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diff --git a/Documentation/doctrees/quick_start.doctree b/Documentation/doctrees/quick_start.doctree
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diff --git a/Documentation/html/.buildinfo b/Documentation/html/.buildinfo
new file mode 100644
index 0000000000000000000000000000000000000000..11176f535a0a18b9caaff112ecccb0b64fd78da0
--- /dev/null
+++ b/Documentation/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 4fe8dea6f5157d998485e509f35babce
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/Documentation/html/.nojekyll b/Documentation/html/.nojekyll
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/Documentation/html/Documentation/Api/api_python.html b/Documentation/html/Documentation/Api/api_python.html
index 32f8149bd11290e8db826c3a8528537c87b39836..ed6d66028a764db53be9dd7d82157093172e72c5 100644
--- a/Documentation/html/Documentation/Api/api_python.html
+++ b/Documentation/html/Documentation/Api/api_python.html
@@ -2215,9 +2215,17 @@ command line.</li>
<dt id="GribUtil.GribUtil">
<em class="property">class </em><code class="descclassname">GribUtil.</code><code class="descname">GribUtil</code><span class="sig-paren">(</span><em>filenames</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/GribUtil.html#GribUtil"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribUtil.GribUtil" title="Permalink to this definition">¶</a></dt>
<dd><p>Class for GRIB utilities (new methods) based on GRIB API</p>
+<p>The GRIB API provides all necessary tools to work directly with the
+grib files. Nevertheless, the GRIB API tools are very basic and are in
+direct connection with the grib files. This class provides some higher
+functions which apply a set of GRIB API tools together in the respective
+context. So, the class initially contains a list of grib files (their
+names) and the using program then applies the methods directly on the
+class objects without having to think about how the actual GRIB API
+tools have to be arranged.</p>
<dl class="method">
<dt id="GribUtil.GribUtil.copy_dummy_msg">
-<code class="descname">copy_dummy_msg</code><span class="sig-paren">(</span><em>filename_in</em>, <em>selectWhere=True</em>, <em>keynames=[]</em>, <em>keyvalues=[]</em>, <em>filemode='w'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/GribUtil.html#GribUtil.copy_dummy_msg"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribUtil.GribUtil.copy_dummy_msg" title="Permalink to this definition">¶</a></dt>
+<code class="descname">copy_dummy_msg</code><span class="sig-paren">(</span><em>filename_in</em>, <em>selectWhere=True</em>, <em>keynames=[]</em>, <em>keyvalues=[]</em>, <em>filemode='wb'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/GribUtil.html#GribUtil.copy_dummy_msg"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribUtil.GribUtil.copy_dummy_msg" title="Permalink to this definition">¶</a></dt>
<dd><p>Add the content of another input grib file to the objects file but
only messages corresponding to keys/values passed to the function.
The selectWhere switch decides if to copy the keys equal to (True) or
@@ -2233,7 +2241,7 @@ different to (False) the keynames/keyvalues list passed to the
function. Default is True.</li>
<li><strong>keynames</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – List of keynames. Default is an empty list.</li>
<li><strong>keyvalues</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – List of keyvalues. Default is an empty list.</li>
-<li><strong>filemode</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Sets the mode for the output file. Default is “w”.</li>
+<li><strong>filemode</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Sets the mode for the output file. Default is “wb”.</li>
</ul>
</td>
</tr>
@@ -2297,7 +2305,7 @@ Default is “my.idx”.</li>
<dl class="method">
<dt id="GribUtil.GribUtil.set_keys">
-<code class="descname">set_keys</code><span class="sig-paren">(</span><em>fromfile</em>, <em>keynames</em>, <em>keyvalues</em>, <em>wherekeynames=[]</em>, <em>wherekeyvalues=[]</em>, <em>strict=False</em>, <em>filemode='w'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/GribUtil.html#GribUtil.set_keys"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribUtil.GribUtil.set_keys" title="Permalink to this definition">¶</a></dt>
+<code class="descname">set_keys</code><span class="sig-paren">(</span><em>fromfile</em>, <em>keynames</em>, <em>keyvalues</em>, <em>wherekeynames=[]</em>, <em>wherekeyvalues=[]</em>, <em>strict=False</em>, <em>filemode='wb'</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/GribUtil.html#GribUtil.set_keys"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GribUtil.GribUtil.set_keys" title="Permalink to this definition">¶</a></dt>
<dd><p>Opens the file to read the grib messages and then write
the selected messages (with wherekeys) to a new output file.
Also, the keyvalues of the passed list of keynames are set.</p>
@@ -2318,7 +2326,7 @@ Default value is an empty list.</li>
<li><strong>strict</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">boolean</span></code>, optional) – Decides if everything from keynames and keyvalues
is written out the grib file (False) or only those
meeting the where statement (True). Default is False.</li>
-<li><strong>filemode</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Sets the mode for the output file. Default is “w”.</li>
+<li><strong>filemode</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">string</span></code>, optional) – Sets the mode for the output file. Default is “wb”.</li>
</ul>
</td>
</tr>
diff --git a/Documentation/html/Documentation/Input/control.html b/Documentation/html/Documentation/Input/control.html
index 35282f89c9cfd477397f60c0d47513ba933de977..6c23a5dc79322e85618d8b7ce9f1a45b29c98ebd 100644
--- a/Documentation/html/Documentation/Input/control.html
+++ b/Documentation/html/Documentation/Input/control.html
@@ -226,6 +226,126 @@ For each main dataset there is an example and additionally some variances in res
in grouped sections with their default values. In <a class="reference internal" href="control_params.html"><span class="doc">The CONTROL parameters</span></a> you can find a more
detailed description with additional hints, possible values and some useful information about
the setting of these parameters.</p>
+<div class="literal-block-wrapper docutils container" id="id1">
+<div class="code-block-caption"><span class="caption-text">CONTROL.documentation</span><a class="headerlink" href="#id1" title="Permalink to this code">¶</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1">################################################################################</span>
+<span class="c1"># Comprehensive list of relevant CONTROL file parameters with</span>
+<span class="c1"># short descriptions and default values. </span>
+<span class="c1">#</span>
+<span class="c1"># For more details on how to select and define parameters </span>
+<span class="c1"># please see Table of CONTROLparameters. </span>
+<span class="c1">#</span>
+<span class="c1"># AUTHOR: Anne Philipp</span>
+<span class="c1"># DATE: 05. February 2019</span>
+<span class="c1">################################################################################</span>
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># USER SECTION:</span>
+<span class="c1"># User specific information for ECMWF server.</span>
+<span class="c1"># Information are needed for storage or data transfer to local gateway server.</span>
+<span class="c1"># (OPTIONAL: INFORMATION ARE KNOWN THROUGH EXTRA FILE AFTER INSTALLATION)</span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+ECUID None
+ECGID None
+DESTINATION None
+GATEWAY None
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># GENERAL SECTION:</span>
+<span class="c1"># Specific storage, notification and data transfer settings.</span>
+<span class="c1"># Selection of ECMWF access interface and extra output options. </span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+DEBUG <span class="m">0</span>
+REQUEST <span class="m">0</span>
+PUBLIC <span class="m">0</span>
+OPER <span class="m">0</span>
+ECSTORAGE <span class="m">0</span>
+ECTRANS <span class="m">0</span>
+PREFIX <span class="s1">'EN'</span>
+ECFSDIR <span class="s1">'ectmp:/${USER}/econdemand/'</span>
+MAILFAIL <span class="o">[</span><span class="s1">'${USER}'</span><span class="o">]</span>
+MAILOPS <span class="o">[</span><span class="s1">'${USER}'</span><span class="o">]</span>
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># TIME SECTION:</span>
+<span class="c1"># Selection of time period and temporal resolution for extraction period.</span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+START_DATE
+END_DATE
+DATE_CHUNK <span class="m">3</span>
+DTIME None
+BASETIME None
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># DATA SECTION:</span>
+<span class="c1"># General description of data set.</span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+CLASS None
+DATASET None
+STREAM None
+NUMBER <span class="s1">'OFF'</span>
+EXPVER <span class="s1">'1'</span>
+FORMAT <span class="s1">'GRIB1'</span>
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># DATA FIELDS SECTION:</span>
+<span class="c1"># Specific selection of field composition regarding type, analysis or forecast </span>
+<span class="c1"># time and the forecast time step.</span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+TYPE None
+TIME None
+STEP None
+MAXSTEP None
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># FLUX DATA FIELDS SECTION:</span>
+<span class="c1"># Specific selection of flux field composition regarding forecast field type</span>
+<span class="c1"># the forecast start times and the maximum forecast step per start time.</span>
+<span class="c1"># Specification of disaggregation method of precipitation data.</span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+ACCTYPE None
+ACCTIME None
+ACCMAXSTEP None
+RRINT <span class="m">0</span>
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># DOMAIN SECTION: </span>
+<span class="c1"># Definition of horizontal area, spatial resolution and vertical levels. </span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+GRID None
+RESOL None
+SMOOTH <span class="m">0</span>
+LEFT None
+LOWER None
+UPPER None
+RIGHT None
+LEVEL None
+LEVELIST None
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># VERTICAL WIND SECTION:</span>
+<span class="c1"># Selection of vertical wind calculation method.</span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+GAUSS <span class="m">0</span>
+ACCURACY <span class="m">24</span>
+OMEGA <span class="m">0</span>
+OMEGADIFF <span class="m">0</span>
+ETA <span class="m">0</span>
+ETADIFF <span class="m">0</span>
+DPDETA <span class="m">1</span>
+ETAPAR <span class="m">77</span>
+
+<span class="c1">#===============================================================================</span>
+<span class="c1"># ADDITIONAL DATA SECTION:</span>
+<span class="c1"># Specification of extra data fields to be extracted.</span>
+<span class="c1">#-------------------------------------------------------------------------------</span>
+CWC <span class="m">0</span>
+WRF <span class="m">0</span>
+DOUBLEELDA <span class="m">0</span>
+ADDPAR None
+</pre></div>
+</div>
+</div>
<div class="toctree-wrapper compound">
</div>
</div>
diff --git a/Documentation/html/Documentation/Input/control_params.html b/Documentation/html/Documentation/Input/control_params.html
index 86a58ba5dcf6df0c8dd0504381c74a08a33c8e97..7c64717bd902826d1edbcd0d2007e0457b2a5a5d 100644
--- a/Documentation/html/Documentation/Input/control_params.html
+++ b/Documentation/html/Documentation/Input/control_params.html
@@ -421,19 +421,6 @@ Possible selections are:
<td><p class="first last">For the ECMWF server it is enough to give ${USER} as input. On local system an actual email is prefered to operate correctly. </p>
</td>
</tr>
-<tr class="row-odd"><td><p class="first last">MAILFAIL</p>
-</td>
-<td><p class="first last">list of String [m1, m2, …]</p>
-</td>
-<td><p class="first last">any number of mail addresses, seperated by comma</p>
-</td>
-<td><p class="first last">[‘”${USER}”]</p>
-</td>
-<td><p class="first last">If there will be an error log on ECMWF servers, the log file will be sent to the list of emails stored in this parameter. The email addresses should be seperated by a comma.</p>
-</td>
-<td><p class="first last">For the ECMWF server it is enough to give ${USER} as input. On local system an actual email is prefered to operate correctly. </p>
-</td>
-</tr>
</tbody>
</table>
</div>
@@ -1091,20 +1078,7 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
</tr>
</thead>
<tbody valign="top">
-<tr class="row-even"><td><p class="first last">WRF</p>
-</td>
-<td><p class="first last">Integer</p>
-</td>
-<td><p class="first last">[0,1]</p>
-</td>
-<td><p class="first last">0</p>
-</td>
-<td><p class="first last">Switch to retrieve additional parameters needed to run WRF (1) or not (0).</p>
-</td>
-<td><p class="first last">Up to now, this is still experimental and not completely tested.</p>
-</td>
-</tr>
-<tr class="row-odd"><td><p class="first last">CWC</p>
+<tr class="row-even"><td><p class="first last">CWC</p>
</td>
<td><p class="first last">Integer</p>
</td>
@@ -1117,7 +1091,7 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
<td><p class="first last"></p>
</td>
</tr>
-<tr class="row-even"><td><p class="first last">DOUBLEELDA</p>
+<tr class="row-odd"><td><p class="first last">DOUBLEELDA</p>
</td>
<td><p class="first last">Integer</p>
</td>
@@ -1130,7 +1104,7 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
<td><p class="first last">Each ensemble member is used to create a new synthesized ensemble member by subtracting 2 * ( current time step value - last time step value ) from the current time step value</p>
</td>
</tr>
-<tr class="row-odd"><td><p class="first last">ADDPAR</p>
+<tr class="row-even"><td><p class="first last">ADDPAR</p>
</td>
<td><p class="first last">String [p1/p2/../pn]</p>
</td>
diff --git a/Documentation/html/Documentation/Input/ecmwf_env.html b/Documentation/html/Documentation/Input/ecmwf_env.html
index 51f47ff03a2d7017d93a6375f3b3244254bdb44b..e54ca2f5b5096dcd87d20fda5a562990405c38de 100644
--- a/Documentation/html/Documentation/Input/ecmwf_env.html
+++ b/Documentation/html/Documentation/Input/ecmwf_env.html
@@ -193,7 +193,7 @@
<div class="section" id="ecmwf-user-credential-file-ecmwf-env">
<h1>ECMWF User Credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code><a class="headerlink" href="#ecmwf-user-credential-file-ecmwf-env" title="Permalink to this headline">¶</a></h1>
-<p>This file contains the user credentials for working on ECMWF servers and transfering files between the ECMWF servers and the local gateway server. It is located in the <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/run</span></code> directory and will be created in the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
+<p>This file contains the user credentials for working on ECMWF servers and transferring files between the ECMWF servers and the local gateway server. It is located in the <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/run</span></code> directory and will be created in the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
<p>This file is based on the template <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV.template</span></code> which is located in the <code class="docutils literal notranslate"><span class="pre">templates</span></code> directory.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
diff --git a/Documentation/html/Documentation/Input/fortran_makefile.html b/Documentation/html/Documentation/Input/fortran_makefile.html
index 0ca4193d7d23e03f86c05de2b517537fcd9b4e21..a0a062ee039ceb62586a22c625adff1fdcfff52f 100644
--- a/Documentation/html/Documentation/Input/fortran_makefile.html
+++ b/Documentation/html/Documentation/Input/fortran_makefile.html
@@ -226,7 +226,7 @@ A list of these <code class="docutils literal notranslate"><span class="pre">Mak
</div>
</div></blockquote>
<p>For instructions on how to adapt the <code class="docutils literal notranslate"><span class="pre">Makefiles</span></code> for the local application mode
-please see <a class="reference internal" href="../../installation.html#ref-install-local"><span class="std std-ref">Local installation</span></a>.</p>
+please see <a class="reference internal" href="../../Installation/local.html#ref-install-local"><span class="std std-ref">Local installation</span></a>.</p>
<div class="toctree-wrapper compound">
</div>
</div>
diff --git a/Documentation/html/Documentation/Input/run.html b/Documentation/html/Documentation/Input/run.html
index 2c49c5224b36eb36a36edb4fd37fe1066d8387b1..bb254bee4ea21d6988ade7a4334481b49dcb719e 100644
--- a/Documentation/html/Documentation/Input/run.html
+++ b/Documentation/html/Documentation/Input/run.html
@@ -477,6 +477,113 @@ the command line parameters and the so-called <code class="docutils literal notr
</div>
<div class="section" id="content-of-run-sh">
<h2>Content of <code class="docutils literal notranslate"><span class="pre">run.sh</span></code><a class="headerlink" href="#content-of-run-sh" title="Permalink to this headline">¶</a></h2>
+<div class="literal-block-wrapper docutils container" id="id2">
+<div class="code-block-caption"><span class="caption-text">run.sh</span><a class="headerlink" href="#id2" title="Permalink to this code">¶</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/bash</span>
+<span class="c1">#</span>
+<span class="c1"># @Author: Anne Philipp</span>
+<span class="c1">#</span>
+<span class="c1"># @Date: October, 4 2018</span>
+<span class="c1">#</span>
+<span class="c1"># @Description: </span>
+<span class="c1">#</span>
+
+
+<span class="c1"># -----------------------------------------------------------------</span>
+<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
+<span class="c1"># </span>
+<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETERS:</span>
+
+<span class="nv">QUEUE</span><span class="o">=</span><span class="s1">'ecgate'</span>
+<span class="nv">START_DATE</span><span class="o">=</span>None
+<span class="nv">END_DATE</span><span class="o">=</span>None
+<span class="nv">DATE_CHUNK</span><span class="o">=</span>None
+<span class="nv">JOB_CHUNK</span><span class="o">=</span><span class="m">3</span>
+<span class="nv">BASETIME</span><span class="o">=</span>None
+<span class="nv">STEP</span><span class="o">=</span>None
+<span class="nv">LEVELIST</span><span class="o">=</span>None
+<span class="nv">AREA</span><span class="o">=</span>None
+<span class="nv">INPUTDIR</span><span class="o">=</span>None
+<span class="nv">OUTPUTDIR</span><span class="o">=</span>None
+<span class="nv">PP_ID</span><span class="o">=</span>None
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.temp'</span>
+<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_OD.OPER.FC.gauss.global'</span>
+<span class="nv">DEBUG</span><span class="o">=</span><span class="m">0</span>
+<span class="nv">REQUEST</span><span class="o">=</span><span class="m">2</span>
+<span class="nv">PUBLIC</span><span class="o">=</span><span class="m">0</span>
+
+<span class="c1"># -----------------------------------------------------------------</span>
+<span class="c1">#</span>
+<span class="c1"># AFTER THIS LINE THE USER DOES NOT HAVE TO CHANGE ANYTHING !!!</span>
+<span class="c1">#</span>
+<span class="c1"># -----------------------------------------------------------------</span>
+
+<span class="c1"># PATH TO SUBMISSION SCRIPT</span>
+<span class="nv">pyscript</span><span class="o">=</span>../Source/Python/submit.py
+
+<span class="c1"># INITIALIZE EMPTY PARAMETERLIST</span>
+<span class="nv">parameterlist</span><span class="o">=</span><span class="s2">""</span>
+
+<span class="c1"># CHECK FOR MORE PARAMETER </span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$START_DATE</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --start_date=</span><span class="nv">$START_DATE</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$END_DATE</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --end_date=</span><span class="nv">$END_DATE</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$DATE_CHUNK</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --date_chunk=</span><span class="nv">$DATE_CHUNK</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$JOB_CHUNK</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --job_chunk=</span><span class="nv">$JOB_CHUNK</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$BASETIME</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --basetime=</span><span class="nv">$BASETIME</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$STEP</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --step=</span><span class="nv">$STEP</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$LEVELIST</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --levelist=</span><span class="nv">$LEVELIST</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$AREA</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --area=</span><span class="nv">$AREA</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$INPUTDIR</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --inputdir=</span><span class="nv">$INPUTDIR</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$OUTPUTDIR</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --outputdir=</span><span class="nv">$OUTPUTDIR</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$PP_ID</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --ppid=</span><span class="nv">$PP_ID</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$JOB_TEMPLATE</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --job_template=</span><span class="nv">$JOB_TEMPLATE</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$QUEUE</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --queue=</span><span class="nv">$QUEUE</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$CONTROLFILE</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --controlfile=</span><span class="nv">$CONTROLFILE</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$DEBUG</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --debug=</span><span class="nv">$DEBUG</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$REQUEST</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --request=</span><span class="nv">$REQUEST</span><span class="s2">"</span>
+<span class="k">fi</span>
+<span class="k">if</span> <span class="o">[</span> -n <span class="s2">"</span><span class="nv">$PUBLIC</span><span class="s2">"</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
+ <span class="nv">parameterlist</span><span class="o">+=</span><span class="s2">" --public=</span><span class="nv">$PUBLIC</span><span class="s2">"</span>
+<span class="k">fi</span>
+
+<span class="c1"># -----------------------------------------------------------------</span>
+<span class="c1"># CALL SCRIPT WITH DETERMINED COMMANDLINE ARGUMENTS</span>
+
+<span class="nv">$pyscript</span> <span class="nv">$parameterlist</span>
+</pre></div>
+</div>
+</div>
</div>
<div class="section" id="usage-of-submit-py-optional">
<span id="ref-install-script"></span><h2>Usage of <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> (optional)<a class="headerlink" href="#usage-of-submit-py-optional" title="Permalink to this headline">¶</a></h2>
diff --git a/Documentation/html/Documentation/Overview/app_modes.html b/Documentation/html/Documentation/Overview/app_modes.html
index 48f897da16773d1d00c2395a0f28ff985ccddd97..ff2839d116a04d6f992f4e2763fdeca2f9eeeff2 100644
--- a/Documentation/html/Documentation/Overview/app_modes.html
+++ b/Documentation/html/Documentation/Overview/app_modes.html
@@ -98,7 +98,6 @@
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="prog_flow.html">Program Flow</a></li>
-<li class="toctree-l3"><a class="reference internal" href="convert.html">CONVERT</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="../input.html">Control & Input Data</a></li>
@@ -198,7 +197,7 @@
<div><ol class="arabic simple" start="2">
<li><dl class="first docutils">
<dt>Gateway (member)</dt>
-<dd>The <strong>Gateway mode</strong> can be used if a local member state gateway server is in place. Then the job scripts can be submitted to the ECMWF Linux member state server via the ECMWF web access tool <code class="docutils literal notranslate"><span class="pre">ecaccess</span></code>. The installation script of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> must be executed at the local gateway server such that the software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory at the ECMWF server and some extra setup is done in the local <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory at the local gateway server. For more information about establishing a gateway server please see section ???. For the <strong>Gateway mode</strong> the necessary environment has to be established which is described in <a class="reference internal" href="../../installation.html#ref-prep-gateway"><span class="std std-ref">Prepare gateway environment</span></a>.</dd>
+<dd>The <strong>Gateway mode</strong> can be used if a local member state gateway server is in place. Then the job scripts can be submitted to the ECMWF Linux member state server via the ECMWF web access tool <code class="docutils literal notranslate"><span class="pre">ecaccess</span></code>. The installation script of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> must be executed at the local gateway server such that the software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory at the ECMWF server and some extra setup is done in the local <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory at the local gateway server. For more information about establishing a gateway server please see section ???. For the <strong>Gateway mode</strong> the necessary environment has to be established which is described in <a class="reference internal" href="../../Installation/gateway.html#ref-prep-gateway"><span class="std std-ref">Prepare gateway environment</span></a>.</dd>
</dl>
</li>
</ol>
@@ -207,12 +206,12 @@
<div><ol class="arabic simple" start="3">
<li><dl class="first docutils">
<dt>Local member</dt>
-<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.html#ref-local-mode"><span class="std std-ref">Local mode</span></a>.</dd>
+<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>
</dl>
</li>
<li><dl class="first docutils">
<dt>Local public</dt>
-<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.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>
+<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>
</dl>
</li>
</ol>
diff --git a/Documentation/html/Ecmwf/access.html b/Documentation/html/Ecmwf/access.html
index fc733d2b4d6d0345a43bfd9ba08878f8e959b454..c67083684f4181895348b5085c641ead66b8cd35 100644
--- a/Documentation/html/Ecmwf/access.html
+++ b/Documentation/html/Ecmwf/access.html
@@ -181,7 +181,7 @@
<dt><strong>Member state user</strong>:</dt>
<dd>This access mode allows the user to work directly on the ECMWF Linux Member State Servers or via a Web Access Toolkit <code class="docutils literal notranslate"><span class="pre">ecaccess</span></code> through a local Member State Gateway Server. This enables the user to have direct and full access to the Mars archive. There might be some limitations in user rights such as the declined access to the latest forecasts. This has to be discussed with the <a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Computing Representative</a>. This user group is also able to work from their local facilities without a gateway server in the same way a <strong>public</strong> user would. The only difference is the connection with the Web API. However, this is automatically selected by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</dd>
<dt><strong>Public user</strong>:</dt>
-<dd>This access mode allows every user to access the ECMWF <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">public datasets</a> from their local facilities. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able (tested for the use with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>) to extract the re-analysis datasets such as ERA-Interim and CERA-20C. The main difference to the <strong>member state user</strong> is the method of access with the Web API and the availability of data. For example, in ERA-Interim there is only a 6-hourly temporal resolution instead of 3 hours. The access method is selected by providing the command line argument “public=1” and providing the MARS keyword “dataset” in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file. Also, the user has to explicitly accept the license of the dataset to be retrieved. This can be done as described in the installation process at section <a class="reference internal" href="../installation.html#ref-licence"><span class="std std-ref">Agree on licences for public datasets</span></a>.</dd>
+<dd>This access mode allows every user to access the ECMWF <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">public datasets</a> from their local facilities. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able (tested for the use with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>) to extract the re-analysis datasets such as ERA-Interim and CERA-20C. The main difference to the <strong>member state user</strong> is the method of access with the Web API and the availability of data. For example, in ERA-Interim there is only a 6-hourly temporal resolution instead of 3 hours. The access method is selected by providing the command line argument “public=1” and providing the MARS keyword “dataset” in the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file. Also, the user has to explicitly accept the license of the dataset to be retrieved. This can be done as described in the installation process at section <a class="reference internal" href="../installation.html#ref-licence"><span class="std std-ref">Licence agreement for public datasets</span></a>.</dd>
</dl>
<div class="admonition note">
<p class="first admonition-title">Note</p>
diff --git a/Documentation/html/Installation/gateway.html b/Documentation/html/Installation/gateway.html
new file mode 100644
index 0000000000000000000000000000000000000000..66494f842cf503d0f9e01ce0ff96238ba7b70e57
--- /dev/null
+++ b/Documentation/html/Installation/gateway.html
@@ -0,0 +1,335 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+ <meta charset="utf-8">
+
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+ <title>Gateway mode installation — flex_extract 7.1 alpha documentation</title>
+
+
+
+
+
+
+
+
+ <script type="text/javascript" src="../_static/js/modernizr.min.js"></script>
+
+
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+ <script type="text/javascript" src="../_static/js/theme.js"></script>
+
+
+
+
+ <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/css/custom.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/css/theme_overrides.css" type="text/css" />
+ <link rel="index" title="Index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="next" title="Local mode installation" href="local.html" />
+ <link rel="prev" title="Remote mode installation" href="remote.html" />
+</head>
+
+<body class="wy-body-for-nav">
+
+
+ <div class="wy-grid-for-nav">
+
+ <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+ <div class="wy-side-scroll">
+ <div class="wy-side-nav-search" >
+
+
+
+ <a href="../index.html" class="icon icon-home"> flex_extract
+
+
+
+ </a>
+
+
+
+
+ <div class="version">
+ 7.1
+ </div>
+
+
+
+
+<div role="search">
+ <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+ <input type="text" name="q" placeholder="Search docs" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+
+
+ </div>
+
+ <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+
+
+
+
+ <p class="caption"><span class="caption-text">Table of Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../installation.html">Installation</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#registration-at-ecmwf">Registration at ECMWF</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
+<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>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#environment-requirements">Environment requirements</a></li>
+<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">
+<li class="toctree-l3"><a class="reference internal" href="remote.html">Remote mode installation</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Gateway mode installation</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#gateway-environment-requirements">Gateway environment requirements</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#prepare-gateway-environment">Prepare gateway environment</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#test-gateway-environment">Test gateway environment</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#gateway-installation">Gateway installation</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="local.html">Local mode installation</a></li>
+</ul>
+</li>
+<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>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#test-installation">Test installation</a></li>
+</ul>
+</li>
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+ <div class="section" id="gateway-mode-installation">
+<h1>Gateway mode installation<a class="headerlink" href="#gateway-mode-installation" title="Permalink to this headline">¶</a></h1>
+<div class="toctree-wrapper compound">
+</div>
+<div class="section" id="gateway-environment-requirements">
+<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>
+<p>The environment on your local system has to provide these software packages
+and libraries, since <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> does only prepare the job script and send
+it to the ECMWF servers:</p>
+<ul class="simple">
+<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>
+<li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
+<li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
+</ul>
+</div>
+<div class="section" id="prepare-gateway-environment">
+<span id="ref-prep-gateway"></span><h2>Prepare gateway environment<a class="headerlink" href="#prepare-gateway-environment" title="Permalink to this headline">¶</a></h2>
+<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.
+The installation was tested on a <em>GNU/Linux Debian buster</em> and an <em>Ubuntu 18.04 Bionic Beaver</em> system.</p>
+<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Linux Debian or Ubuntu system do</span>
+<span class="c1"># (if not already available):</span>
+apt-get install python3
+apt-get install pip
+apt-get install genshi
+apt-get install numpy
+</pre></div>
+</div>
+</div>
+<div class="section" id="test-gateway-environment">
+<span id="ref-test-gateway"></span><h2>Test gateway environment<a class="headerlink" href="#test-gateway-environment" title="Permalink to this headline">¶</a></h2>
+<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>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span>
+<span class="kn">import</span> <span class="nn">genshi</span>
+<span class="kn">import</span> <span class="nn">numpy</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="gateway-installation">
+<span id="ref-install-gateway"></span><h2>Gateway installation<a class="headerlink" href="#gateway-installation" title="Permalink to this headline">¶</a></h2>
+<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>
+<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> please also create an association.
+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>
+<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>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ecaccess-certificate-create
+Please enter your user-id: example_username
+Your passcode: ***
+</pre></div>
+</div>
+<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.
+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>
+<div class="literal-block-wrapper docutils container" id="setup-sh">
+<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>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># -----------------------------------------------------------------</span>
+<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
+<span class="c1">#</span>
+<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
+<span class="c1">#</span>
+<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'ecgate'</span>
+<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'Makefile.gfortran'</span>
+<span class="nv">ECUID</span><span class="o">=</span><span class="s1">'uid'</span>
+<span class="nv">ECGID</span><span class="o">=</span><span class="s1">'gid'</span>
+<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'server.example.edu'</span>
+<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'example@genericSftp'</span>
+<span class="nv">INSTALLDIR</span><span class="o">=</span>None
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
+</pre></div>
+</div>
+</div>
+<p>Afterwards, type:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup.sh
+</pre></div>
+</div>
+<p>to start the installation. You should see the following output at the command line.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
+Create tarball ...
+Job compilation script has been submitted to ecgate <span class="k">for</span> installation in <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_vX.X
+You should get an email with subject <span class="s2">"flexcompile"</span> within the next few minutes!
+</pre></div>
+</div>
+<p>The email content should look like this with a “SUCCESS” statement in the last line:</p>
+<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
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp grphreal.f
+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 ftrafo.f
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
+-rwxr-x---. <span class="m">1</span> USER at <span class="m">353134</span> May <span class="m">23</span> <span class="m">12</span>:27 CONVERT2
+SUCCESS!
+</pre></div>
+</div>
+</div>
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+<li class="toctree-l1 current"><a class="reference internal" href="../installation.html">Installation</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#registration-at-ecmwf">Registration at ECMWF</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
+<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>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#environment-requirements">Environment requirements</a></li>
+<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">
+<li class="toctree-l3"><a class="reference internal" href="remote.html">Remote mode installation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="gateway.html">Gateway mode installation</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Local mode installation</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#local-environment-requirements">Local environment requirements</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#prepare-local-environment">Prepare local environment</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#test-local-environment">Test local environment</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#local-installation">Local installation</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<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>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#test-installation">Test installation</a></li>
+</ul>
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+<li class="toctree-l1"><a class="reference internal" href="../quick_start.html">Quick Start</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../evaluation.html">Evaluation</a></li>
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+
+ <div class="section" id="local-mode-installation">
+<h1>Local mode installation<a class="headerlink" href="#local-mode-installation" title="Permalink to this headline">¶</a></h1>
+<div class="toctree-wrapper compound">
+</div>
+<div class="section" id="local-environment-requirements">
+<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>
+<p>For the local access modes <strong>member</strong> and <strong>public</strong> there is no difference in
+the installation process.</p>
+<p>The environment on your local system has to provide these software packages
+and libraries, since all extraction and preparation is done at the local system:</p>
+<table border="1" class="docutils">
+<colgroup>
+<col width="74%" />
+<col width="26%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>Python part</td>
+<td>Fortran part</td>
+</tr>
+<tr class="row-even"><td><ul class="first last simple">
+<li><a class="reference external" href="https://www.python.org/downloads/">Python3</a></li>
+<li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
+<li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
+<li><a class="reference external" href="https://packages.debian.org/sid/python3-eccodes">eccodes for python</a></li>
+<li><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ecmwf-api-client</a> (everything except ERA5)</li>
+<li><a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> (just for ERA5)</li>
+</ul>
+</td>
+<td><ul class="first last simple">
+<li><a class="reference external" href="https://gcc.gnu.org/wiki/GFortran">gfortran</a></li>
+<li><a class="reference external" href="http://www.fftw.org">fftw3</a></li>
+<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">eccodes</a></li>
+<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">emoslib</a></li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="section" id="prepare-local-environment">
+<span id="ref-prep-local"></span><h2>Prepare local environment<a class="headerlink" href="#prepare-local-environment" title="Permalink to this headline">¶</a></h2>
+<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.
+The installation was tested on a <em>Debian GNU/Linux buster/sid</em> and an <em>Ubuntu 18.04 Bionic Beaver</em> system.</p>
+<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Linux Debian or Ubuntu system do</span>
+<span class="c1"># (if not already available):</span>
+apt-get install python3 <span class="o">(</span>usually available on normal Linux systems<span class="o">)</span>
+apt-get install pip
+apt-get install gfortran
+apt-get install fftw3-dev
+apt-get install libeccodes-dev
+apt-get install libemos-dev
+apt-get install python3-eccodes
+apt-get install genshi
+apt-get install numpy
+pip install cdsapi
+pip install ecmwf-api-client
+</pre></div>
+</div>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p>In case you would like to use Anaconda Python we recommend you follow the installation instructions of
+<a class="reference external" href="https://docs.anaconda.com/anaconda/install/linux/">Anaconda Python Installation for Linux</a> and then install the
+<code class="docutils literal notranslate"><span class="pre">eccodes</span></code> package from <code class="docutils literal notranslate"><span class="pre">conda</span></code> with:</p>
+<div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>conda install conda-forge::python-eccodes
+</pre></div>
+</div>
+</div>
+<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>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<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>
+</div>
+<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>
+<dl class="docutils">
+<dt>ECMWF Web API:</dt>
+<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>
+<dt>CDS API:</dt>
+<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>
+</dl>
+</div>
+<div class="section" id="test-local-environment">
+<span id="ref-test-local"></span><h2>Test local environment<a class="headerlink" href="#test-local-environment" title="Permalink to this headline">¶</a></h2>
+<p>Check the availability of the system packages with <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or <code class="docutils literal notranslate"><span class="pre">rpm</span> <span class="pre">-q</span> <span class="pre"><package_name></span></code>, depending on your system. For example:</p>
+<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>$ dpkg -s libeccodes-dev <span class="p">|</span> grep Status
+<span class="c1"># or</span>
+$ rpm -q libeccodes-dev
+</pre></div>
+</div>
+<p>Afterwards, 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>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span>
+<span class="kn">import</span> <span class="nn">eccodes</span>
+<span class="kn">import</span> <span class="nn">genshi</span>
+<span class="kn">import</span> <span class="nn">numpy</span>
+<span class="kn">import</span> <span class="nn">cdsapi</span>
+<span class="kn">import</span> <span class="nn">ecmwfapi</span>
+</pre></div>
+</div>
+<div class="section" id="test-the-web-api-s">
+<h3>Test the Web API’s<a class="headerlink" href="#test-the-web-api-s" title="Permalink to this headline">¶</a></h3>
+<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>
+<div class="section" id="ecmwf-web-api">
+<h4>ECMWF Web API<a class="headerlink" href="#ecmwf-web-api" title="Permalink to this headline">¶</a></h4>
+<table border="1" class="docutils">
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>Please use this piece of python code for <strong>Member user</strong>:</td>
+<td>Please use this piece of python code for <strong>Public user</strong>:</td>
+</tr>
+<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>
+
+<span class="n">server</span> <span class="o">=</span> <span class="n">ECMWFService</span><span class="p">(</span><span class="s1">'mars'</span><span class="p">)</span>
+
+<span class="n">server</span><span class="o">.</span><span class="n">retrieve</span><span class="p">({</span>
+ <span class="s1">'stream'</span> <span class="p">:</span> <span class="s2">"oper"</span><span class="p">,</span>
+ <span class="s1">'levtype'</span> <span class="p">:</span> <span class="s2">"sfc"</span><span class="p">,</span>
+ <span class="s1">'param'</span> <span class="p">:</span> <span class="s2">"165.128/166.128/167.128"</span><span class="p">,</span>
+ <span class="s1">'dataset'</span> <span class="p">:</span> <span class="s2">"interim"</span><span class="p">,</span>
+ <span class="s1">'step'</span> <span class="p">:</span> <span class="s2">"0"</span><span class="p">,</span>
+ <span class="s1">'grid'</span> <span class="p">:</span> <span class="s2">"0.75/0.75"</span><span class="p">,</span>
+ <span class="s1">'time'</span> <span class="p">:</span> <span class="s2">"00/06/12/18"</span><span class="p">,</span>
+ <span class="s1">'date'</span> <span class="p">:</span> <span class="s2">"2014-07-01/to/2014-07-31"</span><span class="p">,</span>
+ <span class="s1">'type'</span> <span class="p">:</span> <span class="s2">"an"</span><span class="p">,</span>
+ <span class="s1">'class'</span> <span class="p">:</span> <span class="s2">"ei"</span><span class="p">,</span>
+ <span class="s1">'target'</span> <span class="p">:</span> <span class="s2">"download_erainterim_ecmwfapi.grib"</span>
+<span class="p">})</span>
+</pre></div>
+</div>
+</td>
+<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">ECMWFDataServer</span>
+
+<span class="n">server</span> <span class="o">=</span> <span class="n">ECMWFDataServer</span><span class="p">()</span>
+
+<span class="n">server</span><span class="o">.</span><span class="n">retrieve</span><span class="p">({</span>
+ <span class="s1">'stream'</span> <span class="p">:</span> <span class="s2">"enda"</span><span class="p">,</span>
+ <span class="s1">'levtype'</span> <span class="p">:</span> <span class="s2">"sfc"</span><span class="p">,</span>
+ <span class="s1">'param'</span> <span class="p">:</span> <span class="s2">"165.128/166.128/167.128"</span><span class="p">,</span>
+ <span class="s1">'dataset'</span> <span class="p">:</span> <span class="s2">"cera20c"</span><span class="p">,</span>
+ <span class="s1">'step'</span> <span class="p">:</span> <span class="s2">"0"</span><span class="p">,</span>
+ <span class="s1">'grid'</span> <span class="p">:</span> <span class="s2">"1./1."</span><span class="p">,</span>
+ <span class="s1">'time'</span> <span class="p">:</span> <span class="s2">"00/06/12/18"</span><span class="p">,</span>
+ <span class="s1">'date'</span> <span class="p">:</span> <span class="s2">"2000-07-01/to/2000-07-31"</span><span class="p">,</span>
+ <span class="s1">'type'</span> <span class="p">:</span> <span class="s2">"an"</span><span class="p">,</span>
+ <span class="s1">'class'</span> <span class="p">:</span> <span class="s2">"ep"</span><span class="p">,</span>
+ <span class="s1">'target'</span> <span class="p">:</span> <span class="s2">"download_cera20c_ecmwfapi.grib"</span>
+<span class="p">})</span>
+</pre></div>
+</div>
+</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="section" id="cds-api">
+<h4>CDS API<a class="headerlink" href="#cds-api" title="Permalink to this headline">¶</a></h4>
+<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>
+<p>Please use this piece of python code to retrieve a small sample of <em>ERA5</em> pressure levels:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span>
+
+<span class="n">c</span> <span class="o">=</span> <span class="n">cdsapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span>
+
+<span class="n">c</span><span class="o">.</span><span class="n">retrieve</span><span class="p">(</span><span class="s2">"reanalysis-era5-pressure-levels"</span><span class="p">,</span>
+<span class="p">{</span>
+<span class="s2">"variable"</span><span class="p">:</span> <span class="s2">"temperature"</span><span class="p">,</span>
+<span class="s2">"pressure_level"</span><span class="p">:</span> <span class="s2">"1000"</span><span class="p">,</span>
+<span class="s2">"product_type"</span><span class="p">:</span> <span class="s2">"reanalysis"</span><span class="p">,</span>
+<span class="s2">"year"</span><span class="p">:</span> <span class="s2">"2008"</span><span class="p">,</span>
+<span class="s2">"month"</span><span class="p">:</span> <span class="s2">"01"</span><span class="p">,</span>
+<span class="s2">"day"</span><span class="p">:</span> <span class="s2">"01"</span><span class="p">,</span>
+<span class="s2">"time"</span><span class="p">:</span> <span class="s2">"12:00"</span><span class="p">,</span>
+<span class="s2">"format"</span><span class="p">:</span> <span class="s2">"grib"</span>
+<span class="p">},</span>
+<span class="s2">"download_cdsapi.grib"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Afterwards, when you know that the CDS API generally works, you can try to extract some
+data from the MARS archive. From the latest experience we know that this can take a while.</p>
+<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>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span>
+
+<span class="n">c</span> <span class="o">=</span> <span class="n">cdsapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span>
+
+<span class="n">c</span><span class="o">.</span><span class="n">retrieve</span><span class="p">(</span><span class="s1">'reanalysis-era5-complete'</span><span class="p">,</span>
+<span class="p">{</span>
+ <span class="s1">'class'</span> <span class="p">:</span> <span class="s1">'ea'</span><span class="p">,</span>
+ <span class="s1">'expver'</span> <span class="p">:</span> <span class="s1">'1'</span><span class="p">,</span>
+ <span class="s1">'stream'</span> <span class="p">:</span> <span class="s1">'oper'</span><span class="p">,</span>
+ <span class="s1">'type'</span> <span class="p">:</span> <span class="s1">'fc'</span><span class="p">,</span>
+ <span class="s1">'step'</span> <span class="p">:</span> <span class="s1">'3/to/12/by/3'</span><span class="p">,</span>
+ <span class="s1">'param'</span> <span class="p">:</span> <span class="s1">'130.128'</span><span class="p">,</span>
+ <span class="s1">'levtype'</span> <span class="p">:</span> <span class="s1">'ml'</span><span class="p">,</span>
+ <span class="s1">'levelist'</span><span class="p">:</span> <span class="s1">'135/to/137'</span><span class="p">,</span>
+ <span class="s1">'date'</span> <span class="p">:</span> <span class="s1">'2013-01-01'</span><span class="p">,</span>
+ <span class="s1">'time'</span> <span class="p">:</span> <span class="s1">'06/18'</span><span class="p">,</span>
+ <span class="s1">'area'</span> <span class="p">:</span> <span class="s1">'50/-5/40/5'</span><span class="p">,</span>
+ <span class="s1">'grid'</span> <span class="p">:</span> <span class="s1">'1.0/1.0'</span><span class="p">,</span>
+ <span class="s1">'format'</span> <span class="p">:</span> <span class="s1">'grib'</span><span class="p">,</span>
+<span class="p">},</span> <span class="s1">'download_era5_cdsapi.grib'</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+</div>
+<div class="section" id="local-installation">
+<span id="ref-install-local"></span><h2>Local installation<a class="headerlink" href="#local-installation" title="Permalink to this headline">¶</a></h2>
+<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.)
+<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
+the <code class="docutils literal notranslate"><span class="pre">ifort</span></code> compiler:</p>
+<blockquote>
+<div><ul class="simple">
+<li>Makefile.local.gfortran</li>
+<li>Makefile.local.ifort</li>
+</ul>
+</div></blockquote>
+<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
+<code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted with the current version number.</p>
+<div class="admonition caution">
+<p class="first admonition-title">Caution</p>
+<p class="last">It is necessary to adapt <strong>ECCODES_INCLUDE_DIR</strong> and <strong>ECCODES_LIB</strong> in these
+<code class="docutils literal notranslate"><span class="pre">Makefiles</span></code>.</p>
+</div>
+<p>So starting from the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>,
+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
+choice to modify with an editor of your choice. We use the <code class="docutils literal notranslate"><span class="pre">nedit</span></code> in this case.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> flex_extract_vX.X/source/fortran
+nedit Makefile.local.gfortran
+</pre></div>
+</div>
+<p>Edit the pathes to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library on your local machine.</p>
+<div class="admonition caution">
+<p class="first admonition-title">Caution</p>
+<p>This can vary from system to system.
+It is suggested to use a command like</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># for the ECCODES_INCLUDE_DIR path do:</span>
+$ dpkg -L libeccodes-dev <span class="p">|</span> grep eccodes.mod
+<span class="c1"># for the ECCODES_LIB path do:</span>
+$ dpkg -L libeccodes-dev <span class="p">|</span> grep libeccodes.so
+</pre></div>
+</div>
+<p class="last">to find out the path to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library.</p>
+</div>
+<p>Substitute these paths in the <code class="docutils literal notranslate"><span class="pre">Makefile</span></code> for parameters <strong>ECCODES_INCLUDE_DIR</strong>
+and <strong>ECCODES_LIB</strong> and save it.</p>
+<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>
+<span class="nv">ECCODES_INCLUDE_DIR</span><span class="o">=</span>/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
+<span class="nv">ECCODES_LIB</span><span class="o">=</span> -L/usr/lib -leccodes_f90 -leccodes -lm
+</pre></div>
+</div>
+<p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> will be compiled during the
+installation process to get an executable. Therefore the <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>
+has to be set in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script.</p>
+<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
+and adapt the installation parameters in the section labelled with
+“AVAILABLE COMMANDLINE ARGUMENTS TO SET” like shown below.</p>
+<div class="literal-block-wrapper docutils container" id="setup-sh">
+<div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#setup-sh" title="Permalink to this code">¶</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...
+<span class="c1"># -----------------------------------------------------------------</span>
+<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
+<span class="c1">#</span>
+<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
+<span class="c1">#</span>
+<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'local'</span>
+<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'Makefile.local.gfortran'</span>
+<span class="nv">ECUID</span><span class="o">=</span>None
+<span class="nv">ECGID</span><span class="o">=</span>None
+<span class="nv">GATEWAY</span><span class="o">=</span>None
+<span class="nv">DESTINATION</span><span class="o">=</span>None
+<span class="nv">INSTALLDIR</span><span class="o">=</span>None
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
+...
+</pre></div>
+</div>
+</div>
+<p>Afterwards, type:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup.sh
+</pre></div>
+</div>
+<p>to start the installation. You should see the following output at the command line.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
+WARNING: installdir has not been specified
+flex_extract will be installed in here by compiling the Fortran <span class="nb">source</span> in /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/source/fortran
+Install flex_extract_v7.1 software at <span class="nb">local</span> in directory /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1
+
+Using makefile: Makefile.local.gfortran
+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
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp grphreal.f
+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 ftrafo.f
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 rwGRIB2.f90
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 posnam.f
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 preconvert.f90
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -O3 -O3 -fopenmp -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/gcc-4.9.3/grib_api-1.14.3/lib -Bstatic -lgrib_api_f77 -lgrib_api_f90 -lgrib_api -Bdynamic -lm -ljasper -lemosR64
+
+-rwxrwxr-x. <span class="m">1</span> philipa8 tmc <span class="m">282992</span> May <span class="m">23</span> <span class="m">22</span>:27 ./CONVERT2
+</pre></div>
+</div>
+</div>
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+
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+<li class="toctree-l2"><a class="reference internal" href="../installation.html#registration-at-ecmwf">Registration at ECMWF</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
+<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>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#environment-requirements">Environment requirements</a></li>
+<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">
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Remote mode installation</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#remote-environment-requirements">Remote environment requirements</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#prepare-remote-environment">Prepare remote environment</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#remote-installation">Remote installation</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="gateway.html">Gateway mode installation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="local.html">Local mode installation</a></li>
+</ul>
+</li>
+<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>
+<li class="toctree-l2"><a class="reference internal" href="../installation.html#test-installation">Test installation</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../quick_start.html">Quick Start</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
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+ <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+ <div itemprop="articleBody">
+
+ <div class="section" id="remote-mode-installation">
+<h1>Remote mode installation<a class="headerlink" href="#remote-mode-installation" title="Permalink to this headline">¶</a></h1>
+<div class="toctree-wrapper compound">
+</div>
+<div class="section" id="remote-environment-requirements">
+<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>
+<p>The environment for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> on ECMWF servers has to provide these
+software packages and libraries:</p>
+<table border="1" class="docutils">
+<colgroup>
+<col width="61%" />
+<col width="39%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>Python part</td>
+<td>Fortran part</td>
+</tr>
+<tr class="row-even"><td><ul class="first last simple">
+<li><a class="reference external" href="https://www.python.org/downloads/">Python3</a></li>
+<li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
+<li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
+<li><a class="reference external" href="https://packages.debian.org/sid/python3-eccodes">eccodes for python</a></li>
+</ul>
+</td>
+<td><ul class="first last simple">
+<li><a class="reference external" href="https://gcc.gnu.org/wiki/GFortran">gfortran</a></li>
+<li><a class="reference external" href="http://www.fftw.org">fftw3</a></li>
+<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">eccodes</a></li>
+<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">emoslib</a></li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="section" id="prepare-remote-environment">
+<span id="ref-prep-remote"></span><h2>Prepare remote environment<a class="headerlink" href="#prepare-remote-environment" title="Permalink to this headline">¶</a></h2>
+<p>The environment on the ECMWF server (such as <em>ecgate</em> or <em>cca</em>) is already
+prepared. ECMWF server provide all libraries via a module system which is
+going to be selected by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> automatically.</p>
+</div>
+<div class="section" id="remote-installation">
+<span id="ref-install-remote"></span><h2>Remote installation<a class="headerlink" href="#remote-installation" title="Permalink to this headline">¶</a></h2>
+<p>First, log in on one of the ECMWF Linux server, such as <em>ecgate</em> or <em>cca/ccb</em>.
+Substitute <em><ecuid></em> with your ECMWF user name:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ssh -X <ecuid>@ecaccess.ecmwf.int
+</pre></div>
+</div>
+<p>This will lead to the following output on the command line, asking for your
+password:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>Authorized access only.
+
+***************************************************************
+ For further information, read the ECaccess documentation at:
+
+ https://software.ecmwf.int/wiki/display/ECAC/ECaccess+Home
+
+ You can also use ECaccess to load & download files from your
+ EChome, ECscratch or ECfs directories using the ECaccess FTP
+ server:
+
+ ftp://uid@ecaccess.ecmwf.int/
+
+ Please note you must use your UID and ActivID code to login!
+***************************************************************
+
+<ecuid>@131.130.157.5's password: ***
+Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
+
+[<ecuid>@ecgb11 ~]$
+</pre></div>
+</div>
+<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>)
+to the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory of the ECMWF Linux server via <code class="docutils literal notranslate"><span class="pre">scp</span></code>.
+Substitute the <em><localuser></em> and <em><server.edu></em> placeholders with your credentials.
+Untar the file and change into the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp <localuser>@<server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz <span class="nv">$HOME</span>/
+<span class="nb">cd</span> <span class="nv">$HOME</span>
+tar xvf flex_extract_vX.X.tar.gz
+<span class="nb">cd</span> flex_extract_vX.X
+</pre></div>
+</div>
+<p>On these ECMWF servers, it is not necessary to prepare the environment or the
+<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.
+All third party libraries are available from a module system. The <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>
+is optimized for ECMWF servers and the compilation
+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
+batch job queue at ECMWF, does load all relevant modules from the ECMWF’s module system.</p>
+<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
+<code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory for installation.
+Before executing it, it is necessary to adapt some parameters from <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>
+described in <span class="xref std std-doc">Documentation/Input/setup</span>.</p>
+<p>Open <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> with your editor and adapt the values:</p>
+<table border="1" class="docutils">
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>Take this for target = <strong>ectrans</strong></td>
+<td>Take this for target = <strong>cca</strong></td>
+</tr>
+<tr class="row-even"><td><div class="first last highlight-bash notranslate"><div class="highlight"><pre><span></span>...
+<span class="c1"># -----------------------------------------</span>
+<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
+<span class="c1">#</span>
+<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
+<span class="c1">#</span>
+<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'ecgate'</span>
+<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'Makefile.gfortran'</span>
+<span class="nv">ECUID</span><span class="o">=</span><span class="s1">'uid'</span>
+<span class="nv">ECGID</span><span class="o">=</span><span class="s1">'gid'</span>
+<span class="nv">GATEWAY</span><span class="o">=</span>None
+<span class="nv">DESTINATION</span><span class="o">=</span>None
+<span class="nv">INSTALLDIR</span><span class="o">=</span>None
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
+...
+</pre></div>
+</div>
+</td>
+<td><div class="first last highlight-bash notranslate"><div class="highlight"><pre><span></span>...
+<span class="c1"># -----------------------------------------</span>
+<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
+<span class="c1">#</span>
+<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
+<span class="c1">#</span>
+<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'cca'</span>
+<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'Makefile.CRAY'</span>
+<span class="nv">ECUID</span><span class="o">=</span><span class="s1">'uid'</span>
+<span class="nv">ECGID</span><span class="o">=</span><span class="s1">'gid'</span>
+<span class="nv">GATEWAY</span><span class="o">=</span>None
+<span class="nv">DESTINATION</span><span class="o">=</span>None
+<span class="nv">INSTALLDIR</span><span class="o">=</span><span class="s1">''</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
+...
+</pre></div>
+</div>
+</td>
+</tr>
+</tbody>
+</table>
+<p><span class="underline">Please substitute the values of ECUID and ECGID
+with your own credentials and settings.</span></p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">If a local gateway server is available the transfer of files could be done
+via the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. Therefore a valid <em>GATEWAY</em> and <em>DESTINATION</em>
+have to be present and should be set in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file.</p>
+</div>
+<p>Afterwards, type:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>module load python3
+./setup.sh
+</pre></div>
+</div>
+<p>to start the installation. You should see the following output at the command line.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
+Create tarball ...
+Job compilation script has been submitted to ecgate <span class="k">for</span> installation in <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_vX.X
+You should get an email with subject <span class="s2">"flexcompile"</span> within the next few minutes!
+</pre></div>
+</div>
+<p>The email content should look like this with a “SUCCESS” statement in the last line:</p>
+<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
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp grphreal.f
+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 ftrafo.f
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
+gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
+-rwxr-x---. <span class="m">1</span> USER at <span class="m">353134</span> May <span class="m">23</span> <span class="m">12</span>:27 CONVERT2
+SUCCESS!
+</pre></div>
+</div>
+</div>
+</div>
+
+
+ </div>
+
+ </div>
+ <footer>
+
+ <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+
+ <a href="gateway.html" class="btn btn-neutral float-right" title="Gateway mode installation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+
+
+ <a href="../installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+
+ </div>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright 2019, Anne Philipp and Leopold Haimberger
+
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+ </div>
+ </div>
+
+ </section>
+
+ </div>
+
+
+
+ <script type="text/javascript">
+ jQuery(function () {
+ SphinxRtdTheme.Navigation.enable(true);
+ });
+ </script>
+
+
+
+
+
+
+</body>
+</html>
\ No newline at end of file
diff --git a/Documentation/html/Support/faq.html b/Documentation/html/Support/faq.html
index ec37238b156b6dcdfa6492b1f92debcd68c91afc..9f4864f50dfb3feef76261f9fd3c55951dab08d6 100644
--- a/Documentation/html/Support/faq.html
+++ b/Documentation/html/Support/faq.html
@@ -192,7 +192,7 @@ For this case you should follow the following steps:</p>
<li>Install Web API’s <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">CDS API</a> and <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ECMWF Web API</a></li>
<li>Check LD_LIBRARY_PATH environment variable if it contains all paths to the libs</li>
<li>Check available python packages (e.g. import eccodes / import grib_api / import ecmwfapi)</li>
-<li>Start test retrieval (<a class="reference internal" href="../installation.html#ref-test-local"><span class="std std-ref">Test local environment</span></a>)</li>
+<li>Start test retrieval (<a class="reference internal" href="../Installation/local.html#ref-test-local"><span class="std std-ref">Test local environment</span></a>)</li>
<li>Install <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> (<a class="reference internal" href="../installation.html"><span class="doc">Installation</span></a>)</li>
</ol>
</dd>
diff --git a/Documentation/html/_modules/ControlFile.html b/Documentation/html/_modules/ControlFile.html
index 1aedf7d9e40a52e4e5e714601478d10f102ff6ac..d9a507c4bb6233c9158242db4b3ef20407685e73 100644
--- a/Documentation/html/_modules/ControlFile.html
+++ b/Documentation/html/_modules/ControlFile.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for ControlFile</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Leopold Haimberger (University of Vienna)</span>
@@ -185,20 +185,12 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
<span class="c1"># Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span>
-<span class="c1">#</span>
-<span class="c1"># @Class Methods:</span>
-<span class="c1"># __init__</span>
-<span class="c1"># _read_controlfile</span>
-<span class="c1"># __str__</span>
-<span class="c1"># assign_args_to_control</span>
-<span class="c1"># assign_envs_to_control</span>
-<span class="c1"># check_conditions</span>
-<span class="c1"># check_install_conditions</span>
-<span class="c1"># to_list</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># ------------------------------------------------------------------------------</span>
diff --git a/Documentation/html/_modules/EcFlexpart.html b/Documentation/html/_modules/EcFlexpart.html
index 148a8a082897d2e69d85af05e619bbb9c2e392c3..2f9bfe7206c5910055093ac66af4895225e49373 100644
--- a/Documentation/html/_modules/EcFlexpart.html
+++ b/Documentation/html/_modules/EcFlexpart.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for EcFlexpart</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
@@ -203,6 +203,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
@@ -576,15 +578,23 @@
<span class="c1"># ADDITIONAL FIELDS FOR FLEXPART-WRF MODEL (IF QUESTIONED)</span>
<span class="c1"># -----------------------------------------------------------------------</span>
<span class="k">if</span> <span class="n">wrf</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s1">'OG__ML'</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+=</span> <span class="s1">'/Z/VO'</span>
- <span class="k">if</span> <span class="s1">'/D'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s1">'OG__ML'</span><span class="p">][</span><span class="mi">0</span><span class="p">]:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s1">'OG__ML'</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+=</span> <span class="s1">'/D'</span>
+ <span class="c1"># @WRF</span>
+ <span class="c1"># THIS IS NOT YET CORRECTLY IMPLEMENTED !!!</span>
+ <span class="c1">#</span>
+ <span class="c1"># UNDER CONSTRUCTION !!!</span>
+ <span class="c1">#</span>
+
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'WRF VERSION IS UNDER CONSTRUCTION!'</span><span class="p">)</span> <span class="c1"># dummy argument</span>
+
+ <span class="c1">#self.params['OG__ML'][0] += '/Z/VO'</span>
+ <span class="c1">#if '/D' not in self.params['OG__ML'][0]:</span>
+ <span class="c1"># self.params['OG__ML'][0] += '/D'</span>
- <span class="n">wrf_sfc</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'SP'</span><span class="p">,</span><span class="s1">'SKT'</span><span class="p">,</span><span class="s1">'SST'</span><span class="p">,</span><span class="s1">'CI'</span><span class="p">,</span><span class="s1">'STL1'</span><span class="p">,</span><span class="s1">'STL2'</span><span class="p">,</span> <span class="s1">'STL3'</span><span class="p">,</span><span class="s1">'STL4'</span><span class="p">,</span>
- <span class="s1">'SWVL1'</span><span class="p">,</span><span class="s1">'SWVL2'</span><span class="p">,</span><span class="s1">'SWVL3'</span><span class="p">,</span><span class="s1">'SWVL4'</span><span class="p">]</span>
- <span class="k">for</span> <span class="n">par</span> <span class="ow">in</span> <span class="n">wrf_sfc</span><span class="p">:</span>
- <span class="k">if</span> <span class="n">par</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s1">'OG__SL'</span><span class="p">][</span><span class="mi">0</span><span class="p">]:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s1">'OG__SL'</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+=</span> <span class="s1">'/'</span> <span class="o">+</span> <span class="n">par</span>
+ <span class="c1">#wrf_sfc = ['SP','SKT','SST','CI','STL1','STL2', 'STL3','STL4',</span>
+ <span class="c1"># 'SWVL1','SWVL2','SWVL3','SWVL4']</span>
+ <span class="c1">#for par in wrf_sfc:</span>
+ <span class="c1"># if par not in self.params['OG__SL'][0]:</span>
+ <span class="c1"># self.params['OG__SL'][0] += '/' + par</span>
<span class="k">return</span>
@@ -1007,8 +1017,8 @@
<span class="k">if</span> <span class="n">area</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="n">area</span><span class="p">[</span><span class="mi">3</span><span class="p">]:</span>
<span class="n">area</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-=</span> <span class="mi">360</span>
- <span class="n">maxl</span> <span class="o">=</span> <span class="nb">round</span><span class="p">((</span><span class="n">area</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">area</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">/</span> <span class="n">grid</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">+</span> <span class="mi">1</span>
- <span class="n">maxb</span> <span class="o">=</span> <span class="nb">round</span><span class="p">((</span><span class="n">area</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">area</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">/</span> <span class="n">grid</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">maxl</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">round</span><span class="p">((</span><span class="n">area</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">area</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">/</span> <span class="n">grid</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">maxb</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">round</span><span class="p">((</span><span class="n">area</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">area</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">/</span> <span class="n">grid</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span> <span class="o">+</span> <span class="mi">1</span>
<span class="n">stream</span> <span class="o">=</span> <span class="n">namelist_template</span><span class="o">.</span><span class="n">generate</span><span class="p">(</span>
<span class="n">maxl</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">maxl</span><span class="p">),</span>
@@ -1245,9 +1255,9 @@
<span class="n">t_dt</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">'%Y%m</span><span class="si">%d</span><span class="s1">%H'</span><span class="p">)</span> <span class="o">+</span> <span class="n">numbersuffix</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"outputfile = "</span> <span class="o">+</span> <span class="n">fnout</span><span class="p">)</span>
- <span class="n">f_handle</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fnout</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span>
- <span class="n">h_handle</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">hnout</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span>
- <span class="n">g_handle</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">gnout</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span>
+ <span class="n">f_handle</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fnout</span><span class="p">,</span> <span class="s1">'wb'</span><span class="p">)</span>
+ <span class="n">h_handle</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">hnout</span><span class="p">,</span> <span class="s1">'wb'</span><span class="p">)</span>
+ <span class="n">g_handle</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">gnout</span><span class="p">,</span> <span class="s1">'wb'</span><span class="p">)</span>
<span class="c1"># read message for message and store relevant data fields, where</span>
<span class="c1"># data keywords are stored in pars</span>
@@ -1553,13 +1563,13 @@
<span class="c1"># write original time step to flux file as usual</span>
<span class="n">fluxfile</span> <span class="o">=</span> <span class="n">GribUtil</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">inputdir</span><span class="p">,</span> <span class="n">fluxfilename</span><span class="p">))</span>
- <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'a'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'ab'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">wherekeynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'paramId'</span><span class="p">],</span> <span class="n">wherekeyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">142</span><span class="p">],</span>
<span class="n">keynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'perturbationNumber'</span><span class="p">,</span><span class="s1">'date'</span><span class="p">,</span><span class="s1">'time'</span><span class="p">,</span><span class="s1">'stepRange'</span><span class="p">,</span><span class="s1">'values'</span><span class="p">],</span>
<span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="n">inumb</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">date</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">'%Y%m</span><span class="si">%d</span><span class="s1">'</span><span class="p">)),</span>
<span class="n">date</span><span class="o">.</span><span class="n">hour</span><span class="o">*</span><span class="mi">100</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">lsp_new_np</span><span class="p">[</span><span class="n">inumb</span><span class="p">,:,</span><span class="n">it</span><span class="p">]],</span>
<span class="p">)</span>
- <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'a'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'ab'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">wherekeynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'paramId'</span><span class="p">],</span> <span class="n">wherekeyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">143</span><span class="p">],</span>
<span class="n">keynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'perturbationNumber'</span><span class="p">,</span><span class="s1">'date'</span><span class="p">,</span><span class="s1">'time'</span><span class="p">,</span><span class="s1">'stepRange'</span><span class="p">,</span><span class="s1">'values'</span><span class="p">],</span>
<span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="n">inumb</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">date</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">'%Y%m</span><span class="si">%d</span><span class="s1">'</span><span class="p">)),</span>
@@ -1567,13 +1577,13 @@
<span class="p">)</span>
<span class="c1"># rr for first subgrid point is identified by step = 1</span>
- <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'a'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'ab'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">wherekeynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'paramId'</span><span class="p">],</span> <span class="n">wherekeyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">142</span><span class="p">],</span>
<span class="n">keynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'perturbationNumber'</span><span class="p">,</span><span class="s1">'date'</span><span class="p">,</span><span class="s1">'time'</span><span class="p">,</span><span class="s1">'stepRange'</span><span class="p">,</span><span class="s1">'values'</span><span class="p">],</span>
<span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="n">inumb</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">date</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">'%Y%m</span><span class="si">%d</span><span class="s1">'</span><span class="p">)),</span>
<span class="n">date</span><span class="o">.</span><span class="n">hour</span><span class="o">*</span><span class="mi">100</span><span class="p">,</span> <span class="s1">'1'</span><span class="p">,</span> <span class="n">lsp_new_np</span><span class="p">[</span><span class="n">inumb</span><span class="p">,:,</span><span class="n">it</span><span class="o">+</span><span class="mi">1</span><span class="p">]]</span>
<span class="p">)</span>
- <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'a'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'ab'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">wherekeynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'paramId'</span><span class="p">],</span> <span class="n">wherekeyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">143</span><span class="p">],</span>
<span class="n">keynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'perturbationNumber'</span><span class="p">,</span><span class="s1">'date'</span><span class="p">,</span><span class="s1">'time'</span><span class="p">,</span><span class="s1">'stepRange'</span><span class="p">,</span><span class="s1">'values'</span><span class="p">],</span>
<span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="n">inumb</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">date</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">'%Y%m</span><span class="si">%d</span><span class="s1">'</span><span class="p">)),</span>
@@ -1581,13 +1591,13 @@
<span class="p">)</span>
<span class="c1"># rr for second subgrid point is identified by step = 2</span>
- <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'a'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'ab'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">wherekeynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'paramId'</span><span class="p">],</span> <span class="n">wherekeyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">142</span><span class="p">],</span>
<span class="n">keynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'perturbationNumber'</span><span class="p">,</span><span class="s1">'date'</span><span class="p">,</span><span class="s1">'time'</span><span class="p">,</span><span class="s1">'stepRange'</span><span class="p">,</span><span class="s1">'values'</span><span class="p">],</span>
<span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="n">inumb</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">date</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">'%Y%m</span><span class="si">%d</span><span class="s1">'</span><span class="p">)),</span>
<span class="n">date</span><span class="o">.</span><span class="n">hour</span><span class="o">*</span><span class="mi">100</span><span class="p">,</span> <span class="s1">'2'</span><span class="p">,</span> <span class="n">lsp_new_np</span><span class="p">[</span><span class="n">inumb</span><span class="p">,:,</span><span class="n">it</span><span class="o">+</span><span class="mi">2</span><span class="p">]]</span>
<span class="p">)</span>
- <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'a'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">fluxfile</span><span class="o">.</span><span class="n">set_keys</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'ab'</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">wherekeynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'paramId'</span><span class="p">],</span> <span class="n">wherekeyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">143</span><span class="p">],</span>
<span class="n">keynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'perturbationNumber'</span><span class="p">,</span><span class="s1">'date'</span><span class="p">,</span><span class="s1">'time'</span><span class="p">,</span><span class="s1">'stepRange'</span><span class="p">,</span><span class="s1">'values'</span><span class="p">],</span>
<span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="n">inumb</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">date</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">'%Y%m</span><span class="si">%d</span><span class="s1">'</span><span class="p">)),</span>
@@ -1617,10 +1627,10 @@
<span class="n">gribfile</span> <span class="o">=</span> <span class="n">GribUtil</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">inputdir</span><span class="p">,</span><span class="s1">'rr_grib_dummy.grb'</span><span class="p">))</span>
<span class="n">gribfile</span><span class="o">.</span><span class="n">copy_dummy_msg</span><span class="p">(</span><span class="n">ifile</span><span class="p">,</span> <span class="n">keynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'paramId'</span><span class="p">],</span>
- <span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">142</span><span class="p">],</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'w'</span><span class="p">)</span>
+ <span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">142</span><span class="p">],</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'wb'</span><span class="p">)</span>
<span class="n">gribfile</span><span class="o">.</span><span class="n">copy_dummy_msg</span><span class="p">(</span><span class="n">ifile</span><span class="p">,</span> <span class="n">keynames</span><span class="o">=</span><span class="p">[</span><span class="s1">'paramId'</span><span class="p">],</span>
- <span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">143</span><span class="p">],</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'a'</span><span class="p">)</span>
+ <span class="n">keyvalues</span><span class="o">=</span><span class="p">[</span><span class="mi">143</span><span class="p">],</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'ab'</span><span class="p">)</span>
<span class="k">return</span>
@@ -1663,11 +1673,16 @@
<span class="n">end_period</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">strptime</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">end_date</span> <span class="o">+</span> <span class="n">c</span><span class="o">.</span><span class="n">time</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="s1">'%Y%m</span><span class="si">%d</span><span class="s1">%H'</span><span class="p">)</span>
<span class="n">end_period</span> <span class="o">=</span> <span class="n">end_period</span> <span class="o">+</span> <span class="n">timedelta</span><span class="p">(</span><span class="n">hours</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">step</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
- <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">wrf</span><span class="p">:</span>
- <span class="n">table128</span> <span class="o">=</span> <span class="n">init128</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_GRIBTABLE</span><span class="p">)</span>
- <span class="n">wrfpars</span> <span class="o">=</span> <span class="n">to_param_id</span><span class="p">(</span><span class="s1">'sp/mslp/skt/2t/10u/10v/2d/z/lsm/sst/ci/sd/</span><span class="se">\</span>
-<span class="s1"> stl1/stl2/stl3/stl4/swvl1/swvl2/swvl3/swvl4'</span><span class="p">,</span>
- <span class="n">table128</span><span class="p">)</span>
+ <span class="c1"># @WRF</span>
+ <span class="c1"># THIS IS NOT YET CORRECTLY IMPLEMENTED !!!</span>
+ <span class="c1">#</span>
+ <span class="c1"># UNDER CONSTRUCTION !!!</span>
+ <span class="c1">#</span>
+ <span class="c1">#if c.wrf:</span>
+ <span class="c1"># table128 = init128(_config.PATH_GRIBTABLE)</span>
+ <span class="c1"># wrfpars = to_param_id('sp/mslp/skt/2t/10u/10v/2d/z/lsm/sst/ci/sd/\</span>
+ <span class="c1"># stl1/stl2/stl3/stl4/swvl1/swvl2/swvl3/swvl4',</span>
+ <span class="c1"># table128)</span>
<span class="c1"># these numbers are indices for the temporary files "fort.xx"</span>
<span class="c1"># which are used to seperate the grib fields to,</span>
@@ -1719,7 +1734,7 @@
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">fdict</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">fortfile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">inputdir</span><span class="p">,</span> <span class="s1">'fort.'</span> <span class="o">+</span> <span class="n">k</span><span class="p">)</span>
<span class="n">silent_remove</span><span class="p">(</span><span class="n">fortfile</span><span class="p">)</span>
- <span class="n">fdict</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fortfile</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span>
+ <span class="n">fdict</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fortfile</span><span class="p">,</span> <span class="s1">'wb'</span><span class="p">)</span>
<span class="c1">#============================================================================================</span>
<span class="c1"># create correct timestamp from the three time informations</span>
<span class="n">cdate</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">codes_get</span><span class="p">(</span><span class="n">gid</span><span class="p">,</span> <span class="s1">'date'</span><span class="p">))</span>
@@ -1746,11 +1761,16 @@
<span class="k">if</span> <span class="n">timestamp</span> <span class="o"><</span> <span class="n">start_time</span> <span class="ow">or</span> <span class="n">timestamp</span> <span class="o">></span> <span class="n">end_time</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">wrf</span><span class="p">:</span>
- <span class="k">if</span> <span class="s1">'olddate'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">()</span> <span class="ow">or</span> <span class="n">cdate</span> <span class="o">!=</span> <span class="n">olddate</span><span class="p">:</span>
- <span class="n">fwrf</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">outputdir</span><span class="p">,</span>
- <span class="s1">'WRF'</span> <span class="o">+</span> <span class="n">cdate</span> <span class="o">+</span> <span class="s1">'.'</span> <span class="o">+</span> <span class="n">ctime</span> <span class="o">+</span> <span class="s1">'.000.grb2'</span><span class="p">),</span> <span class="s1">'w'</span><span class="p">)</span>
- <span class="n">olddate</span> <span class="o">=</span> <span class="n">cdate</span><span class="p">[:]</span>
+ <span class="c1"># @WRF</span>
+ <span class="c1"># THIS IS NOT YET CORRECTLY IMPLEMENTED !!!</span>
+ <span class="c1">#</span>
+ <span class="c1"># UNDER CONSTRUCTION !!!</span>
+ <span class="c1">#</span>
+ <span class="c1">#if c.wrf:</span>
+ <span class="c1"># if 'olddate' not in locals() or cdate != olddate:</span>
+ <span class="c1"># fwrf = open(os.path.join(c.outputdir,</span>
+ <span class="c1"># 'WRF' + cdate + '.' + ctime + '.000.grb2'), 'wb')</span>
+ <span class="c1"># olddate = cdate[:]</span>
<span class="c1">#============================================================================================</span>
<span class="c1"># savedfields remembers which fields were already used.</span>
<span class="n">savedfields</span> <span class="o">=</span> <span class="p">[]</span>
@@ -1788,11 +1808,16 @@
<span class="n">codes_set</span><span class="p">(</span><span class="n">gid</span><span class="p">,</span> <span class="s1">'paramId'</span><span class="p">,</span> <span class="mi">201031</span><span class="p">)</span>
<span class="n">codes_write</span><span class="p">(</span><span class="n">gid</span><span class="p">,</span> <span class="n">fdict</span><span class="p">[</span><span class="s1">'22'</span><span class="p">])</span>
<span class="n">scwc</span> <span class="o">=</span> <span class="kc">None</span>
- <span class="k">elif</span> <span class="n">c</span><span class="o">.</span><span class="n">wrf</span> <span class="ow">and</span> <span class="n">paramId</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">129</span><span class="p">,</span> <span class="mi">138</span><span class="p">,</span> <span class="mi">155</span><span class="p">]</span> <span class="ow">and</span> \
- <span class="n">levtype</span> <span class="o">==</span> <span class="s1">'hybrid'</span><span class="p">:</span> <span class="c1"># Z, VO, D</span>
- <span class="c1"># do not do anything right now</span>
- <span class="c1"># these are specific parameter for WRF</span>
- <span class="k">pass</span>
+ <span class="c1"># @WRF</span>
+ <span class="c1"># THIS IS NOT YET CORRECTLY IMPLEMENTED !!!</span>
+ <span class="c1">#</span>
+ <span class="c1"># UNDER CONSTRUCTION !!!</span>
+ <span class="c1">#</span>
+ <span class="c1">#elif c.wrf and paramId in [129, 138, 155] and \</span>
+ <span class="c1"># levtype == 'hybrid': # Z, VO, D</span>
+ <span class="c1"># # do not do anything right now</span>
+ <span class="c1"># # these are specific parameter for WRF</span>
+ <span class="c1"># pass</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">paramId</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">savedfields</span><span class="p">:</span>
<span class="c1"># SD/MSL/TCC/10U/10V/2T/2D/Z/LSM/SDOR/CVL/CVH/SR</span>
@@ -1801,18 +1826,22 @@
<span class="n">savedfields</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">paramId</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'duplicate '</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">paramId</span><span class="p">)</span> <span class="o">+</span> <span class="s1">' not written'</span><span class="p">)</span>
-
- <span class="k">try</span><span class="p">:</span>
- <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">wrf</span><span class="p">:</span>
- <span class="c1"># model layer</span>
- <span class="k">if</span> <span class="n">levtype</span> <span class="o">==</span> <span class="s1">'hybrid'</span> <span class="ow">and</span> \
- <span class="n">paramId</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">129</span><span class="p">,</span> <span class="mi">130</span><span class="p">,</span> <span class="mi">131</span><span class="p">,</span> <span class="mi">132</span><span class="p">,</span> <span class="mi">133</span><span class="p">,</span> <span class="mi">138</span><span class="p">,</span> <span class="mi">155</span><span class="p">]:</span>
- <span class="n">codes_write</span><span class="p">(</span><span class="n">gid</span><span class="p">,</span> <span class="n">fwrf</span><span class="p">)</span>
- <span class="c1"># sfc layer</span>
- <span class="k">elif</span> <span class="n">paramId</span> <span class="ow">in</span> <span class="n">wrfpars</span><span class="p">:</span>
- <span class="n">codes_write</span><span class="p">(</span><span class="n">gid</span><span class="p">,</span> <span class="n">fwrf</span><span class="p">)</span>
- <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
- <span class="k">pass</span>
+ <span class="c1"># @WRF</span>
+ <span class="c1"># THIS IS NOT YET CORRECTLY IMPLEMENTED !!!</span>
+ <span class="c1">#</span>
+ <span class="c1"># UNDER CONSTRUCTION !!!</span>
+ <span class="c1">#</span>
+ <span class="c1">#try:</span>
+ <span class="c1"># if c.wrf:</span>
+ <span class="c1"># # model layer</span>
+ <span class="c1"># if levtype == 'hybrid' and \</span>
+ <span class="c1"># paramId in [129, 130, 131, 132, 133, 138, 155]:</span>
+ <span class="c1"># codes_write(gid, fwrf)</span>
+ <span class="c1"># # sfc layer</span>
+ <span class="c1"># elif paramId in wrfpars:</span>
+ <span class="c1"># codes_write(gid, fwrf)</span>
+ <span class="c1">#except AttributeError:</span>
+ <span class="c1"># pass</span>
<span class="n">codes_release</span><span class="p">(</span><span class="n">gid</span><span class="p">)</span>
<span class="n">gid</span> <span class="o">=</span> <span class="n">codes_new_from_index</span><span class="p">(</span><span class="n">iid</span><span class="p">)</span>
@@ -1882,8 +1911,14 @@
<span class="n">shutil</span><span class="o">.</span><span class="n">copyfileobj</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">inputdir</span><span class="p">,</span> <span class="s1">'fort.25'</span><span class="p">),</span>
<span class="s1">'rb'</span><span class="p">),</span> <span class="n">fout</span><span class="p">)</span>
<span class="c1"># ============================================================================================</span>
- <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">wrf</span><span class="p">:</span>
- <span class="n">fwrf</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+
+ <span class="c1"># @WRF</span>
+ <span class="c1"># THIS IS NOT YET CORRECTLY IMPLEMENTED !!!</span>
+ <span class="c1">#</span>
+ <span class="c1"># UNDER CONSTRUCTION !!!</span>
+ <span class="c1">#</span>
+ <span class="c1">#if c.wrf:</span>
+ <span class="c1"># fwrf.close()</span>
<span class="n">codes_index_release</span><span class="p">(</span><span class="n">iid</span><span class="p">)</span>
@@ -1917,6 +1952,7 @@
<span class="c1"># get a list of all prepared output files with control forecast (CF)</span>
<span class="n">CF_filelist</span> <span class="o">=</span> <span class="n">UioFiles</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">'*.N000'</span><span class="p">)</span>
+ <span class="n">CF_filelist</span><span class="o">.</span><span class="n">files</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">CF_filelist</span><span class="o">.</span><span class="n">files</span><span class="p">)</span>
<span class="k">for</span> <span class="n">cffile</span> <span class="ow">in</span> <span class="n">CF_filelist</span><span class="o">.</span><span class="n">files</span><span class="p">:</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">cffile</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
@@ -1930,7 +1966,6 @@
<span class="n">filename</span> <span class="o">=</span> <span class="n">cffile</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'N000'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">maxnum</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
-
<span class="c1"># read an ensemble member</span>
<span class="n">g</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span> <span class="o">+</span> <span class="s1">'N</span><span class="si">{:0>3}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i</span><span class="p">),</span> <span class="s1">'rb'</span><span class="p">)</span>
<span class="c1"># create file for newly calculated ensemble member</span>
diff --git a/Documentation/html/_modules/GribUtil.html b/Documentation/html/_modules/GribUtil.html
index 1f885784848ef97940d44ccebe7d5ddf7b409c2b..a798b8dcc4aa54e1f19ca363cfabaf7e25cd0c0b 100644
--- a/Documentation/html/_modules/GribUtil.html
+++ b/Documentation/html/_modules/GribUtil.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for GribUtil</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
@@ -174,31 +174,15 @@
<span class="c1"># - changed some naming</span>
<span class="c1">#</span>
<span class="c1"># @License:</span>
-<span class="c1"># (C) Copyright 2014-2018.</span>
+<span class="c1"># (C) Copyright 2014-2019.</span>
+<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
-<span class="c1"># This software is licensed under the terms of the Apache Licence Version 2.0</span>
-<span class="c1"># which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.</span>
-<span class="c1">#</span>
-<span class="c1"># @Class Description:</span>
-<span class="c1"># The GRIB API provides all necessary tools to work directly with the</span>
-<span class="c1"># grib files. Nevertheless, the GRIB API tools are very basic and are in</span>
-<span class="c1"># direct connection with the grib files. This class provides some higher</span>
-<span class="c1"># functions which apply a set of GRIB API tools together in the respective</span>
-<span class="c1"># context. So, the class initially contains a list of grib files (their</span>
-<span class="c1"># names) and the using program then applies the methods directly on the</span>
-<span class="c1"># class objects without having to think about how the actual GRIB API</span>
-<span class="c1"># tools have to be arranged.</span>
-<span class="c1">#</span>
-<span class="c1"># @Class Content:</span>
-<span class="c1"># - __init__</span>
-<span class="c1"># - get_keys</span>
-<span class="c1"># - set_keys</span>
-<span class="c1"># - copy_dummy_msg</span>
-<span class="c1"># - index</span>
-<span class="c1">#</span>
-<span class="c1"># @Class Attributes:</span>
-<span class="c1"># - filenames</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
<span class="c1">#</span>
+<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
+<span class="c1"># International License. To view a copy of this license, visit</span>
+<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
+<span class="c1"># Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># ------------------------------------------------------------------------------</span>
@@ -214,6 +198,15 @@
<div class="viewcode-block" id="GribUtil"><a class="viewcode-back" href="../Documentation/Api/api_python.html#GribUtil.GribUtil">[docs]</a><span class="k">class</span> <span class="nc">GribUtil</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Class for GRIB utilities (new methods) based on GRIB API</span>
+
+<span class="sd"> The GRIB API provides all necessary tools to work directly with the</span>
+<span class="sd"> grib files. Nevertheless, the GRIB API tools are very basic and are in</span>
+<span class="sd"> direct connection with the grib files. This class provides some higher</span>
+<span class="sd"> functions which apply a set of GRIB API tools together in the respective</span>
+<span class="sd"> context. So, the class initially contains a list of grib files (their</span>
+<span class="sd"> names) and the using program then applies the methods directly on the</span>
+<span class="sd"> class objects without having to think about how the actual GRIB API</span>
+<span class="sd"> tools have to be arranged.</span>
<span class="sd"> '''</span>
<span class="c1"># --------------------------------------------------------------------------</span>
<span class="c1"># CLASS FUNCTIONS</span>
@@ -259,15 +252,11 @@
<span class="kn">from</span> <span class="nn">eccodes</span> <span class="k">import</span> <span class="p">(</span><span class="n">codes_new_from_file</span><span class="p">,</span> <span class="n">codes_is_defined</span><span class="p">,</span> <span class="n">codes_get</span><span class="p">,</span>
<span class="n">codes_release</span><span class="p">)</span>
- <span class="n">fileid</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filenames</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span>
-
<span class="n">return_list</span> <span class="o">=</span> <span class="p">[]</span>
- <span class="k">while</span> <span class="mi">1</span><span class="p">:</span>
- <span class="n">gid</span> <span class="o">=</span> <span class="n">codes_new_from_file</span><span class="p">(</span><span class="n">fileid</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filenames</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fileid</span><span class="p">:</span>
- <span class="k">if</span> <span class="n">gid</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
- <span class="k">break</span>
+ <span class="n">gid</span> <span class="o">=</span> <span class="n">codes_new_from_file</span><span class="p">(</span><span class="n">fileid</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">wherekeynames</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">wherekeyvalues</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Number of key values and key names must be </span><span class="se">\</span>
@@ -291,13 +280,11 @@
<span class="n">codes_release</span><span class="p">(</span><span class="n">gid</span><span class="p">)</span>
- <span class="n">fileid</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-
<span class="k">return</span> <span class="n">return_list</span></div>
<div class="viewcode-block" id="GribUtil.set_keys"><a class="viewcode-back" href="../Documentation/Api/api_python.html#GribUtil.GribUtil.set_keys">[docs]</a> <span class="k">def</span> <span class="nf">set_keys</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fromfile</span><span class="p">,</span> <span class="n">keynames</span><span class="p">,</span> <span class="n">keyvalues</span><span class="p">,</span> <span class="n">wherekeynames</span><span class="o">=</span><span class="p">[],</span>
- <span class="n">wherekeyvalues</span><span class="o">=</span><span class="p">[],</span> <span class="n">strict</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'w'</span><span class="p">):</span>
+ <span class="n">wherekeyvalues</span><span class="o">=</span><span class="p">[],</span> <span class="n">strict</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'wb'</span><span class="p">):</span>
<span class="sd">'''Opens the file to read the grib messages and then write</span>
<span class="sd"> the selected messages (with wherekeys) to a new output file.</span>
<span class="sd"> Also, the keyvalues of the passed list of keynames are set.</span>
@@ -329,7 +316,7 @@
<span class="sd"> meeting the where statement (True). Default is False.</span>
<span class="sd"> filemode : :obj:`string`, optional</span>
-<span class="sd"> Sets the mode for the output file. Default is "w".</span>
+<span class="sd"> Sets the mode for the output file. Default is "wb".</span>
<span class="sd"> Return</span>
<span class="sd"> ------</span>
@@ -343,14 +330,10 @@
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Give a value for each keyname!"</span><span class="p">)</span>
<span class="n">fout</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filenames</span><span class="p">,</span> <span class="n">filemode</span><span class="p">)</span>
- <span class="n">fin</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fromfile</span><span class="p">)</span>
- <span class="k">while</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">fromfile</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fin</span><span class="p">:</span>
<span class="n">gid</span> <span class="o">=</span> <span class="n">codes_grib_new_from_file</span><span class="p">(</span><span class="n">fin</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">gid</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
- <span class="k">break</span>
-
<span class="n">select</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">wherekey</span> <span class="ow">in</span> <span class="n">wherekeynames</span><span class="p">:</span>
@@ -374,13 +357,12 @@
<span class="n">codes_release</span><span class="p">(</span><span class="n">gid</span><span class="p">)</span>
- <span class="n">fin</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">fout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span></div>
<div class="viewcode-block" id="GribUtil.copy_dummy_msg"><a class="viewcode-back" href="../Documentation/Api/api_python.html#GribUtil.GribUtil.copy_dummy_msg">[docs]</a> <span class="k">def</span> <span class="nf">copy_dummy_msg</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename_in</span><span class="p">,</span> <span class="n">selectWhere</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
- <span class="n">keynames</span><span class="o">=</span><span class="p">[],</span> <span class="n">keyvalues</span><span class="o">=</span><span class="p">[],</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'w'</span><span class="p">):</span>
+ <span class="n">keynames</span><span class="o">=</span><span class="p">[],</span> <span class="n">keyvalues</span><span class="o">=</span><span class="p">[],</span> <span class="n">filemode</span><span class="o">=</span><span class="s1">'wb'</span><span class="p">):</span>
<span class="sd">'''Add the content of another input grib file to the objects file but</span>
<span class="sd"> only messages corresponding to keys/values passed to the function.</span>
<span class="sd"> The selectWhere switch decides if to copy the keys equal to (True) or</span>
@@ -403,7 +385,7 @@
<span class="sd"> List of keyvalues. Default is an empty list.</span>
<span class="sd"> filemode : :obj:`string`, optional</span>
-<span class="sd"> Sets the mode for the output file. Default is "w".</span>
+<span class="sd"> Sets the mode for the output file. Default is "wb".</span>
<span class="sd"> Return</span>
<span class="sd"> ------</span>
@@ -415,16 +397,17 @@
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">keynames</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">keyvalues</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Give a value for each keyname!"</span><span class="p">)</span>
- <span class="n">fin</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename_in</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)</span>
+
<span class="n">fout</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filenames</span><span class="p">,</span> <span class="n">filemode</span><span class="p">)</span>
<span class="n">fields</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="k">while</span> <span class="n">fields</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span>
- <span class="n">gid</span> <span class="o">=</span> <span class="n">codes_grib_new_from_file</span><span class="p">(</span><span class="n">fin</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename_in</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fin</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">fields</span> <span class="o">>=</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">fout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+ <span class="k">return</span>
- <span class="k">if</span> <span class="n">gid</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
- <span class="k">break</span>
+ <span class="n">gid</span> <span class="o">=</span> <span class="n">codes_grib_new_from_file</span><span class="p">(</span><span class="n">fin</span><span class="p">)</span>
<span class="n">select</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
@@ -446,7 +429,6 @@
<span class="n">codes_release</span><span class="p">(</span><span class="n">gid</span><span class="p">)</span>
- <span class="n">fin</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">fout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span></div>
diff --git a/Documentation/html/_modules/MarsRetrieval.html b/Documentation/html/_modules/MarsRetrieval.html
index e809a770e2a9d069282c7bf21cce91d87036e79d..c7f3fe981f99b917ddfc1a703a7325b547a40d86 100644
--- a/Documentation/html/_modules/MarsRetrieval.html
+++ b/Documentation/html/_modules/MarsRetrieval.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for MarsRetrieval</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
@@ -184,6 +184,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
@@ -647,7 +649,7 @@
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">empty_keys</span><span class="p">:</span>
<span class="k">del</span> <span class="n">attrs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
- <span class="n">attrs</span><span class="p">[</span><span class="s1">'ppengine'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'emos'</span>
+<span class="c1"># attrs['ppengine'] = 'emos'</span>
<span class="c1"># MARS request via Python script</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">server</span><span class="p">:</span>
@@ -679,7 +681,7 @@
<span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">attrs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">request_str</span> <span class="o">=</span> <span class="n">request_str</span> <span class="o">+</span> <span class="s1">','</span> <span class="o">+</span> <span class="n">key</span> <span class="o">+</span> <span class="s1">'='</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
<span class="n">request_str</span> <span class="o">+=</span> <span class="s1">',target="'</span> <span class="o">+</span> <span class="n">target</span> <span class="o">+</span> <span class="s1">'"'</span>
- <span class="n">p</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">([</span><span class="s1">'mars'</span><span class="p">,</span> <span class="s1">'-e'</span><span class="p">],</span>
+ <span class="n">p</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">([</span><span class="s1">'mars'</span><span class="p">],</span> <span class="c1">#'-e'],</span>
<span class="n">stdin</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span>
<span class="n">stdout</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span>
<span class="n">stderr</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span>
diff --git a/Documentation/html/_modules/UioFiles.html b/Documentation/html/_modules/UioFiles.html
index 6a16c90648e281b32c5d1a3f4f69c4cf399fbc47..89797a258d434eba58d091f71fda1e38b9fbb406 100644
--- a/Documentation/html/_modules/UioFiles.html
+++ b/Documentation/html/_modules/UioFiles.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for UioFiles</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
@@ -187,6 +187,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
diff --git a/Documentation/html/_modules/checks.html b/Documentation/html/_modules/checks.html
index 138568573bdac0bca5cc4677f6d43b4694527f71..1b6eb598abc06bdbc84496f7a6548affa5c66da5 100644
--- a/Documentation/html/_modules/checks.html
+++ b/Documentation/html/_modules/checks.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for checks</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Philipp (University of Vienna)</span>
@@ -173,6 +173,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
diff --git a/Documentation/html/_modules/disaggregation.html b/Documentation/html/_modules/disaggregation.html
index ac3fbbfae2588c403c5ded67d5718f3c55ae3fbd..f287c99bd9ba3cb147e27227b9c6f92d075eca7d 100644
--- a/Documentation/html/_modules/disaggregation.html
+++ b/Documentation/html/_modules/disaggregation.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for disaggregation</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Philipp (University of Vienna)</span>
@@ -184,6 +184,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
diff --git a/Documentation/html/_modules/get_mars_data.html b/Documentation/html/_modules/get_mars_data.html
index d746890b210cdfc585d29f104a08759e6babc6a1..84f64b35402df649c050a87b5534e186e8b840ef 100644
--- a/Documentation/html/_modules/get_mars_data.html
+++ b/Documentation/html/_modules/get_mars_data.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for get_mars_data</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
@@ -190,6 +190,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
diff --git a/Documentation/html/_modules/install.html b/Documentation/html/_modules/install.html
index 09e2863225bb01d003b4dca65595042fcec9e586..01c07e207c70fa3a5af007ffa4abecb4296daebc 100644
--- a/Documentation/html/_modules/install.html
+++ b/Documentation/html/_modules/install.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for install</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Leopold Haimberger (University of Vienna)</span>
@@ -183,6 +183,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
diff --git a/Documentation/html/_modules/prepare_flexpart.html b/Documentation/html/_modules/prepare_flexpart.html
index fe19a3757179ff2bdea4aac77421ba42ecc4ea37..b568811ac822e345527400efbbbdc7d9e3276f52 100644
--- a/Documentation/html/_modules/prepare_flexpart.html
+++ b/Documentation/html/_modules/prepare_flexpart.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for prepare_flexpart</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
@@ -193,6 +193,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
diff --git a/Documentation/html/_modules/submit.html b/Documentation/html/_modules/submit.html
index 3a078cb966e8f218fc73fb1e436e8b92189ad9ff..2c7d08427518c0ea0f6cf7ec60bef879d0cdc4ff 100644
--- a/Documentation/html/_modules/submit.html
+++ b/Documentation/html/_modules/submit.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for submit</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
@@ -187,6 +187,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
diff --git a/Documentation/html/_modules/tools.html b/Documentation/html/_modules/tools.html
index fdf45138e7245fc55b86122e096449785658532b..bae60765f73eba3fd63f2b080496771b95afee85 100644
--- a/Documentation/html/_modules/tools.html
+++ b/Documentation/html/_modules/tools.html
@@ -160,7 +160,7 @@
<div itemprop="articleBody">
<h1>Source code for tools</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python</span>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">#*******************************************************************************</span>
<span class="c1"># @Author: Anne Philipp (University of Vienna)</span>
@@ -188,6 +188,8 @@
<span class="c1"># (C) Copyright 2014-2019.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
<span class="c1">#</span>
+<span class="c1"># SPDX-License-Identifier: CC-BY-4.0</span>
+<span class="c1">#</span>
<span class="c1"># This work is licensed under the Creative Commons Attribution 4.0</span>
<span class="c1"># International License. To view a copy of this license, visit</span>
<span class="c1"># http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
@@ -922,7 +924,7 @@
<span class="c1"># --- open file ---</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"Opening file for getting information data --- </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">filename</span><span class="p">)</span>
- <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="c1"># load first message from file</span>
<span class="n">gid</span> <span class="o">=</span> <span class="n">codes_grib_new_from_file</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
diff --git a/Documentation/html/_sources/Documentation/Input/ecmwf_env.rst.txt b/Documentation/html/_sources/Documentation/Input/ecmwf_env.rst.txt
index 76acff797808067f4b6be2817b7a486fe7347851..a3232e2c5b7ac760975aba87152fede088e921c5 100644
--- a/Documentation/html/_sources/Documentation/Input/ecmwf_env.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/ecmwf_env.rst.txt
@@ -2,7 +2,7 @@
ECMWF User Credential file ``ECMWF_ENV``
****************************************
-This file contains the user credentials for working on ECMWF servers and transfering files between the ECMWF servers and the local gateway server. It is located in the ``flex_extract_vX.X/run`` directory and will be created in the installation process for the application modes **remote** and **gateway**.
+This file contains the user credentials for working on ECMWF servers and transferring files between the ECMWF servers and the local gateway server. It is located in the ``flex_extract_vX.X/run`` directory and will be created in the installation process for the application modes **remote** and **gateway**.
This file is based on the template ``ECMWF_ENV.template`` which is located in the ``templates`` directory.
diff --git a/Documentation/html/_sources/Installation/gateway.rst.txt b/Documentation/html/_sources/Installation/gateway.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..447685d768a8dcafdb11246230ff3d0cabb06ec4
--- /dev/null
+++ b/Documentation/html/_sources/Installation/gateway.rst.txt
@@ -0,0 +1,172 @@
+*************************
+Gateway mode installation
+*************************
+
+.. role:: underline
+ :class: underline
+
+.. toctree::
+ :hidden:
+ :maxdepth: 3
+
+.. _Python 3: https://docs.python.org/3/
+.. _Python3: https://www.python.org/downloads/
+.. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section
+
+.. _numpy: http://www.numpy.org/
+.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
+.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
+.. _genshi: https://genshi.edgewall.org/
+.. _eccodes for python: https://packages.debian.org/sid/python3-eccodes
+.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _gfortran: https://gcc.gnu.org/wiki/GFortran
+.. _fftw3: http://www.fftw.org
+.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
+.. _emoslib: https://software.ecmwf.int/wiki/display/EMOS/Emoslib
+.. _member state: https://www.ecmwf.int/en/about/who-we-are/member-states
+.. _registration form: https://apps.ecmwf.int/registration/
+.. _CDS API registration: https://cds.climate.copernicus.eu/user/register
+.. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans
+.. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf
+.. _ECMWF's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home
+.. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives
+.. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS
+
+.. _download section: https://www.flexpart.eu/downloads
+
+
+
+.. _ref-gateway-mode:
+
+
+
+.. _ref-req-gateway:
+
+Gateway environment requirements
+================================
+
+The environment on your local system has to provide these software packages
+and libraries, since ``flex_extract`` does only prepare the job script and send
+it to the ECMWF servers:
+
+* `Python3`_ or `Anaconda Python3`_
+* `numpy`_
+* `genshi`_
+
+
+.. _ref-prep-gateway:
+
+Prepare gateway environment
+===========================
+
+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.
+The installation was tested on a *GNU/Linux Debian buster* and an *Ubuntu 18.04 Bionic Beaver* system.
+
+.. code-block:: sh
+
+ # On a Linux Debian or Ubuntu system do
+ # (if not already available):
+ apt-get install python3
+ apt-get install pip
+ apt-get install genshi
+ apt-get install numpy
+
+
+.. _ref-test-gateway:
+
+Test gateway environment
+========================
+
+Check the availability of the python packages by typing ``python3`` in
+a terminal window and run the ``import`` commands in the python shell.
+If there are no error messages, you succeeded in setting up the environment.
+
+.. code-block:: python
+
+ # check in python3 console
+ import genshi
+ import numpy
+
+
+
+.. _ref-install-gateway:
+
+Gateway installation
+====================
+
+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.
+
+Please see `ECMWF's instructions on gateway server`_ to establish the gateway server if not already in place.
+Additionally, to be able to use the Ecaccess file transfer service **ectrans** please also create an association.
+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`_.
+
+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).
+
+.. code-block:: bash
+
+ $ ecaccess-certificate-create
+ Please enter your user-id: example_username
+ Your passcode: ***
+
+``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.
+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.
+
+
+.. code-block:: bash
+ :caption: 'Example settings for a gateway installation.'
+ :name: setup.sh
+
+ # -----------------------------------------------------------------
+ # AVAILABLE COMMANDLINE ARGUMENTS TO SET
+ #
+ # THE USER HAS TO SPECIFY THESE PARAMETER
+ #
+ TARGET='ecgate'
+ MAKEFILE='Makefile.gfortran'
+ ECUID='uid'
+ ECGID='gid'
+ GATEWAY='server.example.edu'
+ DESTINATION='example@genericSftp'
+ INSTALLDIR=None
+ JOB_TEMPLATE='job.template'
+ CONTROLFILE='CONTROL_EA5'
+
+
+Afterwards, type:
+
+.. code-block:: bash
+
+ $ ./setup.sh
+
+to start the installation. You should see the following output at the command line.
+
+
+.. code-block:: bash
+
+ # Output of setup.sh
+ Create tarball ...
+ Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X
+ You should get an email with subject "flexcompile" within the next few minutes!
+
+
+The email content should look like this with a "SUCCESS" statement in the last line:
+
+.. code-block:: bash
+
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
+ -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2
+ SUCCESS!
+
+
+
+
+
+
+
+
diff --git a/Documentation/html/_sources/Installation/local.rst.txt b/Documentation/html/_sources/Installation/local.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca962255c5731cdf907e05f6e08be50802d9eace
--- /dev/null
+++ b/Documentation/html/_sources/Installation/local.rst.txt
@@ -0,0 +1,391 @@
+***********************
+Local mode installation
+***********************
+
+.. role:: underline
+ :class: underline
+
+.. toctree::
+ :hidden:
+ :maxdepth: 2
+
+
+.. _Python 3: https://docs.python.org/3/
+.. _Python3: https://www.python.org/downloads/
+.. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section
+
+.. _numpy: http://www.numpy.org/
+.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
+.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
+.. _genshi: https://genshi.edgewall.org/
+.. _eccodes for python: https://packages.debian.org/sid/python3-eccodes
+.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _gfortran: https://gcc.gnu.org/wiki/GFortran
+.. _fftw3: http://www.fftw.org
+.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
+.. _emoslib: https://software.ecmwf.int/wiki/display/EMOS/Emoslib
+.. _member state: https://www.ecmwf.int/en/about/who-we-are/member-states
+.. _registration form: https://apps.ecmwf.int/registration/
+.. _CDS API registration: https://cds.climate.copernicus.eu/user/register
+.. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans
+.. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf
+.. _ECMWF's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home
+.. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives
+.. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS
+
+.. _download section: https://www.flexpart.eu/downloads
+
+
+
+
+
+.. _ref-local-mode:
+
+
+
+.. _ref-req-local:
+
+Local environment requirements
+==============================
+
+For the local access modes **member** and **public** there is no difference in
+the installation process.
+
+The environment on your local system has to provide these software packages
+and libraries, since all extraction and preparation is done at the local system:
+
++------------------------------------------------+-----------------+
+| Python part | Fortran part |
++------------------------------------------------+-----------------+
+| * `Python3`_ | * `gfortran`_ |
+| * `numpy`_ | * `fftw3`_ |
+| * `genshi`_ | * `eccodes`_ |
+| * `eccodes for python`_ | * `emoslib`_ |
+| * `ecmwf-api-client`_ (everything except ERA5) | |
+| * `cdsapi`_ (just for ERA5) | |
++------------------------------------------------+-----------------+
+
+
+.. _ref-prep-local:
+
+Prepare local environment
+=========================
+
+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.
+The installation was tested on a *Debian GNU/Linux buster/sid* and an *Ubuntu 18.04 Bionic Beaver* system.
+
+.. code-block:: sh
+
+ # On a Linux Debian or Ubuntu system do
+ # (if not already available):
+ apt-get install python3 (usually available on normal Linux systems)
+ apt-get install pip
+ apt-get install gfortran
+ apt-get install fftw3-dev
+ apt-get install libeccodes-dev
+ apt-get install libemos-dev
+ apt-get install python3-eccodes
+ apt-get install genshi
+ apt-get install numpy
+ pip install cdsapi
+ pip install ecmwf-api-client
+
+.. note::
+
+ In case you would like to use Anaconda Python we recommend you follow the installation instructions of
+ `Anaconda Python Installation for Linux <https://docs.anaconda.com/anaconda/install/linux/>`_ and then install the
+ ``eccodes`` package from ``conda`` with:
+
+ .. code-block:: bash
+
+ conda install conda-forge::python-eccodes
+
+
+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``.
+
+.. note::
+
+ Since **public users** currently don't have access to the full *ERA5* dataset they can skip the installation of the ``CDS API``.
+
+Both user groups have to provide key's with their credentials for the Web API's in their home directory. Therefore, follow these instructions:
+
+ECMWF Web API:
+ 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).
+
+CDS API:
+ 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.
+
+
+.. _ref-test-local:
+
+Test local environment
+======================
+
+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:
+
+.. code-block:: sh
+
+ $ dpkg -s libeccodes-dev | grep Status
+ # or
+ $ rpm -q libeccodes-dev
+
+Afterwards, check the availability of the python packages by typing ``python3`` in
+a terminal window and run the ``import`` commands in the python shell. If there are no error messages, you succeeded in setting up the environment.
+
+.. code-block:: python
+
+ # check in python3 console
+ import eccodes
+ import genshi
+ import numpy
+ import cdsapi
+ import ecmwfapi
+
+
+
+Test the Web API's
+------------------
+
+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.
+
+ECMWF Web API
+^^^^^^^^^^^^^
+
+
++----------------------------------------------------------+----------------------------------------------------------+
+|Please use this piece of python code for **Member user**: |Please use this piece of python code for **Public user**: |
++----------------------------------------------------------+----------------------------------------------------------+
+|.. code-block:: python |.. code-block:: python |
+| | |
+| from ecmwfapi import ECMWFService | from ecmwfapi import ECMWFDataServer |
+| | |
+| server = ECMWFService('mars') | server = ECMWFDataServer() |
+| | |
+| server.retrieve({ | server.retrieve({ |
+| 'stream' : "oper", | 'stream' : "enda", |
+| 'levtype' : "sfc", | 'levtype' : "sfc", |
+| 'param' : "165.128/166.128/167.128", | 'param' : "165.128/166.128/167.128", |
+| 'dataset' : "interim", | 'dataset' : "cera20c", |
+| 'step' : "0", | 'step' : "0", |
+| 'grid' : "0.75/0.75", | 'grid' : "1./1.", |
+| 'time' : "00/06/12/18", | 'time' : "00/06/12/18", |
+| 'date' : "2014-07-01/to/2014-07-31", | 'date' : "2000-07-01/to/2000-07-31", |
+| 'type' : "an", | 'type' : "an", |
+| 'class' : "ei", | 'class' : "ep", |
+| 'target' : "download_erainterim_ecmwfapi.grib" | 'target' : "download_cera20c_ecmwfapi.grib" |
+| }) | }) |
++----------------------------------------------------------+----------------------------------------------------------+
+
+
+
+CDS API
+^^^^^^^
+
+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:
+
+Please use this piece of python code to retrieve a small sample of *ERA5* pressure levels:
+
+.. code-block:: python
+
+ import cdsapi
+
+ c = cdsapi.Client()
+
+ c.retrieve("reanalysis-era5-pressure-levels",
+ {
+ "variable": "temperature",
+ "pressure_level": "1000",
+ "product_type": "reanalysis",
+ "year": "2008",
+ "month": "01",
+ "day": "01",
+ "time": "12:00",
+ "format": "grib"
+ },
+ "download_cdsapi.grib")
+
+
+Afterwards, when you know that the CDS API generally works, you can try to extract some
+data from the MARS archive. From the latest experience we know that this can take a while.
+
+.. **Member user**
+
+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!
+
+.. code-block:: python
+
+ import cdsapi
+
+ c = cdsapi.Client()
+
+ c.retrieve('reanalysis-era5-complete',
+ {
+ 'class' : 'ea',
+ 'expver' : '1',
+ 'stream' : 'oper',
+ 'type' : 'fc',
+ 'step' : '3/to/12/by/3',
+ 'param' : '130.128',
+ 'levtype' : 'ml',
+ 'levelist': '135/to/137',
+ 'date' : '2013-01-01',
+ 'time' : '06/18',
+ 'area' : '50/-5/40/5',
+ 'grid' : '1.0/1.0',
+ 'format' : 'grib',
+ }, 'download_era5_cdsapi.grib')
+
+
+.. ********************** COMMENTED OUT FOR FUTURE
+ ********************** PUBLIC RETRIEVAL IS CURRENTLY NOT ACCESSIBLE
+
+ **Public user**
+ Please use this piece of python code:
+
+ .. code-block:: python
+
+ import cdsapi
+
+ c = cdsapi.Client()
+
+ c.retrieve('reanalysis-era5-complete',
+ {
+ 'class' : 'ea',
+ 'dataset' : 'era5',
+ 'expver' : '1',
+ 'stream' : 'oper',
+ 'type' : 'fc',
+ 'step' : '3/to/12/by/3',
+ 'param' : '130.128',
+ 'levtype' : 'ml',
+ 'levelist': '135/to/137',
+ 'date' : '2013-01-01',
+ 'time' : '06/18',
+ 'area' : '50/-5/40/5',
+ 'grid' : '1.0/1.0',
+ 'format' : 'grib',
+ }, 'download_era5_cdsapi.grib')
+
+
+
+
+
+
+.. _ref-install-local:
+
+Local installation
+==================
+
+First prepare the Fortran ``Makefile`` for your environment and set it
+in the ``setup.sh`` script. (See section :ref:`ref-convert` for information on
+the Fortran program.)
+``flex_extract`` has already two ``Makefiles`` prepared for te ``gfortran`` and
+the ``ifort`` compiler:
+
+ * Makefile.local.gfortran
+ * Makefile.local.ifort
+
+They can be found in the path ``flex_extract_vX.X/source/fortran``, where
+``vX.X`` should be substituted with the current version number.
+
+.. caution::
+ It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these
+ ``Makefiles``.
+
+
+So starting from the root directory of ``flex_extract``,
+go to the ``Fortran`` source directory and open the ``Makefile`` of your
+choice to modify with an editor of your choice. We use the ``nedit`` in this case.
+
+.. code-block:: bash
+
+ cd flex_extract_vX.X/source/fortran
+ nedit Makefile.local.gfortran
+
+Edit the pathes to the ``eccodes`` library on your local machine.
+
+.. caution::
+ This can vary from system to system.
+ It is suggested to use a command like
+
+ .. code-block:: bash
+
+ # for the ECCODES_INCLUDE_DIR path do:
+ $ dpkg -L libeccodes-dev | grep eccodes.mod
+ # for the ECCODES_LIB path do:
+ $ dpkg -L libeccodes-dev | grep libeccodes.so
+
+ to find out the path to the ``eccodes`` library.
+
+Substitute these paths in the ``Makefile`` for parameters **ECCODES_INCLUDE_DIR**
+and **ECCODES_LIB** and save it.
+
+.. code-block:: bash
+
+ # these are the paths on a current Debian 10 Testing system (May 2019)
+ ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
+ ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm
+
+
+The Fortran program called ``CONVERT2`` will be compiled during the
+installation process to get an executable. Therefore the ``Makefile``
+has to be set in the ``setup.sh`` script.
+
+In the root directory of ``flex_extract``, open the ``setup.sh`` script
+and adapt the installation parameters in the section labelled with
+"AVAILABLE COMMANDLINE ARGUMENTS TO SET" like shown below.
+
+
+.. code-block:: bash
+ :caption: 'Example settings for a local installation.'
+ :name: setup.sh
+
+ ...
+ # -----------------------------------------------------------------
+ # AVAILABLE COMMANDLINE ARGUMENTS TO SET
+ #
+ # THE USER HAS TO SPECIFY THESE PARAMETER
+ #
+ TARGET='local'
+ MAKEFILE='Makefile.local.gfortran'
+ ECUID=None
+ ECGID=None
+ GATEWAY=None
+ DESTINATION=None
+ INSTALLDIR=None
+ JOB_TEMPLATE='job.template'
+ CONTROLFILE='CONTROL_EA5'
+ ...
+
+
+Afterwards, type:
+
+.. code-block:: bash
+
+ $ ./setup.sh
+
+to start the installation. You should see the following output at the command line.
+
+
+.. code-block:: bash
+
+ # Output of setup.sh
+ WARNING: installdir has not been specified
+ flex_extract will be installed in here by compiling the Fortran source in /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/source/fortran
+ Install flex_extract_v7.1 software at local in directory /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1
+
+ Using makefile: Makefile.local.gfortran
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 rwGRIB2.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 posnam.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 preconvert.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -O3 -O3 -fopenmp -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/gcc-4.9.3/grib_api-1.14.3/lib -Bstatic -lgrib_api_f77 -lgrib_api_f90 -lgrib_api -Bdynamic -lm -ljasper -lemosR64
+
+ -rwxrwxr-x. 1 philipa8 tmc 282992 May 23 22:27 ./CONVERT2
+
+
+
+
+
diff --git a/Documentation/html/_sources/Installation/remote.rst.txt b/Documentation/html/_sources/Installation/remote.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8734e236c9cd52f57cfb2bf8e58fc30e6f6bedcc
--- /dev/null
+++ b/Documentation/html/_sources/Installation/remote.rst.txt
@@ -0,0 +1,204 @@
+************************
+Remote mode installation
+************************
+
+.. role:: underline
+ :class: underline
+
+.. toctree::
+ :hidden:
+ :maxdepth: 2
+
+
+.. _Python 3: https://docs.python.org/3/
+.. _Python3: https://www.python.org/downloads/
+.. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section
+
+.. _numpy: http://www.numpy.org/
+.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
+.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
+.. _genshi: https://genshi.edgewall.org/
+.. _eccodes for python: https://packages.debian.org/sid/python3-eccodes
+.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _gfortran: https://gcc.gnu.org/wiki/GFortran
+.. _fftw3: http://www.fftw.org
+.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
+.. _emoslib: https://software.ecmwf.int/wiki/display/EMOS/Emoslib
+.. _member state: https://www.ecmwf.int/en/about/who-we-are/member-states
+.. _registration form: https://apps.ecmwf.int/registration/
+.. _CDS API registration: https://cds.climate.copernicus.eu/user/register
+.. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans
+.. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf
+.. _ECMWF's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home
+.. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives
+.. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS
+
+.. _download section: https://www.flexpart.eu/downloads
+
+
+.. _ref-remote-mode:
+
+
+.. _ref-req-remote:
+
+Remote environment requirements
+===============================
+
+The environment for ``flex_extract`` on ECMWF servers has to provide these
+software packages and libraries:
+
++---------------------------+-----------------+
+| Python part | Fortran part |
++---------------------------+-----------------+
+| * `Python3`_ | * `gfortran`_ |
+| * `numpy`_ | * `fftw3`_ |
+| * `genshi`_ | * `eccodes`_ |
+| * `eccodes for python`_ | * `emoslib`_ |
++---------------------------+-----------------+
+
+
+.. _ref-prep-remote:
+
+Prepare remote environment
+==========================
+
+The environment on the ECMWF server (such as *ecgate* or *cca*) is already
+prepared. ECMWF server provide all libraries via a module system which is
+going to be selected by ``flex_extract`` automatically.
+
+
+.. _ref-install-remote:
+
+Remote installation
+===================
+
+First, log in on one of the ECMWF Linux server, such as *ecgate* or *cca/ccb*.
+Substitute *<ecuid>* with your ECMWF user name:
+
+.. code-block:: bash
+
+ ssh -X <ecuid>@ecaccess.ecmwf.int
+
+This will lead to the following output on the command line, asking for your
+password:
+
+.. code-block:: bash
+
+ Authorized access only.
+
+ ***************************************************************
+ For further information, read the ECaccess documentation at:
+
+ https://software.ecmwf.int/wiki/display/ECAC/ECaccess+Home
+
+ You can also use ECaccess to load & download files from your
+ EChome, ECscratch or ECfs directories using the ECaccess FTP
+ server:
+
+ ftp://uid@ecaccess.ecmwf.int/
+
+ Please note you must use your UID and ActivID code to login!
+ ***************************************************************
+
+ <ecuid>@131.130.157.5's password: ***
+ Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
+
+ [<ecuid>@ecgb11 ~]$
+
+
+Then, copy the ``flex_extract`` tar ball (from section :ref:`ref-download`)
+to the ``$HOME`` directory of the ECMWF Linux server via ``scp``.
+Substitute the *<localuser>* and *<server.edu>* placeholders with your credentials.
+Untar the file and change into the ``flex_extract`` root directory.
+
+.. code-block:: bash
+
+ scp <localuser>@<server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz $HOME/
+ cd $HOME
+ tar xvf flex_extract_vX.X.tar.gz
+ cd flex_extract_vX.X
+
+
+On these ECMWF servers, it is not necessary to prepare the environment or the
+``Makefile`` for the Fortran program (``CONVERT2``) as described above.
+All third party libraries are available from a module system. The ``Makefile``
+is optimized for ECMWF servers and the compilation
+script ``compilejob.ksh``, which will be submitted by ``flex_extract`` to the
+batch job queue at ECMWF, does load all relevant modules from the ECMWF's module system.
+
+So there is just the need to execute the ``setup.sh`` script from the
+``flex_extract`` root directory for installation.
+Before executing it, it is necessary to adapt some parameters from ``setup.sh``
+described in :doc:`Documentation/Input/setup`.
+
+Open ``setup.sh`` with your editor and adapt the values:
+
++----------------------------------------------+----------------------------------------------+
+| Take this for target = **ectrans** | Take this for target = **cca** |
++----------------------------------------------+----------------------------------------------+
+| .. code-block:: bash | .. code-block:: bash |
+| | |
+| ... | ... |
+| # -----------------------------------------| # -----------------------------------------|
+| # AVAILABLE COMMANDLINE ARGUMENTS TO SET | # AVAILABLE COMMANDLINE ARGUMENTS TO SET |
+| # | # |
+| # THE USER HAS TO SPECIFY THESE PARAMETER | # THE USER HAS TO SPECIFY THESE PARAMETER |
+| # | # |
+| TARGET='ecgate' | TARGET='cca' |
+| MAKEFILE='Makefile.gfortran' | MAKEFILE='Makefile.CRAY' |
+| ECUID='uid' | ECUID='uid' |
+| ECGID='gid' | ECGID='gid' |
+| GATEWAY=None | GATEWAY=None |
+| DESTINATION=None | DESTINATION=None |
+| INSTALLDIR=None | INSTALLDIR='' |
+| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
+| ... | ... |
++----------------------------------------------+----------------------------------------------+
+
+:underline:`Please substitute the values of ECUID and ECGID
+with your own credentials and settings.`
+
+.. note::
+
+ If a local gateway server is available the transfer of files could be done
+ via the ``ECaccess`` commands. Therefore a valid *GATEWAY* and *DESTINATION*
+ have to be present and should be set in the ``setup.sh`` file.
+
+
+Afterwards, type:
+
+.. code-block:: bash
+
+ module load python3
+ ./setup.sh
+
+to start the installation. You should see the following output at the command line.
+
+
+.. code-block:: bash
+
+ # Output of setup.sh
+ Create tarball ...
+ Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X
+ You should get an email with subject "flexcompile" within the next few minutes!
+
+
+The email content should look like this with a "SUCCESS" statement in the last line:
+
+.. code-block:: bash
+
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
+ -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2
+ SUCCESS!
+
+
+
+
+
diff --git a/Documentation/html/_sources/index.rst.txt b/Documentation/html/_sources/index.rst.txt
index fcba97c2957916aeb62160c40fce64bf48241832..bea0b26583a0ac8c46e44fe21bdc74ce7adc4038 100644
--- a/Documentation/html/_sources/index.rst.txt
+++ b/Documentation/html/_sources/index.rst.txt
@@ -128,7 +128,7 @@ Welcome to ``flex_extract``'s user documentation!
Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
.. toctree::
- :maxdepth: 3
+ :maxdepth: 4
:caption: Table of Contents:
installation
diff --git a/Documentation/html/_sources/installation.rst.txt b/Documentation/html/_sources/installation.rst.txt
index 839721d05758a9fc78124150de23e56ef41c90c5..e1f4f13f80acd1d6c8840ee6141af1b7043bba87 100644
--- a/Documentation/html/_sources/installation.rst.txt
+++ b/Documentation/html/_sources/installation.rst.txt
@@ -8,6 +8,7 @@ Installation
.. toctree::
:hidden:
:maxdepth: 2
+
.. _Python 3: https://docs.python.org/3/
.. _Python3: https://www.python.org/downloads/
@@ -36,59 +37,68 @@ Installation
-``flex_extract`` is a software package which contains a mix of Python and Shell scripts as well as a Fortran program. These components rely on a couple of third party libraries which need to be prepared first before starting the installation process. For now, the software is only tested for a Linux/Unix environment. Feel free to try it out on other platforms.
+The ``flex_extract`` software package contains python and shell scripts as well as a Fortran program. These components rely on several libraries which need to be available before starting the installation process. Currently, the software is only tested for a GNU/Linux environment. Feel free to try it out on other platforms.
-Start with the decision of which `user group <Ecmwf/access>`_ you belong to and follow the instructions at :ref:`ref-registration` to get an account at ECMWF. Considering your user group and the method of applying ``flex_extract`` there appear to be 4 application modes:
+At first, go to the `user group <Ecmwf/access.html>`_ section and decide which group you belong to and follow the instructions at :ref:`ref-registration` to obtain an account at ECMWF (if you don't have it already). Depending on the user group and the way to access the ECWMF MARS archive, there are four possible :doc:`Documentation/Overview/app_modes`:
-- Remote (for member state users only) :ref:`[installation]<ref-remote-mode>`
-- Gateway (for member state users only) :ref:`[installation]<ref-gateway-mode>`
-- Local member :ref:`[installation]<ref-local-mode>`
-- Local public :ref:`[installation]<ref-local-mode>`
+- Remote (member-state users only) :ref:`[installation]<ref-remote-mode>`
+- Gateway (member-state users only) :ref:`[installation]<ref-gateway-mode>`
+- Local, member-state user :ref:`[installation]<ref-local-mode>`
+- Local, public user :ref:`[installation]<ref-local-mode>`
-More information can be found in :doc:`Documentation/Overview/app_modes`.
+Please follow the link :doc:`Documentation/Overview/app_modes` to get a description of the modes.
.. note::
If you encounter any problems in the installation process, you can ask for :doc:`support`.
-
-
-
-
+
+
+
+
.. _ref-registration:
Registration at ECMWF
=====================
-Decide which user group you belong to and follow the instructions for registration:
+The registration depends on the :doc:`Documentation/Overview/app_modes` and in case of the local mode also on the data set you'd like to retrieve. The following table gives an overview where you need to register.
-**Member state user**:
- To get a member-state user account, users have to be a resident of a `member state`_. In that case, you can contact your `Computing Representative`_ for granting access. If you would like to use the local application mode to retrieve **ERA5** data you'd have to register at the `Copernicus Climate Data Store <https://cds.climate.copernicus.eu/user/register>`_ also.
++--------------+------------------------------------+--------------+
+| | Member-state user | Public user |
+| +---------+----------+---------------+--------------+
+| Data sets |Remote |Gateway |Local | Local |
++--------------+---------+----------+---------------+--------------+
+| Operational | 1 | 1 | 1,2 | - |
++--------------+---------+----------+---------------+--------------+
+| ERA-Interim | 1 | 1 | 1,2 | 2 |
++--------------+---------+----------+---------------+--------------+
+| CERA-20C | 1 | 1 | 1,2 | 2 |
++--------------+---------+----------+---------------+--------------+
+| ERA5 | 1 | 1 | 3 | - |
++--------------+---------+----------+---------------+--------------+
-**Public user**:
- To be able to download public datasets with ``flex_extract`` such as **ERA-Interim** and **CERA-20C** (**ERA5** is not supported via ECMWF Web API anymore), the public user has to create an account at ECMWF.
- Use the registration at the ECMWF website by filling out this `registration form`.
-
- .. note::
- In the future retrievement of *ERA5* will be possible via the CDS API for public users also. Then a registration at the `Copernicus Climate Data Store <https://cds.climate.copernicus.eu/user/register>`_ is needed in addition.
-
-
+
+Registration options:
+
+ 1.) Access through a member-state user account granted by the `Computing Representative`_. The credentials have to be provided during installation.
+ 2.) Access through the ECMWF Web API. Need to sign in at `ECMWF Web API <https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home>`_ and configure the ECMWF key as described. Member-state users can sign in with their credentials from the `Computing Representative`_ and public users have to fill out the `registration form`_ to get an account.
+ 3.) Access through the `CDS API <https://cds.climate.copernicus.eu/api-how-to>`_. Extra registration for member-state users is required at `Copernicus Climate Data Store <https://cds.climate.copernicus.eu/user/register>`_ including the configurations of the CDS key as described. This mode is currently not available for public users. See the note at `user group <Ecmwf/access.html>`_ for information.
+
.. _ref-licence:
-Agree on licences for public datasets
+Licence agreement for public datasets
=====================================
-Each public dataset which is intended to be downloaded by ``flex_extract`` has its own licence which has to be accepted, regardless of the user group.
+Each ECMWF public dataset has its own licence which has to be accepted, regardless of the user group.
For the *ERA-Interim* and *CERA-20C* datasets this can be done at the ECMWF website `Available ECMWF Public Datasets <https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets>`_. Log in and follow the licence links on the right side for each dataset and accept it.
-For the *ERA5* dataset this has to be done at the `Climate Data Store (CDS) website <https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset>`_. Log in with your credentials and then select on the left panel the product type "Reanalysis" for finding *ERA5* datasets. Then follow the link of a title with *ERA5* (anyone) to the full dataset record, click on tab "Download data" and scroll down. There is a section "Terms of use" where you have to click the :underline:`Accept terms` button.
-
+For the *ERA5* dataset this has to be done at the `Climate Data Store (CDS) website <https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset>`_. Log in and select, on the left panel, product type "Reanalysis" for finding *ERA5* datasets. Then follow any link with *ERA5* to the full dataset record, click on tab "Download data" and scroll down. There is a section "Terms of use" where you have to click the :underline:`Accept terms` button.
@@ -99,26 +109,21 @@ For the *ERA5* dataset this has to be done at the `Climate Data Store (CDS) webs
Download ``flex_extract``
=========================
-There are 2 options to download ``flex_extract``:
+There are two options to download ``flex_extract``:
tar ball
- You can download the latest prepared release tar ball from the `download section`_
- of our ``FLEXPART`` community website and then untar the file. Substitute
- the **<ID>** in the ``wget`` command with the ID-number of the ``flex_extract``
- release tar ball in the list of downloads at the community website.
-
-
+ You can download a tar ball with the latest release from the `flex_extract page <https://www.flexpart.eu/wiki/FpInputMetEcmwf>`_ from our ``FLEXPART`` community website and then untar the file.
+
.. code-block:: bash
- wget https://www.flexpart.eu/downloads/<ID>
tar -xvf <flex_extract_vX.X.tar>
-git repo
- Or you can clone the current release version from our git repository master branch.
+git repo
+ Alternatively, if you have ``git`` installed on your machine, and if you are interested to keep the code in a version control system, you may clone the latest version from our git repository master branch.
.. code-block:: bash
- $ git clone https://www.flexpart.eu/gitmob/flexpart
+ $ git clone --single-branch --branch master https://www.flexpart.eu/gitmob/flexpart
@@ -129,27 +134,11 @@ git repo
Environment requirements
========================
-This is a list of the general environment requirements for ``flex_extract``.
-What is required exactly for each application mode will be described in the specifc installation section.
+The software required for running ``flex_extract`` depends on the :doc:`Documentation/Overview/app_modes` and therefore is described in the respective specific installation sections.
-To run the python part of ``flex_extract`` a `Python 3`_ environment is needed.
-We tested ``flex_extract`` with a normal Linux Python package distribution and Anaconda Python.
-Except for `Python3`_ all are python packages which can be installed via ``pip``.
-
-* `Python3`_ or `Anaconda Python3`_
-* `numpy`_
-* `ecmwf-api-client`_ (Web Interface to ECMWF servers for datasets except ERA5)
-* `cdsapi`_ (Web Interface to `C3S <https://climate.copernicus.eu/>`_ servers for ERA5)
-* `genshi`_
-* `eccodes for python`_
-
-For the Fortran part of ``flex_extract`` we need the following distribution packages:
-
-* `gfortran`_
-* `fftw3`_
-* `eccodes`_
-* `emoslib`_
+Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries.
+We tested ``flex_extract`` with the python3 package from the the GNU/Linux distribution and Anaconda Python. The required python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).
@@ -161,705 +150,49 @@ For the Fortran part of ``flex_extract`` we need the following distribution pack
Installation of ``flex_extract``
================================
-The actual installation of ``flex_extract`` will be done by executing a `Shell` script called ``setup.sh``.
-It defines some parameters and calls a Python script by giving the parameters as command line arguments.
-More information on the script and its parameters can be found at :doc:`Documentation/Input/setup`.
+The actual installation of ``flex_extract`` is done by executing a shell script called ``setup.sh``.
+It defines some parameters and calls a Python script passing the parameters as command line arguments. For details, see :doc:`Documentation/Input/setup`.
For each application mode installation section we describe the requirements for the explicit
environment and how it is installed, test if it works and how the actual ``flex_extract``
installation has to be done. At the users local side not all software has to be present for ``flex_extract``.
+Select one of the following modes to install:
-
-
-
-.. _ref-remote-mode:
-
-Remote mode
------------
-
-.. _ref-req-remote:
-
-Remote environment requirements
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The environment for ``flex_extract`` on ECMWF servers has to provide these
-software packages and libraries:
-
-+---------------------------+-----------------+
-| Python part | Fortran part |
-+---------------------------+-----------------+
-| * `Python3`_ | * `gfortran`_ |
-| * `numpy`_ | * `fftw3`_ |
-| * `genshi`_ | * `eccodes`_ |
-| * `eccodes for python`_ | * `emoslib`_ |
-+---------------------------+-----------------+
-
-
-.. _ref-prep-remote:
-
-Prepare remote environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The environment on the ECMWF server (such as *ecgate* or *cca*) is already
-prepared. ECMWF server provide all libraries via a module system which is
-going to be selected by ``flex_extract`` automatically.
-
-
-.. _ref-install-remote:
-
-Remote installation
-^^^^^^^^^^^^^^^^^^^
-
-First, log in on one of the ECMWF Linux server, such as *ecgate* or *cca/ccb*.
-Substitute *<ecuid>* with your ECMWF user name:
-
-.. code-block:: bash
-
- ssh -X <ecuid>@ecaccess.ecmwf.int
-
-This will lead to the following output on the command line, asking for your
-password:
-
-.. code-block:: bash
-
- Authorized access only.
-
- ***************************************************************
- For further information, read the ECaccess documentation at:
-
- https://software.ecmwf.int/wiki/display/ECAC/ECaccess+Home
-
- You can also use ECaccess to load & download files from your
- EChome, ECscratch or ECfs directories using the ECaccess FTP
- server:
-
- ftp://uid@ecaccess.ecmwf.int/
-
- Please note you must use your UID and ActivID code to login!
- ***************************************************************
-
- <ecuid>@131.130.157.5's password: ***
- Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
-
- [<ecuid>@ecgb11 ~]$
-
-
-Then, copy the ``flex_extract`` tar ball (from section :ref:`ref-download`)
-to the ``$HOME`` directory of the ECMWF Linux server via ``scp``.
-Substitute the *<localuser>* and *<server.edu>* placeholders with your credentials.
-Untar the file and change into the ``flex_extract`` root directory.
-
-.. code-block:: bash
-
- scp <localuser>@<server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz $HOME/
- cd $HOME
- tar xvf flex_extract_vX.X.tar.gz
- cd flex_extract_vX.X
-
-
-On these ECMWF servers, it is not necessary to prepare the environment or the
-``Makefile`` for the Fortran program (``CONVERT2``) as described above.
-All third party libraries are available from a module system. The ``Makefile``
-is optimized for ECMWF servers and the compilation
-script ``compilejob.ksh``, which will be submitted by ``flex_extract`` to the
-batch job queue at ECMWF, does load all relevant modules from the ECMWF's module system.
-
-So there is just the need to execute the ``setup.sh`` script from the
-``flex_extract`` root directory for installation.
-Before executing it, it is necessary to adapt some parameters from ``setup.sh``
-described in :doc:`Documentation/Input/setup`.
-
-Open ``setup.sh`` with your editor and adapt the values:
-
-+----------------------------------------------+----------------------------------------------+
-| Take this for target = **ectrans** | Take this for target = **cca** |
-+----------------------------------------------+----------------------------------------------+
-| .. code-block:: bash | .. code-block:: bash |
-| | |
-| ... | ... |
-| # -----------------------------------------| # -----------------------------------------|
-| # AVAILABLE COMMANDLINE ARGUMENTS TO SET | # AVAILABLE COMMANDLINE ARGUMENTS TO SET |
-| # | # |
-| # THE USER HAS TO SPECIFY THESE PARAMETER | # THE USER HAS TO SPECIFY THESE PARAMETER |
-| # | # |
-| TARGET='ecgate' | TARGET='cca' |
-| MAKEFILE='Makefile.gfortran' | MAKEFILE='Makefile.CRAY' |
-| ECUID='uid' | ECUID='uid' |
-| ECGID='gid' | ECGID='gid' |
-| GATEWAY=None | GATEWAY=None |
-| DESTINATION=None | DESTINATION=None |
-| INSTALLDIR=None | INSTALLDIR='' |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
-| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
-| ... | ... |
-+----------------------------------------------+----------------------------------------------+
-
-:underline:`Please substitute the values of ECUID and ECGID
-with your own credentials and settings.`
-
-.. note::
-
- If a local gateway server is available the transfer of files could be done
- via the ``ECaccess`` commands. Therefore a valid *GATEWAY* and *DESTINATION*
- have to be present and should be set in the ``setup.sh`` file.
-
-
-Afterwards, type:
-
-.. code-block:: bash
-
- module load python3
- ./setup.sh
-
-to start the installation. You should see the following output at the command line.
-
-
-.. code-block:: bash
-
- # Output of setup.sh
- Create tarball ...
- Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X
- You should get an email with subject "flexcompile" within the next few minutes!
-
-
-The email content should look like this with a "SUCCESS" statement in the last line:
-
-.. code-block:: bash
-
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
- -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2
- SUCCESS!
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-.. _ref-gateway-mode:
-
-Gateway mode
-------------
-
-
-.. _ref-req-gateway:
-
-Gateway environment requirements
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The environment on your local system has to provide these software packages
-and libraries, since ``flex_extract`` does only prepare the job script and send
-it to the ECMWF servers:
-
-* `Python3`_ or `Anaconda Python3`_
-* `numpy`_
-* `genshi`_
-
-
-.. _ref-prep-gateway:
-
-Prepare gateway environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-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.
-The installation was tested on a *GNU/Linux Debian buster* and an *Ubuntu 18.04 Bionic Beaver* system.
-
-.. code-block:: sh
-
- # On a Linux Debian or Ubuntu system do
- # (if not already available):
- apt-get install python3
- apt-get install pip
- apt-get install genshi
- apt-get install numpy
-
-
-.. _ref-test-gateway:
-
-Test gateway environment
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Check the availability of the python packages by typing ``python3`` in
-a terminal window and run the ``import`` commands in the python shell.
-If there are no error messages, you succeeded in setting up the environment.
-
-.. code-block:: python
-
- # check in python3 console
- import genshi
- import numpy
-
-
-
-.. _ref-install-gateway:
-
-Gateway installation
-^^^^^^^^^^^^^^^^^^^^
-
-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.
-
-Please see `ECMWF's instructions on gateway server`_ to establish the gateway server if not already in place.
-Additionally, to be able to use the Ecaccess file transfer service **ectrans** please also create an association.
-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`_.
-
-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).
-
-.. code-block:: bash
-
- $ ecaccess-certificate-create
- Please enter your user-id: example_username
- Your passcode: ***
-
-``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.
-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.
-
-
-.. code-block:: bash
- :caption: 'Example settings for a gateway installation.'
- :name: setup.sh
-
- # -----------------------------------------------------------------
- # AVAILABLE COMMANDLINE ARGUMENTS TO SET
- #
- # THE USER HAS TO SPECIFY THESE PARAMETER
- #
- TARGET='ecgate'
- MAKEFILE='Makefile.gfortran'
- ECUID='uid'
- ECGID='gid'
- GATEWAY='server.example.edu'
- DESTINATION='example@genericSftp'
- INSTALLDIR=None
- JOB_TEMPLATE='job.template'
- CONTROLFILE='CONTROL_EA5'
-
-
-Afterwards, type:
-
-.. code-block:: bash
-
- $ ./setup.sh
-
-to start the installation. You should see the following output at the command line.
-
-
-.. code-block:: bash
-
- # Output of setup.sh
- Create tarball ...
- Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X
- You should get an email with subject "flexcompile" within the next few minutes!
-
-
-The email content should look like this with a "SUCCESS" statement in the last line:
-
-.. code-block:: bash
-
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
- -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2
- SUCCESS!
-
-
-
-
-
+ :doc:`Installation/remote`
+ :doc:`Installation/gateway`
-
-
-
-
-
-
-
-
-
-
-
-
-.. _ref-local-mode:
-
-Local mode
-----------
-
-
-
-.. _ref-req-local:
-
-Local environment requirements
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-For the local access modes **member** and **public** there is no difference in
-the installation process.
-
-The environment on your local system has to provide these software packages
-and libraries, since all extraction and preparation is done at the local system:
-
-+------------------------------------------------+-----------------+
-| Python part | Fortran part |
-+------------------------------------------------+-----------------+
-| * `Python3`_ | * `gfortran`_ |
-| * `numpy`_ | * `fftw3`_ |
-| * `genshi`_ | * `eccodes`_ |
-| * `eccodes for python`_ | * `emoslib`_ |
-| * `ecmwf-api-client`_ (everything except ERA5) | |
-| * `cdsapi`_ (just for ERA5) | |
-+------------------------------------------------+-----------------+
-
-
-.. _ref-prep-local:
-
-Prepare local environment
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-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.
-The installation was tested on a *Debian GNU/Linux buster/sid* and an *Ubuntu 18.04 Bionic Beaver* system.
-
-.. code-block:: sh
-
- # On a Linux Debian or Ubuntu system do
- # (if not already available):
- apt-get install python3 (usually available on normal Linux systems)
- apt-get install pip
- apt-get install gfortran
- apt-get install fftw3-dev
- apt-get install libeccodes-dev
- apt-get install libemos-dev
- apt-get install python3-eccodes
- apt-get install genshi
- apt-get install numpy
- pip install cdsapi
- pip install ecmwf-api-client
-
-.. note::
-
- In case you would like to use Anaconda Python we recommend you follow the installation instructions of
- `Anaconda Python Installation for Linux <https://docs.anaconda.com/anaconda/install/linux/>`_ and then install the
- ``eccodes`` package from ``conda`` with:
-
- .. code-block:: bash
-
- conda install conda-forge::python-eccodes
+ :doc:`Installation/local`
-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``.
-
-.. note::
-
- Since **public users** currently don't have access to the full *ERA5* dataset they can skip the installation of the ``CDS API``.
-
-Both user groups have to provide key's with their credentials for the Web API's in their home directory. Therefore, follow these instructions:
-
-ECMWF Web API:
- 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).
-
-CDS API:
- 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.
-
-
-.. _ref-test-local:
-
-Test local environment
-^^^^^^^^^^^^^^^^^^^^^^
-
-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:
-
-.. code-block:: sh
-
- $ dpkg -s libeccodes-dev | grep Status
- # or
- $ rpm -q libeccodes-dev
-
-Afterwards, check the availability of the python packages by typing ``python3`` in
-a terminal window and run the ``import`` commands in the python shell. If there are no error messages, you succeeded in setting up the environment.
-
-.. code-block:: python
-
- # check in python3 console
- import eccodes
- import genshi
- import numpy
- import cdsapi
- import ecmwfapi
-
-
-
-Test the Web API's
-""""""""""""""""""
-
-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.
-
-ECMWF Web API
-"""""""""""""
-
-
-+----------------------------------------------------------+----------------------------------------------------------+
-|Please use this piece of python code for **Member user**: |Please use this piece of python code for **Public user**: |
-+----------------------------------------------------------+----------------------------------------------------------+
-|.. code-block:: python |.. code-block:: python |
-| | |
-| from ecmwfapi import ECMWFService | from ecmwfapi import ECMWFDataServer |
-| | |
-| server = ECMWFService('mars') | server = ECMWFDataServer() |
-| | |
-| server.retrieve({ | server.retrieve({ |
-| 'stream' : "oper", | 'stream' : "enda", |
-| 'levtype' : "sfc", | 'levtype' : "sfc", |
-| 'param' : "165.128/166.128/167.128", | 'param' : "165.128/166.128/167.128", |
-| 'dataset' : "interim", | 'dataset' : "cera20c", |
-| 'step' : "0", | 'step' : "0", |
-| 'grid' : "0.75/0.75", | 'grid' : "1./1.", |
-| 'time' : "00/06/12/18", | 'time' : "00/06/12/18", |
-| 'date' : "2014-07-01/to/2014-07-31", | 'date' : "2000-07-01/to/2000-07-31", |
-| 'type' : "an", | 'type' : "an", |
-| 'class' : "ei", | 'class' : "ep", |
-| 'target' : "download_erainterim_ecmwfapi.grib" | 'target' : "download_cera20c_ecmwfapi.grib" |
-| }) | }) |
-+----------------------------------------------------------+----------------------------------------------------------+
-
-
-
-CDS API
-"""""""
-
-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:
-
-Please use this piece of python code to retrieve a small sample of *ERA5* pressure levels:
-
-.. code-block:: python
-
- import cdsapi
-
- c = cdsapi.Client()
+.. toctree::
+ :hidden:
+ :maxdepth: 2
- c.retrieve("reanalysis-era5-pressure-levels",
- {
- "variable": "temperature",
- "pressure_level": "1000",
- "product_type": "reanalysis",
- "year": "2008",
- "month": "01",
- "day": "01",
- "time": "12:00",
- "format": "grib"
- },
- "download_cdsapi.grib")
-
-
-Afterwards, when you know that the CDS API generally works, you can try to extract some
-data from the MARS archive. From the latest experience we know that this can take a while.
-
-.. **Member user**
+ Installation/remote
+ Installation/gateway
+ Installation/local
-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!
-.. code-block:: python
- import cdsapi
-
- c = cdsapi.Client()
-
- c.retrieve('reanalysis-era5-complete',
- {
- 'class' : 'ea',
- 'expver' : '1',
- 'stream' : 'oper',
- 'type' : 'fc',
- 'step' : '3/to/12/by/3',
- 'param' : '130.128',
- 'levtype' : 'ml',
- 'levelist': '135/to/137',
- 'date' : '2013-01-01',
- 'time' : '06/18',
- 'area' : '50/-5/40/5',
- 'grid' : '1.0/1.0',
- 'format' : 'grib',
- }, 'download_era5_cdsapi.grib')
-
-
-.. ********************** COMMENTED OUT FOR FUTURE
- ********************** PUBLIC RETRIEVAL IS CURRENTLY NOT ACCESSIBLE
-
- **Public user**
- Please use this piece of python code:
-
- .. code-block:: python
-
- import cdsapi
-
- c = cdsapi.Client()
-
- c.retrieve('reanalysis-era5-complete',
- {
- 'class' : 'ea',
- 'dataset' : 'era5',
- 'expver' : '1',
- 'stream' : 'oper',
- 'type' : 'fc',
- 'step' : '3/to/12/by/3',
- 'param' : '130.128',
- 'levtype' : 'ml',
- 'levelist': '135/to/137',
- 'date' : '2013-01-01',
- 'time' : '06/18',
- 'area' : '50/-5/40/5',
- 'grid' : '1.0/1.0',
- 'format' : 'grib',
- }, 'download_era5_cdsapi.grib')
-.. _ref-install-local:
-Local installation
-^^^^^^^^^^^^^^^^^^
-First prepare the Fortran ``Makefile`` for your environment and set it
-in the ``setup.sh`` script. (See section :ref:`ref-convert` for information on
-the Fortran program.)
-``flex_extract`` has already two ``Makefiles`` prepared for te ``gfortran`` and
-the ``ifort`` compiler:
- * Makefile.local.gfortran
- * Makefile.local.ifort
-They can be found in the path ``flex_extract_vX.X/source/fortran``, where
-``vX.X`` should be substituted with the current version number.
-.. caution::
- It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these
- ``Makefiles``.
-So starting from the root directory of ``flex_extract``,
-go to the ``Fortran`` source directory and open the ``Makefile`` of your
-choice to modify with an editor of your choice. We use the ``nedit`` in this case.
-
-.. code-block:: bash
-
- cd flex_extract_vX.X/source/fortran
- nedit Makefile.local.gfortran
-
-Edit the pathes to the ``eccodes`` library on your local machine.
-
-.. caution::
- This can vary from system to system.
- It is suggested to use a command like
-
- .. code-block:: bash
-
- # for the ECCODES_INCLUDE_DIR path do:
- $ dpkg -L libeccodes-dev | grep eccodes.mod
- # for the ECCODES_LIB path do:
- $ dpkg -L libeccodes-dev | grep libeccodes.so
-
- to find out the path to the ``eccodes`` library.
-
-Substitute these paths in the ``Makefile`` for parameters **ECCODES_INCLUDE_DIR**
-and **ECCODES_LIB** and save it.
-
-.. code-block:: bash
-
- # these are the paths on a current Debian 10 Testing system (May 2019)
- ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
- ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm
-
-The Fortran program called ``CONVERT2`` will be compiled during the
-installation process to get an executable. Therefore the ``Makefile``
-has to be set in the ``setup.sh`` script.
-
-In the root directory of ``flex_extract``, open the ``setup.sh`` script
-and adapt the installation parameters in the section labelled with
-"AVAILABLE COMMANDLINE ARGUMENTS TO SET" like shown below.
-
-
-.. code-block:: bash
- :caption: 'Example settings for a local installation.'
- :name: setup.sh
-
- ...
- # -----------------------------------------------------------------
- # AVAILABLE COMMANDLINE ARGUMENTS TO SET
- #
- # THE USER HAS TO SPECIFY THESE PARAMETER
- #
- TARGET='local'
- MAKEFILE='Makefile.local.gfortran'
- ECUID=None
- ECGID=None
- GATEWAY=None
- DESTINATION=None
- INSTALLDIR=None
- JOB_TEMPLATE='job.template'
- CONTROLFILE='CONTROL_EA5'
- ...
-
-
-Afterwards, type:
-
-.. code-block:: bash
-
- $ ./setup.sh
-
-to start the installation. You should see the following output at the command line.
-.. code-block:: bash
-
- # Output of setup.sh
- WARNING: installdir has not been specified
- flex_extract will be installed in here by compiling the Fortran source in /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/source/fortran
- Install flex_extract_v7.1 software at local in directory /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1
-
- Using makefile: Makefile.local.gfortran
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 rwGRIB2.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 posnam.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 preconvert.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -O3 -O3 -fopenmp -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/gcc-4.9.3/grib_api-1.14.3/lib -Bstatic -lgrib_api_f77 -lgrib_api_f90 -lgrib_api -Bdynamic -lm -ljasper -lemosR64
-
- -rwxrwxr-x. 1 philipa8 tmc 282992 May 23 22:27 ./CONVERT2
-
-
-
-
-
``Flex_extract`` in combination with ``FLEXPART``
=================================================
@@ -911,7 +244,7 @@ The installation was successfull if it showed the following output:
readlatlon: 4 records read
SUCCESSFULLY FINISHED CONVERT_PRE: CONGRATULATIONS
-Now go back to the root directoy:
+Now go back to the root directory:
.. code-block:: bash
diff --git a/Documentation/html/_sources/quick_start.rst.txt b/Documentation/html/_sources/quick_start.rst.txt
index cc1a51a166df08a91ed210a8708484790d229db3..a34faa12ec79b748418c485b5fc577611551b3b8 100644
--- a/Documentation/html/_sources/quick_start.rst.txt
+++ b/Documentation/html/_sources/quick_start.rst.txt
@@ -336,7 +336,7 @@ It is then available from 1st January 1979 to 31st August 2019. The ``etadot`` i
.. todo::
- @LEO: please check the complete describtion and functionality of the CONTROL FILEs
+ @LEO: please check the complete description and functionality of the CONTROL FILEs
Operational data
----------------
diff --git a/Documentation/html/index.html b/Documentation/html/index.html
index 010eb75761637e5bb931abaed316b34deb2f942c..13443c9ee2ba5544b795e23963a1f9524c45e505 100644
--- a/Documentation/html/index.html
+++ b/Documentation/html/index.html
@@ -284,15 +284,10 @@ Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="installation.html#registration-at-ecmwf">Registration at ECMWF</a></li>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#agree-on-licences-for-public-datasets">Agree on licences for public datasets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="installation.html#environment-requirements">Environment requirements</a></li>
-<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><ul>
-<li class="toctree-l3"><a class="reference internal" href="installation.html#remote-mode">Remote mode</a></li>
-<li class="toctree-l3"><a class="reference internal" href="installation.html#gateway-mode">Gateway mode</a></li>
-<li class="toctree-l3"><a class="reference internal" href="installation.html#local-mode">Local mode</a></li>
-</ul>
-</li>
+<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>
<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>
<li class="toctree-l2"><a class="reference internal" href="installation.html#test-installation">Test installation</a><ul>
<li class="toctree-l3"><a class="reference internal" href="installation.html#fortran-program-test">Fortran program test</a></li>
diff --git a/Documentation/html/installation.html b/Documentation/html/installation.html
index bf009725bf5725d5f1e8cf2aec8deaba5ae8d956..4179fa52d83cff6774a622ea7c69d698f5a1d982 100644
--- a/Documentation/html/installation.html
+++ b/Documentation/html/installation.html
@@ -38,8 +38,8 @@
<link rel="stylesheet" href="_static/css/theme_overrides.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="next" title="Quick Start" href="quick_start.html" />
- <link rel="prev" title="<no title>" href="index.html" />
+ <link rel="next" title="Remote mode installation" href="Installation/remote.html" />
+ <link rel="prev" title="Welcome to flex_extract’s user documentation!" href="index.html" />
</head>
<body class="wy-body-for-nav">
@@ -91,30 +91,13 @@
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#registration-at-ecmwf">Registration at ECMWF</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#agree-on-licences-for-public-datasets">Agree on licences for public datasets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
<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>
<li class="toctree-l2"><a class="reference internal" href="#environment-requirements">Environment requirements</a></li>
<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>
-<li class="toctree-l3"><a class="reference internal" href="#remote-mode">Remote mode</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#remote-environment-requirements">Remote environment requirements</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#prepare-remote-environment">Prepare remote environment</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#remote-installation">Remote installation</a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#gateway-mode">Gateway mode</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#gateway-environment-requirements">Gateway environment requirements</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#prepare-gateway-environment">Prepare gateway environment</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#test-gateway-environment">Test gateway environment</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#gateway-installation">Gateway installation</a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#local-mode">Local mode</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#local-environment-requirements">Local environment requirements</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#prepare-local-environment">Prepare local environment</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#test-local-environment">Test local environment</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#local-installation">Local installation</a></li>
-</ul>
-</li>
+<li class="toctree-l3"><a class="reference internal" href="Installation/remote.html">Remote mode installation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="Installation/gateway.html">Gateway mode installation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="Installation/local.html">Local mode installation</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#flex-extract-in-combination-with-flexpart"><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> in combination with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code></a></li>
@@ -202,665 +185,123 @@
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
-<p><code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is a software package which contains a mix of Python and Shell scripts as well as a Fortran program. These components rely on a couple of third party libraries which need to be prepared first before starting the installation process. For now, the software is only tested for a Linux/Unix environment. Feel free to try it out on other platforms.</p>
-<p>Start with the decision of which <a class="reference external" href="Ecmwf/access">user group</a> you belong to and follow the instructions at <a class="reference internal" href="#ref-registration"><span class="std std-ref">Registration at ECMWF</span></a> to get an account at ECMWF. Considering your user group and the method of applying <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> there appear to be 4 application modes:</p>
+<p>The <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> software package contains python and shell scripts as well as a Fortran program. These components rely on several libraries which need to be available before starting the installation process. Currently, the software is only tested for a GNU/Linux environment. Feel free to try it out on other platforms.</p>
+<p>At first, go to the <a class="reference external" href="Ecmwf/access.html">user group</a> section and decide which group you belong to and follow the instructions at <a class="reference internal" href="#ref-registration"><span class="std std-ref">Registration at ECMWF</span></a> to obtain an account at ECMWF (if you don’t have it already). Depending on the user group and the way to access the ECWMF MARS archive, there are four possible <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a>:</p>
<ul class="simple">
-<li>Remote (for member state users only) <a class="reference internal" href="#ref-remote-mode"><span class="std std-ref">[installation]</span></a></li>
-<li>Gateway (for member state users only) <a class="reference internal" href="#ref-gateway-mode"><span class="std std-ref">[installation]</span></a></li>
-<li>Local member <a class="reference internal" href="#ref-local-mode"><span class="std std-ref">[installation]</span></a></li>
-<li>Local public <a class="reference internal" href="#ref-local-mode"><span class="std std-ref">[installation]</span></a></li>
+<li>Remote (member-state users only) <a class="reference internal" href="Installation/remote.html#ref-remote-mode"><span class="std std-ref">[installation]</span></a></li>
+<li>Gateway (member-state users only) <a class="reference internal" href="Installation/gateway.html#ref-gateway-mode"><span class="std std-ref">[installation]</span></a></li>
+<li>Local, member-state user <a class="reference internal" href="Installation/local.html#ref-local-mode"><span class="std std-ref">[installation]</span></a></li>
+<li>Local, public user <a class="reference internal" href="Installation/local.html#ref-local-mode"><span class="std std-ref">[installation]</span></a></li>
</ul>
-<p>More information can be found in <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a>.</p>
+<p>Please follow the link <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> to get a description of the modes.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you encounter any problems in the installation process, you can ask for <a class="reference internal" href="support.html"><span class="doc">Support</span></a>.</p>
</div>
<div class="section" id="registration-at-ecmwf">
<span id="ref-registration"></span><h2>Registration at ECMWF<a class="headerlink" href="#registration-at-ecmwf" title="Permalink to this headline">¶</a></h2>
-<p>Decide which user group you belong to and follow the instructions for registration:</p>
-<dl class="docutils">
-<dt><strong>Member state user</strong>:</dt>
-<dd>To get a member-state user account, users have to be a resident of a <a class="reference external" href="https://www.ecmwf.int/en/about/who-we-are/member-states">member state</a>. In that case, you can contact your <a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Computing Representative</a> for granting access. If you would like to use the local application mode to retrieve <strong>ERA5</strong> data you’d have to register at the <a class="reference external" href="https://cds.climate.copernicus.eu/user/register">Copernicus Climate Data Store</a> also.</dd>
-<dt><strong>Public user</strong>:</dt>
-<dd><p class="first">To be able to download public datasets with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> such as <strong>ERA-Interim</strong> and <strong>CERA-20C</strong> (<strong>ERA5</strong> is not supported via ECMWF Web API anymore), the public user has to create an account at ECMWF.
-Use the registration at the ECMWF website by filling out this <cite>registration form</cite>.</p>
-<div class="last admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">In the future retrievement of <em>ERA5</em> will be possible via the CDS API for public users also. Then a registration at the <a class="reference external" href="https://cds.climate.copernicus.eu/user/register">Copernicus Climate Data Store</a> is needed in addition.</p>
-</div>
-</dd>
-</dl>
-</div>
-<div class="section" id="agree-on-licences-for-public-datasets">
-<span id="ref-licence"></span><h2>Agree on licences for public datasets<a class="headerlink" href="#agree-on-licences-for-public-datasets" title="Permalink to this headline">¶</a></h2>
-<p>Each public dataset which is intended to be downloaded by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> has its own licence which has to be accepted, regardless of the user group.</p>
-<p>For the <em>ERA-Interim</em> and <em>CERA-20C</em> datasets this can be done at the ECMWF website <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">Available ECMWF Public Datasets</a>. Log in and follow the licence links on the right side for each dataset and accept it.</p>
-<p>For the <em>ERA5</em> dataset this has to be done at the <a class="reference external" href="https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset">Climate Data Store (CDS) website</a>. Log in with your credentials and then select on the left panel the product type “Reanalysis” for finding <em>ERA5</em> datasets. Then follow the link of a title with <em>ERA5</em> (anyone) to the full dataset record, click on tab “Download data” and scroll down. There is a section “Terms of use” where you have to click the <span class="underline">Accept terms</span> button.</p>
-</div>
-<div class="section" id="download-flex-extract">
-<span id="ref-download"></span><h2>Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code><a class="headerlink" href="#download-flex-extract" title="Permalink to this headline">¶</a></h2>
-<p>There are 2 options to download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>:</p>
-<dl class="docutils">
-<dt>tar ball</dt>
-<dd><p class="first">You can download the latest prepared release tar ball from the <a class="reference external" href="https://www.flexpart.eu/downloads">download section</a>
-of our <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> community website and then untar the file. Substitute
-the <strong><ID></strong> in the <code class="docutils literal notranslate"><span class="pre">wget</span></code> command with the ID-number of the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>
-release tar ball in the list of downloads at the community website.</p>
-<div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>wget https://www.flexpart.eu/downloads/<ID>
-tar -xvf <flex_extract_vX.X.tar>
-</pre></div>
-</div>
-</dd>
-<dt>git repo</dt>
-<dd><p class="first">Or you can clone the current release version from our git repository master branch.</p>
-<div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>$ git clone https://www.flexpart.eu/gitmob/flexpart
-</pre></div>
-</div>
-</dd>
-</dl>
-</div>
-<div class="section" id="environment-requirements">
-<span id="ref-requirements"></span><h2>Environment requirements<a class="headerlink" href="#environment-requirements" title="Permalink to this headline">¶</a></h2>
-<p>This is a list of the general environment requirements for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.
-What is required exactly for each application mode will be described in the specifc installation section.</p>
-<p>To run the python part of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> a <a class="reference external" href="https://docs.python.org/3/">Python 3</a> environment is needed.
-We tested <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with a normal Linux Python package distribution and Anaconda Python.
-Except for <a class="reference external" href="https://www.python.org/downloads/">Python3</a> all are python packages which can be installed via <code class="docutils literal notranslate"><span class="pre">pip</span></code>.</p>
-<ul class="simple">
-<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>
-<li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
-<li><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ecmwf-api-client</a> (Web Interface to ECMWF servers for datasets except ERA5)</li>
-<li><a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> (Web Interface to <a class="reference external" href="https://climate.copernicus.eu/">C3S</a> servers for ERA5)</li>
-<li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
-<li><a class="reference external" href="https://packages.debian.org/sid/python3-eccodes">eccodes for python</a></li>
-</ul>
-<p>For the Fortran part of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> we need the following distribution packages:</p>
-<ul class="simple">
-<li><a class="reference external" href="https://gcc.gnu.org/wiki/GFortran">gfortran</a></li>
-<li><a class="reference external" href="http://www.fftw.org">fftw3</a></li>
-<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">eccodes</a></li>
-<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">emoslib</a></li>
-</ul>
-</div>
-<div class="section" id="installation-of-flex-extract">
-<span id="ref-install-fe"></span><h2>Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code><a class="headerlink" href="#installation-of-flex-extract" title="Permalink to this headline">¶</a></h2>
-<p>The actual installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> will be done by executing a <cite>Shell</cite> script called <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.
-It defines some parameters and calls a Python script by giving the parameters as command line arguments.
-More information on the script and its parameters can be found at <a class="reference internal" href="Documentation/Input/setup.html"><span class="doc">The Installation Script - setup.sh</span></a>.</p>
-<p>For each application mode installation section we describe the requirements for the explicit
-environment and how it is installed, test if it works and how the actual <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>
-installation has to be done. At the users local side not all software has to be present for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
-<div class="section" id="remote-mode">
-<span id="ref-remote-mode"></span><h3>Remote mode<a class="headerlink" href="#remote-mode" title="Permalink to this headline">¶</a></h3>
-<div class="section" id="remote-environment-requirements">
-<span id="ref-req-remote"></span><h4>Remote environment requirements<a class="headerlink" href="#remote-environment-requirements" title="Permalink to this headline">¶</a></h4>
-<p>The environment for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> on ECMWF servers has to provide these
-software packages and libraries:</p>
+<p>The registration depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application Modes</span></a> and in case of the local mode also on the data set you’d like to retrieve. The following table gives an overview where you need to register.</p>
<table border="1" class="docutils">
<colgroup>
-<col width="61%" />
-<col width="39%" />
+<col width="23%" />
+<col width="15%" />
+<col width="16%" />
+<col width="24%" />
+<col width="23%" />
</colgroup>
<tbody valign="top">
-<tr class="row-odd"><td>Python part</td>
-<td>Fortran part</td>
+<tr class="row-odd"><td rowspan="2">Data sets</td>
+<td colspan="3">Member-state user</td>
+<td>Public user</td>
</tr>
-<tr class="row-even"><td><ul class="first last simple">
-<li><a class="reference external" href="https://www.python.org/downloads/">Python3</a></li>
-<li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
-<li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
-<li><a class="reference external" href="https://packages.debian.org/sid/python3-eccodes">eccodes for python</a></li>
-</ul>
-</td>
+<tr class="row-even"><td>Remote</td>
+<td>Gateway</td>
+<td>Local</td>
+<td>Local</td>
+</tr>
+<tr class="row-odd"><td>Operational</td>
+<td>1</td>
+<td>1</td>
+<td>1,2</td>
<td><ul class="first last simple">
-<li><a class="reference external" href="https://gcc.gnu.org/wiki/GFortran">gfortran</a></li>
-<li><a class="reference external" href="http://www.fftw.org">fftw3</a></li>
-<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">eccodes</a></li>
-<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">emoslib</a></li>
+<li></li>
</ul>
</td>
</tr>
-</tbody>
-</table>
-</div>
-<div class="section" id="prepare-remote-environment">
-<span id="ref-prep-remote"></span><h4>Prepare remote environment<a class="headerlink" href="#prepare-remote-environment" title="Permalink to this headline">¶</a></h4>
-<p>The environment on the ECMWF server (such as <em>ecgate</em> or <em>cca</em>) is already
-prepared. ECMWF server provide all libraries via a module system which is
-going to be selected by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> automatically.</p>
-</div>
-<div class="section" id="remote-installation">
-<span id="ref-install-remote"></span><h4>Remote installation<a class="headerlink" href="#remote-installation" title="Permalink to this headline">¶</a></h4>
-<p>First, log in on one of the ECMWF Linux server, such as <em>ecgate</em> or <em>cca/ccb</em>.
-Substitute <em><ecuid></em> with your ECMWF user name:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ssh -X <ecuid>@ecaccess.ecmwf.int
-</pre></div>
-</div>
-<p>This will lead to the following output on the command line, asking for your
-password:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>Authorized access only.
-
-***************************************************************
- For further information, read the ECaccess documentation at:
-
- https://software.ecmwf.int/wiki/display/ECAC/ECaccess+Home
-
- You can also use ECaccess to load & download files from your
- EChome, ECscratch or ECfs directories using the ECaccess FTP
- server:
-
- ftp://uid@ecaccess.ecmwf.int/
-
- Please note you must use your UID and ActivID code to login!
-***************************************************************
-
-<ecuid>@131.130.157.5's password: ***
-Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
-
-[<ecuid>@ecgb11 ~]$
-</pre></div>
-</div>
-<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="#ref-download"><span class="std std-ref">Download flex_extract</span></a>)
-to the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory of the ECMWF Linux server via <code class="docutils literal notranslate"><span class="pre">scp</span></code>.
-Substitute the <em><localuser></em> and <em><server.edu></em> placeholders with your credentials.
-Untar the file and change into the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp <localuser>@<server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz <span class="nv">$HOME</span>/
-<span class="nb">cd</span> <span class="nv">$HOME</span>
-tar xvf flex_extract_vX.X.tar.gz
-<span class="nb">cd</span> flex_extract_vX.X
-</pre></div>
-</div>
-<p>On these ECMWF servers, it is not necessary to prepare the environment or the
-<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.
-All third party libraries are available from a module system. The <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>
-is optimized for ECMWF servers and the compilation
-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
-batch job queue at ECMWF, does load all relevant modules from the ECMWF’s module system.</p>
-<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
-<code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory for installation.
-Before executing it, it is necessary to adapt some parameters from <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>
-described in <a class="reference internal" href="Documentation/Input/setup.html"><span class="doc">The Installation Script - setup.sh</span></a>.</p>
-<p>Open <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> with your editor and adapt the values:</p>
-<table border="1" class="docutils">
-<colgroup>
-<col width="50%" />
-<col width="50%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td>Take this for target = <strong>ectrans</strong></td>
-<td>Take this for target = <strong>cca</strong></td>
+<tr class="row-even"><td>ERA-Interim</td>
+<td>1</td>
+<td>1</td>
+<td>1,2</td>
+<td>2</td>
</tr>
-<tr class="row-even"><td><div class="first last highlight-bash notranslate"><div class="highlight"><pre><span></span>...
-<span class="c1"># -----------------------------------------</span>
-<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
-<span class="c1">#</span>
-<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
-<span class="c1">#</span>
-<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'ecgate'</span>
-<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'Makefile.gfortran'</span>
-<span class="nv">ECUID</span><span class="o">=</span><span class="s1">'uid'</span>
-<span class="nv">ECGID</span><span class="o">=</span><span class="s1">'gid'</span>
-<span class="nv">GATEWAY</span><span class="o">=</span>None
-<span class="nv">DESTINATION</span><span class="o">=</span>None
-<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
-<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
-...
-</pre></div>
-</div>
-</td>
-<td><div class="first last highlight-bash notranslate"><div class="highlight"><pre><span></span>...
-<span class="c1"># -----------------------------------------</span>
-<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
-<span class="c1">#</span>
-<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
-<span class="c1">#</span>
-<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'cca'</span>
-<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'Makefile.CRAY'</span>
-<span class="nv">ECUID</span><span class="o">=</span><span class="s1">'uid'</span>
-<span class="nv">ECGID</span><span class="o">=</span><span class="s1">'gid'</span>
-<span class="nv">GATEWAY</span><span class="o">=</span>None
-<span class="nv">DESTINATION</span><span class="o">=</span>None
-<span class="nv">INSTALLDIR</span><span class="o">=</span><span class="s1">''</span>
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
-<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
-...
-</pre></div>
-</div>
-</td>
+<tr class="row-odd"><td>CERA-20C</td>
+<td>1</td>
+<td>1</td>
+<td>1,2</td>
+<td>2</td>
</tr>
-</tbody>
-</table>
-<p><span class="underline">Please substitute the values of ECUID and ECGID
-with your own credentials and settings.</span></p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">If a local gateway server is available the transfer of files could be done
-via the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. Therefore a valid <em>GATEWAY</em> and <em>DESTINATION</em>
-have to be present and should be set in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file.</p>
-</div>
-<p>Afterwards, type:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>module load python3
-./setup.sh
-</pre></div>
-</div>
-<p>to start the installation. You should see the following output at the command line.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
-Create tarball ...
-Job compilation script has been submitted to ecgate <span class="k">for</span> installation in <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_vX.X
-You should get an email with subject <span class="s2">"flexcompile"</span> within the next few minutes!
-</pre></div>
-</div>
-<p>The email content should look like this with a “SUCCESS” statement in the last line:</p>
-<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
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp grphreal.f
-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 ftrafo.f
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
--rwxr-x---. <span class="m">1</span> USER at <span class="m">353134</span> May <span class="m">23</span> <span class="m">12</span>:27 CONVERT2
-SUCCESS!
-</pre></div>
-</div>
-</div>
-</div>
-<div class="section" id="gateway-mode">
-<span id="ref-gateway-mode"></span><h3>Gateway mode<a class="headerlink" href="#gateway-mode" title="Permalink to this headline">¶</a></h3>
-<div class="section" id="gateway-environment-requirements">
-<span id="ref-req-gateway"></span><h4>Gateway environment requirements<a class="headerlink" href="#gateway-environment-requirements" title="Permalink to this headline">¶</a></h4>
-<p>The environment on your local system has to provide these software packages
-and libraries, since <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> does only prepare the job script and send
-it to the ECMWF servers:</p>
-<ul class="simple">
-<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>
-<li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
-<li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
-</ul>
-</div>
-<div class="section" id="prepare-gateway-environment">
-<span id="ref-prep-gateway"></span><h4>Prepare gateway environment<a class="headerlink" href="#prepare-gateway-environment" title="Permalink to this headline">¶</a></h4>
-<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.
-The installation was tested on a <em>GNU/Linux Debian buster</em> and an <em>Ubuntu 18.04 Bionic Beaver</em> system.</p>
-<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Linux Debian or Ubuntu system do</span>
-<span class="c1"># (if not already available):</span>
-apt-get install python3
-apt-get install pip
-apt-get install genshi
-apt-get install numpy
-</pre></div>
-</div>
-</div>
-<div class="section" id="test-gateway-environment">
-<span id="ref-test-gateway"></span><h4>Test gateway environment<a class="headerlink" href="#test-gateway-environment" title="Permalink to this headline">¶</a></h4>
-<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>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span>
-<span class="kn">import</span> <span class="nn">genshi</span>
-<span class="kn">import</span> <span class="nn">numpy</span>
-</pre></div>
-</div>
-</div>
-<div class="section" id="gateway-installation">
-<span id="ref-install-gateway"></span><h4>Gateway installation<a class="headerlink" href="#gateway-installation" title="Permalink to this headline">¶</a></h4>
-<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>
-<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> please also create an association.
-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>
-<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>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ecaccess-certificate-create
-Please enter your user-id: example_username
-Your passcode: ***
-</pre></div>
-</div>
-<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.
-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>
-<div class="literal-block-wrapper docutils container" id="setup-sh">
-<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>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># -----------------------------------------------------------------</span>
-<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
-<span class="c1">#</span>
-<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
-<span class="c1">#</span>
-<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'ecgate'</span>
-<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'Makefile.gfortran'</span>
-<span class="nv">ECUID</span><span class="o">=</span><span class="s1">'uid'</span>
-<span class="nv">ECGID</span><span class="o">=</span><span class="s1">'gid'</span>
-<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'server.example.edu'</span>
-<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'example@genericSftp'</span>
-<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
-<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
-</pre></div>
-</div>
-</div>
-<p>Afterwards, type:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup.sh
-</pre></div>
-</div>
-<p>to start the installation. You should see the following output at the command line.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
-Create tarball ...
-Job compilation script has been submitted to ecgate <span class="k">for</span> installation in <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_vX.X
-You should get an email with subject <span class="s2">"flexcompile"</span> within the next few minutes!
-</pre></div>
-</div>
-<p>The email content should look like this with a “SUCCESS” statement in the last line:</p>
-<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
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp grphreal.f
-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 ftrafo.f
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
--rwxr-x---. <span class="m">1</span> USER at <span class="m">353134</span> May <span class="m">23</span> <span class="m">12</span>:27 CONVERT2
-SUCCESS!
-</pre></div>
-</div>
-</div>
-</div>
-<div class="section" id="local-mode">
-<span id="ref-local-mode"></span><h3>Local mode<a class="headerlink" href="#local-mode" title="Permalink to this headline">¶</a></h3>
-<div class="section" id="local-environment-requirements">
-<span id="ref-req-local"></span><h4>Local environment requirements<a class="headerlink" href="#local-environment-requirements" title="Permalink to this headline">¶</a></h4>
-<p>For the local access modes <strong>member</strong> and <strong>public</strong> there is no difference in
-the installation process.</p>
-<p>The environment on your local system has to provide these software packages
-and libraries, since all extraction and preparation is done at the local system:</p>
-<table border="1" class="docutils">
-<colgroup>
-<col width="74%" />
-<col width="26%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td>Python part</td>
-<td>Fortran part</td>
-</tr>
-<tr class="row-even"><td><ul class="first last simple">
-<li><a class="reference external" href="https://www.python.org/downloads/">Python3</a></li>
-<li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
-<li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
-<li><a class="reference external" href="https://packages.debian.org/sid/python3-eccodes">eccodes for python</a></li>
-<li><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ecmwf-api-client</a> (everything except ERA5)</li>
-<li><a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> (just for ERA5)</li>
-</ul>
-</td>
+<tr class="row-even"><td>ERA5</td>
+<td>1</td>
+<td>1</td>
+<td>3</td>
<td><ul class="first last simple">
-<li><a class="reference external" href="https://gcc.gnu.org/wiki/GFortran">gfortran</a></li>
-<li><a class="reference external" href="http://www.fftw.org">fftw3</a></li>
-<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">eccodes</a></li>
-<li><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">emoslib</a></li>
+<li></li>
</ul>
</td>
</tr>
</tbody>
</table>
+<p>Registration options:</p>
+<blockquote>
+<div><p>1.) Access through a member-state user account granted by the <a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Computing Representative</a>. The credentials have to be provided during installation.</p>
+<p>2.) Access through the ECMWF Web API. Need to sign in at <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ECMWF Web API</a> and configure the ECMWF key as described. Member-state users can sign in with their credentials from the <a class="reference external" href="https://www.ecmwf.int/en/about/contact-us/computing-representatives">Computing Representative</a> and public users have to fill out the <a class="reference external" href="https://apps.ecmwf.int/registration/">registration form</a> to get an account.</p>
+<p>3.) Access through the <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">CDS API</a>. Extra registration for member-state users is required at <a class="reference external" href="https://cds.climate.copernicus.eu/user/register">Copernicus Climate Data Store</a> including the configurations of the CDS key as described. This mode is currently not available for public users. See the note at <a class="reference external" href="Ecmwf/access.html">user group</a> for information.</p>
+</div></blockquote>
</div>
-<div class="section" id="prepare-local-environment">
-<span id="ref-prep-local"></span><h4>Prepare local environment<a class="headerlink" href="#prepare-local-environment" title="Permalink to this headline">¶</a></h4>
-<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.
-The installation was tested on a <em>Debian GNU/Linux buster/sid</em> and an <em>Ubuntu 18.04 Bionic Beaver</em> system.</p>
-<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Linux Debian or Ubuntu system do</span>
-<span class="c1"># (if not already available):</span>
-apt-get install python3 <span class="o">(</span>usually available on normal Linux systems<span class="o">)</span>
-apt-get install pip
-apt-get install gfortran
-apt-get install fftw3-dev
-apt-get install libeccodes-dev
-apt-get install libemos-dev
-apt-get install python3-eccodes
-apt-get install genshi
-apt-get install numpy
-pip install cdsapi
-pip install ecmwf-api-client
-</pre></div>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>In case you would like to use Anaconda Python we recommend you follow the installation instructions of
-<a class="reference external" href="https://docs.anaconda.com/anaconda/install/linux/">Anaconda Python Installation for Linux</a> and then install the
-<code class="docutils literal notranslate"><span class="pre">eccodes</span></code> package from <code class="docutils literal notranslate"><span class="pre">conda</span></code> with:</p>
-<div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>conda install conda-forge::python-eccodes
-</pre></div>
-</div>
-</div>
-<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>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<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>
+<div class="section" id="licence-agreement-for-public-datasets">
+<span id="ref-licence"></span><h2>Licence agreement for public datasets<a class="headerlink" href="#licence-agreement-for-public-datasets" title="Permalink to this headline">¶</a></h2>
+<p>Each ECMWF public dataset has its own licence which has to be accepted, regardless of the user group.</p>
+<p>For the <em>ERA-Interim</em> and <em>CERA-20C</em> datasets this can be done at the ECMWF website <a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets">Available ECMWF Public Datasets</a>. Log in and follow the licence links on the right side for each dataset and accept it.</p>
+<p>For the <em>ERA5</em> dataset this has to be done at the <a class="reference external" href="https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset">Climate Data Store (CDS) website</a>. Log in and select, on the left panel, product type “Reanalysis” for finding <em>ERA5</em> datasets. Then follow any link with <em>ERA5</em> to the full dataset record, click on tab “Download data” and scroll down. There is a section “Terms of use” where you have to click the <span class="underline">Accept terms</span> button.</p>
</div>
-<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>
+<div class="section" id="download-flex-extract">
+<span id="ref-download"></span><h2>Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code><a class="headerlink" href="#download-flex-extract" title="Permalink to this headline">¶</a></h2>
+<p>There are two options to download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>:</p>
<dl class="docutils">
-<dt>ECMWF Web API:</dt>
-<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>
-<dt>CDS API:</dt>
-<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>
-</dl>
-</div>
-<div class="section" id="test-local-environment">
-<span id="ref-test-local"></span><h4>Test local environment<a class="headerlink" href="#test-local-environment" title="Permalink to this headline">¶</a></h4>
-<p>Check the availability of the system packages with <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or <code class="docutils literal notranslate"><span class="pre">rpm</span> <span class="pre">-q</span> <span class="pre"><package_name></span></code>, depending on your system. For example:</p>
-<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>$ dpkg -s libeccodes-dev <span class="p">|</span> grep Status
-<span class="c1"># or</span>
-$ rpm -q libeccodes-dev
-</pre></div>
-</div>
-<p>Afterwards, 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>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span>
-<span class="kn">import</span> <span class="nn">eccodes</span>
-<span class="kn">import</span> <span class="nn">genshi</span>
-<span class="kn">import</span> <span class="nn">numpy</span>
-<span class="kn">import</span> <span class="nn">cdsapi</span>
-<span class="kn">import</span> <span class="nn">ecmwfapi</span>
-</pre></div>
-</div>
-<div class="section" id="test-the-web-api-s">
-<h5>Test the Web API’s<a class="headerlink" href="#test-the-web-api-s" title="Permalink to this headline">¶</a></h5>
-<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>
-</div>
-<div class="section" id="ecmwf-web-api">
-<h5>ECMWF Web API<a class="headerlink" href="#ecmwf-web-api" title="Permalink to this headline">¶</a></h5>
-<table border="1" class="docutils">
-<colgroup>
-<col width="50%" />
-<col width="50%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td>Please use this piece of python code for <strong>Member user</strong>:</td>
-<td>Please use this piece of python code for <strong>Public user</strong>:</td>
-</tr>
-<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>
-
-<span class="n">server</span> <span class="o">=</span> <span class="n">ECMWFService</span><span class="p">(</span><span class="s1">'mars'</span><span class="p">)</span>
-
-<span class="n">server</span><span class="o">.</span><span class="n">retrieve</span><span class="p">({</span>
- <span class="s1">'stream'</span> <span class="p">:</span> <span class="s2">"oper"</span><span class="p">,</span>
- <span class="s1">'levtype'</span> <span class="p">:</span> <span class="s2">"sfc"</span><span class="p">,</span>
- <span class="s1">'param'</span> <span class="p">:</span> <span class="s2">"165.128/166.128/167.128"</span><span class="p">,</span>
- <span class="s1">'dataset'</span> <span class="p">:</span> <span class="s2">"interim"</span><span class="p">,</span>
- <span class="s1">'step'</span> <span class="p">:</span> <span class="s2">"0"</span><span class="p">,</span>
- <span class="s1">'grid'</span> <span class="p">:</span> <span class="s2">"0.75/0.75"</span><span class="p">,</span>
- <span class="s1">'time'</span> <span class="p">:</span> <span class="s2">"00/06/12/18"</span><span class="p">,</span>
- <span class="s1">'date'</span> <span class="p">:</span> <span class="s2">"2014-07-01/to/2014-07-31"</span><span class="p">,</span>
- <span class="s1">'type'</span> <span class="p">:</span> <span class="s2">"an"</span><span class="p">,</span>
- <span class="s1">'class'</span> <span class="p">:</span> <span class="s2">"ei"</span><span class="p">,</span>
- <span class="s1">'target'</span> <span class="p">:</span> <span class="s2">"download_erainterim_ecmwfapi.grib"</span>
-<span class="p">})</span>
-</pre></div>
-</div>
-</td>
-<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">ECMWFDataServer</span>
-
-<span class="n">server</span> <span class="o">=</span> <span class="n">ECMWFDataServer</span><span class="p">()</span>
-
-<span class="n">server</span><span class="o">.</span><span class="n">retrieve</span><span class="p">({</span>
- <span class="s1">'stream'</span> <span class="p">:</span> <span class="s2">"enda"</span><span class="p">,</span>
- <span class="s1">'levtype'</span> <span class="p">:</span> <span class="s2">"sfc"</span><span class="p">,</span>
- <span class="s1">'param'</span> <span class="p">:</span> <span class="s2">"165.128/166.128/167.128"</span><span class="p">,</span>
- <span class="s1">'dataset'</span> <span class="p">:</span> <span class="s2">"cera20c"</span><span class="p">,</span>
- <span class="s1">'step'</span> <span class="p">:</span> <span class="s2">"0"</span><span class="p">,</span>
- <span class="s1">'grid'</span> <span class="p">:</span> <span class="s2">"1./1."</span><span class="p">,</span>
- <span class="s1">'time'</span> <span class="p">:</span> <span class="s2">"00/06/12/18"</span><span class="p">,</span>
- <span class="s1">'date'</span> <span class="p">:</span> <span class="s2">"2000-07-01/to/2000-07-31"</span><span class="p">,</span>
- <span class="s1">'type'</span> <span class="p">:</span> <span class="s2">"an"</span><span class="p">,</span>
- <span class="s1">'class'</span> <span class="p">:</span> <span class="s2">"ep"</span><span class="p">,</span>
- <span class="s1">'target'</span> <span class="p">:</span> <span class="s2">"download_cera20c_ecmwfapi.grib"</span>
-<span class="p">})</span>
-</pre></div>
-</div>
-</td>
-</tr>
-</tbody>
-</table>
-</div>
-<div class="section" id="cds-api">
-<h5>CDS API<a class="headerlink" href="#cds-api" title="Permalink to this headline">¶</a></h5>
-<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>
-<p>Please use this piece of python code to retrieve a small sample of <em>ERA5</em> pressure levels:</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span>
-
-<span class="n">c</span> <span class="o">=</span> <span class="n">cdsapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span>
-
-<span class="n">c</span><span class="o">.</span><span class="n">retrieve</span><span class="p">(</span><span class="s2">"reanalysis-era5-pressure-levels"</span><span class="p">,</span>
-<span class="p">{</span>
-<span class="s2">"variable"</span><span class="p">:</span> <span class="s2">"temperature"</span><span class="p">,</span>
-<span class="s2">"pressure_level"</span><span class="p">:</span> <span class="s2">"1000"</span><span class="p">,</span>
-<span class="s2">"product_type"</span><span class="p">:</span> <span class="s2">"reanalysis"</span><span class="p">,</span>
-<span class="s2">"year"</span><span class="p">:</span> <span class="s2">"2008"</span><span class="p">,</span>
-<span class="s2">"month"</span><span class="p">:</span> <span class="s2">"01"</span><span class="p">,</span>
-<span class="s2">"day"</span><span class="p">:</span> <span class="s2">"01"</span><span class="p">,</span>
-<span class="s2">"time"</span><span class="p">:</span> <span class="s2">"12:00"</span><span class="p">,</span>
-<span class="s2">"format"</span><span class="p">:</span> <span class="s2">"grib"</span>
-<span class="p">},</span>
-<span class="s2">"download_cdsapi.grib"</span><span class="p">)</span>
+<dt>tar ball</dt>
+<dd><p class="first">You can download a tar ball with the latest release from the <a class="reference external" href="https://www.flexpart.eu/wiki/FpInputMetEcmwf">flex_extract page</a> from our <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> community website and then untar the file.</p>
+<div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>tar -xvf <flex_extract_vX.X.tar>
</pre></div>
</div>
-<p>Afterwards, when you know that the CDS API generally works, you can try to extract some
-data from the MARS archive. From the latest experience we know that this can take a while.</p>
-<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>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cdsapi</span>
-
-<span class="n">c</span> <span class="o">=</span> <span class="n">cdsapi</span><span class="o">.</span><span class="n">Client</span><span class="p">()</span>
-
-<span class="n">c</span><span class="o">.</span><span class="n">retrieve</span><span class="p">(</span><span class="s1">'reanalysis-era5-complete'</span><span class="p">,</span>
-<span class="p">{</span>
- <span class="s1">'class'</span> <span class="p">:</span> <span class="s1">'ea'</span><span class="p">,</span>
- <span class="s1">'expver'</span> <span class="p">:</span> <span class="s1">'1'</span><span class="p">,</span>
- <span class="s1">'stream'</span> <span class="p">:</span> <span class="s1">'oper'</span><span class="p">,</span>
- <span class="s1">'type'</span> <span class="p">:</span> <span class="s1">'fc'</span><span class="p">,</span>
- <span class="s1">'step'</span> <span class="p">:</span> <span class="s1">'3/to/12/by/3'</span><span class="p">,</span>
- <span class="s1">'param'</span> <span class="p">:</span> <span class="s1">'130.128'</span><span class="p">,</span>
- <span class="s1">'levtype'</span> <span class="p">:</span> <span class="s1">'ml'</span><span class="p">,</span>
- <span class="s1">'levelist'</span><span class="p">:</span> <span class="s1">'135/to/137'</span><span class="p">,</span>
- <span class="s1">'date'</span> <span class="p">:</span> <span class="s1">'2013-01-01'</span><span class="p">,</span>
- <span class="s1">'time'</span> <span class="p">:</span> <span class="s1">'06/18'</span><span class="p">,</span>
- <span class="s1">'area'</span> <span class="p">:</span> <span class="s1">'50/-5/40/5'</span><span class="p">,</span>
- <span class="s1">'grid'</span> <span class="p">:</span> <span class="s1">'1.0/1.0'</span><span class="p">,</span>
- <span class="s1">'format'</span> <span class="p">:</span> <span class="s1">'grib'</span><span class="p">,</span>
-<span class="p">},</span> <span class="s1">'download_era5_cdsapi.grib'</span><span class="p">)</span>
+</dd>
+<dt>git repo</dt>
+<dd><p class="first">Alternatively, if you have <code class="docutils literal notranslate"><span class="pre">git</span></code> installed on your machine, and if you are interested to keep the code in a version control system, you may clone the latest version from our git repository master branch.</p>
+<div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>$ git clone --single-branch --branch master https://www.flexpart.eu/gitmob/flexpart
</pre></div>
</div>
+</dd>
+</dl>
</div>
+<div class="section" id="environment-requirements">
+<span id="ref-requirements"></span><h2>Environment requirements<a class="headerlink" href="#environment-requirements" title="Permalink to this headline">¶</a></h2>
+<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>
+<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.
+We tested <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the python3 package from the the GNU/Linux distribution and Anaconda Python. The required python3 modules should prefarably be installed as distribution packages, or alternatively using Python’s own package manager <code class="docutils literal notranslate"><span class="pre">pip</span></code> (this may mess up some aspects of your python installation, especially if you use <code class="docutils literal notranslate"><span class="pre">pip</span></code> as root. Think about using virtual environments.).</p>
</div>
-<div class="section" id="local-installation">
-<span id="ref-install-local"></span><h4>Local installation<a class="headerlink" href="#local-installation" title="Permalink to this headline">¶</a></h4>
-<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.)
-<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
-the <code class="docutils literal notranslate"><span class="pre">ifort</span></code> compiler:</p>
+<div class="section" id="installation-of-flex-extract">
+<span id="ref-install-fe"></span><h2>Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code><a class="headerlink" href="#installation-of-flex-extract" title="Permalink to this headline">¶</a></h2>
+<p>The actual installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is done by executing a shell script called <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.
+It defines some parameters and calls a Python script passing the parameters as command line arguments. For details, see <a class="reference internal" href="Documentation/Input/setup.html"><span class="doc">The Installation Script - setup.sh</span></a>.</p>
+<p>For each application mode installation section we describe the requirements for the explicit
+environment and how it is installed, test if it works and how the actual <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>
+installation has to be done. At the users local side not all software has to be present for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</p>
+<p>Select one of the following modes to install:</p>
<blockquote>
-<div><ul class="simple">
-<li>Makefile.local.gfortran</li>
-<li>Makefile.local.ifort</li>
-</ul>
+<div><p><a class="reference internal" href="Installation/remote.html"><span class="doc">Remote mode installation</span></a></p>
+<p><a class="reference internal" href="Installation/gateway.html"><span class="doc">Gateway mode installation</span></a></p>
+<p><a class="reference internal" href="Installation/local.html"><span class="doc">Local mode installation</span></a></p>
</div></blockquote>
-<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
-<code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted with the current version number.</p>
-<div class="admonition caution">
-<p class="first admonition-title">Caution</p>
-<p class="last">It is necessary to adapt <strong>ECCODES_INCLUDE_DIR</strong> and <strong>ECCODES_LIB</strong> in these
-<code class="docutils literal notranslate"><span class="pre">Makefiles</span></code>.</p>
-</div>
-<p>So starting from the root directory of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>,
-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
-choice to modify with an editor of your choice. We use the <code class="docutils literal notranslate"><span class="pre">nedit</span></code> in this case.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> flex_extract_vX.X/source/fortran
-nedit Makefile.local.gfortran
-</pre></div>
-</div>
-<p>Edit the pathes to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library on your local machine.</p>
-<div class="admonition caution">
-<p class="first admonition-title">Caution</p>
-<p>This can vary from system to system.
-It is suggested to use a command like</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># for the ECCODES_INCLUDE_DIR path do:</span>
-$ dpkg -L libeccodes-dev <span class="p">|</span> grep eccodes.mod
-<span class="c1"># for the ECCODES_LIB path do:</span>
-$ dpkg -L libeccodes-dev <span class="p">|</span> grep libeccodes.so
-</pre></div>
-</div>
-<p class="last">to find out the path to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library.</p>
-</div>
-<p>Substitute these paths in the <code class="docutils literal notranslate"><span class="pre">Makefile</span></code> for parameters <strong>ECCODES_INCLUDE_DIR</strong>
-and <strong>ECCODES_LIB</strong> and save it.</p>
-<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>
-<span class="nv">ECCODES_INCLUDE_DIR</span><span class="o">=</span>/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
-<span class="nv">ECCODES_LIB</span><span class="o">=</span> -L/usr/lib -leccodes_f90 -leccodes -lm
-</pre></div>
-</div>
-<p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> will be compiled during the
-installation process to get an executable. Therefore the <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>
-has to be set in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script.</p>
-<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
-and adapt the installation parameters in the section labelled with
-“AVAILABLE COMMANDLINE ARGUMENTS TO SET” like shown below.</p>
-<div class="literal-block-wrapper docutils container" id="id2">
-<div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#id2" title="Permalink to this code">¶</a></div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...
-<span class="c1"># -----------------------------------------------------------------</span>
-<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
-<span class="c1">#</span>
-<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
-<span class="c1">#</span>
-<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'local'</span>
-<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">'Makefile.local.gfortran'</span>
-<span class="nv">ECUID</span><span class="o">=</span>None
-<span class="nv">ECGID</span><span class="o">=</span>None
-<span class="nv">GATEWAY</span><span class="o">=</span>None
-<span class="nv">DESTINATION</span><span class="o">=</span>None
-<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
-<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
-...
-</pre></div>
-</div>
-</div>
-<p>Afterwards, type:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup.sh
-</pre></div>
-</div>
-<p>to start the installation. You should see the following output at the command line.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
-WARNING: installdir has not been specified
-flex_extract will be installed in here by compiling the Fortran <span class="nb">source</span> in /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/source/fortran
-Install flex_extract_v7.1 software at <span class="nb">local</span> in directory /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1
-
-Using makefile: Makefile.local.gfortran
-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
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -g -O3 -fopenmp grphreal.f
-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 ftrafo.f
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 rwGRIB2.f90
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 posnam.f
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 preconvert.f90
-gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert<span class="o">=</span>big-endian -O3 -O3 -fopenmp -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/gcc-4.9.3/grib_api-1.14.3/lib -Bstatic -lgrib_api_f77 -lgrib_api_f90 -lgrib_api -Bdynamic -lm -ljasper -lemosR64
-
--rwxrwxr-x. <span class="m">1</span> philipa8 tmc <span class="m">282992</span> May <span class="m">23</span> <span class="m">22</span>:27 ./CONVERT2
-</pre></div>
-</div>
-</div>
+<div class="toctree-wrapper compound">
</div>
</div>
<div class="section" id="flex-extract-in-combination-with-flexpart">
@@ -896,7 +337,7 @@ STATISTICS: <span class="m">98842</span>.4598 <span class="m">98709</span>.7359
SUCCESSFULLY FINISHED CONVERT_PRE: CONGRATULATIONS
</pre></div>
</div>
-<p>Now go back to the root directoy:</p>
+<p>Now go back to the root directory:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> ../../../
</pre></div>
</div>
@@ -917,10 +358,10 @@ SUCCESSFULLY FINISHED CONVERT_PRE: CONGRATULATIONS
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="quick_start.html" class="btn btn-neutral float-right" title="Quick Start" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+ <a href="Installation/remote.html" class="btn btn-neutral float-right" title="Remote mode installation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="index.html" class="btn btn-neutral float-left" title="<no title>" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="index.html" class="btn btn-neutral float-left" title="Welcome to flex_extract’s user documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/objects.inv b/Documentation/html/objects.inv
index 0a37771f29c00bdd29e8499519cc2ffa6d6dd2b1..49a8afa10517c80bea1e92e9904c34965af48369 100644
Binary files a/Documentation/html/objects.inv and b/Documentation/html/objects.inv differ
diff --git a/Documentation/html/quick_start.html b/Documentation/html/quick_start.html
index 7947b6abe505da2c7293c00e5dd7a5ee8c32c75a..58e68ac5697190566304d604f4bb195952d99bae 100644
--- a/Documentation/html/quick_start.html
+++ b/Documentation/html/quick_start.html
@@ -39,7 +39,7 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="ECMWF Data" href="ecmwf_data.html" />
- <link rel="prev" title="Installation" href="installation.html" />
+ <link rel="prev" title="Local mode installation" href="Installation/local.html" />
</head>
<body class="wy-body-for-nav">
@@ -475,7 +475,7 @@ The forecast starting time is <code class="docutils literal notranslate"><span c
It is then available from 1st January 1979 to 31st August 2019. The <code class="docutils literal notranslate"><span class="pre">etadot</span></code> is not available in this dataset. Therefore <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> must select the <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> parameter to retrieve the divergence field in addition. The vertical velocity is the calculated with the continuity equation in the Fortran program <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code>. Since the analysis fields are only available for every 6th hour, the dataset can be made 3 hourly by adding forecast fields in between. No ensemble members are available.</p>
<div class="admonition-todo admonition" id="index-0">
<p class="first admonition-title">Todo</p>
-<p class="last">@LEO: please check the complete describtion and functionality of the CONTROL FILEs</p>
+<p class="last">@LEO: please check the complete description and functionality of the CONTROL FILEs</p>
</div>
</div>
<div class="section" id="operational-data">
@@ -629,7 +629,7 @@ RIGHT <span class="m">180</span>.
<a href="ecmwf_data.html" class="btn btn-neutral float-right" title="ECMWF Data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="Installation/local.html" class="btn btn-neutral float-left" title="Local mode installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/Documentation/html/searchindex.js b/Documentation/html/searchindex.js
index 57fde9886973c501f9a4ef35e4490c11e4aaddec..a4fe9d4a88dc614e5d0f875b8477c46ae17c3dbc 100644
--- a/Documentation/html/searchindex.js
+++ b/Documentation/html/searchindex.js
@@ -1 +1 @@
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Documentation","Fortran\u2019s Auto Generated Documentation","Python\u2019s Auto Generated Documentation","CONTROL file changes","The Compilation Jobscript <code class=\"docutils literal notranslate\"><span class=\"pre\">compilejob.ksh</span></code>","The CONTROL file","The CONTROL parameters","ECMWF User Credential file <code class=\"docutils literal notranslate\"><span class=\"pre\">ECMWF_ENV</span></code>","CONTROL file examples","The Fortran Makefile - <code class=\"docutils literal notranslate\"><span class=\"pre\">CONVERT2</span></code>","The Jobscript <code class=\"docutils literal notranslate\"><span class=\"pre\">job.ksh</span></code>","The executable Script - <code class=\"docutils literal notranslate\"><span class=\"pre\">run.sh</span></code>","The Installation Script - <code class=\"docutils literal notranslate\"><span class=\"pre\">setup.sh</span></code>","Templates","Application Modes","Program Flow","Auto Generated Documentation","Disaggregation of Flux Data","Control & Input Data","Output Data","Overview","Vertical Coordinate","Access Modes","Link Collection for Quick finder","Hints to specify dataset retrieval","Available Datasets for Member State users","Available Datasets for Public users","Metrics","Static Code Analysis","Testcases","Gateway mode installation","Local mode installation","Remote mode installation","FAQ - Frequently asked questions","Known Bugs and Issues","Developer Team","Changelog","Developer Guide","Documentation","ECMWF Data","Evaluation","Welcome to <code class=\"docutils literal notranslate\"><span class=\"pre\">flex_extract</span></code>\u2019s user documentation!","Installation","Quick Start","Support","ToDos"],titleterms:{"class":2,"new":[19,36],"public":[26,42,43],"static":28,CDS:31,The:[4,5,6,9,10,11,12],access:22,adapt:[],addit:[0,6,19],adjust:43,agre:[],agreement:42,analysi:28,api:31,applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calcul:21,can:[24,33],cera:43,chang:[3,36],changelog:36,check:2,code:28,collect:23,combin:[42,43],comparison:29,compil:4,compilejob:[4,13],content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert2:[9,19],convert:13,coordin:21,credenti:7,dai:[],data:[6,17,18,19,24,25,39,43],dataset:[24,25,26,42,43],definit:43,delight:[],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:[30,31,32,42],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:[30,31,32,42],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}})
\ No newline at end of file
diff --git a/Documentation/html/todo.html b/Documentation/html/todo.html
index 678d096985bd03484c9c69994819b2ce7081bb6d..075ca43f265d4750a1404bab0ded2f3705fb8123 100644
--- a/Documentation/html/todo.html
+++ b/Documentation/html/todo.html
@@ -165,7 +165,7 @@
<h1>ToDos<a class="headerlink" href="#todos" title="Permalink to this headline">¶</a></h1>
<div class="admonition-todo admonition">
<p class="first admonition-title">Todo</p>
-<p class="last">@LEO: please check the complete describtion and functionality of the CONTROL FILEs</p>
+<p class="last">@LEO: please check the complete description and functionality of the CONTROL FILEs</p>
</div>
<p class="todo-source">(The <a class="reference internal" href="quick_start.html#index-0"><em>original entry</em></a> is located in /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/For_developers/Sphinx/source/quick_start.rst, line 337.)</p>
<div class="admonition-todo admonition">
diff --git a/For_developers/Sphinx/source/Documentation/Input/ecmwf_env.rst b/For_developers/Sphinx/source/Documentation/Input/ecmwf_env.rst
index 76acff797808067f4b6be2817b7a486fe7347851..a3232e2c5b7ac760975aba87152fede088e921c5 100644
--- a/For_developers/Sphinx/source/Documentation/Input/ecmwf_env.rst
+++ b/For_developers/Sphinx/source/Documentation/Input/ecmwf_env.rst
@@ -2,7 +2,7 @@
ECMWF User Credential file ``ECMWF_ENV``
****************************************
-This file contains the user credentials for working on ECMWF servers and transfering files between the ECMWF servers and the local gateway server. It is located in the ``flex_extract_vX.X/run`` directory and will be created in the installation process for the application modes **remote** and **gateway**.
+This file contains the user credentials for working on ECMWF servers and transferring files between the ECMWF servers and the local gateway server. It is located in the ``flex_extract_vX.X/run`` directory and will be created in the installation process for the application modes **remote** and **gateway**.
This file is based on the template ``ECMWF_ENV.template`` which is located in the ``templates`` directory.
diff --git a/For_developers/Sphinx/source/Installation/gateway.rst b/For_developers/Sphinx/source/Installation/gateway.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c452eb6b5868150e55aa6ae16ef28a30e41b96a9
--- /dev/null
+++ b/For_developers/Sphinx/source/Installation/gateway.rst
@@ -0,0 +1,168 @@
+*************************
+Gateway mode installation
+*************************
+
+.. role:: underline
+ :class: underline
+
+.. toctree::
+ :hidden:
+ :maxdepth: 2
+
+.. _Python 3: https://docs.python.org/3/
+.. _Python3: https://www.python.org/downloads/
+.. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section
+
+.. _numpy: http://www.numpy.org/
+.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
+.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
+.. _genshi: https://genshi.edgewall.org/
+.. _eccodes for python: https://packages.debian.org/sid/python3-eccodes
+.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _gfortran: https://gcc.gnu.org/wiki/GFortran
+.. _fftw3: http://www.fftw.org
+.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
+.. _emoslib: https://software.ecmwf.int/wiki/display/EMOS/Emoslib
+.. _member state: https://www.ecmwf.int/en/about/who-we-are/member-states
+.. _registration form: https://apps.ecmwf.int/registration/
+.. _CDS API registration: https://cds.climate.copernicus.eu/user/register
+.. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans
+.. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf
+.. _ECMWF's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home
+.. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives
+.. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS
+
+.. _download section: https://www.flexpart.eu/downloads
+
+
+
+.. _ref-gateway-mode:
+
+
+
+.. _ref-req-gateway:
+
+Gateway mode - dependencies
+===========================
+
+* `Python3`_
+* `numpy`_
+* `genshi`_
+
+
+.. _ref-prep-gateway:
+
+Prepare gateway environment
+===========================
+
+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.
+
+Please see `ECMWF's instructions on gateway server`_ to establish the gateway server if not already in place. Additionally, to be able to use the ECaccess file transfer service **ectrans** it is necessary to create a so-called association. The easiest way is to visit the ECaccess Member State Gateway website (e.g. https://msgatway.ecmwf.int) and follow the instructions in the short `ECaccess Presentation`_ (page 17 ff.). Additional documentation can be found on the `ECMWF ectrans site`_.
+
+The next step is to create an *ecaccess certificate* to be able to send and receive files from and to the ECMWF server. You can do this by using the ``ecaccess-certificate-create`` command on the gateway server. You will be prompted for your ECMWF member state user name and a password (generated by a token). This certificate has to be renewed periodically (every 7 days).
+
+
+.. code-block:: bash
+
+ $ ecaccess-certificate-create
+ Please enter your user-id: example_username
+ Your passcode: ***
+
+
+
+The easiest way to install all required packages is to use the package management system of your Linux distribution which required admin rights.
+The installation was tested under *GNU/Linux Debian buster* and *Ubuntu 18.04 Bionic Beaver*.
+
+.. code-block:: sh
+
+
+ # 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):
+ # (if not already available):
+ apt-get install python3
+ apt-get install python3-genshi
+ apt-get install python3-numpy
+
+
+.. _ref-test-gateway:
+
+Test gateway environment
+========================
+
+Check the availability of the python packages by typing ``python3`` in
+a terminal window and run the ``import`` commands in the python shell.
+If there are no error messages, you succeeded in setting up the environment.
+
+.. code-block:: python
+
+ # check in python3 console
+ import genshi
+ import numpy
+
+
+
+.. _ref-install-gateway:
+
+Gateway installation
+====================
+
+``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.
+The job script, send to the job queue via the ECaccess software, loads the required modules from the module system. For enabling the file transfer via the gateway, you have to set the *ECUID*, *ECGID*, *GATEWAY* and *DESTINATION* parameter values.
+
+
+.. code-block:: bash
+ :caption: 'Example settings for a gateway installation.'
+ :name: setup.sh
+
+ # -----------------------------------------------------------------
+ # AVAILABLE COMMANDLINE ARGUMENTS TO SET
+ #
+ # THE USER HAS TO SPECIFY THESE PARAMETER
+ #
+ TARGET='ecgate'
+ MAKEFILE='makefile.gfortran'
+ ECUID='uid'
+ ECGID='gid'
+ GATEWAY='localserver.tld'
+ DESTINATION='association_name@genericSftp'
+ INSTALLDIR=None
+ JOB_TEMPLATE='job.template'
+ CONTROLFILE='CONTROL_EA5'
+
+
+Afterwards, type:
+
+.. code-block:: bash
+
+ $ ./setup.sh
+
+to start the installation. You should see the following on standard output.
+
+
+.. code-block:: bash
+
+ # Output of setup.sh
+ Create tarball ...
+ Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X
+ You should get an email with subject "flexcompile" within the next few minutes!
+
+``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:
+
+.. code-block:: bash
+
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
+ -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2
+ SUCCESS!
+
+
+
+
+
+
+
+
diff --git a/For_developers/Sphinx/source/Installation/local.rst b/For_developers/Sphinx/source/Installation/local.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d0276bf56a2f8443c7241302fe7c43c4b6cc77f8
--- /dev/null
+++ b/For_developers/Sphinx/source/Installation/local.rst
@@ -0,0 +1,381 @@
+***********************
+Local mode installation
+***********************
+
+.. role:: underline
+ :class: underline
+
+.. toctree::
+ :hidden:
+ :maxdepth: 2
+
+
+.. _Python 3: https://docs.python.org/3/
+.. _Python3: https://www.python.org/downloads/
+.. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section
+
+.. _numpy: http://www.numpy.org/
+.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
+.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
+.. _genshi: https://genshi.edgewall.org/
+.. _eccodes for python: https://packages.debian.org/sid/python3-eccodes
+.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _gfortran: https://gcc.gnu.org/wiki/GFortran
+.. _fftw3: http://www.fftw.org
+.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
+.. _emoslib: https://software.ecmwf.int/wiki/display/EMOS/Emoslib
+.. _member state: https://www.ecmwf.int/en/about/who-we-are/member-states
+.. _registration form: https://apps.ecmwf.int/registration/
+.. _CDS API registration: https://cds.climate.copernicus.eu/user/register
+.. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans
+.. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf
+.. _ECMWF's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home
+.. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives
+.. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS
+
+.. _download section: https://www.flexpart.eu/downloads
+
+
+
+
+
+.. _ref-local-mode:
+
+
+
+.. _ref-req-local:
+
+Local mode - dependencies
+=========================
+
+The installation is the same for the access modes **member** and **public**.
+
+The environment on your local system has to provide these software packages
+and libraries, since the preparation of the extraction and the post-processing is done on the local machine:
+
++------------------------------------------------+-----------------+
+| Python part | Fortran part |
++------------------------------------------------+-----------------+
+| * `Python3`_ | * `gfortran`_ |
+| * `numpy`_ | * `fftw3`_ |
+| * `genshi`_ | * `eccodes`_ |
+| * `eccodes for python`_ | * `emoslib`_ |
+| * `ecmwf-api-client`_ (everything except ERA5) | |
+| * `cdsapi`_ (just for ERA5) | |
++------------------------------------------------+-----------------+
+
+
+.. _ref-prep-local:
+
+Prepare local environment
+=========================
+
+The easiest way to install all required packages is to use the package management system of your Linux distribution which requires admin rights.
+The installation was tested on a *Debian GNU/Linux buster* and an *Ubuntu 18.04 Bionic Beaver* system.
+
+.. code-block:: sh
+
+ # 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):
+ # (if not already available):
+ apt-get install python3 (usually already available on GNU/Linux systems)
+ apt-get install python3-eccodes
+ apt-get install python3-genshi
+ apt-get install python3-numpy
+ apt-get install gfortran
+ apt-get install fftw3-dev
+ apt-get install libeccodes-dev
+ apt-get install libemos-dev
+ # Some of these packages will pull in further packages as dependencies. This is fine, and some are even needed by ``flex_extract''.
+
+
+ # 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:
+ apt-get install pip
+ pip install cdsapi
+ pip install ecmwf-api-client
+
+.. note::
+
+ In case you would like to use Anaconda Python we recommend you follow the installation instructions of
+ `Anaconda Python Installation for Linux <https://docs.anaconda.com/anaconda/install/linux/>`_ and then install the
+ ``eccodes`` package from ``conda`` with:
+
+ .. code-block:: bash
+
+ conda install conda-forge::python-eccodes
+
+The CDS API (cdsapi) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.
+
+.. note::
+
+ Since **public users** currently don't have access to the full *ERA5* dataset they can skip the installation of the ``CDS API``.
+
+Both user groups have to provide keys with their credentials for the Web API's in their home directory. Therefore, follow these instructions:
+
+ECMWF Web API:
+ 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).
+
+CDS API:
+ 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.
+
+
+.. _ref-test-local:
+
+Test local environment
+======================
+
+Check the availability of the python packages by typing ``python3`` in a terminal window and run the ``import`` commands in the python shell. If there are no error messages, you succeeded in setting up the environment.
+
+.. code-block:: python
+
+ # check in python3 console
+ import eccodes
+ import genshi
+ import numpy
+ import cdsapi
+ import ecmwfapi
+
+
+
+Test the Web API's
+------------------
+
+You can start very simple test retrievals for both Web APIs to be sure that everything works. This is recommended to minimise the range of possible errors using ``flex_extract`` later on.
+
+
+ECMWF Web API
+^^^^^^^^^^^^^
+
+
++----------------------------------------------------------+----------------------------------------------------------+
+|Please use this piece of Python code for **Member user**: |Please use this piece of Python code for **Public user**: |
++----------------------------------------------------------+----------------------------------------------------------+
+|.. code-block:: python |.. code-block:: python |
+| | |
+| from ecmwfapi import ECMWFService | from ecmwfapi import ECMWFDataServer |
+| | |
+| server = ECMWFService('mars') | server = ECMWFDataServer() |
+| | |
+| server.retrieve({ | server.retrieve({ |
+| 'stream' : "oper", | 'stream' : "enda", |
+| 'levtype' : "sfc", | 'levtype' : "sfc", |
+| 'param' : "165.128/166.128/167.128", | 'param' : "165.128/166.128/167.128", |
+| 'dataset' : "interim", | 'dataset' : "cera20c", |
+| 'step' : "0", | 'step' : "0", |
+| 'grid' : "0.75/0.75", | 'grid' : "1./1.", |
+| 'time' : "00/06/12/18", | 'time' : "00/06/12/18", |
+| 'date' : "2014-07-01/to/2014-07-31", | 'date' : "2000-07-01/to/2000-07-31", |
+| 'type' : "an", | 'type' : "an", |
+| 'class' : "ei", | 'class' : "ep", |
+| 'target' : "download_erainterim_ecmwfapi.grib" | 'target' : "download_cera20c_ecmwfapi.grib" |
+| }) | }) |
++----------------------------------------------------------+----------------------------------------------------------+
+
+
+
+CDS API
+^^^^^^^
+
+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):
+
+Please use this piece of Python code to retrieve a small sample of *ERA5* pressure levels:
+
+.. code-block:: python
+
+ import cdsapi
+
+ c = cdsapi.Client()
+
+ c.retrieve("reanalysis-era5-pressure-levels",
+ {
+ "variable": "temperature",
+ "pressure_level": "1000",
+ "product_type": "reanalysis",
+ "year": "2008",
+ "month": "01",
+ "day": "01",
+ "time": "12:00",
+ "format": "grib"
+ },
+ "download_cdsapi.grib")
+
+
+If you know that your CDS API works, you can try to extract some data from MARS.
+
+.. **Member-state user**
+
+Please use this piece of Python code to retrieve a small *ERA5* data sample as a **member-state user**! The **Public user** do not have access to the full *ERA5* dataset!
+
+.. code-block:: python
+
+ import cdsapi
+
+ c = cdsapi.Client()
+
+ c.retrieve('reanalysis-era5-complete',
+ {
+ 'class' : 'ea',
+ 'expver' : '1',
+ 'stream' : 'oper',
+ 'type' : 'fc',
+ 'step' : '3/to/12/by/3',
+ 'param' : '130.128',
+ 'levtype' : 'ml',
+ 'levelist': '135/to/137',
+ 'date' : '2013-01-01',
+ 'time' : '06/18',
+ 'area' : '50/-5/40/5',
+ 'grid' : '1.0/1.0',
+ 'format' : 'grib',
+ }, 'download_era5_cdsapi.grib')
+
+
+.. ********************** COMMENTED OUT FOR FUTURE
+ ********************** PUBLIC RETRIEVAL IS CURRENTLY NOT ACCESSIBLE
+
+ **Public user**
+ Please use this piece of Python code:
+
+ .. code-block:: python
+
+ import cdsapi
+
+ c = cdsapi.Client()
+
+ c.retrieve('reanalysis-era5-complete',
+ {
+ 'class' : 'ea',
+ 'dataset' : 'era5',
+ 'expver' : '1',
+ 'stream' : 'oper',
+ 'type' : 'fc',
+ 'step' : '3/to/12/by/3',
+ 'param' : '130.128',
+ 'levtype' : 'ml',
+ 'levelist': '135/to/137',
+ 'date' : '2013-01-01',
+ 'time' : '06/18',
+ 'area' : '50/-5/40/5',
+ 'grid' : '1.0/1.0',
+ 'format' : 'grib',
+ }, 'download_era5_cdsapi.grib')
+
+
+
+
+
+
+.. _ref-install-local:
+
+Local installation
+==================
+
+First prepare the Fortran ``makefile`` for your environment and set it in the ``setup.sh`` script. (See section :ref:`ref-convert` for information on the Fortran program.)
+``flex_extract`` comes with two ``makefiles`` prepared for the ``gfortran`` and
+the ``ifort`` compiler. The ``gfortran`` version assumes that ``eccodes`` and ``emoslib`` are installed as distribution packages.
+
+ * makefile.local.gfortran
+ * makefile.local.ifort
+
+They can be found at ``flex_extract_vX.X/Source/Fortran``, where
+``vX.X`` should be substituted with the current version number.
+
+.. caution::
+ It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these
+ ``makefiles`` if other than standard paths are used.
+
+So starting from the root directory of ``flex_extract``,
+go to the ``Fortran`` source directory and open the ``makefile`` of your
+choice to modify with an editor of your choice. We use the ``nedit`` in this case.
+
+.. code-block:: bash
+
+ cd flex_extract_vX.X/Source/Fortran
+ nedit makefile.local.gfortran
+
+Edit the paths to the ``eccodes`` library on your local machine.
+
+
+.. caution::
+ This can vary from system to system.
+ It is suggested to use a command like
+
+ .. code-block:: bash
+
+ # for the ECCODES_INCLUDE_DIR path do:
+ $ dpkg -L libeccodes-dev | grep eccodes.mod
+ # for the ECCODES_LIB path do:
+ $ dpkg -L libeccodes-dev | grep libeccodes.so
+
+ to find out the path to the ``eccodes`` library.
+
+Substitute these paths in the ``makefile`` for parameters **ECCODES_INCLUDE_DIR**
+and **ECCODES_LIB** and save it.
+
+.. code-block:: bash
+
+ # these are the paths on a current Debian 10 Testing system (May 2019)
+ ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
+ ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm
+
+
+The Fortran program called ``CONVERT2`` will be compiled during the
+installation process.Therefore the name of the ``makefile`` to be used needs to be given in ``setup.sh``.
+
+In the root directory of ``flex_extract``, open the ``setup.sh`` script
+and adapt the installation parameters in the section labelled with
+"AVAILABLE COMMANDLINE ARGUMENTS TO SET" like shown below.
+
+
+.. code-block:: bash
+ :caption: 'Example settings for a local installation.'
+ :name: setup.sh
+
+ ...
+ # -----------------------------------------------------------------
+ # AVAILABLE COMMANDLINE ARGUMENTS TO SET
+ #
+ # THE USER HAS TO SPECIFY THESE PARAMETER
+ #
+ TARGET='local'
+ MAKEFILE='makefile.local.gfortran'
+ ECUID=None
+ ECGID=None
+ GATEWAY=None
+ DESTINATION=None
+ INSTALLDIR=None
+ JOB_TEMPLATE='job.template'
+ CONTROLFILE='CONTROL_EA5'
+ ...
+
+
+Afterwards, type:
+
+.. code-block:: bash
+
+ $ ./setup.sh
+
+to start the installation. You should see the following standard output.
+
+
+.. code-block:: bash
+
+ # Output of setup.sh
+ WARNING: installdir has not been specified
+ flex_extract will be installed in here by compiling the Fortran source in /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/source/fortran
+ Install flex_extract_v7.1 software at local in directory /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1
+
+ Using makefile: Makefile.local.gfortran
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 rwGRIB2.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 posnam.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 preconvert.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -O3 -O3 -fopenmp -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/gcc-4.9.3/grib_api-1.14.3/lib -Bstatic -lgrib_api_f77 -lgrib_api_f90 -lgrib_api -Bdynamic -lm -ljasper -lemosR64
+
+ -rwxrwxr-x. 1 philipa8 tmc 282992 May 23 22:27 ./CONVERT2
+
+
+
+
+
diff --git a/For_developers/Sphinx/source/Installation/remote.rst b/For_developers/Sphinx/source/Installation/remote.rst
new file mode 100644
index 0000000000000000000000000000000000000000..b2e4d42a856f995e0722e764aabd08f40e9fb4c0
--- /dev/null
+++ b/For_developers/Sphinx/source/Installation/remote.rst
@@ -0,0 +1,188 @@
+************************
+Remote mode installation
+************************
+
+.. role:: underline
+ :class: underline
+
+.. toctree::
+ :hidden:
+ :maxdepth: 2
+
+
+.. _Python 3: https://docs.python.org/3/
+.. _Python3: https://www.python.org/downloads/
+.. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section
+
+.. _numpy: http://www.numpy.org/
+.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
+.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
+.. _genshi: https://genshi.edgewall.org/
+.. _eccodes for python: https://packages.debian.org/sid/python3-eccodes
+.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _gfortran: https://gcc.gnu.org/wiki/GFortran
+.. _fftw3: http://www.fftw.org
+.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
+.. _emoslib: https://software.ecmwf.int/wiki/display/EMOS/Emoslib
+.. _member state: https://www.ecmwf.int/en/about/who-we-are/member-states
+.. _registration form: https://apps.ecmwf.int/registration/
+.. _CDS API registration: https://cds.climate.copernicus.eu/user/register
+.. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans
+.. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf
+.. _ECMWF's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home
+.. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives
+.. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS
+
+.. _download section: https://www.flexpart.eu/downloads
+
+
+.. _ref-remote-mode:
+
+
+.. _ref-req-remote:
+
+Remote mode - dependencies
+==========================
+
+The following software is required, and already available at the ECMWF servers:
+
++---------------------------+-----------------+
+| Python part | Fortran part |
++---------------------------+-----------------+
+| * `Python3`_ | * `gfortran`_ |
+| * `numpy`_ | * `fftw3`_ |
+| * `genshi`_ | * `eccodes`_ |
+| * `eccodes for python`_ | * `emoslib`_ |
++---------------------------+-----------------+
+
+
+.. _ref-prep-remote:
+
+Prepare remote environment
+==========================
+
+ECMWF servers provide all libraries via a module system. Loading the required modules is already built into ``flex_extract`` and no user action is needed.
+
+
+.. _ref-install-remote:
+
+Remote installation
+===================
+
+First, log in on one of the ECMWF servers, such as *ecgate* or *cca/ccb*.
+Substitute *<ecuid>* with your ECMWF user name:
+
+.. code-block:: bash
+
+ ssh -X <ecuid>@ecaccess.ecmwf.int
+
+This will lead to the following output on the command line, asking for your
+password:
+
+.. code-block:: bash
+
+ Authorized access only.
+
+ ***************************************************************
+ For further information, read the ECaccess documentation at:
+
+ https://software.ecmwf.int/wiki/display/ECAC/ECaccess+Home
+
+ You can also use ECaccess to load & download files from your
+ EChome, ECscratch or ECfs directories using the ECaccess FTP
+ server:
+
+ ftp://uid@ecaccess.ecmwf.int/
+
+ Please note you must use your UID and ActivID code to login!
+ ***************************************************************
+
+ <ecuid>@<ipname/address>'s password: ***
+ Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
+
+ [<ecuid>@ecgb11 ~]$
+
+Substitute the *<localuser>* and *<localmachine.tld>* placeholders with your local user name and the IP name or address of your local machine.
+Untar the file and change into the ``flex_extract`` root directory.
+
+.. code-block:: bash
+
+ scp <localuser>@<localmachine.tld>:</path/to/tarfile/>flex_extract_vX.X.tar.gz $HOME/
+ cd $HOME
+ tar xvf flex_extract_vX.X.tar.gz
+ cd flex_extract_vX.X
+
+
+
+Execute the ``setup.sh`` script from the ``flex_extract``'s root directory.
+Before executing it, it is necessary to adapt some parameters from ``setup.sh``
+described in :doc:`Documentation/Input/setup`.
+
+Open ``setup.sh`` with your preferred editor (e.g., ``nano'') and adapt the values:
+
++----------------------------------------------+----------------------------------------------+
+| Use this for target = **ectrans** | Use this for target = **cca** |
++----------------------------------------------+----------------------------------------------+
+| .. code-block:: bash | .. code-block:: bash |
+| | |
+| ... | ... |
+| # -----------------------------------------| # -----------------------------------------|
+| # AVAILABLE COMMANDLINE ARGUMENTS TO SET | # AVAILABLE COMMANDLINE ARGUMENTS TO SET |
+| # | # |
+| # THE USER HAS TO SPECIFY THESE PARAMETER | # THE USER HAS TO SPECIFY THESE PARAMETER |
+| # | # |
+| TARGET='ecgate' | TARGET='cca' |
+| MAKEFILE='Makefile.gfortran' | MAKEFILE='Makefile.CRAY' |
+| ECUID='uid' | ECUID='uid' |
+| ECGID='gid' | ECGID='gid' |
+| GATEWAY=None | GATEWAY=None |
+| DESTINATION=None | DESTINATION=None |
+| INSTALLDIR=None | INSTALLDIR='' |
+| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
+| ... | ... |
++----------------------------------------------+----------------------------------------------+
+
+:underline:`Please substitute the values of ECUID and ECGID
+with your own ones (look at any of your files with ``ls -l'' to see uid and gid).`
+
+.. note::
+
+ 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).
+
+Afterwards, type:
+
+.. code-block:: bash
+
+ module load python3
+ ./setup.sh
+
+to start the installation. You should see the following on standard output.
+
+
+.. code-block:: bash
+
+ # Output of setup.sh
+ Create tarball ...
+ Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X
+ You should get an email with subject "flexcompile" within the next few minutes!
+
+
+``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:
+
+.. code-block:: bash
+
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
+ gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
+ -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2
+ SUCCESS!
+
+
+
+
+
diff --git a/For_developers/Sphinx/source/conf.py b/For_developers/Sphinx/source/conf.py
index aa18d419bd2a7b209794ce924943b1c48e52aa63..9a5c21f9f2b9daf8096e7effdd0b5652c2755762 100644
--- a/For_developers/Sphinx/source/conf.py
+++ b/For_developers/Sphinx/source/conf.py
@@ -19,6 +19,7 @@ sys.path.insert(0, os.path.abspath('../../../Source/Python/Mods'))
sys.path.insert(0, os.path.abspath('../../../Source/Python/Classes'))
sys.path.insert(0, os.path.abspath('_static/python'))
+sys.setrecursionlimit(1500)
#fortran_src = [f for f in os.listdir('../../../source/fortran') if '.f90' in f or '.f' in f]
#print(fortran_src)
diff --git a/For_developers/Sphinx/source/index.rst b/For_developers/Sphinx/source/index.rst
index fcba97c2957916aeb62160c40fce64bf48241832..bea0b26583a0ac8c46e44fe21bdc74ce7adc4038 100644
--- a/For_developers/Sphinx/source/index.rst
+++ b/For_developers/Sphinx/source/index.rst
@@ -128,7 +128,7 @@ Welcome to ``flex_extract``'s user documentation!
Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
.. toctree::
- :maxdepth: 3
+ :maxdepth: 4
:caption: Table of Contents:
installation
diff --git a/For_developers/Sphinx/source/installation.rst b/For_developers/Sphinx/source/installation.rst
index 839721d05758a9fc78124150de23e56ef41c90c5..a65057f9347f1bf3ae34740210df1295ce47f70b 100644
--- a/For_developers/Sphinx/source/installation.rst
+++ b/For_developers/Sphinx/source/installation.rst
@@ -8,6 +8,7 @@ Installation
.. toctree::
:hidden:
:maxdepth: 2
+
.. _Python 3: https://docs.python.org/3/
.. _Python3: https://www.python.org/downloads/
@@ -36,59 +37,68 @@ Installation
-``flex_extract`` is a software package which contains a mix of Python and Shell scripts as well as a Fortran program. These components rely on a couple of third party libraries which need to be prepared first before starting the installation process. For now, the software is only tested for a Linux/Unix environment. Feel free to try it out on other platforms.
+The ``flex_extract`` software package contains python and shell scripts as well as a Fortran program. These components rely on several libraries which need to be available before starting the installation process. Currently, the software is only tested for a GNU/Linux environment. Feel free to try it out on other platforms.
-Start with the decision of which `user group <Ecmwf/access>`_ you belong to and follow the instructions at :ref:`ref-registration` to get an account at ECMWF. Considering your user group and the method of applying ``flex_extract`` there appear to be 4 application modes:
+At first, go to the `user group <Ecmwf/access.html>`_ section and decide which group you belong to and follow the instructions at :ref:`ref-registration` to obtain an account at ECMWF (if you don't have it already). Depending on the user group and the way to access the ECWMF MARS archive, there are four possible :doc:`Documentation/Overview/app_modes`:
-- Remote (for member state users only) :ref:`[installation]<ref-remote-mode>`
-- Gateway (for member state users only) :ref:`[installation]<ref-gateway-mode>`
-- Local member :ref:`[installation]<ref-local-mode>`
-- Local public :ref:`[installation]<ref-local-mode>`
+- Remote (member-state users only) :ref:`[installation]<ref-remote-mode>`
+- Gateway (member-state users only) :ref:`[installation]<ref-gateway-mode>`
+- Local, member-state user :ref:`[installation]<ref-local-mode>`
+- Local, public user :ref:`[installation]<ref-local-mode>`
-More information can be found in :doc:`Documentation/Overview/app_modes`.
+Please follow the link :doc:`Documentation/Overview/app_modes` to get a description of the modes.
.. note::
If you encounter any problems in the installation process, you can ask for :doc:`support`.
-
-
-
-
+
+
+
+
.. _ref-registration:
Registration at ECMWF
=====================
-Decide which user group you belong to and follow the instructions for registration:
+The registration depends on the :doc:`Documentation/Overview/app_modes` and in case of the local mode also on the data set you'd like to retrieve. The following table gives an overview where you need to register.
-**Member state user**:
- To get a member-state user account, users have to be a resident of a `member state`_. In that case, you can contact your `Computing Representative`_ for granting access. If you would like to use the local application mode to retrieve **ERA5** data you'd have to register at the `Copernicus Climate Data Store <https://cds.climate.copernicus.eu/user/register>`_ also.
++--------------+------------------------------------+--------------+
+| | Member-state user | Public user |
+| +---------+----------+---------------+--------------+
+| Data sets |Remote |Gateway |Local | Local |
++--------------+---------+----------+---------------+--------------+
+| Operational | 1 | 1 | 1,2 | - |
++--------------+---------+----------+---------------+--------------+
+| ERA-Interim | 1 | 1 | 1,2 | 2 |
++--------------+---------+----------+---------------+--------------+
+| CERA-20C | 1 | 1 | 1,2 | 2 |
++--------------+---------+----------+---------------+--------------+
+| ERA5 | 1 | 1 | 3 | - |
++--------------+---------+----------+---------------+--------------+
-**Public user**:
- To be able to download public datasets with ``flex_extract`` such as **ERA-Interim** and **CERA-20C** (**ERA5** is not supported via ECMWF Web API anymore), the public user has to create an account at ECMWF.
- Use the registration at the ECMWF website by filling out this `registration form`.
-
- .. note::
- In the future retrievement of *ERA5* will be possible via the CDS API for public users also. Then a registration at the `Copernicus Climate Data Store <https://cds.climate.copernicus.eu/user/register>`_ is needed in addition.
-
-
+
+Registration options:
+
+ 1.) Access through a member-state user account granted by the `Computing Representative`_. The credentials have to be provided during installation.
+ 2.) Access through the ECMWF Web API. Need to sign in at `ECMWF Web API <https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home>`_ and configure the ECMWF key as described. Member-state users can sign in with their credentials from the `Computing Representative`_ and public users have to fill out the `registration form`_ to get an account.
+ 3.) Access through the `CDS API <https://cds.climate.copernicus.eu/api-how-to>`_. Extra registration for member-state users is required at `Copernicus Climate Data Store <https://cds.climate.copernicus.eu/user/register>`_ including the configurations of the CDS key as described. This mode is currently not available for public users. See the note at `user group <Ecmwf/access.html>`_ for information.
+
.. _ref-licence:
-Agree on licences for public datasets
+Licence agreement for public datasets
=====================================
-Each public dataset which is intended to be downloaded by ``flex_extract`` has its own licence which has to be accepted, regardless of the user group.
+Each ECMWF public dataset has its own licence which has to be accepted, regardless of the user group.
For the *ERA-Interim* and *CERA-20C* datasets this can be done at the ECMWF website `Available ECMWF Public Datasets <https://confluence.ecmwf.int/display/WEBAPI/Available+ECMWF+Public+Datasets>`_. Log in and follow the licence links on the right side for each dataset and accept it.
-For the *ERA5* dataset this has to be done at the `Climate Data Store (CDS) website <https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset>`_. Log in with your credentials and then select on the left panel the product type "Reanalysis" for finding *ERA5* datasets. Then follow the link of a title with *ERA5* (anyone) to the full dataset record, click on tab "Download data" and scroll down. There is a section "Terms of use" where you have to click the :underline:`Accept terms` button.
-
+For the *ERA5* dataset this has to be done at the `Climate Data Store (CDS) website <https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset>`_. Log in and select, on the left panel, product type "Reanalysis" for finding *ERA5* datasets. Then follow any link with *ERA5* to the full dataset record, click on tab "Download data" and scroll down. There is a section "Terms of use" where you have to click the :underline:`Accept terms` button.
@@ -99,26 +109,21 @@ For the *ERA5* dataset this has to be done at the `Climate Data Store (CDS) webs
Download ``flex_extract``
=========================
-There are 2 options to download ``flex_extract``:
+There are two options to download ``flex_extract``:
tar ball
- You can download the latest prepared release tar ball from the `download section`_
- of our ``FLEXPART`` community website and then untar the file. Substitute
- the **<ID>** in the ``wget`` command with the ID-number of the ``flex_extract``
- release tar ball in the list of downloads at the community website.
-
-
+ You can download a tar ball with the latest release from the `flex_extract page <https://www.flexpart.eu/wiki/FpInputMetEcmwf>`_ from our ``FLEXPART`` community website and then untar the file.
+
.. code-block:: bash
- wget https://www.flexpart.eu/downloads/<ID>
tar -xvf <flex_extract_vX.X.tar>
-git repo
- Or you can clone the current release version from our git repository master branch.
+git repo
+ Alternatively, if you have ``git`` installed on your machine, and if you are interested to keep the code in a version control system, you may clone the latest version from our git repository master branch.
.. code-block:: bash
- $ git clone https://www.flexpart.eu/gitmob/flexpart
+ $ git clone --single-branch --branch master https://www.flexpart.eu/gitmob/flexpart
@@ -126,30 +131,21 @@ git repo
.. _ref-requirements:
-Environment requirements
-========================
-
-This is a list of the general environment requirements for ``flex_extract``.
-What is required exactly for each application mode will be described in the specifc installation section.
+Dependencies
+============
+The software required for running ``flex_extract`` depends on the :doc:`Documentation/Overview/app_modes` and therefore is described in the respective specific installation sections.
-To run the python part of ``flex_extract`` a `Python 3`_ environment is needed.
-We tested ``flex_extract`` with a normal Linux Python package distribution and Anaconda Python.
-Except for `Python3`_ all are python packages which can be installed via ``pip``.
-
-* `Python3`_ or `Anaconda Python3`_
-* `numpy`_
-* `ecmwf-api-client`_ (Web Interface to ECMWF servers for datasets except ERA5)
-* `cdsapi`_ (Web Interface to `C3S <https://climate.copernicus.eu/>`_ servers for ERA5)
-* `genshi`_
-* `eccodes for python`_
-
-For the Fortran part of ``flex_extract`` we need the following distribution packages:
-
-* `gfortran`_
-* `fftw3`_
-* `eccodes`_
-* `emoslib`_
+Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries.
+We tested ``flex_extract`` with the python3 package from the the GNU/Linux distribution and Anaconda Python. The required python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).
+
+Before installing the system packages check the availability with ``dpkg -s <package-name> | grep Status`` or ``rpm -q <package_name>``, depending on your system. For example:
+
+.. code-block:: sh
+
+ $ dpkg -s libeccodes-dev | grep Status
+ # or
+ $ rpm -q libeccodes-dev
@@ -161,712 +157,54 @@ For the Fortran part of ``flex_extract`` we need the following distribution pack
Installation of ``flex_extract``
================================
-The actual installation of ``flex_extract`` will be done by executing a `Shell` script called ``setup.sh``.
-It defines some parameters and calls a Python script by giving the parameters as command line arguments.
-More information on the script and its parameters can be found at :doc:`Documentation/Input/setup`.
+The actual installation of ``flex_extract`` is done by executing a shell script called ``setup.sh``.
+It defines some parameters and calls a Python script passing the parameters as command line arguments. For details, see :doc:`Documentation/Input/setup`.
For each application mode installation section we describe the requirements for the explicit
environment and how it is installed, test if it works and how the actual ``flex_extract``
installation has to be done. At the users local side not all software has to be present for ``flex_extract``.
+Select one of the following modes to install:
-
-
-
-.. _ref-remote-mode:
-
-Remote mode
------------
-
-.. _ref-req-remote:
-
-Remote environment requirements
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The environment for ``flex_extract`` on ECMWF servers has to provide these
-software packages and libraries:
+ :doc:`Installation/remote`
-+---------------------------+-----------------+
-| Python part | Fortran part |
-+---------------------------+-----------------+
-| * `Python3`_ | * `gfortran`_ |
-| * `numpy`_ | * `fftw3`_ |
-| * `genshi`_ | * `eccodes`_ |
-| * `eccodes for python`_ | * `emoslib`_ |
-+---------------------------+-----------------+
-
-
-.. _ref-prep-remote:
-
-Prepare remote environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The environment on the ECMWF server (such as *ecgate* or *cca*) is already
-prepared. ECMWF server provide all libraries via a module system which is
-going to be selected by ``flex_extract`` automatically.
-
-
-.. _ref-install-remote:
-
-Remote installation
-^^^^^^^^^^^^^^^^^^^
-
-First, log in on one of the ECMWF Linux server, such as *ecgate* or *cca/ccb*.
-Substitute *<ecuid>* with your ECMWF user name:
-
-.. code-block:: bash
-
- ssh -X <ecuid>@ecaccess.ecmwf.int
-
-This will lead to the following output on the command line, asking for your
-password:
-
-.. code-block:: bash
-
- Authorized access only.
-
- ***************************************************************
- For further information, read the ECaccess documentation at:
-
- https://software.ecmwf.int/wiki/display/ECAC/ECaccess+Home
-
- You can also use ECaccess to load & download files from your
- EChome, ECscratch or ECfs directories using the ECaccess FTP
- server:
-
- ftp://uid@ecaccess.ecmwf.int/
-
- Please note you must use your UID and ActivID code to login!
- ***************************************************************
-
- <ecuid>@131.130.157.5's password: ***
- Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
-
- [<ecuid>@ecgb11 ~]$
-
-
-Then, copy the ``flex_extract`` tar ball (from section :ref:`ref-download`)
-to the ``$HOME`` directory of the ECMWF Linux server via ``scp``.
-Substitute the *<localuser>* and *<server.edu>* placeholders with your credentials.
-Untar the file and change into the ``flex_extract`` root directory.
-
-.. code-block:: bash
-
- scp <localuser>@<server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz $HOME/
- cd $HOME
- tar xvf flex_extract_vX.X.tar.gz
- cd flex_extract_vX.X
-
-
-On these ECMWF servers, it is not necessary to prepare the environment or the
-``Makefile`` for the Fortran program (``CONVERT2``) as described above.
-All third party libraries are available from a module system. The ``Makefile``
-is optimized for ECMWF servers and the compilation
-script ``compilejob.ksh``, which will be submitted by ``flex_extract`` to the
-batch job queue at ECMWF, does load all relevant modules from the ECMWF's module system.
-
-So there is just the need to execute the ``setup.sh`` script from the
-``flex_extract`` root directory for installation.
-Before executing it, it is necessary to adapt some parameters from ``setup.sh``
-described in :doc:`Documentation/Input/setup`.
-
-Open ``setup.sh`` with your editor and adapt the values:
-
-+----------------------------------------------+----------------------------------------------+
-| Take this for target = **ectrans** | Take this for target = **cca** |
-+----------------------------------------------+----------------------------------------------+
-| .. code-block:: bash | .. code-block:: bash |
-| | |
-| ... | ... |
-| # -----------------------------------------| # -----------------------------------------|
-| # AVAILABLE COMMANDLINE ARGUMENTS TO SET | # AVAILABLE COMMANDLINE ARGUMENTS TO SET |
-| # | # |
-| # THE USER HAS TO SPECIFY THESE PARAMETER | # THE USER HAS TO SPECIFY THESE PARAMETER |
-| # | # |
-| TARGET='ecgate' | TARGET='cca' |
-| MAKEFILE='Makefile.gfortran' | MAKEFILE='Makefile.CRAY' |
-| ECUID='uid' | ECUID='uid' |
-| ECGID='gid' | ECGID='gid' |
-| GATEWAY=None | GATEWAY=None |
-| DESTINATION=None | DESTINATION=None |
-| INSTALLDIR=None | INSTALLDIR='' |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
-| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
-| ... | ... |
-+----------------------------------------------+----------------------------------------------+
-
-:underline:`Please substitute the values of ECUID and ECGID
-with your own credentials and settings.`
-
-.. note::
-
- If a local gateway server is available the transfer of files could be done
- via the ``ECaccess`` commands. Therefore a valid *GATEWAY* and *DESTINATION*
- have to be present and should be set in the ``setup.sh`` file.
-
-
-Afterwards, type:
-
-.. code-block:: bash
-
- module load python3
- ./setup.sh
-
-to start the installation. You should see the following output at the command line.
+ :doc:`Installation/gateway`
-
-.. code-block:: bash
-
- # Output of setup.sh
- Create tarball ...
- Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X
- You should get an email with subject "flexcompile" within the next few minutes!
-
-
-The email content should look like this with a "SUCCESS" statement in the last line:
-
-.. code-block:: bash
-
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
- -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2
- SUCCESS!
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+ :doc:`Installation/local`
-
-
-
-.. _ref-gateway-mode:
-
-Gateway mode
-------------
-
-
-.. _ref-req-gateway:
-
-Gateway environment requirements
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The environment on your local system has to provide these software packages
-and libraries, since ``flex_extract`` does only prepare the job script and send
-it to the ECMWF servers:
-
-* `Python3`_ or `Anaconda Python3`_
-* `numpy`_
-* `genshi`_
-
-
-.. _ref-prep-gateway:
-
-Prepare gateway environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-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.
-The installation was tested on a *GNU/Linux Debian buster* and an *Ubuntu 18.04 Bionic Beaver* system.
-
-.. code-block:: sh
-
- # On a Linux Debian or Ubuntu system do
- # (if not already available):
- apt-get install python3
- apt-get install pip
- apt-get install genshi
- apt-get install numpy
-
-
-.. _ref-test-gateway:
-
-Test gateway environment
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Check the availability of the python packages by typing ``python3`` in
-a terminal window and run the ``import`` commands in the python shell.
-If there are no error messages, you succeeded in setting up the environment.
-
-.. code-block:: python
-
- # check in python3 console
- import genshi
- import numpy
-
-
-
-.. _ref-install-gateway:
-
-Gateway installation
-^^^^^^^^^^^^^^^^^^^^
-
-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.
-
-Please see `ECMWF's instructions on gateway server`_ to establish the gateway server if not already in place.
-Additionally, to be able to use the Ecaccess file transfer service **ectrans** please also create an association.
-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`_.
-
-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).
-
-.. code-block:: bash
-
- $ ecaccess-certificate-create
- Please enter your user-id: example_username
- Your passcode: ***
-
-``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.
-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.
-
-
-.. code-block:: bash
- :caption: 'Example settings for a gateway installation.'
- :name: setup.sh
-
- # -----------------------------------------------------------------
- # AVAILABLE COMMANDLINE ARGUMENTS TO SET
- #
- # THE USER HAS TO SPECIFY THESE PARAMETER
- #
- TARGET='ecgate'
- MAKEFILE='Makefile.gfortran'
- ECUID='uid'
- ECGID='gid'
- GATEWAY='server.example.edu'
- DESTINATION='example@genericSftp'
- INSTALLDIR=None
- JOB_TEMPLATE='job.template'
- CONTROLFILE='CONTROL_EA5'
-
-
-Afterwards, type:
-
-.. code-block:: bash
-
- $ ./setup.sh
-
-to start the installation. You should see the following output at the command line.
-
-
-.. code-block:: bash
-
- # Output of setup.sh
- Create tarball ...
- Job compilation script has been submitted to ecgate for installation in ${HOME}/flex_extract_vX.X
- You should get an email with subject "flexcompile" within the next few minutes!
-
-
-The email content should look like this with a "SUCCESS" statement in the last line:
-
-.. code-block:: bash
-
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g rwGRIB2.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g posnam.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -I. -I/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/include -g preconvert.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -g -O3 -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/eccodes/2.12.0/GNU/6.3.0/lib -leccodes_f90 -leccodes -ljasper -lpthread -L/usr/local/apps/jasper/1.900.1/LP64/lib -ljasper -lm -L/usr/local/apps/libemos/000455/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/libemos/000455/GNU/6.3.0/lib -lemos.R64.D64.I32 -L/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -Wl,-rpath,/usr/local/apps/fftw/3.3.4/GNU/6.3.0/lib -lfftw3
- -rwxr-x---. 1 USER at 353134 May 23 12:27 CONVERT2
- SUCCESS!
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-.. _ref-local-mode:
-
-Local mode
-----------
-
-
-
-.. _ref-req-local:
-
-Local environment requirements
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-For the local access modes **member** and **public** there is no difference in
-the installation process.
-
-The environment on your local system has to provide these software packages
-and libraries, since all extraction and preparation is done at the local system:
-
-+------------------------------------------------+-----------------+
-| Python part | Fortran part |
-+------------------------------------------------+-----------------+
-| * `Python3`_ | * `gfortran`_ |
-| * `numpy`_ | * `fftw3`_ |
-| * `genshi`_ | * `eccodes`_ |
-| * `eccodes for python`_ | * `emoslib`_ |
-| * `ecmwf-api-client`_ (everything except ERA5) | |
-| * `cdsapi`_ (just for ERA5) | |
-+------------------------------------------------+-----------------+
-
-
-.. _ref-prep-local:
-
-Prepare local environment
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-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.
-The installation was tested on a *Debian GNU/Linux buster/sid* and an *Ubuntu 18.04 Bionic Beaver* system.
-
-.. code-block:: sh
-
- # On a Linux Debian or Ubuntu system do
- # (if not already available):
- apt-get install python3 (usually available on normal Linux systems)
- apt-get install pip
- apt-get install gfortran
- apt-get install fftw3-dev
- apt-get install libeccodes-dev
- apt-get install libemos-dev
- apt-get install python3-eccodes
- apt-get install genshi
- apt-get install numpy
- pip install cdsapi
- pip install ecmwf-api-client
-
-.. note::
-
- In case you would like to use Anaconda Python we recommend you follow the installation instructions of
- `Anaconda Python Installation for Linux <https://docs.anaconda.com/anaconda/install/linux/>`_ and then install the
- ``eccodes`` package from ``conda`` with:
-
- .. code-block:: bash
-
- conda install conda-forge::python-eccodes
-
-
-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``.
-
-.. note::
-
- Since **public users** currently don't have access to the full *ERA5* dataset they can skip the installation of the ``CDS API``.
-
-Both user groups have to provide key's with their credentials for the Web API's in their home directory. Therefore, follow these instructions:
-
-ECMWF Web API:
- 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).
-
-CDS API:
- 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.
-
-
-.. _ref-test-local:
-
-Test local environment
-^^^^^^^^^^^^^^^^^^^^^^
-
-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:
-
-.. code-block:: sh
-
- $ dpkg -s libeccodes-dev | grep Status
- # or
- $ rpm -q libeccodes-dev
-
-Afterwards, check the availability of the python packages by typing ``python3`` in
-a terminal window and run the ``import`` commands in the python shell. If there are no error messages, you succeeded in setting up the environment.
-
-.. code-block:: python
-
- # check in python3 console
- import eccodes
- import genshi
- import numpy
- import cdsapi
- import ecmwfapi
-
-
-
-Test the Web API's
-""""""""""""""""""
-
-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.
-
-ECMWF Web API
-"""""""""""""
-
-
-+----------------------------------------------------------+----------------------------------------------------------+
-|Please use this piece of python code for **Member user**: |Please use this piece of python code for **Public user**: |
-+----------------------------------------------------------+----------------------------------------------------------+
-|.. code-block:: python |.. code-block:: python |
-| | |
-| from ecmwfapi import ECMWFService | from ecmwfapi import ECMWFDataServer |
-| | |
-| server = ECMWFService('mars') | server = ECMWFDataServer() |
-| | |
-| server.retrieve({ | server.retrieve({ |
-| 'stream' : "oper", | 'stream' : "enda", |
-| 'levtype' : "sfc", | 'levtype' : "sfc", |
-| 'param' : "165.128/166.128/167.128", | 'param' : "165.128/166.128/167.128", |
-| 'dataset' : "interim", | 'dataset' : "cera20c", |
-| 'step' : "0", | 'step' : "0", |
-| 'grid' : "0.75/0.75", | 'grid' : "1./1.", |
-| 'time' : "00/06/12/18", | 'time' : "00/06/12/18", |
-| 'date' : "2014-07-01/to/2014-07-31", | 'date' : "2000-07-01/to/2000-07-31", |
-| 'type' : "an", | 'type' : "an", |
-| 'class' : "ei", | 'class' : "ep", |
-| 'target' : "download_erainterim_ecmwfapi.grib" | 'target' : "download_cera20c_ecmwfapi.grib" |
-| }) | }) |
-+----------------------------------------------------------+----------------------------------------------------------+
-
-
-
-CDS API
-"""""""
-
-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:
-
-Please use this piece of python code to retrieve a small sample of *ERA5* pressure levels:
-
-.. code-block:: python
-
- import cdsapi
-
- c = cdsapi.Client()
+.. toctree::
+ :hidden:
+ :maxdepth: 2
- c.retrieve("reanalysis-era5-pressure-levels",
- {
- "variable": "temperature",
- "pressure_level": "1000",
- "product_type": "reanalysis",
- "year": "2008",
- "month": "01",
- "day": "01",
- "time": "12:00",
- "format": "grib"
- },
- "download_cdsapi.grib")
-
+ Installation/remote
+ Installation/gateway
+ Installation/local
-Afterwards, when you know that the CDS API generally works, you can try to extract some
-data from the MARS archive. From the latest experience we know that this can take a while.
-.. **Member user**
-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!
-.. code-block:: python
-
- import cdsapi
-
- c = cdsapi.Client()
-
- c.retrieve('reanalysis-era5-complete',
- {
- 'class' : 'ea',
- 'expver' : '1',
- 'stream' : 'oper',
- 'type' : 'fc',
- 'step' : '3/to/12/by/3',
- 'param' : '130.128',
- 'levtype' : 'ml',
- 'levelist': '135/to/137',
- 'date' : '2013-01-01',
- 'time' : '06/18',
- 'area' : '50/-5/40/5',
- 'grid' : '1.0/1.0',
- 'format' : 'grib',
- }, 'download_era5_cdsapi.grib')
-
-
-.. ********************** COMMENTED OUT FOR FUTURE
- ********************** PUBLIC RETRIEVAL IS CURRENTLY NOT ACCESSIBLE
-
- **Public user**
- Please use this piece of python code:
- .. code-block:: python
- import cdsapi
-
- c = cdsapi.Client()
-
- c.retrieve('reanalysis-era5-complete',
- {
- 'class' : 'ea',
- 'dataset' : 'era5',
- 'expver' : '1',
- 'stream' : 'oper',
- 'type' : 'fc',
- 'step' : '3/to/12/by/3',
- 'param' : '130.128',
- 'levtype' : 'ml',
- 'levelist': '135/to/137',
- 'date' : '2013-01-01',
- 'time' : '06/18',
- 'area' : '50/-5/40/5',
- 'grid' : '1.0/1.0',
- 'format' : 'grib',
- }, 'download_era5_cdsapi.grib')
-.. _ref-install-local:
-Local installation
-^^^^^^^^^^^^^^^^^^
-First prepare the Fortran ``Makefile`` for your environment and set it
-in the ``setup.sh`` script. (See section :ref:`ref-convert` for information on
-the Fortran program.)
-``flex_extract`` has already two ``Makefiles`` prepared for te ``gfortran`` and
-the ``ifort`` compiler:
- * Makefile.local.gfortran
- * Makefile.local.ifort
-They can be found in the path ``flex_extract_vX.X/source/fortran``, where
-``vX.X`` should be substituted with the current version number.
-
-.. caution::
- It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these
- ``Makefiles``.
-
-
-So starting from the root directory of ``flex_extract``,
-go to the ``Fortran`` source directory and open the ``Makefile`` of your
-choice to modify with an editor of your choice. We use the ``nedit`` in this case.
-
-.. code-block:: bash
-
- cd flex_extract_vX.X/source/fortran
- nedit Makefile.local.gfortran
-
-Edit the pathes to the ``eccodes`` library on your local machine.
-
-.. caution::
- This can vary from system to system.
- It is suggested to use a command like
-
- .. code-block:: bash
-
- # for the ECCODES_INCLUDE_DIR path do:
- $ dpkg -L libeccodes-dev | grep eccodes.mod
- # for the ECCODES_LIB path do:
- $ dpkg -L libeccodes-dev | grep libeccodes.so
-
- to find out the path to the ``eccodes`` library.
-
-Substitute these paths in the ``Makefile`` for parameters **ECCODES_INCLUDE_DIR**
-and **ECCODES_LIB** and save it.
-
-.. code-block:: bash
-
- # these are the paths on a current Debian 10 Testing system (May 2019)
- ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
- ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm
-
-The Fortran program called ``CONVERT2`` will be compiled during the
-installation process to get an executable. Therefore the ``Makefile``
-has to be set in the ``setup.sh`` script.
-
-In the root directory of ``flex_extract``, open the ``setup.sh`` script
-and adapt the installation parameters in the section labelled with
-"AVAILABLE COMMANDLINE ARGUMENTS TO SET" like shown below.
-
-
-.. code-block:: bash
- :caption: 'Example settings for a local installation.'
- :name: setup.sh
-
- ...
- # -----------------------------------------------------------------
- # AVAILABLE COMMANDLINE ARGUMENTS TO SET
- #
- # THE USER HAS TO SPECIFY THESE PARAMETER
- #
- TARGET='local'
- MAKEFILE='Makefile.local.gfortran'
- ECUID=None
- ECGID=None
- GATEWAY=None
- DESTINATION=None
- INSTALLDIR=None
- JOB_TEMPLATE='job.template'
- CONTROLFILE='CONTROL_EA5'
- ...
-
-
-Afterwards, type:
-
-.. code-block:: bash
-
- $ ./setup.sh
-
-to start the installation. You should see the following output at the command line.
-.. code-block:: bash
-
- # Output of setup.sh
- WARNING: installdir has not been specified
- flex_extract will be installed in here by compiling the Fortran source in /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/source/fortran
- Install flex_extract_v7.1 software at local in directory /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1
-
- Using makefile: Makefile.local.gfortran
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp phgrreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp grphreal.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -g -O3 -fopenmp ftrafo.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 rwGRIB2.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 posnam.f
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 preconvert.f90
- gfortran -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore -ffixed-line-length-132 -fopenmp -fconvert=big-endian -O3 -O3 -fopenmp -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/gcc-4.9.3/grib_api-1.14.3/lib -Bstatic -lgrib_api_f77 -lgrib_api_f90 -lgrib_api -Bdynamic -lm -ljasper -lemosR64
-
- -rwxrwxr-x. 1 philipa8 tmc 282992 May 23 22:27 ./CONVERT2
-
-
-
-
-
``Flex_extract`` in combination with ``FLEXPART``
=================================================
-Some users might like 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.
+Some users might wish to incorporate ``flex_extract`` directly into the ``FLEXPART`` distribution. Then the installation path has to be changed by setting the parameter `installdir` in the ``setup.sh`` file to the ``script`` directory in the ``FLEXPART`` root directoy.
@@ -884,22 +222,20 @@ Test installation
Fortran program test
--------------------
-To check if the compilation of the Fortran program ``CONVERT2`` was successful
-a quick program call on a minimal prepared dataset can be done.
+To check whether the Fortran program ``CONVERT2`` has been compiled and runs properly, it can be applied to a prepared minimal dataset.
-For this, go from the ``flex_extract`` root directory to the test
-directory and call the executable of the Fortran program.
+For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Convert/`` directory and execute the Fortran program.
.. note::
Remember that you might have to log in at the ECMWF server if you used the installation for the **remote** or **gateway** mode. There you find the ``flex_extract`` root directory in your ``$HOME`` directory.
.. code-block:: bash
- cd test/Installation/Convert
- # call the Fortran progam without arguments
- ../../../source/fortran/CONVERT2
+ cd Testing/Installation/Convert
+ # execute the Fortran progam without arguments
+ ../../../Source/Fortran/CONVERT2
-The installation was successfull if it showed the following output:
+The installation was successfull if you obtain on standard output:
.. code-block:: bash
@@ -911,7 +247,7 @@ The installation was successfull if it showed the following output:
readlatlon: 4 records read
SUCCESSFULLY FINISHED CONVERT_PRE: CONGRATULATIONS
-Now go back to the root directoy:
+Now go back to the root directory:
.. code-block:: bash
diff --git a/For_developers/Sphinx/source/quick_start.rst b/For_developers/Sphinx/source/quick_start.rst
index cc1a51a166df08a91ed210a8708484790d229db3..a34faa12ec79b748418c485b5fc577611551b3b8 100644
--- a/For_developers/Sphinx/source/quick_start.rst
+++ b/For_developers/Sphinx/source/quick_start.rst
@@ -336,7 +336,7 @@ It is then available from 1st January 1979 to 31st August 2019. The ``etadot`` i
.. todo::
- @LEO: please check the complete describtion and functionality of the CONTROL FILEs
+ @LEO: please check the complete description and functionality of the CONTROL FILEs
Operational data
----------------