Changeset d720895 in flex_extract.git


Ignore:
Timestamp:
Dec 19, 2019, 8:12:11 PM (4 years ago)
Author:
Anne Philipp <anne.philipp@…>
Branches:
master, ctbto, dev
Children:
e70c85f
Parents:
76c37a9
Message:

updated online docu

Location:
Documentation/html
Files:
36 added
17 edited

Legend:

Unmodified
Added
Removed

  • Documentation/html/Documentation/Input/run.html

    r30f7911 rd720895  
    487487<span class="c1">#</span>
    488488<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>
    492504<span class="c1"># -----------------------------------------------------------------</span>
    493505<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
    … …  
    508520<span class="nv">PP_ID</span><span class="o">=</span>None
    509521<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">&#39;job.temp&#39;</span>
    510 <span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">&#39;CONTROL_OD.OPER.FC.gauss.global&#39;</span>
     522<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">&#39;CONTROL_EA5&#39;</span>
    511523<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>
    513525<span class="nv">PUBLIC</span><span class="o">=</span><span class="m">0</span>
    514526

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

    rba99230 rd720895  
    348348<span class="c1">#    This file defines the flex_extract&#39;s available installation</span>
    349349<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>
    353362<span class="c1">#</span>
    354363<span class="c1"># -----------------------------------------------------------------</span>
    … …  
    358367<span class="c1">#</span>
    359368<span class="nv">TARGET</span><span class="o">=</span><span class="s1">&#39;ecgate&#39;</span>
    360 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">&#39;Makefile.gfortran&#39;</span>
     369<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">&#39;makefile.eccodes&#39;</span>
    361370<span class="nv">ECUID</span><span class="o">=</span><span class="s1">&#39;km4a&#39;</span>
    362371<span class="nv">ECGID</span><span class="o">=</span><span class="s1">&#39;at&#39;</span>

  • Documentation/html/Documentation/Input/templates.html

    rba99230 rd720895  
    252252On 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>.
    253253For 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>
    255255<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>
    256256<div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
    … …  
    336336On 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>.
    337337For 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>
    339339<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>
    340340<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  
    189189<li><dl class="first docutils">
    190190<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>
    192192</dl>
    193193</li>
    … …  
    207207<li><dl class="first docutils">
    208208<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>
    210210</dl>
    211211</li>
    212212<li><dl class="first docutils">
    213213<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>
    215215</dl>
    216216</li>

  • Documentation/html/Documentation/overview.html

    rba99230 rd720895  
    193193<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>
    194194<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>
    196196<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>
    197197<div class="toctree-wrapper compound">

  • Documentation/html/Installation/gateway.html

    r30f7911 rd720895  
    9494<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
    9595<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>
    9797<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">
    9898<li class="toctree-l3"><a class="reference internal" href="remote.html">Remote mode installation</a></li>
    9999<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>
    101101<li class="toctree-l4"><a class="reference internal" href="#prepare-gateway-environment">Prepare gateway environment</a></li>
    102102<li class="toctree-l4"><a class="reference internal" href="#test-gateway-environment">Test gateway environment</a></li>
    … …  
    190190<div class="toctree-wrapper compound">
    191191</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>
    197194<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>
    199196<li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
    200197<li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
    … …  
    203200<div class="section" id="prepare-gateway-environment">
    204201<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
     206Please enter your user-id: example_username
     207Your 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.
     211The 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>
    208213<span class="c1"># (if not already available):</span>
    209214apt-get install python3
    210 apt-get install pip
    211 apt-get install genshi
    212 apt-get install numpy
     215apt-get install python3-genshi
     216apt-get install python3-numpy
    213217</pre></div>
    214218</div>
    … …  
    227231<div class="section" id="gateway-installation">
    228232<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.
     234The 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>
    241235<div class="literal-block-wrapper docutils container" id="setup-sh">
    242236<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>
    … …  
    247241<span class="c1">#</span>
    248242<span class="nv">TARGET</span><span class="o">=</span><span class="s1">&#39;ecgate&#39;</span>
    249 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">&#39;Makefile.gfortran&#39;</span>
     243<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">&#39;makefile.gfortran&#39;</span>
    250244<span class="nv">ECUID</span><span class="o">=</span><span class="s1">&#39;uid&#39;</span>
    251245<span class="nv">ECGID</span><span class="o">=</span><span class="s1">&#39;gid&#39;</span>
    252 <span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">&#39;server.example.edu&#39;</span>
    253 <span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">&#39;example@genericSftp&#39;</span>
     246<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">&#39;localserver.tld&#39;</span>
     247<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">&#39;association_name@genericSftp&#39;</span>
    254248<span class="nv">INSTALLDIR</span><span class="o">=</span>None
    255249<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">&#39;job.template&#39;</span>
    … …  
    262256</pre></div>
    263257</div>
    264 <p>to start the installation. You should see the following output at the command line.</p>
     258<p>to start the installation. You should see the following on standard output.</p>
    265259<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
    266260Create tarball ...
    … …  
    269263</pre></div>
    270264</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>
    272266<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
    273267gfortran   -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  
    9494<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
    9595<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>
    9797<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">
    9898<li class="toctree-l3"><a class="reference internal" href="remote.html">Remote mode installation</a></li>
    9999<li class="toctree-l3"><a class="reference internal" href="gateway.html">Gateway mode installation</a></li>
    100100<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>
    102102<li class="toctree-l4"><a class="reference internal" href="#prepare-local-environment">Prepare local environment</a></li>
    103103<li class="toctree-l4"><a class="reference internal" href="#test-local-environment">Test local environment</a></li>
    … …  
    190190<div class="toctree-wrapper compound">
    191191</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>
    196195<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>
     196and libraries, since the preparation of the extraction and the post-processing is done on the local machine:</p>
    198197<table border="1" class="docutils">
    199198<colgroup>
    … …  
    227226<div class="section" id="prepare-local-environment">
    228227<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 with admin 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.
     229The 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>
    232231<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&#39;&#39;.</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
    244247</pre></div>
    245248</div>
    … …  
    253256</div>
    254257</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>
    256259<div class="admonition note">
    257260<p class="first admonition-title">Note</p>
    258261<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>
    259262</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>
    261264<dl class="docutils">
    262265<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 point 1 (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>
    264267<dt>CDS API:</dt>
    265268<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>
    … …  
    268271<div class="section" id="test-local-environment">
    269272<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">&lt;package-name&gt;</span> <span class="pre">|</span>&#160; <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">&lt;package_name&gt;</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>
    278274<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span>
    279275<span class="kn">import</span> <span class="nn">eccodes</span>
    … …  
    286282<div class="section" id="test-the-web-api-s">
    287283<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>
    289285<div class="section" id="ecmwf-web-api">
    290286<h4>ECMWF Web API<a class="headerlink" href="#ecmwf-web-api" title="Permalink to this headline">¶</a></h4>
    … …  
    295291</colgroup>
    296292<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>
    299295</tr>
    300296<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>
    … …  
    344340<div class="section" id="cds-api">
    345341<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>
    348344<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span>
    349345
    … …  
    364360</pre></div>
    365361</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>
    369364<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span>
    370365
    … …  
    394389<div class="section" id="local-installation">
    395390<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
     393the <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>
    401394<blockquote>
    402395<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>
    405398</ul>
    406399</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>, where
     400<p>They can be found at <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Fortran</span></code>, where
    408401<code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted with the current version number.</p>
    409402<div class="admonition caution">
    410403<p class="first admonition-title">Caution</p>
    411404<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>
    413406</div>
    414407<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 your
     408go 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
    416409choice 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/fortran
    418 nedit Makefile.local.gfortran
    419 </pre></div>
    420 </div>
    421 <p>Edit the pathes 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
     411nedit 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>
    422415<div class="admonition caution">
    423416<p class="first admonition-title">Caution</p>
    … …  
    432425<p class="last">to find out the path to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library.</p>
    433426</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>
    435428and <strong>ECCODES_LIB</strong> and save it.</p>
    436429<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>
    … …  
    440433</div>
    441434<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>
     435installation 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>
    444436<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
    445437and adapt the installation parameters in the section labelled with
    … …  
    454446<span class="c1">#</span>
    455447<span class="nv">TARGET</span><span class="o">=</span><span class="s1">&#39;local&#39;</span>
    456 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">&#39;Makefile.local.gfortran&#39;</span>
     448<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">&#39;makefile.local.gfortran&#39;</span>
    457449<span class="nv">ECUID</span><span class="o">=</span>None
    458450<span class="nv">ECGID</span><span class="o">=</span>None
    … …  
    470462</pre></div>
    471463</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>
    473465<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
    474466WARNING: installdir has not been specified

  • Documentation/html/Installation/remote.html

    r30f7911 rd720895  
    9494<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
    9595<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>
    9797<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">
    9898<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>
    100100<li class="toctree-l4"><a class="reference internal" href="#prepare-remote-environment">Prepare remote environment</a></li>
    101101<li class="toctree-l4"><a class="reference internal" href="#remote-installation">Remote installation</a></li>
    … …  
    189189<div class="toctree-wrapper compound">
    190190</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>
    195194<table border="1" class="docutils">
    196195<colgroup>
    … …  
    222221<div class="section" id="prepare-remote-environment">
    223222<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>
    227224</div>
    228225<div class="section" id="remote-installation">
    229226<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>.
    231228Substitute <em>&lt;ecuid&gt;</em> with your ECMWF user name:</p>
    232229<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ssh -X &lt;ecuid&gt;@ecaccess.ecmwf.int
    … …  
    251248***************************************************************
    252249
    253 &lt;ecuid&gt;@131.130.157.5&#39;s password: ***
     250&lt;ecuid&gt;@&lt;ipname/address&gt;&#39;s password: ***
    254251Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
    255252
    … …  
    257254</pre></div>
    258255</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">$HOME</span></code> directory of the ECMWF Linux server via <code class="docutils literal notranslate"><span class="pre">scp</span></code>.
    261 Substitute the <em>&lt;localuser&gt;</em> and <em>&lt;server.edu&gt;</em> placeholders with your credentials.
     256<p>Substitute the <em>&lt;localuser&gt;</em> and <em>&lt;localmachine.tld&gt;</em> placeholders with your local user name and the IP name or address of your local machine.
    262257Untar the file and change into the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory.</p>
    263 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp &lt;localuser&gt;@&lt;server.edu&gt;:/path/to/tarfile/flex_extract_vX.X.tar.gz  <span class="nv">$HOME</span>/
     258<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp &lt;localuser&gt;@&lt;localmachine.tld&gt;:&lt;/path/to/tarfile/&gt;flex_extract_vX.X.tar.gz  <span class="nv">$HOME</span>/
    264259<span class="nb">cd</span> <span class="nv">$HOME</span>
    265260tar xvf flex_extract_vX.X.tar.gz
    … …  
    267262</pre></div>
    268263</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.
    277265Before executing it, it is necessary to adapt some parameters from <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>
    278266described 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 editor and 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>
    280268<table border="1" class="docutils">
    281269<colgroup>
    … …  
    284272</colgroup>
    285273<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>
    288276</tr>
    289277<tr class="row-even"><td><div class="first last highlight-bash notranslate"><div class="highlight"><pre><span></span>...
    … …  
    329317</table>
    330318<p><span class="underline">Please substitute the values of ECUID and ECGID
    331 with your own credentials and settings.</span></p>
     319with your own ones (look at any of your files with ``ls -l’’ to see uid and gid).</span></p>
    332320<div class="admonition note">
    333321<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>
    337323</div>
    338324<p>Afterwards, type:</p>
    … …  
    341327</pre></div>
    342328</div>
    343 <p>to start the installation. You should see the following output at the command line.</p>
     329<p>to start the installation. You should see the following on standard output.</p>
    344330<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
    345331Create tarball ...
    … …  
    348334</pre></div>
    349335</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>
    351337<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
    352338gfortran   -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  
    537537              <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">&#39;*.h&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span>
    538538    <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">&#39;Makefile*&#39;</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">&#39;makefile*&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span>
    540540    <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>
    541541

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

    r30f7911 rd720895  
    88.. toctree::
    99    :hidden:
    10     :maxdepth: 3
     10    :maxdepth: 2
    1111   
    1212.. _Python 3: https://docs.python.org/3/
    … …  
    4343.. _ref-req-gateway:
    4444 
    45 Gateway environment requirements
    46 ================================
     45Gateway mode - dependencies
     46===========================
    4747
    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`_
    5349* `numpy`_
    5450* `genshi`_
    … …  
    6056===========================
    6157
    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.
     58In 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
     60Please 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
     62The 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   
     73The easiest way to install all required packages is to use the package management system of your Linux distribution which required admin rights.
     74The installation was tested under *GNU/Linux Debian buster* and *Ubuntu 18.04 Bionic Beaver*.
    6475
    6576.. code-block:: sh
    6677
    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):
    6880   # (if not already available):
    6981   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   
    7485
    7586.. _ref-test-gateway:
    … …  
    7788Test gateway environment
    7889========================
    79  
     90
    8091Check the availability of the python packages by typing ``python3`` in
    8192a terminal window and run the ``import`` commands in the python shell.
    8293If there are no error messages, you succeeded in setting up the environment.
    83 
     94 
    8495.. code-block:: python
    8596   
    … …  
    95106====================
    96107
    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.
     109The 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.
    106110   
    107    $ ecaccess-certificate-create
    108    Please enter your user-id: example_username
    109    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  
    114111
    115112.. code-block:: bash
    … …  
    123120    #
    124121    TARGET='ecgate'
    125     MAKEFILE='Makefile.gfortran'
     122    MAKEFILE='makefile.gfortran'
    126123    ECUID='uid'
    127124    ECGID='gid'
    128     GATEWAY='server.example.edu'
    129     DESTINATION='example@genericSftp'
     125    GATEWAY='localserver.tld'
     126    DESTINATION='association_name@genericSftp'
    130127    INSTALLDIR=None
    131128    JOB_TEMPLATE='job.template'
    … …  
    139136   $ ./setup.sh
    140137   
    141 to start the installation. You should see the following output at the command line.
     138to start the installation. You should see the following on standard output.
    142139   
    143140   
    … …  
    149146   You should get an email with subject "flexcompile" within the next few minutes!
    150147
    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:
    153149
    154150.. code-block:: bash

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

    r30f7911 rd720895  
    4646.. _ref-req-local:
    4747 
    48 Local environment requirements
    49 ==============================
    50 
    51 For the local access modes **member** and **public** there is no difference in
    52 the installation process.
     48Local mode - dependencies
     49=========================
     50
     51The installation is the same for the access modes **member** and **public**.
    5352
    5453The 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:
     54and libraries, since the preparation of the extraction and the post-processing is done on the local machine:
    5655
    5756+------------------------------------------------+-----------------+
    … …  
    7271=========================
    7372
    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 with admin rights.
    75 The installation was tested on a *Debian GNU/Linux buster/sid* and an *Ubuntu 18.04 Bionic Beaver* system.
     73The easiest way to install all required packages is to use the package management system of your Linux distribution  which requires admin rights.
     74The installation was tested on a *Debian GNU/Linux buster* and an *Ubuntu 18.04 Bionic Beaver* system.
    7675
    7776.. code-block:: sh
    7877
    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
    8384   apt-get install gfortran
    8485   apt-get install fftw3-dev
    8586   apt-get install libeccodes-dev
    8687   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
    9093   pip install cdsapi
    9194   pip install ecmwf-api-client
    92 
     95   
    9396.. note::
    9497
    … …  
    99102    .. code-block:: bash
    100103
    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   
     106The 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
     112Both user groups have to provide keys with their credentials for the Web API's in their home directory. Therefore, follow these instructions:
    105113       
    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    
    112114ECMWF 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 point 1 (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).
    114116     
    115117CDS API:
    116118   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   
    119121.. _ref-test-local:
    120122   
    … …  
    122124======================
    123125
    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.
     126Check 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.
    134127
    135128.. code-block:: python
    … …  
    147140------------------
    148141
    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.
     142You 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
    150144
    151145ECMWF Web API
    … …  
    154148
    155149+----------------------------------------------------------+----------------------------------------------------------+
    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**: |
    157151+----------------------------------------------------------+----------------------------------------------------------+
    158152|.. code-block:: python                                    |.. code-block:: python                                    |
    … …  
    182176^^^^^^^
    183177
    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:
     178Extraction 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
     180Please use this piece of Python code to retrieve a small sample of *ERA5* pressure levels:
    187181
    188182.. code-block:: python
    … …  
    205199    "download_cdsapi.grib")
    206200
    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   
     202If you know that your CDS API works, you can try to extract some data from MARS.
     203
     204.. **Member-state user**
     205
     206Please 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!
    214207
    215208.. code-block:: python
    … …  
    241234   
    242235    **Public user**
    243     Please use this piece of python code:
     236    Please use this piece of Python code:
    244237
    245238    .. code-block:: python
    … …  
    277270==================
    278271
    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
     272First 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
     274the ``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 
     279They can be found at ``flex_extract_vX.X/Source/Fortran``, where
    289280``vX.X`` should be substituted with the current version number.
    290281
    291282.. caution::   
    292283   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.
    295285
    296286So starting from the root directory of ``flex_extract``,
    297 go to the ``Fortran`` source directory and open the ``Makefile`` of your
     287go to the ``Fortran`` source directory and open the ``makefile`` of your
    298288choice to modify with an editor of your choice. We use the ``nedit`` in this case.
    299289
    300290.. code-block:: bash
    301291
    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 
     295Edit the paths to the ``eccodes`` library on your local machine.
     296
    306297
    307298.. caution::
    … …  
    318309   to find out the path to the ``eccodes`` library.
    319310   
    320 Substitute these paths in the ``Makefile`` for parameters **ECCODES_INCLUDE_DIR**
     311Substitute these paths in the ``makefile`` for parameters **ECCODES_INCLUDE_DIR**
    321312and **ECCODES_LIB** and save it.
    322313
    … …  
    329320   
    330321The 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.
     322installation process.Therefore the name of the ``makefile`` to be used needs to be given in  ``setup.sh``.
    333323
    334324In the root directory of ``flex_extract``, open the ``setup.sh`` script
    … …  
    348338   #
    349339   TARGET='local'
    350    MAKEFILE='Makefile.local.gfortran'
     340   MAKEFILE='makefile.local.gfortran'
    351341   ECUID=None
    352342   ECGID=None
    … …  
    365355   $ ./setup.sh
    366356   
    367 to start the installation. You should see the following output at the command line.
     357to start the installation. You should see the following standard output.
    368358   
    369359   

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    4242.. _ref-req-remote:
    4343 
    44 Remote environment requirements
    45 ===============================
     44Remote mode - dependencies
     45==========================
    4646
    47 The environment for ``flex_extract`` on ECMWF servers has to provide these
    48 software packages and libraries:
     47The following software is required, and already available at the ECMWF servers:
    4948   
    5049+---------------------------+-----------------+
    … …  
    6362==========================
    6463 
    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.
     64ECMWF servers provide all libraries via a module system. Loading the required modules is already built into ``flex_extract`` and no user action is needed.
    6865
    6966
    … …  
    7370===================
    7471
    75 First, log in on one of the ECMWF Linux server, such as *ecgate* or *cca/ccb*.
     72First, log in on one of the ECMWF servers, such as *ecgate* or *cca/ccb*.
    7673Substitute *<ecuid>* with your ECMWF user name:
    7774
    … …  
    10198   ***************************************************************
    10299
    103    <ecuid>@131.130.157.5's password: ***
     100   <ecuid>@<ipname/address>'s password: ***
    104101   Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
    105102
    106103   [<ecuid>@ecgb11 ~]$
    107104   
     105Substitute the *<localuser>* and *<localmachine.tld>* placeholders with your local user name and the IP name or address of your local machine.
     106Untar the file and change into the ``flex_extract`` root directory.
    108107   
    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 
    114108.. code-block:: bash
    115109
    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/
    117111   cd $HOME
    118112   tar xvf flex_extract_vX.X.tar.gz
    … …  
    120114   
    121115
    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   
     117Execute the ``setup.sh`` script from the ``flex_extract``'s root directory.
    131118Before executing it, it is necessary to adapt some parameters from ``setup.sh``
    132119described in :doc:`Documentation/Input/setup`.
    133120
    134 Open ``setup.sh`` with your editor and adapt the values: 
    135 
     121Open ``setup.sh`` with your preferred editor (e.g., ``nano'') and adapt the values: 
     122   
    136123+----------------------------------------------+----------------------------------------------+   
    137 |   Take this for target = **ectrans**         |  Take this for target = **cca**              |
     124|   Use this for target = **ectrans**          |   Use this for target = **cca**              |
    138125+----------------------------------------------+----------------------------------------------+
    139126| .. code-block:: bash                         | .. code-block:: bash                         |
    … …  
    158145
    159146:underline:`Please substitute the values of ECUID and ECGID
    160 with your own credentials and settings.`
     147with your own ones (look at any of your files with ``ls -l'' to see uid and gid).`
    161148
    162149.. note::
    163150
    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).
    168152
    169153Afterwards, type:
    … …  
    174158   ./setup.sh
    175159   
    176 to start the installation. You should see the following output at the command line.
     160to start the installation. You should see the following on standard output.
    177161   
    178162   
    … …  
    185169
    186170   
    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:
    188172
    189173.. code-block:: bash

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    132132.. _ref-requirements:
    133133 
    134 Environment requirements
    135 ========================
     134Dependencies
     135============
    136136
    137137The 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 
    139138   
    140139Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries.
    141140We 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
     142Before 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
    142149
    143150
    … …  
    198205=================================================
    199206
    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.
     207Some 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.
    203208
    204209
    … …  
    218223--------------------
    219224
    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.
     225To check whether the Fortran program ``CONVERT2`` has been compiled and runs properly, it can be applied to a prepared minimal dataset.
     226
     227For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Convert/`` directory and execute the Fortran program.
    225228
    226229.. note::
    … …  
    229232.. code-block:: bash
    230233   
    231    cd test/Installation/Convert
    232    # call the Fortran progam without arguments
    233    ../../../source/fortran/CONVERT2
    234 
    235 The installation was successfull if it showed the following output:
     234   cd Testing/Installation/Convert
     235   # execute the Fortran progam without arguments
     236   ../../../Source/Fortran/CONVERT2
     237
     238The installation was successfull if you obtain on standard output:
    236239
    237240.. code-block:: bash

  • Documentation/html/index.html

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    287287<li class="toctree-l2"><a class="reference internal" href="installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
    288288<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>
    290290<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>
    291291<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

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    9494<li class="toctree-l2"><a class="reference internal" href="#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
    9595<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>
    9797<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>
    9898<li class="toctree-l3"><a class="reference internal" href="Installation/remote.html">Remote mode installation</a></li>
    … …  
    283283</dl>
    284284</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>
    287287<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>
    288288<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.
    289289We 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">&lt;package-name&gt;</span> <span class="pre">|</span>&#160; <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">&lt;package_name&gt;</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>
    290296</div>
    291297<div class="section" id="installation-of-flex-extract">
    … …  
    307313<div class="section" id="flex-extract-in-combination-with-flexpart">
    308314<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>
    312316</div>
    313317<div class="section" id="test-installation">
    … …  
    315319<div class="section" id="fortran-program-test">
    316320<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>
    321323<div class="admonition note">
    322324<p class="first admonition-title">Note</p>
    323325<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>
    324326</div>
    325 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> test/Installation/Convert
    326 <span class="c1"># call the Fortran progam without arguments</span>
    327 ../../../source/fortran/CONVERT2
    328 </pre></div>
    329 </div>
    330 <p>The installation was successfull if it showed the following output:</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>
    331333<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> readspectral:            <span class="m">1</span>  records <span class="nb">read</span>
    332334 readlatlon:            <span class="m">8</span>  records <span class="nb">read</span>

  • Documentation/html/searchindex.js

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    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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 &amp; 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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