From d72089559ba8d16d2cf31482c3bc1e074448cdd1 Mon Sep 17 00:00:00 2001
From: Anne Philipp <anne.philipp@univie.ac.at>
Date: Thu, 19 Dec 2019 21:12:11 +0100
Subject: [PATCH] updated online docu
---
.../html/Documentation/Input/run.html | 20 ++-
.../html/Documentation/Input/setup.html | 17 ++-
.../html/Documentation/Input/templates.html | 4 +-
.../Documentation/Overview/app_modes.html | 6 +-
.../html/Documentation/overview.html | 2 +-
Documentation/html/Installation/gateway.html | 56 ++++----
Documentation/html/Installation/local.html | 108 ++++++++--------
Documentation/html/Installation/remote.html | 50 +++-----
Documentation/html/_modules/install.html | 2 +-
.../_sources/Installation/gateway.rst.txt | 74 +++++------
.../html/_sources/Installation/local.rst.txt | 120 ++++++++----------
.../html/_sources/Installation/remote.rst.txt | 52 +++-----
.../html/_sources/installation.rst.txt | 31 +++--
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...379b867d7c69c85310a4f24e5228f-le64.cache-3 | Bin 0 -> 5208 bytes
Documentation/html/index.html | 2 +-
Documentation/html/installation.html | 30 +++--
Documentation/html/objects.inv | Bin 7172 -> 7175 bytes
Documentation/html/searchindex.js | 2 +-
53 files changed, 272 insertions(+), 304 deletions(-)
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diff --git a/Documentation/html/Documentation/Input/run.html b/Documentation/html/Documentation/Input/run.html
index bb254be..e7bb568 100644
--- a/Documentation/html/Documentation/Input/run.html
+++ b/Documentation/html/Documentation/Input/run.html
@@ -486,9 +486,21 @@ the command line parameters and the so-called <code class="docutils literal notr
<span class="c1"># @Date: October, 4 2018</span>
<span class="c1">#</span>
<span class="c1"># @Description: </span>
+<span class="c1"># This script defines the available command-line parameters</span>
+<span class="c1"># for running flex_extract and combines them for the execution </span>
+<span class="c1"># of the Python program. It also does some checks to </span>
+<span class="c1"># guarantee necessary parameters were set and consistent.</span>
+<span class="c1">#</span>
+<span class="c1"># @Licence:</span>
+<span class="c1"># (C) Copyright 2014-2019.</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"># -----------------------------------------------------------------</span>
<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
<span class="c1"># </span>
@@ -507,9 +519,9 @@ the command line parameters and the so-called <code class="docutils literal notr
<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">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</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">REQUEST</span><span class="o">=</span><span class="m">0</span>
<span class="nv">PUBLIC</span><span class="o">=</span><span class="m">0</span>
<span class="c1"># -----------------------------------------------------------------</span>
diff --git a/Documentation/html/Documentation/Input/setup.html b/Documentation/html/Documentation/Input/setup.html
index 979f65f..6bf0a9a 100644
--- a/Documentation/html/Documentation/Input/setup.html
+++ b/Documentation/html/Documentation/Input/setup.html
@@ -347,9 +347,18 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<span class="c1"># @Description: </span>
<span class="c1"># This file defines the flex_extract's available installation</span>
<span class="c1"># parameters and puts them together for the call of the actual </span>
-<span class="c1"># python installation script. </span>
-<span class="c1"># It also does some checks to guarantees necessary parameters </span>
-<span class="c1"># were set.</span>
+<span class="c1"># python installation script. It also does some checks to </span>
+<span class="c1"># guarantee necessary parameters were set.</span>
+<span class="c1">#</span>
+<span class="c1"># @Licence:</span>
+<span class="c1"># (C) Copyright 2014-2019.</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"># -----------------------------------------------------------------</span>
<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
@@ -357,7 +366,7 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETERS</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">MAKEFILE</span><span class="o">=</span><span class="s1">'makefile.eccodes'</span>
<span class="nv">ECUID</span><span class="o">=</span><span class="s1">'km4a'</span>
<span class="nv">ECGID</span><span class="o">=</span><span class="s1">'at'</span>
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'srvx8.img.univie.ac.at'</span>
diff --git a/Documentation/html/Documentation/Input/templates.html b/Documentation/html/Documentation/Input/templates.html
index 350d298..65aaf8f 100644
--- a/Documentation/html/Documentation/Input/templates.html
+++ b/Documentation/html/Documentation/Input/templates.html
@@ -251,7 +251,7 @@ DESTINATION <span class="nv">$destination_name</span>
<p>At the beginning some directives for the batch system are set.
On the <strong>ecgate</strong> server the <code class="docutils literal notranslate"><span class="pre">SBATCH</span></code> comments are the directives for the SLURM workload manager. A description of the single lines can be found at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs">SLURM directives</a>.
For the high performance computers <strong>cca</strong> and <strong>ccb</strong> the <code class="docutils literal notranslate"><span class="pre">PBS</span></code> comments are necessary and can be view at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS">PBS directives</a>.</p>
-<p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Environment requirements</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>
+<p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>
<p>Afterwards the installation steps as such are done. Including the generation of the root directory, putting files in place, compiling the Fortran program and sending a log file via email.</p>
<div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
@@ -335,7 +335,7 @@ ls -l <span class="nv">$fortran_program</span> >>flexcompile
<p>At the beginning some directives for the batch system are set.
On the <strong>ecgate</strong> server the <code class="docutils literal notranslate"><span class="pre">SBATCH</span></code> comments are the directives for the SLURM workload manager. A description of the single lines can be found at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Writing+SLURM+jobs">SLURM directives</a>.
For the high performance computers <strong>cca</strong> and <strong>ccb</strong> the <code class="docutils literal notranslate"><span class="pre">PBS</span></code> comments are necessary and can be view at <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Batch+environment%3A++PBS">PBS directives</a>.</p>
-<p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Environment requirements</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>
+<p>The software environment requirements mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> are prepared by loading the corresponding modules depending in the <code class="docutils literal notranslate"><span class="pre">HOST</span></code>. It should not be changed without testing.</p>
<p>Afterwards the run directory and the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file are created and <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> is executed. In the end a log file is send via email.</p>
<div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
diff --git a/Documentation/html/Documentation/Overview/app_modes.html b/Documentation/html/Documentation/Overview/app_modes.html
index ff2839d..31dfda0 100644
--- a/Documentation/html/Documentation/Overview/app_modes.html
+++ b/Documentation/html/Documentation/Overview/app_modes.html
@@ -188,7 +188,7 @@
<div><ol class="arabic simple">
<li><dl class="first docutils">
<dt>Remote (member)</dt>
-<dd>In the <strong>Remote mode</strong> the user works directly on ECMWF Linux member state server, such as <code class="docutils literal notranslate"><span class="pre">ecgate</span></code> or <code class="docutils literal notranslate"><span class="pre">cca</span></code>. The software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory. The user does not need to install any of the additional third-party libraries mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Environment requirements</span></a> as ECMWF provides everything with environment modules. The module selection will be done automatically in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</dd>
+<dd>In the <strong>Remote mode</strong> the user works directly on ECMWF Linux member state server, such as <code class="docutils literal notranslate"><span class="pre">ecgate</span></code> or <code class="docutils literal notranslate"><span class="pre">cca</span></code>. The software will be installed in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory. The user does not need to install any of the additional third-party libraries mentioned in <a class="reference internal" href="../../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a> as ECMWF provides everything with environment modules. The module selection will be done automatically in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>.</dd>
</dl>
</li>
</ol>
@@ -206,12 +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/local.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 - dependencies</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/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>
+<dd>Scripts are installed and executed on a local machine, either in the current <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directory or in a path given to the installation script. Under this scenario a software environment similar to that at ECMWF is required. Additionally, Web API’s have to be installed to access ECMWF server. The complete installation process is described in <a class="reference internal" href="../../Installation/local.html#ref-local-mode"><span class="std std-ref">Local mode - dependencies</span></a>. In this case a direct registration at ECMWF is necessary and the user has to accept a specific license agreement for each dataset he/she intends to retrieve.</dd>
</dl>
</li>
</ol>
diff --git a/Documentation/html/Documentation/overview.html b/Documentation/html/Documentation/overview.html
index d5a5ee9..24d7d27 100644
--- a/Documentation/html/Documentation/overview.html
+++ b/Documentation/html/Documentation/overview.html
@@ -192,7 +192,7 @@ The software retrieves the minimal number of parameters <code class="docutils li
</dl>
<p>Additionally, it has some Korn shell scripts which are used to set the environment and batch job features on ECMWF servers for the <em>gateway</em> and <em>remote</em> mode. See <a class="reference internal" href="Overview/app_modes.html"><span class="doc">Application Modes</span></a> for information of application modes.</p>
<p>A number of Shell scripts are wrapped around the software package for easy installation and fast job submission.</p>
-<p>The software depends on a number of third-party libraries which can be found in <a class="reference internal" href="../installation.html#ref-requirements"><span class="std std-ref">Environment requirements</span></a>.</p>
+<p>The software depends on a number of third-party libraries which can be found in <a class="reference internal" href="../installation.html#ref-requirements"><span class="std std-ref">Dependencies</span></a>.</p>
<p>Some details on the tasks and program worksteps are described in <a class="reference internal" href="Overview/prog_flow.html"><span class="doc">Program Flow</span></a>.</p>
<div class="toctree-wrapper compound">
</div>
diff --git a/Documentation/html/Installation/gateway.html b/Documentation/html/Installation/gateway.html
index 66494f8..0f4e077 100644
--- a/Documentation/html/Installation/gateway.html
+++ b/Documentation/html/Installation/gateway.html
@@ -93,11 +93,11 @@
<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"><a class="reference internal" href="../installation.html#dependencies">Dependencies</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="#gateway-mode-dependencies">Gateway mode - dependencies</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>
@@ -189,27 +189,31 @@
<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>
+<div class="section" id="gateway-mode-dependencies">
+<span id="ref-req-gateway"></span><span id="ref-gateway-mode"></span><h2>Gateway mode - dependencies<a class="headerlink" href="#gateway-mode-dependencies" title="Permalink to this headline">¶</a></h2>
<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="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>
</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>
+<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> it is necessary to create a so-called association. The easiest way is to visit the ECaccess Member State Gateway website (e.g. <a class="reference external" href="https://msgatway.ecmwf.int">https://msgatway.ecmwf.int</a>) and follow the instructions in the short <a class="reference external" href="https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf">ECaccess Presentation</a> (page 17 ff.). Additional documentation can be found on the <a class="reference external" href="https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans">ECMWF ectrans site</a>.</p>
+<p>The next step is to create an <em>ecaccess certificate</em> to be able to send and receive files from and to the ECMWF server. You can do this by using the <code class="docutils literal notranslate"><span class="pre">ecaccess-certificate-create</span></code> command on the gateway server. You will be prompted for your ECMWF member state user name and a password (generated by a token). This certificate has to be renewed periodically (every 7 days).</p>
+<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>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 <em>GNU/Linux Debian buster</em> and <em>Ubuntu 18.04 Bionic Beaver</em>.</p>
+<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># On a Debian or Debian-derived sytem (e. g. Ubuntu) system you may use the following commands (or equivalent commands of your preferred package manager):</span>
<span class="c1"># (if not already available):</span>
apt-get install python3
-apt-get install pip
-apt-get install genshi
-apt-get install numpy
+apt-get install python3-genshi
+apt-get install python3-numpy
</pre></div>
</div>
</div>
@@ -226,18 +230,8 @@ If there are no error messages, you succeeded in setting up the environment.</p>
</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>
+<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, loads the required modules from the module system. For enabling the file transfer via the gateway, you have to set the <em>ECUID</em>, <em>ECGID</em>, <em>GATEWAY</em> and <em>DESTINATION</em> parameter values.</p>
<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>
@@ -246,11 +240,11 @@ The job script, send to the job queue via the ECaccess software, selects again a
<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">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">GATEWAY</span><span class="o">=</span><span class="s1">'localserver.tld'</span>
+<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'association_name@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>
@@ -261,14 +255,14 @@ The job script, send to the job queue via the ECaccess software, selects again a
<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>
+<p>to start the installation. You should see the following on standard output.</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>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the email address connectd to the user account on ECMWF servers. The email content should look like this with a “SUCCESS” statement in the last line:</p>
<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
diff --git a/Documentation/html/Installation/local.html b/Documentation/html/Installation/local.html
index bcd7c37..d454436 100644
--- a/Documentation/html/Installation/local.html
+++ b/Documentation/html/Installation/local.html
@@ -93,12 +93,12 @@
<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"><a class="reference internal" href="../installation.html#dependencies">Dependencies</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="#local-mode-dependencies">Local mode - dependencies</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>
@@ -189,12 +189,11 @@
<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>
+<div class="section" id="local-mode-dependencies">
+<span id="ref-req-local"></span><span id="ref-local-mode"></span><h2>Local mode - dependencies<a class="headerlink" href="#local-mode-dependencies" title="Permalink to this headline">¶</a></h2>
+<p>The installation is the same for the access modes <strong>member</strong> and <strong>public</strong>.</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>
+and libraries, since the preparation of the extraction and the post-processing is done on the local machine:</p>
<table border="1" class="docutils">
<colgroup>
<col width="74%" />
@@ -226,21 +225,25 @@ and libraries, since all extraction and preparation is done at the local system:
</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>
+<p>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 <em>Debian GNU/Linux 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 Debian or Debian-derived sytem (e. g. Ubuntu) system you may use the following commands (or equivalent commands of your preferred package manager):</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
+ apt-get install python3 <span class="o">(</span>usually already available on GNU/Linux systems<span class="o">)</span>
+ 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
+<span class="c1"># Some of these packages will pull in further packages as dependencies. This is fine, and some are even needed by ``flex_extract''.</span>
+
+
+<span class="c1"># As currently the CDS and ECMWF API packages are not available as Debian packages, they need to be installed outside of the Debian (Ubuntu etc.) package management system. The recommended way is:</span>
+ apt-get install pip
+ pip install cdsapi
+ pip install ecmwf-api-client
</pre></div>
</div>
<div class="admonition note">
@@ -252,29 +255,22 @@ pip install ecmwf-api-client
</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>
+<p>The CDS API (cdsapi) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.</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>
+<p>Both user groups have to provide keys with their credentials for the Web API’s in their home directory. Therefore, follow these instructions:</p>
<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>
+<dd>Go to <a class="reference external" href="https://confluence.ecmwf.int//display/WEBAPI/Access+MARS">MARS access</a> website and log in with your credentials. Afterwards, on this site in section “Install ECMWF KEY” the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file <cite>.ecmwfapirc</cite> in your home directory).</dd>
<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>
+<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">eccodes</span>
<span class="kn">import</span> <span class="nn">genshi</span>
@@ -285,7 +281,7 @@ a terminal window and run the <code class="docutils literal notranslate"><span c
</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>
+<p>You can start very simple test retrievals for both Web APIs to be sure that everything works. This is recommended to minimise the range of possible errors using <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> later on.</p>
<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">
@@ -294,8 +290,8 @@ a terminal window and run the <code class="docutils literal notranslate"><span c
<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 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>
@@ -343,8 +339,8 @@ a terminal window and run the <code class="docutils literal notranslate"><span c
</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>
+<p>Extraction of ERA5 data via CDS API might take time as currently there is a high demand for ERA5 data. Therefore, as a simple test for the API just retrieve pressure-level data (even if that is NOT what we need for FLEXPART), as they are stored on disk and don’t need to be retrieved from MARS (which is the time-consuming action):</p>
+<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>
@@ -363,9 +359,8 @@ a terminal window and run the <code class="docutils literal notranslate"><span c
<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>
+<p>If you know that your CDS API works, you can try to extract some data from MARS.</p>
+<p>Please use this piece of Python code to retrieve a small <em>ERA5</em> data sample as a <strong>member-state user</strong>! The <strong>Public user</strong> do not have access to the full <em>ERA5</em> dataset!</p>
<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>
@@ -393,32 +388,30 @@ data from the MARS archive. From the latest experience we know that this can tak
</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>
+<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> comes with two <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> prepared for the <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> and
+the <code class="docutils literal notranslate"><span class="pre">ifort</span></code> compiler. The <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> version assumes that <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> and <code class="docutils literal notranslate"><span class="pre">emoslib</span></code> are installed as distribution packages.</p>
<blockquote>
<div><ul class="simple">
-<li>Makefile.local.gfortran</li>
-<li>Makefile.local.ifort</li>
+<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
+<p>They can be found at <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>
+<code class="docutils literal notranslate"><span class="pre">makefiles</span></code> if other than standard paths are used.</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
+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
+<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>
+<p>Edit the paths 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.
@@ -431,7 +424,7 @@ $ dpkg -L libeccodes-dev <span class="p">|</span> grep libeccodes.so
</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>
+<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/
@@ -439,8 +432,7 @@ and <strong>ECCODES_LIB</strong> and save it.</p>
</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>
+installation process.Therefore the name of the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> to be used needs to be given in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.</p>
<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>
@@ -453,7 +445,7 @@ and adapt the installation parameters in the section labelled with
<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">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
@@ -469,7 +461,7 @@ and adapt the installation parameters in the section labelled with
<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>
+<p>to start the installation. You should see the following standard output.</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
diff --git a/Documentation/html/Installation/remote.html b/Documentation/html/Installation/remote.html
index 29d3bb7..5350789 100644
--- a/Documentation/html/Installation/remote.html
+++ b/Documentation/html/Installation/remote.html
@@ -93,10 +93,10 @@
<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"><a class="reference internal" href="../installation.html#dependencies">Dependencies</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="#remote-mode-dependencies">Remote mode - dependencies</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>
@@ -188,10 +188,9 @@
<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>
+<div class="section" id="remote-mode-dependencies">
+<span id="ref-req-remote"></span><span id="ref-remote-mode"></span><h2>Remote mode - dependencies<a class="headerlink" href="#remote-mode-dependencies" title="Permalink to this headline">¶</a></h2>
+<p>The following software is required, and already available at the ECMWF servers:</p>
<table border="1" class="docutils">
<colgroup>
<col width="61%" />
@@ -221,13 +220,11 @@ software packages and libraries:</p>
</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>
+<p>ECMWF servers provide all libraries via a module system. Loading the required modules is already built into <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> and no user action is needed.</p>
</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>.
+<p>First, log in on one of the ECMWF servers, 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>
@@ -250,41 +247,32 @@ password:</p>
Please note you must use your UID and ActivID code to login!
***************************************************************
-<ecuid>@131.130.157.5's password: ***
+<ecuid>@<ipname/address>'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">$HOME</span></code> directory of the ECMWF Linux server via <code class="docutils literal notranslate"><span class="pre">scp</span></code>.
-Substitute the <em><localuser></em> and <em><server.edu></em> placeholders with your credentials.
+<p>Substitute the <em><localuser></em> and <em><localmachine.tld></em> placeholders with your local user name and the IP name or address of your local machine.
Untar the file and change into the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp <localuser>@<server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz <span class="nv">$HOME</span>/
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp <localuser>@<localmachine.tld>:</path/to/tarfile/>flex_extract_vX.X.tar.gz <span class="nv">$HOME</span>/
<span class="nb">cd</span> <span class="nv">$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.
+<p>Execute the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>’s root directory.
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>
+<p>Open <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> with your preferred editor (e.g., <a href="#id1"><span class="problematic" id="id2">``</span></a>nano’‘) and adapt the values:</p>
<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-odd"><td>Use this for target = <strong>ectrans</strong></td>
+<td>Use 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>
@@ -328,26 +316,24 @@ described in <span class="xref std std-doc">Documentation/Input/setup</span>.</p
</tbody>
</table>
<p><span class="underline">Please substitute the values of ECUID and ECGID
-with your own credentials and settings.</span></p>
+with your own ones (look at any of your files with ``ls -l’’ to see uid and gid).</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>
+<p class="last">If a local gateway server is available, files can be transferred with <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. In that case, a valid <em>GATEWAY</em> and <em>DESTINATION</em> have to be present in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file (even if not used, the lines must not be deleted).</p>
</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>
+<p>to start the installation. You should see the following on standard output.</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>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the email address connectd to the user account on ECMWF servers. The email content should look like this with a “SUCCESS” statement in the last line:</p>
<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
diff --git a/Documentation/html/_modules/install.html b/Documentation/html/_modules/install.html
index 01c07e2..371bd1e 100644
--- a/Documentation/html/_modules/install.html
+++ b/Documentation/html/_modules/install.html
@@ -536,7 +536,7 @@
<span class="n">hfiles</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">relpath</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">ecd</span><span class="p">)</span>
<span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">UioFiles</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_REL_FORTRAN_SRC</span><span class="p">,</span> <span class="s1">'*.h'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span>
<span class="n">makefiles</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">relpath</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">ecd</span><span class="p">)</span>
- <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">UioFiles</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_REL_FORTRAN_SRC</span><span class="p">,</span> <span class="s1">'Makefile*'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">UioFiles</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_REL_FORTRAN_SRC</span><span class="p">,</span> <span class="s1">'makefile*'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span>
<span class="n">jobdir</span> <span class="o">=</span> <span class="p">[</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_REL_JOBSCRIPTS</span><span class="p">]</span>
<span class="c1"># concatenate single lists to one for a better looping</span>
diff --git a/Documentation/html/_sources/Installation/gateway.rst.txt b/Documentation/html/_sources/Installation/gateway.rst.txt
index 447685d..c452eb6 100644
--- a/Documentation/html/_sources/Installation/gateway.rst.txt
+++ b/Documentation/html/_sources/Installation/gateway.rst.txt
@@ -7,7 +7,7 @@ Gateway mode installation
.. toctree::
:hidden:
- :maxdepth: 3
+ :maxdepth: 2
.. _Python 3: https://docs.python.org/3/
.. _Python3: https://www.python.org/downloads/
@@ -42,14 +42,10 @@ Gateway mode installation
.. _ref-req-gateway:
-Gateway environment requirements
-================================
+Gateway mode - dependencies
+===========================
-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`_
+* `Python3`_
* `numpy`_
* `genshi`_
@@ -59,28 +55,43 @@ it to the ECMWF servers:
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.
+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 Linux Debian or Ubuntu system do
+
+ # 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 pip
- apt-get install genshi
- apt-get install numpy
-
+ 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
@@ -94,23 +105,9 @@ If there are no error messages, you succeeded in setting up the environment.
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, 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.
-``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.'
@@ -122,11 +119,11 @@ The job script, send to the job queue via the ECaccess software, selects again a
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='ecgate'
- MAKEFILE='Makefile.gfortran'
+ MAKEFILE='makefile.gfortran'
ECUID='uid'
ECGID='gid'
- GATEWAY='server.example.edu'
- DESTINATION='example@genericSftp'
+ GATEWAY='localserver.tld'
+ DESTINATION='association_name@genericSftp'
INSTALLDIR=None
JOB_TEMPLATE='job.template'
CONTROLFILE='CONTROL_EA5'
@@ -138,7 +135,7 @@ Afterwards, type:
$ ./setup.sh
-to start the installation. You should see the following output at the command line.
+to start the installation. You should see the following on standard output.
.. code-block:: bash
@@ -148,8 +145,7 @@ to start the installation. You should see the following output at the command li
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:
+``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
diff --git a/Documentation/html/_sources/Installation/local.rst.txt b/Documentation/html/_sources/Installation/local.rst.txt
index ca96225..d0276bf 100644
--- a/Documentation/html/_sources/Installation/local.rst.txt
+++ b/Documentation/html/_sources/Installation/local.rst.txt
@@ -45,14 +45,13 @@ Local mode installation
.. _ref-req-local:
-Local environment requirements
-==============================
+Local mode - dependencies
+=========================
-For the local access modes **member** and **public** there is no difference in
-the installation process.
+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 all extraction and preparation is done at the local system:
+and libraries, since the preparation of the extraction and the post-processing is done on the local machine:
+------------------------------------------------+-----------------+
| Python part | Fortran part |
@@ -71,25 +70,29 @@ and libraries, since all extraction and preparation is done at the local system:
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.
+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 Linux Debian or Ubuntu system do
- # (if not already available):
- apt-get install python3 (usually available on normal Linux systems)
- apt-get install pip
+ # 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
- apt-get install python3-eccodes
- apt-get install genshi
- apt-get install numpy
+ # 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
@@ -98,39 +101,29 @@ The installation was tested on a *Debian GNU/Linux buster/sid* and an *Ubuntu 18
.. 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``.
-
+ 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 key's with their credentials for the Web API's in their home directory. Therefore, follow these instructions:
-
+
+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 point 1 (save the key in a file `.ecmwfapirc` in your home directory).
+ 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 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.
+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
@@ -146,14 +139,15 @@ a terminal window and run the ``import`` commands in the python shell. If there
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.
+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**: |
+|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 |
| | |
@@ -181,9 +175,9 @@ ECMWF Web API
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:
+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:
+Please use this piece of Python code to retrieve a small sample of *ERA5* pressure levels:
.. code-block:: python
@@ -204,13 +198,12 @@ Please use this piece of python code to retrieve a small sample of *ERA5* pressu
},
"download_cdsapi.grib")
+
+If you know that your CDS API works, you can try to extract some data from MARS.
-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**
+.. **Member-state 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!
+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
@@ -240,7 +233,7 @@ Please use this piece of python code to retrieve a small *ERA5* data sample as a
********************** PUBLIC RETRIEVAL IS CURRENTLY NOT ACCESSIBLE
**Public user**
- Please use this piece of python code:
+ Please use this piece of Python code:
.. code-block:: python
@@ -276,33 +269,31 @@ Please use this piece of python code to retrieve a small *ERA5* data sample as a
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
+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.
-They can be found in the path ``flex_extract_vX.X/source/fortran``, where
+ * 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``.
-
+ ``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
+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
+ cd flex_extract_vX.X/Source/Fortran
+ nedit makefile.local.gfortran
+
+Edit the paths to the ``eccodes`` library on your local machine.
-Edit the pathes to the ``eccodes`` library on your local machine.
.. caution::
This can vary from system to system.
@@ -317,7 +308,7 @@ Edit the pathes to the ``eccodes`` library on your local machine.
to find out the path to the ``eccodes`` library.
-Substitute these paths in the ``Makefile`` for parameters **ECCODES_INCLUDE_DIR**
+Substitute these paths in the ``makefile`` for parameters **ECCODES_INCLUDE_DIR**
and **ECCODES_LIB** and save it.
.. code-block:: bash
@@ -328,8 +319,7 @@ and **ECCODES_LIB** and save it.
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.
+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
@@ -347,7 +337,7 @@ and adapt the installation parameters in the section labelled with
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='local'
- MAKEFILE='Makefile.local.gfortran'
+ MAKEFILE='makefile.local.gfortran'
ECUID=None
ECGID=None
GATEWAY=None
@@ -364,7 +354,7 @@ Afterwards, type:
$ ./setup.sh
-to start the installation. You should see the following output at the command line.
+to start the installation. You should see the following standard output.
.. code-block:: bash
diff --git a/Documentation/html/_sources/Installation/remote.rst.txt b/Documentation/html/_sources/Installation/remote.rst.txt
index 8734e23..b2e4d42 100644
--- a/Documentation/html/_sources/Installation/remote.rst.txt
+++ b/Documentation/html/_sources/Installation/remote.rst.txt
@@ -41,11 +41,10 @@ Remote mode installation
.. _ref-req-remote:
-Remote environment requirements
-===============================
+Remote mode - dependencies
+==========================
-The environment for ``flex_extract`` on ECMWF servers has to provide these
-software packages and libraries:
+The following software is required, and already available at the ECMWF servers:
+---------------------------+-----------------+
| Python part | Fortran part |
@@ -62,9 +61,7 @@ software packages and libraries:
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.
+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:
@@ -72,7 +69,7 @@ going to be selected by ``flex_extract`` automatically.
Remote installation
===================
-First, log in on one of the ECMWF Linux server, such as *ecgate* or *cca/ccb*.
+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
@@ -100,41 +97,31 @@ password:
Please note you must use your UID and ActivID code to login!
***************************************************************
- <ecuid>@131.130.157.5's password: ***
+ <ecuid>@<ipname/address>'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.
+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>@<server.edu>:/path/to/tarfile/flex_extract_vX.X.tar.gz $HOME/
+ 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
-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.
+
+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 editor and adapt the values:
-
+Open ``setup.sh`` with your preferred editor (e.g., ``nano'') and adapt the values:
+
+----------------------------------------------+----------------------------------------------+
-| Take this for target = **ectrans** | Take this for target = **cca** |
+| Use this for target = **ectrans** | Use this for target = **cca** |
+----------------------------------------------+----------------------------------------------+
| .. code-block:: bash | .. code-block:: bash |
| | |
@@ -157,14 +144,11 @@ Open ``setup.sh`` with your editor and adapt the values:
+----------------------------------------------+----------------------------------------------+
:underline:`Please substitute the values of ECUID and ECGID
-with your own credentials and settings.`
+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 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.
-
+ 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:
@@ -173,7 +157,7 @@ Afterwards, type:
module load python3
./setup.sh
-to start the installation. You should see the following output at the command line.
+to start the installation. You should see the following on standard output.
.. code-block:: bash
@@ -184,7 +168,7 @@ to start the installation. You should see the following output at the command li
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:
+``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
diff --git a/Documentation/html/_sources/installation.rst.txt b/Documentation/html/_sources/installation.rst.txt
index e1f4f13..a65057f 100644
--- a/Documentation/html/_sources/installation.rst.txt
+++ b/Documentation/html/_sources/installation.rst.txt
@@ -131,15 +131,22 @@ git repo
.. _ref-requirements:
-Environment requirements
-========================
+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.
-
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
+
@@ -197,9 +204,7 @@ Select one of the following modes to install:
``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.
@@ -217,22 +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
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diff --git a/Documentation/html/index.html b/Documentation/html/index.html
index 13443c9..419c432 100644
--- a/Documentation/html/index.html
+++ b/Documentation/html/index.html
@@ -286,7 +286,7 @@ Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</p>
<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"><a class="reference internal" href="installation.html#dependencies">Dependencies</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></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>
diff --git a/Documentation/html/installation.html b/Documentation/html/installation.html
index 4179fa5..5793d58 100644
--- a/Documentation/html/installation.html
+++ b/Documentation/html/installation.html
@@ -93,7 +93,7 @@
<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="#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="#dependencies">Dependencies</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="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>
@@ -282,11 +282,17 @@
</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>
+<div class="section" id="dependencies">
+<span id="ref-requirements"></span><h2>Dependencies<a class="headerlink" href="#dependencies" 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>
+<p>Before installing the system packages check the availability with <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or <code class="docutils literal notranslate"><span class="pre">rpm</span> <span class="pre">-q</span> <span class="pre"><package_name></span></code>, depending on your system. For example:</p>
+<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>
</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>
@@ -306,28 +312,24 @@ installation has to be done. At the users local side not all software has to be
</div>
<div class="section" id="flex-extract-in-combination-with-flexpart">
<h2><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> in combination with <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code><a class="headerlink" href="#flex-extract-in-combination-with-flexpart" title="Permalink to this headline">¶</a></h2>
-<p>Some users might like to incorporate <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly into the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>
-distribution. Then the installation path has to be changed by setting the parameter
-<cite>installdir</cite> in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file to the <code class="docutils literal notranslate"><span class="pre">script</span></code> directory in the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> root directoy.</p>
+<p>Some users might wish to incorporate <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> directly into the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> distribution. Then the installation path has to be changed by setting the parameter <cite>installdir</cite> in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file to the <code class="docutils literal notranslate"><span class="pre">script</span></code> directory in the <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> root directoy.</p>
</div>
<div class="section" id="test-installation">
<span id="ref-testinstallfe"></span><h2>Test installation<a class="headerlink" href="#test-installation" title="Permalink to this headline">¶</a></h2>
<div class="section" id="fortran-program-test">
<h3>Fortran program test<a class="headerlink" href="#fortran-program-test" title="Permalink to this headline">¶</a></h3>
-<p>To check if the compilation of the Fortran program <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> was successful
-a quick program call on a minimal prepared dataset can be done.</p>
-<p>For this, go from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory to the test
-directory and call the executable of the Fortran program.</p>
+<p>To check whether the Fortran program <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> has been compiled and runs properly, it can be applied to a prepared minimal dataset.</p>
+<p>For this, go from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory to the <code class="docutils literal notranslate"><span class="pre">Testing/Installation/Convert/</span></code> directory and execute the Fortran program.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Remember that you might have to log in at the ECMWF server if you used the installation for the <strong>remote</strong> or <strong>gateway</strong> mode. There you find the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory in your <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory.</p>
</div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> test/Installation/Convert
-<span class="c1"># call the Fortran progam without arguments</span>
-../../../source/fortran/CONVERT2
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> Testing/Installation/Convert
+<span class="c1"># execute the Fortran progam without arguments</span>
+../../../Source/Fortran/CONVERT2
</pre></div>
</div>
-<p>The installation was successfull if it showed the following output:</p>
+<p>The installation was successfull if you obtain on standard output:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> readspectral: <span class="m">1</span> records <span class="nb">read</span>
readlatlon: <span class="m">8</span> records <span class="nb">read</span>
STATISTICS: <span class="m">98842</span>.4598 <span class="m">98709</span>.7359 <span class="m">5120</span>.5385
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index a4fe9d4..3e9a2b6 100644
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Documentation","Fortran\u2019s Auto Generated Documentation","Python\u2019s Auto Generated Documentation","CONTROL file changes","The Compilation Jobscript <code class=\"docutils literal notranslate\"><span class=\"pre\">compilejob.ksh</span></code>","The CONTROL file","The CONTROL parameters","ECMWF User Credential file <code class=\"docutils literal notranslate\"><span class=\"pre\">ECMWF_ENV</span></code>","CONTROL file examples","The Fortran Makefile - <code class=\"docutils literal notranslate\"><span class=\"pre\">CONVERT2</span></code>","The Jobscript <code class=\"docutils literal notranslate\"><span class=\"pre\">job.ksh</span></code>","The executable Script - <code class=\"docutils literal notranslate\"><span class=\"pre\">run.sh</span></code>","The Installation Script - <code class=\"docutils literal notranslate\"><span class=\"pre\">setup.sh</span></code>","Templates","Application Modes","Program Flow","Auto Generated Documentation","Disaggregation of Flux Data","Control & Input Data","Output Data","Overview","Vertical Coordinate","Access Modes","Link Collection for Quick finder","Hints to specify dataset retrieval","Available Datasets for Member State users","Available Datasets for Public users","Metrics","Static Code Analysis","Testcases","Gateway mode installation","Local mode installation","Remote mode installation","FAQ - Frequently asked questions","Known Bugs and Issues","Developer Team","Changelog","Developer Guide","Documentation","ECMWF Data","Evaluation","Welcome to <code class=\"docutils literal notranslate\"><span class=\"pre\">flex_extract</span></code>\u2019s user documentation!","Installation","Quick Start","Support","ToDos"],titleterms:{"class":2,"new":[19,36],"public":[26,42,43],"static":28,CDS:31,The:[4,5,6,9,10,11,12],access:22,adapt:[],addit:[0,6,19],adjust:43,agre:[],agreement:42,analysi:28,api:31,applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calcul:21,can:[24,33],cera:43,chang:[3,36],changelog:36,check:2,code:28,collect:23,combin:[42,43],comparison:29,compil:4,compilejob:[4,13],content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert2:[9,19],convert:13,coordin:21,credenti:7,dai:[],data:[6,17,18,19,24,25,39,43],dataset:[24,25,26,42,43],definit:43,delight:[],depend:[30,31,32,42],develop:[35,37],diagramm:0,differ:15,disagg:[],disaggreg:[2,17,19],distribut:33,document:[0,1,2,16,38,41],doe:[4,10],domain:6,done:[],download:42,ecflexpart:2,ecmwf:[7,31,39,42],ecmwf_env:[7,13],ensembl:19,environ:[30,31,32],equat:21,era:43,evalu:40,exampl:[4,5,8,10,15],execut:11,faq:[33,44],featur:[36,43],field:[6,17,19],file:[3,5,6,7,8,19,21,29,43],find:24,finder:23,fix:36,flex_extract:[41,42],flexpart:[19,42],flow:15,flux:[6,17,19],forecast:19,format:5,fort:19,fortran:[1,9,19,42],frequent:33,from:[21,33],frozen:[],full:42,gatewai:[30,43],gener:[1,2,6,15,16],get_mars_data:2,grib:[19,29],gributil:2,guid:37,half:[],hint:[24,43],horizont:21,host:[],how:24,index:19,input:[18,19],instal:[2,12,30,31,32,33,42],interim:43,issu:[34,44],job:[10,13,43],jobscript:[4,10],known:[34,44],ksh:[4,10],level:25,librari:33,licenc:42,link:23,list:44,local:[15,31,43],mail:44,makefil:9,mar:[19,21,29],marsretriev:2,member:[15,25],method:[],metric:27,mix:[],mode:[14,15,22,30,31,32,43],model:25,modul:2,need:[],old:[],older:17,onlin:0,oper:43,option:[11,12],out:24,output:[19,21],overview:20,packag:33,paramet:[6,11,12,21,43],parti:33,pre:21,precip:[],precipit:[17,19],predict:19,prepar:[21,30,31,32,43],prepare_flexpart:2,program:[2,15,19,42],pure:19,python:2,question:33,quick:[23,43],registr:42,releas:36,remot:[32,43],report:44,request:[19,29],requir:[],rest:17,retriev:24,run:11,script:[4,11,12],section:6,select:43,sequenc:0,server:[],set:15,setup:12,softwar:0,some:43,specif:43,specifi:24,sphinx:0,standard:19,start:43,state:25,submiss:11,submit:[2,11],support:44,surfac:25,system:44,team:35,temp:13,templat:13,temporari:19,test:[30,31,42],testcas:29,third:33,ticket:44,time:6,todo:[43,45],tool:2,uiofil:2,updat:0,usag:[11,12],user:[6,7,15,25,26,41],using:21,veloc:21,version:17,versu:[],vertic:[6,19,21],web:31,welcom:41,what:[4,10,24,33],why:[],wind:[6,21],workflow:15}})
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