server`_ to establish the gateway server if not already in place. 100 Additionally, to be able to use the Ecaccess file transfer service **ectrans** please also create an association. 101 The easiest way is to visit the ECaccess Member State Gateway website (e.g. msgatway.ecmwf.int) and follow the instructions in the short `ECaccess Presentation`_ (page 17 ff.). Additional documentation can be found on the `ECMWF ectrans site`_. 102 103 After everything is set up you have to create an *ecaccess certificate* to be able to send and receive files from and to the ECMWF server. You can do this by using the ``ecaccess-certificate-create`` command on the gateway server. You will be prompted for your ECMWF member state user name and a password (which will be usually generated by a Token). This certificate has to be re-newed periodically (every 7 days). 104 105 .. code-block:: bash 108 ``Flex_extract`` will be run on an ECMWF server which makes the setup the same as for the **remote mode**. In the ``setup.sh`` script `[ref] <Documentation/Input/setup.html>`_, select the ``makefile.gfortran`` for the ``CONVERT2`` Fortran program and the ECMWF server (*target*) you would like to use. 109 The job script, send to the job queue via the ECaccess software, loads the required modules from the module system. For enabling the file transfer via the gateway, you have to set the *ECUID*, *ECGID*, *GATEWAY* and *DESTINATION* parameter values. 106 110 107 $ ecaccess-certificate-create108 Please enter your user-id: example_username109 Your passcode: ***110 111 ``Flex_extract`` will be run on an ECMWF server which makes the setup the same as for the **remote mode**. In the ``setup.sh`` script `[ref] <Documentation/Input/setup.html>`_, select the ``Makefile.gfortran`` for the ``CONVERT2`` Fortran program and the ECMWF server (*target*) you would like to use.112 The job script, send to the job queue via the ECaccess software, selects again automatically the correct libraries from the module system. For enableing the file transfer you have to set the *ECUID*, *ECGID*, *GATEWAY* and *DESTINATION* parameter values.113 114 111 115 112 .. code-block:: bash … … 123 120 # 124 121 TARGET='ecgate' 125 MAKEFILE=' Makefile.gfortran'122 MAKEFILE='makefile.gfortran' 126 123 ECUID='uid' 127 124 ECGID='gid' 128 GATEWAY=' server.example.edu'129 DESTINATION=' example@genericSftp'125 GATEWAY='localserver.tld' 126 DESTINATION='association_name@genericSftp' 130 127 INSTALLDIR=None 131 128 JOB_TEMPLATE='job.template' … … 139 136 $ ./setup.sh 140 137 141 to start the installation. You should see the following o utput at the command line.138 to start the installation. You should see the following on standard output. 142 139 143 140 … … 149 146 You should get an email with subject "flexcompile" within the next few minutes! 150 147 151 152 The email content should look like this with a "SUCCESS" statement in the last line: 148 ``Flex_extract`` uses the email address connectd to the user account on ECMWF servers. The email content should look like this with a "SUCCESS" statement in the last line: 153 149 154 150 .. code-block:: bash -
Documentation/html/_sources/Installation/local.rst.txt
r30f7911 rd720895 46 46 .. _ref-req-local: 47 47 48 Local environment requirements 49 ============================== 50 51 For the local access modes **member** and **public** there is no difference in 52 the installation process. 48 Local mode - dependencies 49 ========================= 50 51 The installation is the same for the access modes **member** and **public**. 53 52 54 53 The environment on your local system has to provide these software packages 55 and libraries, since all extraction and preparation is done at the local system:54 and libraries, since the preparation of the extraction and the post-processing is done on the local machine: 56 55 57 56 +------------------------------------------------+-----------------+ … … 72 71 ========================= 73 72 74 The easiest way to install all required packages is to use the package management system of your Linux distribution . To do so, it is necessary to use a user withadmin rights.75 The installation was tested on a *Debian GNU/Linux buster /sid* and an *Ubuntu 18.04 Bionic Beaver* system.73 The easiest way to install all required packages is to use the package management system of your Linux distribution which requires admin rights. 74 The installation was tested on a *Debian GNU/Linux buster* and an *Ubuntu 18.04 Bionic Beaver* system. 76 75 77 76 .. code-block:: sh 78 77 79 # On a Linux Debian or Ubuntu system do 80 # (if not already available): 81 apt-get install python3 (usually available on normal Linux systems) 82 apt-get install pip 78 # On a Debian or Debian-derived sytem (e. g. Ubuntu) system you may use the following commands (or equivalent commands of your preferred package manager): 79 # (if not already available): 80 apt-get install python3 (usually already available on GNU/Linux systems) 81 apt-get install python3-eccodes 82 apt-get install python3-genshi 83 apt-get install python3-numpy 83 84 apt-get install gfortran 84 85 apt-get install fftw3-dev 85 86 apt-get install libeccodes-dev 86 87 apt-get install libemos-dev 87 apt-get install python3-eccodes 88 apt-get install genshi 89 apt-get install numpy 88 # Some of these packages will pull in further packages as dependencies. This is fine, and some are even needed by ``flex_extract''. 89 90 91 # As currently the CDS and ECMWF API packages are not available as Debian packages, they need to be installed outside of the Debian (Ubuntu etc.) package management system. The recommended way is: 92 apt-get install pip 90 93 pip install cdsapi 91 94 pip install ecmwf-api-client 92 95 93 96 .. note:: 94 97 … … 99 102 .. code-block:: bash 100 103 101 conda install conda-forge::python-eccodes 102 103 104 The CDS API (cdsapi) and the ECMWF Web API (ecmwf-api-client) have both to be installed since ERA5 can only be retrieved with the ``CDS API`` and all other datasets with the ``ECMWF Web API``. 104 conda install conda-forge::python-eccodes 105 106 The CDS API (cdsapi) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets. 107 108 .. note:: 109 110 Since **public users** currently don't have access to the full *ERA5* dataset they can skip the installation of the ``CDS API``. 111 112 Both user groups have to provide keys with their credentials for the Web API's in their home directory. Therefore, follow these instructions: 105 113 106 .. note::107 108 Since **public users** currently don't have access to the full *ERA5* dataset they can skip the installation of the ``CDS API``.109 110 Both user groups have to provide key's with their credentials for the Web API's in their home directory. Therefore, follow these instructions:111 112 114 ECMWF Web API: 113 Go to `MARS access`_ website and log in with your credentials. Afterwards, on this site in section "Install ECMWF KEY" the key for the ECMWF Web API should be listed. Please follow the instructions in this section under point1 (save the key in a file `.ecmwfapirc` in your home directory).115 Go to `MARS access`_ website and log in with your credentials. Afterwards, on this site in section "Install ECMWF KEY" the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file `.ecmwfapirc` in your home directory). 114 116 115 117 CDS API: 116 118 Go to 'CDS API registration'_ and register there too. Log in at the `cdsapi`_ website and follow the instructions at section "Install the CDS API key" to save your credentials in a `.cdsapirc` file. 117 118 119 120 119 121 .. _ref-test-local: 120 122 … … 122 124 ====================== 123 125 124 Check the availability of the system packages with ``dpkg -s <package-name> | grep Status`` or ``rpm -q <package_name>``, depending on your system. For example: 125 126 .. code-block:: sh 127 128 $ dpkg -s libeccodes-dev | grep Status 129 # or 130 $ rpm -q libeccodes-dev 131 132 Afterwards, check the availability of the python packages by typing ``python3`` in 133 a terminal window and run the ``import`` commands in the python shell. If there are no error messages, you succeeded in setting up the environment. 126 Check the availability of the python packages by typing ``python3`` in a terminal window and run the ``import`` commands in the python shell. If there are no error messages, you succeeded in setting up the environment. 134 127 135 128 .. code-block:: python … … 147 140 ------------------ 148 141 149 You can start very simple test retrievals for both Web API's to be sure that everything works. This is recommended to minimize the range of possible errors using ``flex_extract`` later on. 142 You can start very simple test retrievals for both Web APIs to be sure that everything works. This is recommended to minimise the range of possible errors using ``flex_extract`` later on. 143 150 144 151 145 ECMWF Web API … … 154 148 155 149 +----------------------------------------------------------+----------------------------------------------------------+ 156 |Please use this piece of python code for **Member user**: |Please use this piece of python code for **Public user**: |150 |Please use this piece of Python code for **Member user**: |Please use this piece of Python code for **Public user**: | 157 151 +----------------------------------------------------------+----------------------------------------------------------+ 158 152 |.. code-block:: python |.. code-block:: python | … … 182 176 ^^^^^^^ 183 177 184 Since ERA5 extraction with CDS API might take some time due to the very high number of requests, you can start by retrieving some online stored pressure levels (not from MARS). This is usually much faster and gives a quick result to find out if the web API works: 185 186 Please use this piece of python code to retrieve a small sample of *ERA5* pressure levels:178 Extraction of ERA5 data via CDS API might take time as currently there is a high demand for ERA5 data. Therefore, as a simple test for the API just retrieve pressure-level data (even if that is NOT what we need for FLEXPART), as they are stored on disk and don't need to be retrieved from MARS (which is the time-consuming action): 179 180 Please use this piece of Python code to retrieve a small sample of *ERA5* pressure levels: 187 181 188 182 .. code-block:: python … … 205 199 "download_cdsapi.grib") 206 200 207 208 Afterwards, when you know that the CDS API generally works, you can try to extract some 209 data from the MARS archive. From the latest experience we know that this can take a while. 210 211 .. **Member user** 212 213 Please use this piece of python code to retrieve a small *ERA5* data sample as a **member user**! The **public user** doesn't have access to the full *ERA5* dataset! 201 202 If you know that your CDS API works, you can try to extract some data from MARS. 203 204 .. **Member-state user** 205 206 Please use this piece of Python code to retrieve a small *ERA5* data sample as a **member-state user**! The **Public user** do not have access to the full *ERA5* dataset! 214 207 215 208 .. code-block:: python … … 241 234 242 235 **Public user** 243 Please use this piece of python code:236 Please use this piece of Python code: 244 237 245 238 .. code-block:: python … … 277 270 ================== 278 271 279 First prepare the Fortran ``Makefile`` for your environment and set it 280 in the ``setup.sh`` script. (See section :ref:`ref-convert` for information on 281 the Fortran program.) 282 ``flex_extract`` has already two ``Makefiles`` prepared for te ``gfortran`` and 283 the ``ifort`` compiler: 284 285 * Makefile.local.gfortran 286 * Makefile.local.ifort 287 288 They can be found in the path ``flex_extract_vX.X/source/fortran``, where 272 First prepare the Fortran ``makefile`` for your environment and set it in the ``setup.sh`` script. (See section :ref:`ref-convert` for information on the Fortran program.) 273 ``flex_extract`` comes with two ``makefiles`` prepared for the ``gfortran`` and 274 the ``ifort`` compiler. The ``gfortran`` version assumes that ``eccodes`` and ``emoslib`` are installed as distribution packages. 275 276 * makefile.local.gfortran 277 * makefile.local.ifort 278 279 They can be found at ``flex_extract_vX.X/Source/Fortran``, where 289 280 ``vX.X`` should be substituted with the current version number. 290 281 291 282 .. caution:: 292 283 It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these 293 ``Makefiles``. 294 284 ``makefiles`` if other than standard paths are used. 295 285 296 286 So starting from the root directory of ``flex_extract``, 297 go to the ``Fortran`` source directory and open the `` Makefile`` of your287 go to the ``Fortran`` source directory and open the ``makefile`` of your 298 288 choice to modify with an editor of your choice. We use the ``nedit`` in this case. 299 289 300 290 .. code-block:: bash 301 291 302 cd flex_extract_vX.X/source/fortran 303 nedit Makefile.local.gfortran 304 305 Edit the pathes to the ``eccodes`` library on your local machine. 292 cd flex_extract_vX.X/Source/Fortran 293 nedit makefile.local.gfortran 294 295 Edit the paths to the ``eccodes`` library on your local machine. 296 306 297 307 298 .. caution:: … … 318 309 to find out the path to the ``eccodes`` library. 319 310 320 Substitute these paths in the `` Makefile`` for parameters **ECCODES_INCLUDE_DIR**311 Substitute these paths in the ``makefile`` for parameters **ECCODES_INCLUDE_DIR** 321 312 and **ECCODES_LIB** and save it. 322 313 … … 329 320 330 321 The Fortran program called ``CONVERT2`` will be compiled during the 331 installation process to get an executable. Therefore the ``Makefile`` 332 has to be set in the ``setup.sh`` script. 322 installation process.Therefore the name of the ``makefile`` to be used needs to be given in ``setup.sh``. 333 323 334 324 In the root directory of ``flex_extract``, open the ``setup.sh`` script … … 348 338 # 349 339 TARGET='local' 350 MAKEFILE=' Makefile.local.gfortran'340 MAKEFILE='makefile.local.gfortran' 351 341 ECUID=None 352 342 ECGID=None … … 365 355 $ ./setup.sh 366 356 367 to start the installation. You should see the following output at the command line.357 to start the installation. You should see the following standard output. 368 358 369 359 -
Documentation/html/_sources/Installation/remote.rst.txt
r30f7911 rd720895 42 42 .. _ref-req-remote: 43 43 44 Remote environment requirements45 ========================== =====44 Remote mode - dependencies 45 ========================== 46 46 47 The environment for ``flex_extract`` on ECMWF servers has to provide these 48 software packages and libraries: 47 The following software is required, and already available at the ECMWF servers: 49 48 50 49 +---------------------------+-----------------+ … … 63 62 ========================== 64 63 65 The environment on the ECMWF server (such as *ecgate* or *cca*) is already 66 prepared. ECMWF server provide all libraries via a module system which is 67 going to be selected by ``flex_extract`` automatically. 64 ECMWF servers provide all libraries via a module system. Loading the required modules is already built into ``flex_extract`` and no user action is needed. 68 65 69 66 … … 73 70 =================== 74 71 75 First, log in on one of the ECMWF Linux server, such as *ecgate* or *cca/ccb*.72 First, log in on one of the ECMWF servers, such as *ecgate* or *cca/ccb*. 76 73 Substitute *<ecuid>* with your ECMWF user name: 77 74 … … 101 98 *************************************************************** 102 99 103 <ecuid>@ 131.130.157.5's password: ***100 <ecuid>@<ipname/address>'s password: *** 104 101 Select hostname (ecgate, cca, ccb) [ecgate]: ecgate 105 102 106 103 [<ecuid>@ecgb11 ~]$ 107 104 105 Substitute the *<localuser>* and *<localmachine.tld>* placeholders with your local user name and the IP name or address of your local machine. 106 Untar the file and change into the ``flex_extract`` root directory. 108 107 109 Then, copy the ``flex_extract`` tar ball (from section :ref:`ref-download`)110 to the ``$HOME`` directory of the ECMWF Linux server via ``scp``.111 Substitute the *<localuser>* and *<server.edu>* placeholders with your credentials.112 Untar the file and change into the ``flex_extract`` root directory.113 114 108 .. code-block:: bash 115 109 116 scp <localuser>@< server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz $HOME/110 scp <localuser>@<localmachine.tld>:</path/to/tarfile/>flex_extract_vX.X.tar.gz $HOME/ 117 111 cd $HOME 118 112 tar xvf flex_extract_vX.X.tar.gz … … 120 114 121 115 122 On these ECMWF servers, it is not necessary to prepare the environment or the 123 ``Makefile`` for the Fortran program (``CONVERT2``) as described above. 124 All third party libraries are available from a module system. The ``Makefile`` 125 is optimized for ECMWF servers and the compilation 126 script ``compilejob.ksh``, which will be submitted by ``flex_extract`` to the 127 batch job queue at ECMWF, does load all relevant modules from the ECMWF's module system. 128 129 So there is just the need to execute the ``setup.sh`` script from the 130 ``flex_extract`` root directory for installation. 116 117 Execute the ``setup.sh`` script from the ``flex_extract``'s root directory. 131 118 Before executing it, it is necessary to adapt some parameters from ``setup.sh`` 132 119 described in :doc:`Documentation/Input/setup`. 133 120 134 Open ``setup.sh`` with your editorand adapt the values:135 121 Open ``setup.sh`` with your preferred editor (e.g., ``nano'') and adapt the values: 122 136 123 +----------------------------------------------+----------------------------------------------+ 137 | Take this for target = **ectrans** | Take this for target = **cca** |124 | Use this for target = **ectrans** | Use this for target = **cca** | 138 125 +----------------------------------------------+----------------------------------------------+ 139 126 | .. code-block:: bash | .. code-block:: bash | … … 158 145 159 146 :underline:`Please substitute the values of ECUID and ECGID 160 with your own credentials and settings.`147 with your own ones (look at any of your files with ``ls -l'' to see uid and gid).` 161 148 162 149 .. note:: 163 150 164 If a local gateway server is available the transfer of files could be done 165 via the ``ECaccess`` commands. Therefore a valid *GATEWAY* and *DESTINATION* 166 have to be present and should be set in the ``setup.sh`` file. 167 151 If a local gateway server is available, files can be transferred with ``ECaccess`` commands. In that case, a valid *GATEWAY* and *DESTINATION* have to be present in the ``setup.sh`` file (even if not used, the lines must not be deleted). 168 152 169 153 Afterwards, type: … … 174 158 ./setup.sh 175 159 176 to start the installation. You should see the following o utput at the command line.160 to start the installation. You should see the following on standard output. 177 161 178 162 … … 185 169 186 170 187 The email content should look like this with a "SUCCESS" statement in the last line:171 ``Flex_extract`` uses the email address connectd to the user account on ECMWF servers. The email content should look like this with a "SUCCESS" statement in the last line: 188 172 189 173 .. code-block:: bash -
Documentation/html/_sources/installation.rst.txt
r30f7911 rd720895 132 132 .. _ref-requirements: 133 133 134 Environment requirements135 ============ ============134 Dependencies 135 ============ 136 136 137 137 The software required for running ``flex_extract`` depends on the :doc:`Documentation/Overview/app_modes` and therefore is described in the respective specific installation sections. 138 139 138 140 139 Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries. 141 140 We tested ``flex_extract`` 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 ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.). 141 142 Before installing the system packages check the availability with ``dpkg -s <package-name> | grep Status`` or ``rpm -q <package_name>``, depending on your system. For example: 143 144 .. code-block:: sh 145 146 $ dpkg -s libeccodes-dev | grep Status 147 # or 148 $ rpm -q libeccodes-dev 142 149 143 150 … … 198 205 ================================================= 199 206 200 Some users might like to incorporate ``flex_extract`` directly into the ``FLEXPART`` 201 distribution. Then the installation path has to be changed by setting the parameter 202 `installdir` in the ``setup.sh`` file to the ``script`` directory in the ``FLEXPART`` root directoy. 207 Some users might wish to incorporate ``flex_extract`` directly into the ``FLEXPART`` distribution. Then the installation path has to be changed by setting the parameter `installdir` in the ``setup.sh`` file to the ``script`` directory in the ``FLEXPART`` root directoy. 203 208 204 209 … … 218 223 -------------------- 219 224 220 To check if the compilation of the Fortran program ``CONVERT2`` was successful 221 a quick program call on a minimal prepared dataset can be done. 222 223 For this, go from the ``flex_extract`` root directory to the test 224 directory and call the executable of the Fortran program. 225 To check whether the Fortran program ``CONVERT2`` has been compiled and runs properly, it can be applied to a prepared minimal dataset. 226 227 For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Convert/`` directory and execute the Fortran program. 225 228 226 229 .. note:: … … 229 232 .. code-block:: bash 230 233 231 cd test/Installation/Convert232 # callthe Fortran progam without arguments233 ../../../ source/fortran/CONVERT2234 235 The installation was successfull if it showed the followingoutput:234 cd Testing/Installation/Convert 235 # execute the Fortran progam without arguments 236 ../../../Source/Fortran/CONVERT2 237 238 The installation was successfull if you obtain on standard output: 236 239 237 240 .. code-block:: bash -
Documentation/html/index.html
r30f7911 rd720895 287 287 <li class="toctree-l2"><a class="reference internal" href="installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> 288 288 <li class="toctree-l2"><a class="reference internal" href="installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> 289 <li class="toctree-l2"><a class="reference internal" href="installation.html# environment-requirements">Environment requirements</a></li>289 <li class="toctree-l2"><a class="reference internal" href="installation.html#dependencies">Dependencies</a></li> 290 290 <li class="toctree-l2"><a class="reference internal" href="installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li> 291 291 <li class="toctree-l2"><a class="reference internal" href="installation.html#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> -
Documentation/html/installation.html
r30f7911 rd720895 94 94 <li class="toctree-l2"><a class="reference internal" href="#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li> 95 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> 96 <li class="toctree-l2"><a class="reference internal" href="# environment-requirements">Environment requirements</a></li>96 <li class="toctree-l2"><a class="reference internal" href="#dependencies">Dependencies</a></li> 97 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> 98 98 <li class="toctree-l3"><a class="reference internal" href="Installation/remote.html">Remote mode installation</a></li> … … 283 283 </dl> 284 284 </div> 285 <div class="section" id=" environment-requirements">286 <span id="ref-requirements"></span><h2> Environment requirements<a class="headerlink" href="#environment-requirements" title="Permalink to this headline">¶</a></h2>285 <div class="section" id="dependencies"> 286 <span id="ref-requirements"></span><h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2> 287 287 <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> 288 288 <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. 289 289 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> 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> 291 <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>$ dpkg -s libeccodes-dev <span class="p">|</span> grep Status 292 <span class="c1"># or</span> 293 $ rpm -q libeccodes-dev 294 </pre></div> 295 </div> 290 296 </div> 291 297 <div class="section" id="installation-of-flex-extract"> … … 307 313 <div class="section" id="flex-extract-in-combination-with-flexpart"> 308 314 <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> 309 <p>Some users might like 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> 310 distribution. Then the installation path has to be changed by setting the parameter 311 <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> 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> 312 316 </div> 313 317 <div class="section" id="test-installation"> … … 315 319 <div class="section" id="fortran-program-test"> 316 320 <h3>Fortran program test<a class="headerlink" href="#fortran-program-test" title="Permalink to this headline">¶</a></h3> 317 <p>To check if the compilation of the Fortran program <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> was successful 318 a quick program call on a minimal prepared dataset can be done.</p> 319 <p>For this, go from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory to the test 320 directory and call the executable of the Fortran program.</p> 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> 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> 321 323 <div class="admonition note"> 322 324 <p class="first admonition-title">Note</p> 323 325 <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> 324 326 </div> 325 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> test/Installation/Convert326 <span class="c1"># callthe Fortran progam without arguments</span>327 ../../../ source/fortran/CONVERT2328 </pre></div> 329 </div> 330 <p>The installation was successfull if it showed the followingoutput:</p>327 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> Testing/Installation/Convert 328 <span class="c1"># execute the Fortran progam without arguments</span> 329 ../../../Source/Fortran/CONVERT2 330 </pre></div> 331 </div> 332 <p>The installation was successfull if you obtain on standard output:</p> 331 333 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> readspectral: <span class="m">1</span> records <span class="nb">read</span> 332 334 readlatlon: <span class="m">8</span> records <span class="nb">read</span> -
Documentation/html/searchindex.js
r30f7911 rd720895 1 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:[2,19,20,43],dry:17,dtime:[2,3,5,6,10,43],due:[6,11,12,17,31,43],durat:43,dure:[2,4,9,12,13,15,18,31,42],each:[2,5,6,10,11,13,14,17,19,39,42,43],earlier:[],easi:[17,18,20,43],easier:[18,22,43],easiest:[30,31],easili:[2,11],east:[2,11],eastern:2,eastward:[17,19],ec_api:[2,10],ec_memory_per_task:[4,10,13],ec_threads_per_task:[4,10,13],ecac:32,ecaccess:[2,4,10,12,13,14,15,22,23,30,32,43],ecaccess_do_not_remov:[4,10,13,43],eccod:[4,10,12,13,23,30,31,32,33,36],eccodes_include_dir:[9,31],eccodes_lib:[9,31],ecd:2,ecf:[2,6,32],ecfsdir:[2,5,6,10],ecg:[4,10,13],ecgat:[2,4,6,9,10,11,12,13,14,21,30,32,43],ecgb11:[32,43],ecgb:[4,10,13],ecgid:[2,5,6,7,10,12,13,30,31,32,43],echo:[4,12,13],echom:32,ecmf:19,ecmwf:[2,4,5,6,9,10,11,12,13,14,15,17,18,19,20,21,22,23,30,32,33,36,41,43],ecmwf_env:[2,11,12,18,43],ecmwf_grib1_table_128:[],ecmwfapi:[31,33],ecmwfapirc:31,ecmwfdata7:[],ecmwfdata:[],ecmwfdataserv:[2,31],ecmwfservic:[2,31],ecnam:12,econdemand:[2,5,6,10],ecscratch:32,ecstorag:[2,5,6,10],ectmp:[2,5,6,10],ectran:[2,5,6,10,15,30,32,43],ecuid:[2,5,6,7,10,12,13,30,31,32,43],ecwmf:42,edg:12,edit:[19,31],editor:[31,32],edu:[30,32],effect:[13,21,43],effici:[13,17,19,43],egat:12,ei15080900:[],ei15080903:[],ei15080906:[],ei15080909:[],ei15080912:[],ei15080915:[],ei15080918:[],ei15080921:[],ei_exampl:[],einweisung:[],einzelnen:[],either:[2,6,11,14,15,43],elda:[2,6,8,36,43],element:[2,3],els:[4,10,12,13],email:[2,4,6,10,13,30,32,43,44],emo:[4,10,13],emoslib:[21,23,31,32,33],empti:[2,11,12],enabl:[22,30,43],encount:42,end:[2,4,6,10,11,13,17,19,43],end_dat:[2,5,6,10,11,17,43],end_period:2,enda:[10,19,31,43],endian:[30,31,32],endif:17,endo:6,enfo:[6,8,36,43],enough:[6,39,43],ens:[8,43],ensembl:[2,6,23,36,43],ensemble_memb:19,ensur:21,enter:[30,43],entri:[2,11,45],env:[2,4,13],environ:[2,4,6,10,11,12,13,14,20,33,41,43,44],environment:[2,35,43],enyymmddhh:[],eof:[10,13],equal:[2,6,11,21,43],equat:[2,6,17,43],equidistantli:17,era5:[2,5,6,21,22,23,31,42,43],era:[5,6,11,19,21,22,23,36,41,42],error:[2,4,10,12,13,21,30,31,43],error_msg:2,esac:[4,10,13],escap:13,especi:[21,39,42,43],establish:[14,30],eta:[2,5,6,8,10,19,21,38,43],etadiff:[2,5,6,10,21,43],etadot:[2,6,19,43],etadothigh2:[],etapar:[2,5,6,10],etayymmddhh:[6,21],etc:44,europ:43,european:[20,39,41],evalu:41,even:[17,21,43],event:17,eventu:[11,15],everi:[22,30,43],everyon:6,everyth:[0,2,14,30,31,43],ewss:[17,19],exact:[2,17,43],exactli:[],exampl:[2,3,6,7,11,17,18,19,22,23,30,31,39,43],example_usernam:30,exce:43,exceed:43,excelt:0,except:[2,6,21,31,43],execut:[2,9,10,12,13,14,15,18,19,31,32,42],execute_subprocess:2,exedir:2,exist:[2,6,11,43],exit:[2,11,12],expect:[2,43],expens:[6,21],experi:[6,31,43,44],experienc:43,experiment:[],explain:[43,45],explan:43,explanait:43,explic:20,explicit:[22,42],explicitli:[6,20,22,43],express:2,expver:[2,5,6,10,19,31],extend:43,extens:[0,2,6,17],extra:[2,5,6,14,19,36,42,43],extract:[2,5,6,19,21,22,31,43,45],f90:[30,31,32,36],f_i:17,facil:[22,30],factor:[],fail:[2,4,6,10,13,43],failur:43,fals:2,familiar:43,faq:41,far:6,fast:20,faster:[18,22,31,44],fcgg__sl:[],fcog__ml:[],fcog__sl:[],fcog_acc_sl:19,fconvert:[30,31,32],fcrai:[30,31,32],fcsh__ml:[],fcsh__sl:[],fdefault:[30,31,32],feasibl:21,featur:[2,6,20,41,44],februari:5,fedir:2,feel:42,felder:[],fell:[],few:[6,30,32,43],fewer:43,ffix:[30,31,32],fftw3:[31,32],fftw:[23,30,32,33],field:[2,5,11,15,20,21,23,36,41,43,45],field_typ:19,fig:17,figur:[14,17,43],file1:2,file2:2,file:[0,2,4,9,10,11,12,13,15,17,18,20,22,23,30,31,32,36,39,41,42,44,45],filemod:2,filenam:[2,17,19,43],filename_in:2,filepath:2,fill:[6,42,43],filter:[2,17],find:[5,31,39,42,43],finder:39,fine:21,finer:[3,21],finish:[42,43],first:[2,5,6,11,17,31,32,36,39,42,43],fit:2,fix:[4,10,17,41],flex:[10,13,43],flex_ecmwf:[4,10,13],flex_extract:[0,2,4,5,6,8,9,10,11,12,13,14,15,17,18,19,20,21,22,30,31,32,33,39,43,44],flex_extract_v7:[10,13,19,31,45],flex_extract_v:[4,13],flex_extract_vx:[5,7,8,9,11,12,13,18,30,31,32,42,43],flexcompil:[4,13,30,32],flexextract:[10,19,31,45],flexextractdir:2,flexpart:[2,6,11,15,17,20,21,22,41,43,44],flexpart_root:[4,13],flexpart_root_script:[4,13],flexpartdir:12,flextra:[2,20,21,41],flow:[2,11,12,20],flux:[2,5,15,21,38,43],fluxpar:[],fluxyyyymmddhh:17,flxacc2:17,fno:[30,31,32],follow:[2,5,7,12,13,15,17,18,19,21,30,31,32,33,39,42,43],font:0,fontpath:0,fopenmp:[30,31,32],for_develop:[0,45],forecast:[2,5,6,11,17,20,21,22,23,39,41,43,45],forecast_step:19,forescast:43,forg:31,forget:33,form:[6,42],format:[2,6,10,12,15,17,19,20,31,43],formul:17,fort:[2,13],fortran90:[12,21],fortran:[0,2,4,12,13,15,16,17,18,20,30,31,32,36,38,41,43],fortran_program:13,found:[2,5,6,9,13,19,20,21,30,31,43,44],four:[2,42],fp_root:2,fp_root_path:13,fp_root_script:13,fpdir:2,frac32:17,frac:17,framework:[13,30],free:42,frequent:[41,44],friendli:[],frog:[],from:[2,3,4,5,6,10,11,12,13,14,15,17,18,19,20,22,23,30,31,32,36,39,41,42,43,44],fromfil:2,fsr:19,ftime:2,ftp:32,ftrafo:[30,31,32],ftype:2,fulfil:17,full:[2,6,11,12,21,22,31,39,41,43],fulli:39,further: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Documentation","Fortran\u2019s Auto Generated Documentation","Python\u2019s Auto Generated Documentation","CONTROL file changes","The Compilation Jobscript <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 - <code class=\"docutils literal notranslate\"><span class=\"pre\">CONVERT2</span></code>","The Jobscript <code class=\"docutils literal notranslate\"><span class=\"pre\">job.ksh</span></code>","The executable Script - <code class=\"docutils literal notranslate\"><span class=\"pre\">run.sh</span></code>","The Installation Script - <code class=\"docutils literal notranslate\"><span class=\"pre\">setup.sh</span></code>","Templates","Application Modes","Program Flow","Auto Generated Documentation","Disaggregation of Flux Data","Control & Input Data","Output Data","Overview","Vertical Coordinate","Access Modes","Link Collection for Quick finder","Hints to specify dataset retrieval","Available Datasets for Member State users","Available Datasets for Public users","Metrics","Static Code Analysis","Testcases","Gateway mode installation","Local mode installation","Remote mode installation","FAQ - Frequently asked questions","Known Bugs and Issues","Developer Team","Changelog","Developer Guide","Documentation","ECMWF Data","Evaluation","Welcome to <code class=\"docutils literal notranslate\"><span class=\"pre\">flex_extract</span></code>\u2019s user documentation!","Installation","Quick Start","Support","ToDos"],titleterms:{"class":2,"new":[19,36],"public":[26,42,43],"static":28,CDS:31,The:[4,5,6,9,10,11,12],access:22,adapt:[],addit:[0,6,19],adjust:43,agre:[],agreement:42,analysi:28,api:31,applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calcul:21,can:[24,33],cera:43,chang:[3,36],changelog:36,check:2,code:28,collect:23,combin:[42,43],comparison:29,compil:4,compilejob:[4,13],content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert2:[9,19],convert:13,coordin:21,credenti:7,dai:[],data:[6,17,18,19,24,25,39,43],dataset:[24,25,26,42,43],definit:43,delight:[],depend:[30,31,32,42],develop:[35,37],diagramm:0,differ:15,disagg:[],disaggreg:[2,17,19],distribut:33,document:[0,1,2,16,38,41],doe:[4,10],domain:6,done:[],download:42,ecflexpart:2,ecmwf:[7,31,39,42],ecmwf_env:[7,13],ensembl:19,environ:[30,31,32],equat:21,era:43,evalu:40,exampl:[4,5,8,10,15],execut:11,faq:[33,44],featur:[36,43],field:[6,17,19],file:[3,5,6,7,8,19,21,29,43],find:24,finder:23,fix:36,flex_extract:[41,42],flexpart:[19,42],flow:15,flux:[6,17,19],forecast:19,format:5,fort:19,fortran:[1,9,19,42],frequent:33,from:[21,33],frozen:[],full:42,gatewai:[30,43],gener:[1,2,6,15,16],get_mars_data:2,grib:[19,29],gributil:2,guid:37,half:[],hint:[24,43],horizont:21,host:[],how:24,index:19,input:[18,19],instal:[2,12,30,31,32,33,42],interim:43,issu:[34,44],job:[10,13,43],jobscript:[4,10],known:[34,44],ksh:[4,10],level:25,librari:33,licenc:42,link:23,list:44,local:[15,31,43],mail:44,makefil:9,mar:[19,21,29],marsretriev:2,member:[15,25],method:[],metric:27,mix:[],mode:[14,15,22,30,31,32,43],model:25,modul:2,need:[],old:[],older:17,onlin:0,oper:43,option:[11,12],out:24,output:[19,21],overview:20,packag:33,paramet:[6,11,12,21,43],parti:33,pre:21,precip:[],precipit:[17,19],predict:19,prepar:[21,30,31,32,43],prepare_flexpart:2,program:[2,15,19,42],pure:19,python:2,question:33,quick:[23,43],registr:42,releas:36,remot:[32,43],report:44,request:[19,29],requir:[],rest:17,retriev:24,run:11,script:[4,11,12],section:6,select:43,sequenc:0,server:[],set:15,setup:12,softwar:0,some:43,specif:43,specifi:24,sphinx:0,standard:19,start:43,state:25,submiss:11,submit:[2,11],support:44,surfac:25,system:44,team:35,temp:13,templat:13,temporari:19,test:[30,31,42],testcas:29,third:33,ticket:44,time:6,todo:[43,45],tool:2,uiofil:2,updat:0,usag:[11,12],user:[6,7,15,25,26,41],using:21,veloc:21,version:17,versu:[],vertic:[6,19,21],web:31,welcom:41,what:[4,10,24,33],why:[],wind:[6,21],workflow:15}})
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