diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9a1c4c7aa0219937ffbdd02aff9494e022f84cd4
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,11 @@
+image: python:3.7-alpine
+
+pages:
+ stage: deploy
+ script:
+ - cp -r Documentation/html public
+ artifacts:
+ paths:
+ - public
+ only:
+ - master
diff --git a/Documentation/html/Documentation/Api/api_python.html b/Documentation/html/Documentation/Api/api_python.html
index ddf3bf648c45021210910aaad608241f858e1371..311ac81e9118000d01ab5e6657bde52cd506fb44 100644
--- a/Documentation/html/Documentation/Api/api_python.html
+++ b/Documentation/html/Documentation/Api/api_python.html
@@ -2492,6 +2492,28 @@ command line.</p></li>
<div class="section" id="module-tools">
<span id="tools"></span><h3><a class="toc-backref" href="#id15">tools</a><a class="headerlink" href="#module-tools" title="Permalink to this headline">¶</a></h3>
<p>This module contains a collection of diverse tasks within flex_extract.</p>
+<dl class="function">
+<dt id="tools.check_for_string_in_file">
+<code class="sig-prename descclassname">tools.</code><code class="sig-name descname">check_for_string_in_file</code><span class="sig-paren">(</span><em class="sig-param">filepath</em>, <em class="sig-param">search_string</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#check_for_string_in_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.check_for_string_in_file" title="Permalink to this definition">¶</a></dt>
+<dd><p>Search for a specific string in a file and return True if
+the string was found.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filepath</strong> (<em>str</em>) – The full file path which is to be examined.</p></li>
+<li><p><strong>search_string</strong> (<em>str</em>) – The string which is looked up for in the file.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>True : String was found
+False : String was not found</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p>Boolean</p>
+</dd>
+</dl>
+</dd></dl>
+
<dl class="function">
<dt id="tools.clean_up">
<code class="sig-prename descclassname">tools.</code><code class="sig-name descname">clean_up</code><span class="sig-paren">(</span><em class="sig-param">c</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#clean_up"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.clean_up" title="Permalink to this definition">¶</a></dt>
@@ -2735,6 +2757,21 @@ then the Python type None is returned, otherwise the string itself.</p>
</dl>
</dd></dl>
+<dl class="function">
+<dt id="tools.overwrite_lines_in_file">
+<code class="sig-prename descclassname">tools.</code><code class="sig-name descname">overwrite_lines_in_file</code><span class="sig-paren">(</span><em class="sig-param">filepath</em>, <em class="sig-param">search_string</em>, <em class="sig-param">sub_string</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#overwrite_lines_in_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.overwrite_lines_in_file" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overwrites lines which contain the given search string with the
+substitution string.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>search_string</strong> (<em>str</em>) – The string which is looked up for in the file.</p></li>
+<li><p><strong>sub_string</strong> (<em>str</em>) – The string which overwrites the search string.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
<dl class="function">
<dt id="tools.product">
<code class="sig-prename descclassname">tools.</code><code class="sig-name descname">product</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwds</em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/tools.html#product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tools.product" title="Permalink to this definition">¶</a></dt>
diff --git a/Documentation/html/Documentation/Input/setup.html b/Documentation/html/Documentation/Input/setup.html
index 044f102e9e638c1ac74ec4047173a665177102fe..0a3f215761d74543c2e7d9c3e6e087b44b9f1ea8 100644
--- a/Documentation/html/Documentation/Input/setup.html
+++ b/Documentation/html/Documentation/Input/setup.html
@@ -234,9 +234,9 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<tbody>
<tr class="row-even"><td><p>TARGET</p></td>
<td><p>String</p></td>
-<td><p>local, ecgate, cca, ccb</p></td>
+<td><p>local, syslocal, ecgate, cca, ccb</p></td>
<td><p>None</p></td>
-<td><p>Defines the flex_extract application mode to be used. Local = local mode; ecgate = Remote or Gateway mode, cca or ccb = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here.</p></td>
+<td><p>Defines the flex_extract application mode to be used. Local = local mode; ecgate = Remote or Gateway mode, cca or ccb = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here. Syslocal = seperates the executables and user application files during installation. Paths are selectable through INSTALLDIR and SYSINSTALLDIR</p></td>
</tr>
<tr class="row-odd"><td><p>MAKEFILE</p></td>
<td><p>String</p></td>
@@ -274,13 +274,19 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<td><p>$HOME on ECMWF server and current flex_extract root path on local machine</p></td>
<td><p>Root path where flex_extract should be installed. It will always be $HOME on ECMWF servers and if not set for the local mode, it will be the current flex_extract root path on local servers. </p></td>
</tr>
-<tr class="row-odd"><td><p>JOB_TEMPLATE</p></td>
+<tr class="row-odd"><td><p>SYSINSTALLDIR</p></td>
+<td><p>String</p></td>
+<td><p>a full path </p></td>
+<td><p>None</p></td>
+<td><p>This will be the same as INSTALLDIR if TARGET=local. Otherwise, the executable files are stored in this path. If it is choosen to be in a system path, don’t forget to start the script with admin rights. </p></td>
+</tr>
+<tr class="row-even"><td><p>JOB_TEMPLATE</p></td>
<td><p>String</p></td>
<td><p>installscript.template</p></td>
<td><p>installscript.template</p></td>
<td><p>The rudimentary template file to create a batch job template for submission to ECMWF servers. Should not be changed because it is already optimised for ECMWF servers. (Remote and Gateway mode)</p></td>
</tr>
-<tr class="row-even"><td><p>CONTROLFILE</p></td>
+<tr class="row-odd"><td><p>CONTROLFILE</p></td>
<td><p>String</p></td>
<td><p>any CONTROL file</p></td>
<td><p>CONTROL_EA5</p></td>
@@ -401,6 +407,7 @@ we see again all possible command line parameters.</p>
usage: install.py <span class="o">[</span>-h<span class="o">]</span> <span class="o">[</span>--target INSTALL_TARGET<span class="o">]</span> <span class="o">[</span>--makefile MAKEFILE<span class="o">]</span>
<span class="o">[</span>--ecuid ECUID<span class="o">]</span> <span class="o">[</span>--ecgid ECGID<span class="o">]</span> <span class="o">[</span>--gateway GATEWAY<span class="o">]</span>
<span class="o">[</span>--destination DESTINATION<span class="o">]</span> <span class="o">[</span>--installdir INSTALLDIR<span class="o">]</span>
+ <span class="o">[</span>--sysinstalldir SYSINSTALLDIR<span class="o">]</span>
<span class="o">[</span>--job_template JOB_TEMPLATE<span class="o">]</span> <span class="o">[</span>--controlfile CONTROLFILE<span class="o">]</span>
Install flex_extract software locally or on ECMWF machines
@@ -408,7 +415,7 @@ Install flex_extract software locally or on ECMWF machines
optional arguments:
-h, --help show this <span class="nb">help</span> message and <span class="nb">exit</span>
--target INSTALL_TARGET
- Valid targets: <span class="nb">local</span> <span class="p">|</span> ecgate <span class="p">|</span> cca , the latter two
+ Valid targets: syslocal <span class="p">|</span> <span class="nb">local</span> <span class="p">|</span> ecgate <span class="p">|</span> cca , the latter two
are at ECMWF <span class="o">(</span>default: None<span class="o">)</span>
--makefile MAKEFILE Name of makefile to compile the Fortran
code. <span class="o">(</span>default depends on <span class="sb">`</span>target<span class="sb">`</span>: <span class="nb">local</span> - makefile_local_gfortran,
@@ -422,6 +429,9 @@ optional arguments:
--installdir INSTALLDIR
Root directory where flex_extract will be installed
to. <span class="o">(</span>default: None<span class="o">)</span>
+ --sysinstalldir SYSINSTALLDIR
+ System installation path<span class="p">;</span> where executables are
+ stored. <span class="o">(</span>default: None<span class="o">)</span>
--job_template JOB_TEMPLATE
The rudimentary template file to create a batch job
template <span class="k">for</span> submission to ECMWF servers. <span class="o">(</span>default:
diff --git a/Documentation/html/Installation/local.html b/Documentation/html/Installation/local.html
index e15f365863c01a6bf3966ced27de745aa566e539..244a0d730301938b84f54b25a94fa6680b18dcec 100644
--- a/Documentation/html/Installation/local.html
+++ b/Documentation/html/Installation/local.html
@@ -103,6 +103,7 @@
<li class="toctree-l4"><a class="reference internal" href="#preparing-the-local-environment">Preparing the local environment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#testing-the-local-environment">Testing the local environment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#local-installation">Local installation</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#local-system-installation">Local system installation</a></li>
</ul>
</li>
</ul>
@@ -394,14 +395,14 @@ and then install the <code class="docutils literal notranslate"><span class="pre
<span id="ref-install-local"></span><h2>Local installation<a class="headerlink" href="#local-installation" title="Permalink to this headline">¶</a></h2>
<p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> will be compiled during the
installation process. A suitable makefile (<code class="docutils literal notranslate"><span class="pre">makefile_local_gfortran</span></code>) for the compilation is set by default.
-This may be overwritten by the <code class="docutils literal notranslate"><span class="pre">MAKEFILE</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.</p>
-<p>However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>
+This may be overwritten by the <code class="docutils literal notranslate"><span class="pre">MAKEFILE</span></code> parameter in <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code>.</p>
+<p>However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code>
For details on the makefile and how to adapt them, see <a class="reference internal" href="../Documentation/Input/fortran_makefile.html#ref-convert"><span class="std std-ref">Fortran Makefile</span></a>.</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
+<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_local.sh</span></code> script
with an editor and adapt the installation parameters in the section labelled with
“AVAILABLE COMMANDLINE ARGUMENTS TO SET” as shown below:</p>
-<div class="literal-block-wrapper docutils container" id="setup-sh">
-<div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#setup-sh" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="setup-local-sh">
+<div class="code-block-caption"><span class="caption-text">‘Example settings for a local installation.’</span><a class="headerlink" href="#setup-local-sh" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...
<span class="c1"># -----------------------------------------------------------------</span>
<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
@@ -415,6 +416,7 @@ with an editor and adapt the installation parameters in the section labelled wit
<span class="nv">GATEWAY</span><span class="o">=</span>None
<span class="nv">DESTINATION</span><span class="o">=</span>None
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
+<span class="nv">SYSINSTALLDIR</span><span class="o">=</span>None
<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">''</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
@@ -422,11 +424,11 @@ with an editor and adapt the installation parameters in the section labelled wit
</div>
</div>
<p>Afterwards, type:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup.sh
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./setup_local.sh
</pre></div>
</div>
<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>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup_local.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 <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran
Install flex_extract_v7.1 software at <span class="nb">local</span> in directory <path-to-flex_extract>/flex_extract_v7.1
@@ -445,6 +447,58 @@ lrwxrwxrwx. <span class="m">1</span> <username> tmc <span class="m">20</sp
</pre></div>
</div>
</div>
+<div class="section" id="local-system-installation">
+<h2>Local system installation<a class="headerlink" href="#local-system-installation" title="Permalink to this headline">¶</a></h2>
+<p>There is also the possibility to separate the software executables from the user application files. For doing so, the <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> parameter can be set to “syslocal” and the additional parameter <code class="docutils literal notranslate"><span class="pre">SYSINSTALLDIR</span></code> in the <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code> has to be specified. This new path will contain the Fortran and Python executables of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. If you chose to set a system path for this, please start the script as root.
+The user directory for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>, which basically consists of everything except the <code class="docutils literal notranslate"><span class="pre">Source</span></code> directory, will be installed into <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code>.
+In this installation mode, an extra (hidden) <code class="docutils literal notranslate"><span class="pre">.setup.rc</span></code> file will be generated in the <code class="docutils literal notranslate"><span class="pre">Run</span></code> directory. It contains the necessary settings for running the local system mode.</p>
+<p>Despite the change in the <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> parameter, the meaning of <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code> and the additional <code class="docutils literal notranslate"><span class="pre">SYSINSTALLDIR</span></code>, the steps for installation are the same as in the local installation mentioned above. For example, modify the <code class="docutils literal notranslate"><span class="pre">setup_local.sh</span></code> file as follows:</p>
+<div class="literal-block-wrapper docutils container" id="id1">
+<div class="code-block-caption"><span class="caption-text">‘Example settings for a local system installation.’</span><a class="headerlink" href="#id1" title="Permalink to this code">¶</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>...
+<span class="c1"># -----------------------------------------------------------------</span>
+<span class="c1"># AVAILABLE COMMANDLINE ARGUMENTS TO SET</span>
+<span class="c1">#</span>
+<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
+<span class="c1">#</span>
+<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'syslocal'</span>
+<span class="nv">MAKEFILE</span><span class="o">=</span><name_of_your_makefile>
+<span class="nv">ECUID</span><span class="o">=</span>None
+<span class="nv">ECGID</span><span class="o">=</span>None
+<span class="nv">GATEWAY</span><span class="o">=</span>None
+<span class="nv">DESTINATION</span><span class="o">=</span>None
+<span class="nv">INSTALLDIR</span><span class="o">=</span><span class="nv">$HOME</span>
+<span class="nv">SYSINSTALLDIR</span><span class="o">=</span>/usr/bin/
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">''</span>
+<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
+...
+</pre></div>
+</div>
+</div>
+<p>Afterwards, type:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ sudo ./setup_local.sh
+</pre></div>
+</div>
+<p>to start the installation. You should see the following standard output.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>Flex_extract will be installed in <<span class="nv">$HOME</span>>
+Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2
+
+Using makefile: makefile_local_gfortran
+/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./rwgrib2.f90
+/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./phgrreal.f90
+/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./grphreal.f90
+/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./ftrafo.f90
+/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./calc_etadot.f90
+/usr/local/bin/gfortran -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian -c ./posnam.f90
+/usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march<span class="o">=</span>native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp
+ln -sf calc_etadot_fast.out calc_etadot
+
+lrwxrwxrwx. <span class="m">1</span> <username> tmc <span class="m">20</span> <span class="m">27</span>. Okt <span class="m">23</span>:25 ./calc_etadot -> calc_etadot_fast.out
+SUCCESS: INSTALLATION FINISHED!
+</pre></div>
+</div>
+<p>You can now change into the user directory specified in <code class="docutils literal notranslate"><span class="pre">INSTALLDIR</span></code> and find a <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X</span></code> directory there.</p>
+</div>
</div>
diff --git a/Documentation/html/_modules/ControlFile.html b/Documentation/html/_modules/ControlFile.html
index cce975fb272c3c6ad2e3cf43da7bcc1a94ffeca7..349d7b400a83195702ab89792f1e6aff77e5f475 100644
--- a/Documentation/html/_modules/ControlFile.html
+++ b/Documentation/html/_modules/ControlFile.html
@@ -182,6 +182,8 @@
<span class="c1"># - outsourced the commandline argument assignments to control attributes</span>
<span class="c1"># June 2020 - Anne Philipp</span>
<span class="c1"># - update default makefile to None</span>
+<span class="c1"># August 2020 - Leopold Haimberger</span>
+<span class="c1"># - added a class parameter for system installation path</span>
<span class="c1">#</span>
<span class="c1"># @License:</span>
<span class="c1"># (C) Copyright 2014-2020.</span>
@@ -565,6 +567,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">flexextractdir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span>
<span class="bp">self</span><span class="o">.</span><span class="n">exedir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span>
<span class="bp">self</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makefile</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">destination</span> <span class="o">=</span> <span class="kc">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">gateway</span> <span class="o">=</span> <span class="kc">None</span>
diff --git a/Documentation/html/_modules/install.html b/Documentation/html/_modules/install.html
index 2c18a49a2efd7d92160580fa102f095fbb0d50f2..9bf89f534be34da421318ea262955f923d86969b 100644
--- a/Documentation/html/_modules/install.html
+++ b/Documentation/html/_modules/install.html
@@ -180,9 +180,14 @@
<span class="c1"># - use of tarfile package in python</span>
<span class="c1"># June 2020 - Anne Philipp</span>
<span class="c1"># - renamed "convert" functions to "fortran" functions</span>
-<span class="c1"># - reconfigured mk_tarball to select *.template files instead </span>
+<span class="c1"># - reconfigured mk_tarball to select *.template files instead</span>
<span class="c1"># of *.nl and *.temp</span>
<span class="c1"># - added check for makefile settings</span>
+<span class="c1"># August 2020 - Leopold Haimberger</span>
+<span class="c1"># - added a new installation section for system installation (if-else block)</span>
+<span class="c1"># - read new argument from command line</span>
+<span class="c1"># - write .setup.rc for a system installation into Run directory</span>
+<span class="c1"># - copy executables to system path and user files to user path</span>
<span class="c1">#</span>
<span class="c1"># @License:</span>
<span class="c1"># (C) Copyright 2014-2020.</span>
@@ -236,6 +241,7 @@
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">subprocess</span>
<span class="kn">import</span> <span class="nn">tarfile</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
<span class="kn">from</span> <span class="nn">argparse</span> <span class="kn">import</span> <span class="n">ArgumentParser</span><span class="p">,</span> <span class="n">ArgumentDefaultsHelpFormatter</span>
<span class="c1"># software specific classes and modules from flex_extract</span>
@@ -243,7 +249,8 @@
<span class="kn">from</span> <span class="nn">Classes.ControlFile</span> <span class="kn">import</span> <span class="n">ControlFile</span>
<span class="kn">from</span> <span class="nn">Classes.UioFiles</span> <span class="kn">import</span> <span class="n">UioFiles</span>
<span class="kn">from</span> <span class="nn">Mods.tools</span> <span class="kn">import</span> <span class="p">(</span><span class="n">make_dir</span><span class="p">,</span> <span class="n">put_file_to_ecserver</span><span class="p">,</span> <span class="n">submit_job_to_ecserver</span><span class="p">,</span>
- <span class="n">silent_remove</span><span class="p">,</span> <span class="n">execute_subprocess</span><span class="p">,</span> <span class="n">none_or_str</span><span class="p">)</span>
+ <span class="n">silent_remove</span><span class="p">,</span> <span class="n">execute_subprocess</span><span class="p">,</span> <span class="n">none_or_str</span><span class="p">,</span>
+ <span class="n">overwrite_lines_in_file</span><span class="p">,</span> <span class="n">check_for_string_in_file</span><span class="p">)</span>
<span class="c1"># ------------------------------------------------------------------------------</span>
<span class="c1"># FUNCTIONS</span>
@@ -264,11 +271,13 @@
<span class="n">c</span><span class="o">.</span><span class="n">assign_args_to_control</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
<span class="n">check_install_conditions</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">'local'</span><span class="p">:</span> <span class="c1"># ecgate or cca</span>
+ <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'local'</span><span class="p">,</span> <span class="s1">'syslocal'</span><span class="p">]:</span> <span class="c1"># ecgate or cca</span>
<span class="n">install_via_gateway</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span> <span class="c1"># local</span>
<span class="n">install_local</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"SUCCESS: INSTALLATION FINISHED!"</span><span class="p">)</span>
+
<span class="k">return</span></div>
<div class="viewcode-block" id="get_install_cmdline_args"><a class="viewcode-back" href="../Documentation/Api/api_python.html#install.get_install_cmdline_args">[docs]</a><span class="k">def</span> <span class="nf">get_install_cmdline_args</span><span class="p">():</span>
@@ -289,7 +298,7 @@
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--target'</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">'install_target'</span><span class="p">,</span>
<span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
- <span class="n">help</span><span class="o">=</span><span class="s2">"Valid targets: local | ecgate | cca , </span><span class="se">\</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Valid targets: syslocal | local | ecgate | cca , </span><span class="se">\</span>
<span class="s2"> the latter two are at ECMWF"</span><span class="p">)</span>
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--makefile"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"makefile"</span><span class="p">,</span>
<span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -311,8 +320,12 @@
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--installdir"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"installdir"</span><span class="p">,</span>
<span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
- <span class="n">help</span><span class="o">=</span><span class="s1">'Root directory of the '</span>
+ <span class="n">help</span><span class="o">=</span><span class="s1">'Root (user) directory of the '</span>
<span class="s1">'flex_extract installation'</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--sysinstalldir"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"sysinstalldir"</span><span class="p">,</span>
+ <span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s1">'System installation path; where '</span>
+ <span class="s1">'executables are stored.'</span><span class="p">)</span>
<span class="c1"># arguments for job submission to ECMWF, only needed by submit.py</span>
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--job_template"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s1">'job_template'</span><span class="p">,</span>
@@ -389,16 +402,24 @@
<span class="n">tar_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">,</span>
<span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">'.tar'</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">==</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">:</span>
- <span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: installdir has not been specified'</span><span class="p">)</span>
- <span class="nb">print</span><span class="p">(</span><span class="s1">'flex_extract will be installed in here by compiling the '</span> <span class="o">+</span>
- <span class="s1">'Fortran source in '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span><span class="p">)</span>
- <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span><span class="p">)</span>
- <span class="k">else</span><span class="p">:</span> <span class="c1"># creates the target working directory for flex_extract</span>
- <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expandvars</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">expanduser</span><span class="p">(</span>
- <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">))</span>
- <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">!=</span> \
- <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">):</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</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">expandvars</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">expanduser</span><span class="p">(</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)))</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</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">expandvars</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">expanduser</span><span class="p">(</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)))</span>
+
+ <span class="c1"># this is standard installation into a single directory</span>
+ <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">==</span> <span class="s1">'local'</span><span class="p">:</span>
+
+ <span class="c1"># installation into the current directory</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">==</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: installdir has not been specified'</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'flex_extract will be installed in current dir by compiling the '</span> <span class="o">+</span>
+ <span class="s1">'Fortran source in '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FORTRAN_SRC</span><span class="p">)</span>
+ <span class="c1"># installation into a different path</span>
+ <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">!=</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="p">:</span>
+
+ <span class="c1"># creates the target working directory for flex_extract</span>
<span class="n">mk_tarball</span><span class="p">(</span><span class="n">tar_file</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span><span class="p">)</span>
<span class="n">make_dir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span>
<span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span><span class="p">))</span>
@@ -409,13 +430,92 @@
<span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</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="c1"># Create Fortran executable</span>
- <span class="nb">print</span><span class="p">(</span><span class="s1">'Install '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">' software at '</span> <span class="o">+</span>
- <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">+</span> <span class="s1">' in directory '</span> <span class="o">+</span>
- <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
-
- <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)</span>
- <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span>
+ <span class="c1"># Create Fortran executable</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'Install '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">' software at '</span> <span class="o">+</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">+</span> <span class="s1">' in directory '</span> <span class="o">+</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)</span>
+ <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s1">'../../'</span><span class="p">)</span>
+ <span class="c1"># make sure that the correct calling of submit.py script is in run_local.sh</span>
+ <span class="n">overwrite_lines_in_file</span><span class="p">(</span><span class="s1">'Run/run_local.sh'</span><span class="p">,</span>
+ <span class="s1">'pyscript='</span><span class="p">,</span> <span class="s1">'pyscript=../Source/Python/submit.py</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="c1"># this is system installation were executables and user files are separated</span>
+ <span class="k">elif</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">==</span> <span class="s1">'syslocal'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">==</span> <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="p">:</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'ERROR: System installation path is equal to user '</span>
+ <span class="s1">'installation path.</span><span class="se">\n</span><span class="s1"> Please change either the system '</span>
+ <span class="s1">'installation path or use installation target "local".'</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span> <span class="o">==</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'Flex_extract will be installed in current directory!'</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span> <span class="c1"># install user part in different dir</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'Flex_extract will be installed in '</span> <span class="o">+</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="p">)</span>
+
+ <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">):</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)</span>
+
+ <span class="c1"># copy all files except Python and Fortranfiles to this dir</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">,</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span> <span class="n">symlinks</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'Source'</span><span class="p">))</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'.git'</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">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span> <span class="s1">'*~'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">:</span>
+ <span class="n">silent_remove</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+
+ <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'setup.sh'</span><span class="p">))</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'setup_local.sh'</span><span class="p">))</span>
+
+ <span class="c1"># configure run_local script correctly</span>
+ <span class="c1"># check if source of system config file is already in run_local.sh,</span>
+ <span class="c1"># if not, add it</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">check_for_string_in_file</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'Run/run_local.sh'</span><span class="p">),</span>
+ <span class="s1">'source .setup.rc'</span><span class="p">):</span>
+ <span class="n">overwrite_lines_in_file</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'Run/run_local.sh'</span><span class="p">),</span>
+ <span class="s1">'# PATH TO SUBMISSION SCRIPT'</span><span class="p">,</span>
+ <span class="s1">'# PATH TO SUBMISSION SCRIPT</span><span class="se">\n</span><span class="s1">source '</span><span class="o">+</span><span class="n">_config</span><span class="o">.</span><span class="n">FILE_SYS_CONFIG</span><span class="o">+</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+ <span class="c1"># make sure that the correct calling of submit.py script is in run_local.sh</span>
+ <span class="n">overwrite_lines_in_file</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">,</span><span class="s1">'Run/run_local.sh'</span><span class="p">),</span>
+ <span class="s1">'pyscript='</span><span class="p">,</span> <span class="s1">'pyscript=submit.py</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="c1"># change permission for file to executable</span>
+ <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">'chmod'</span><span class="p">,</span> <span class="s1">'0775'</span><span class="p">,</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">),</span><span class="s1">'Run/run_local.sh'</span><span class="p">)])</span>
+
+
+ <span class="c1"># create systemdir</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span><span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">):</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span>
+
+ <span class="c1"># create setup file for running flex_extract with system installation</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">),</span><span class="s1">'Run/.setup.rc'</span><span class="p">),</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
+ <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'#!/bin/bash </span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'export FLEXEXTRACT_USER_DIR='</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">)</span><span class="o">+</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'export PATH='</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span><span class="o">+</span><span class="s1">'/Python:$</span><span class="si">{PATH}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'export PATH='</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span><span class="o">+</span><span class="s1">':$</span><span class="si">{PATH}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="c1"># copy all Python and Fortranfiles to this dir</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_SOURCES</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span> <span class="n">symlinks</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span><span class="s1">'Fortran'</span><span class="p">))</span>
+ <span class="c1"># Create Fortran executable</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'Install '</span> <span class="o">+</span> <span class="n">_config</span><span class="o">.</span><span class="n">FLEXEXTRACT_DIRNAME</span> <span class="o">+</span> <span class="s1">' software as '</span> <span class="o">+</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">+</span> <span class="s1">' in directory '</span> <span class="o">+</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="n">del_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)</span>
+ <span class="n">mk_fortran_build</span><span class="p">(</span><span class="s1">'.'</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">)</span>
+
+ <span class="n">outfile</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</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="s1">'.'</span><span class="p">,</span><span class="s1">'*.out'</span><span class="p">)</span><span class="o">.</span><span class="n">files</span><span class="p">]</span>
+ <span class="n">test</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span><span class="s1">'calc_etadot'</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">outfile</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: Multiple executables for Fortran code are available!'</span><span class="p">)</span>
+ <span class="c1"># move executable one dir up and delete Fortran dir</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s1">'..'</span><span class="p">)</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="n">outfile</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">,</span><span class="s1">'calc_etadot'</span><span class="p">))</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">),</span><span class="s1">'Fortran'</span><span class="p">))</span>
<span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span><span class="p">)</span>
<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">tar_file</span><span class="p">):</span>
@@ -450,7 +550,7 @@
<span class="nb">print</span><span class="p">(</span><span class="s1">'use -h or --help for help'</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="ow">and</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">!=</span> <span class="s1">'local'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="ow">and</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'local'</span><span class="p">,</span> <span class="s1">'syslocal'</span><span class="p">]:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">ecgid</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">ecuid</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Please enter your ECMWF user id and group id '</span>
<span class="s1">' with command line options --ecuid --ecgid'</span><span class="p">)</span>
@@ -466,9 +566,16 @@
<span class="s1">'local gateway server possible!'</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">:</span>
<span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="s1">'$</span><span class="si">{HOME}</span><span class="s1">'</span>
- <span class="k">else</span><span class="p">:</span> <span class="c1"># local</span>
+ <span class="k">elif</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">==</span> <span class="s1">'local'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">:</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span>
+ <span class="k">elif</span> <span class="n">c</span><span class="o">.</span><span class="n">install_target</span> <span class="o">==</span> <span class="s1">'syslocal'</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">installdir</span><span class="p">:</span>
<span class="n">c</span><span class="o">.</span><span class="n">installdir</span> <span class="o">=</span> <span class="n">_config</span><span class="o">.</span><span class="n">PATH_FLEXEXTRACT_DIR</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">sysinstalldir</span><span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s1">'ERROR: System installation was selected but '</span>
+ <span class="s1">'no system installation path was defined.'</span><span class="p">)</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">makefile</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: no makefile was specified.'</span><span class="p">)</span>
@@ -484,7 +591,7 @@
<span class="nb">print</span><span class="p">(</span><span class="s1">'WARNING: default makefile selected: makefile_cray'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">pass</span>
-
+
<span class="k">return</span></div>
@@ -876,7 +983,7 @@
<span class="nb">print</span><span class="p">(</span><span class="s1">'ERROR: makefile call failed:'</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">'ls'</span><span class="p">,</span> <span class="s1">'-l'</span><span class="p">,</span>
+ <span class="n">execute_subprocess</span><span class="p">([</span><span class="s1">'ls'</span><span class="p">,</span> <span class="s1">'-l'</span><span class="p">,</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">src_path</span><span class="p">,</span> <span class="n">_config</span><span class="o">.</span><span class="n">FORTRAN_EXECUTABLE</span><span class="p">)],</span>
<span class="n">error_msg</span><span class="o">=</span><span class="s1">'FORTRAN EXECUTABLE COULD NOT BE FOUND!'</span><span class="p">)</span>
diff --git a/Documentation/html/_modules/submit.html b/Documentation/html/_modules/submit.html
index 324208d8dfd77cfe279ee46d00bc4965bb02dd34..fb196102400c95cfd1e79d6949c365e3b14d899b 100644
--- a/Documentation/html/_modules/submit.html
+++ b/Documentation/html/_modules/submit.html
@@ -275,7 +275,7 @@
<span class="c1"># send files to ECMWF server</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">submit</span><span class="p">(</span><span class="n">job_template</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">queue</span><span class="p">)</span>
- <span class="n">exit_message</span> <span class="o">=</span> <span class="s1">'FLEX_EXTRACT JOB SCRIPT IS SUBMITED!'</span>
+ <span class="n">exit_message</span> <span class="o">=</span> <span class="s1">'FLEX_EXTRACT JOB SCRIPT IS SUBMITTED!'</span>
<span class="n">normal_exit</span><span class="p">(</span><span class="n">exit_message</span><span class="p">)</span>
diff --git a/Documentation/html/_modules/tools.html b/Documentation/html/_modules/tools.html
index 2bdf28aeb91309dc578c18a61e0b781820e87a03..59a13582655472fbcdaeb3c52c607a57ff30128a 100644
--- a/Documentation/html/_modules/tools.html
+++ b/Documentation/html/_modules/tools.html
@@ -184,6 +184,10 @@
<span class="c1"># put_file_to_ecserver, submit_job_to_ecserver, get_informations,</span>
<span class="c1"># get_dimensions, execute_subprocess, none_or_int, none_or_str</span>
<span class="c1">#</span>
+<span class="c1"># August 2020 - Leopold Haimberger (University of Vienna)</span>
+<span class="c1"># - added function to check if a specific string is in a file</span>
+<span class="c1"># - added function to overwrite lines in a file which contain specific string</span>
+<span class="c1">#</span>
<span class="c1"># @License:</span>
<span class="c1"># (C) Copyright 2014-2020.</span>
<span class="c1"># Anne Philipp, Leopold Haimberger</span>
@@ -410,7 +414,7 @@
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--queue"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"queue"</span><span class="p">,</span>
<span class="nb">type</span><span class="o">=</span><span class="n">none_or_str</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">help</span><span class="o">=</span><span class="s1">'The name of the ECMWF server name where the'</span>
- <span class="s1">'job script is to be submitted '</span>
+ <span class="s1">'job script is to be submitted '</span>
<span class="s1">'(e.g. ecgate | cca | ccb)'</span><span class="p">)</span>
<span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
@@ -785,7 +789,7 @@
<div class="viewcode-block" id="make_dir"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.make_dir">[docs]</a><span class="k">def</span> <span class="nf">make_dir</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span>
<span class="sd">'''Creates a directory.</span>
-<span class="sd"> If the directory already exists, an information is printed and the creation </span>
+<span class="sd"> If the directory already exists, an information is printed and the creation</span>
<span class="sd"> skipped. The program stops only if there is another problem.</span>
<span class="sd"> Parameters</span>
@@ -1017,8 +1021,8 @@
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> cmd_list : list of str</span>
-<span class="sd"> A list of the components for the command line execution. </span>
-<span class="sd"> They will be concatenated with blank space for the command </span>
+<span class="sd"> A list of the components for the command line execution.</span>
+<span class="sd"> They will be concatenated with blank space for the command</span>
<span class="sd"> to be submitted, like ['mv', file1, file2] for mv file1 file2.</span>
<span class="sd"> Return</span>
@@ -1071,6 +1075,62 @@
<span class="k">return</span> <span class="n">start_period</span><span class="p">,</span> <span class="n">end_period</span></div>
+
+
+<div class="viewcode-block" id="check_for_string_in_file"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.check_for_string_in_file">[docs]</a><span class="k">def</span> <span class="nf">check_for_string_in_file</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">search_string</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Search for a specific string in a file and return True if</span>
+<span class="sd"> the string was found.</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filepath : str</span>
+<span class="sd"> The full file path which is to be examined.</span>
+
+<span class="sd"> search_string : str</span>
+<span class="sd"> The string which is looked up for in the file.</span>
+
+<span class="sd"> Return</span>
+<span class="sd"> ------</span>
+<span class="sd"> Boolean :</span>
+<span class="sd"> True : String was found</span>
+<span class="sd"> False : String was not found</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fio</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">search_string</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
+ <span class="k">return</span> <span class="kc">True</span>
+ <span class="k">return</span> <span class="kc">False</span></div>
+
+
+<div class="viewcode-block" id="overwrite_lines_in_file"><a class="viewcode-back" href="../Documentation/Api/api_python.html#tools.overwrite_lines_in_file">[docs]</a><span class="k">def</span> <span class="nf">overwrite_lines_in_file</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">search_string</span><span class="p">,</span> <span class="n">sub_string</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Overwrites lines which contain the given search string with the</span>
+<span class="sd"> substitution string.</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> search_string : str</span>
+<span class="sd"> The string which is looked up for in the file.</span>
+
+<span class="sd"> sub_string : str</span>
+<span class="sd"> The string which overwrites the search string.</span>
+
+<span class="sd"> Return</span>
+<span class="sd"> ------</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">fio</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fio</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">search_string</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
+ <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">sub_string</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">fio</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+
+ <span class="k">return</span></div>
+
</pre></div>
</div>
diff --git a/Documentation/html/_sources/Documentation/Input/setup.rst.txt b/Documentation/html/_sources/Documentation/Input/setup.rst.txt
index ee4469db9cd5714bf31c3a16b20a16a90e1cfcc8..3ef2879177ba5fb22698bf2898df8d1e0f822c85 100644
--- a/Documentation/html/_sources/Documentation/Input/setup.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/setup.rst.txt
@@ -164,6 +164,7 @@ we see again all possible command line parameters.
usage: install.py [-h] [--target INSTALL_TARGET] [--makefile MAKEFILE]
[--ecuid ECUID] [--ecgid ECGID] [--gateway GATEWAY]
[--destination DESTINATION] [--installdir INSTALLDIR]
+ [--sysinstalldir SYSINSTALLDIR]
[--job_template JOB_TEMPLATE] [--controlfile CONTROLFILE]
Install flex_extract software locally or on ECMWF machines
@@ -171,7 +172,7 @@ we see again all possible command line parameters.
optional arguments:
-h, --help show this help message and exit
--target INSTALL_TARGET
- Valid targets: local | ecgate | cca , the latter two
+ Valid targets: syslocal | local | ecgate | cca , the latter two
are at ECMWF (default: None)
--makefile MAKEFILE Name of makefile to compile the Fortran
code. (default depends on `target`: local - makefile_local_gfortran,
@@ -185,6 +186,9 @@ we see again all possible command line parameters.
--installdir INSTALLDIR
Root directory where flex_extract will be installed
to. (default: None)
+ --sysinstalldir SYSINSTALLDIR
+ System installation path; where executables are
+ stored. (default: None)
--job_template JOB_TEMPLATE
The rudimentary template file to create a batch job
template for submission to ECMWF servers. (default:
@@ -197,6 +201,7 @@ we see again all possible command line parameters.
+
.. toctree::
:hidden:
:maxdepth: 2
diff --git a/Documentation/html/_sources/Installation/local.rst.txt b/Documentation/html/_sources/Installation/local.rst.txt
index 879a974aa189fee86182db257e2526924a972e28..6874a05a8dc6fc1a1ba9723a51a36dedf4d785bd 100644
--- a/Documentation/html/_sources/Installation/local.rst.txt
+++ b/Documentation/html/_sources/Installation/local.rst.txt
@@ -265,20 +265,20 @@ Local installation
The Fortran program called ``calc_etadot`` will be compiled during the
installation process. A suitable makefile (``makefile_local_gfortran``) for the compilation is set by default.
-This may be overwritten by the ``MAKEFILE`` parameter in ``setup.sh``.
+This may be overwritten by the ``MAKEFILE`` parameter in ``setup_local.sh``.
-However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup.sh``
+However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup_local.sh``
For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`.
-In the root directory of ``flex_extract``, open the ``setup.sh`` script
+In the root directory of ``flex_extract``, open the ``setup_local.sh`` script
with an editor and adapt the installation parameters in the section labelled with
"AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below:
.. code-block:: bash
:caption: 'Example settings for a local installation.'
- :name: setup.sh
+ :name: setup_local.sh
...
# -----------------------------------------------------------------
@@ -293,6 +293,7 @@ with an editor and adapt the installation parameters in the section labelled wit
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
+ SYSINSTALLDIR=None
JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
@@ -302,14 +303,14 @@ Afterwards, type:
.. code-block:: bash
- $ ./setup.sh
+ $ ./setup_local.sh
to start the installation. You should see the following standard output.
.. code-block:: bash
- # Output of setup.sh
+ # Output of setup_local.sh
WARNING: installdir has not been specified
flex_extract will be installed in here by compiling the Fortran source in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran
Install flex_extract_v7.1 software at local in directory <path-to-flex_extract>/flex_extract_v7.1
@@ -326,3 +327,65 @@ to start the installation. You should see the following standard output.
lrwxrwxrwx. 1 <username> tmc 20 Aug 12 10:59 ./calc_etadot -> calc_etadot_fast.out
+
+Local system installation
+=========================
+
+There is also the possibility to separate the software executables from the user application files. For doing so, the ``TARGET`` parameter can be set to "syslocal" and the additional parameter ``SYSINSTALLDIR`` in the ``setup_local.sh`` has to be specified. This new path will contain the Fortran and Python executables of ``flex_extract``. If you chose to set a system path for this, please start the script as root.
+The user directory for ``flex_extract``, which basically consists of everything except the ``Source`` directory, will be installed into ``INSTALLDIR``.
+In this installation mode, an extra (hidden) ``.setup.rc`` file will be generated in the ``Run`` directory. It contains the necessary settings for running the local system mode.
+
+Despite the change in the ``TARGET`` parameter, the meaning of ``INSTALLDIR`` and the additional ``SYSINSTALLDIR``, the steps for installation are the same as in the local installation mentioned above. For example, modify the ``setup_local.sh`` file as follows:
+
+
+.. code-block:: bash
+ :caption: 'Example settings for a local system installation.'
+ :name: setup_local.sh
+
+ ...
+ # -----------------------------------------------------------------
+ # AVAILABLE COMMANDLINE ARGUMENTS TO SET
+ #
+ # THE USER HAS TO SPECIFY THESE PARAMETER
+ #
+ TARGET='syslocal'
+ MAKEFILE=<name_of_your_makefile>
+ ECUID=None
+ ECGID=None
+ GATEWAY=None
+ DESTINATION=None
+ INSTALLDIR=$HOME
+ SYSINSTALLDIR=/usr/bin/
+ JOB_TEMPLATE=''
+ CONTROLFILE='CONTROL_EA5'
+ ...
+
+
+Afterwards, type:
+
+.. code-block:: bash
+
+ $ sudo ./setup_local.sh
+
+to start the installation. You should see the following standard output.
+
+.. code-block:: bash
+
+ Flex_extract will be installed in <$HOME>
+ Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2
+
+ Using makefile: makefile_local_gfortran
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./rwgrib2.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./phgrreal.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./grphreal.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./ftrafo.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./calc_etadot.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./posnam.f90
+ /usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp
+ ln -sf calc_etadot_fast.out calc_etadot
+
+ lrwxrwxrwx. 1 <username> tmc 20 27. Okt 23:25 ./calc_etadot -> calc_etadot_fast.out
+ SUCCESS: INSTALLATION FINISHED!
+
+
+You can now change into the user directory specified in ``INSTALLDIR`` and find a ``flex_extract_vX.X`` directory there.
diff --git a/Documentation/html/genindex.html b/Documentation/html/genindex.html
index a6913b97eabf38674fb88c261a4fa2fda95a33a4..4f906be9f37e343e74b6eaecb253d26185ba7730 100644
--- a/Documentation/html/genindex.html
+++ b/Documentation/html/genindex.html
@@ -272,6 +272,8 @@
<li><a href="Documentation/Api/api_python.html#checks.check_dates">check_dates() (in module checks)</a>
</li>
<li><a href="Documentation/Api/api_python.html#get_mars_data.check_dates_for_nonflux_fc_times">check_dates_for_nonflux_fc_times() (in module get_mars_data)</a>
+</li>
+ <li><a href="Documentation/Api/api_python.html#tools.check_for_string_in_file">check_for_string_in_file() (in module tools)</a>
</li>
<li><a href="Documentation/Api/api_python.html#checks.check_grid">check_grid() (in module checks)</a>
</li>
@@ -649,13 +651,15 @@
</li>
<li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.omegadiff">omegadiff (ControlFile.ControlFile attribute)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.oper">oper (ControlFile.ControlFile attribute)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="Documentation/Api/api_python.html#ControlFile.ControlFile.outputdir">outputdir (ControlFile.ControlFile attribute)</a>
</li>
<li><a href="Documentation/Api/api_python.html#EcFlexpart.EcFlexpart.outputfilelist">outputfilelist (EcFlexpart.EcFlexpart attribute)</a>
+</li>
+ <li><a href="Documentation/Api/api_python.html#tools.overwrite_lines_in_file">overwrite_lines_in_file() (in module tools)</a>
</li>
</ul></td>
</tr></table>
diff --git a/Documentation/html/objects.inv b/Documentation/html/objects.inv
index 80c1a3f56a4d658d479e7aa3791ed555561e97e3..5a8b1bf520c9ff04fab4160648fc99240df41c28 100644
Binary files a/Documentation/html/objects.inv and b/Documentation/html/objects.inv differ
diff --git a/Documentation/html/searchindex.js b/Documentation/html/searchindex.js
index 4313b2f3418f857510a6c0caa0bf1eb050cc5ffb..efec657071025c0ac5750628893c5652fddad8c2 100644
--- a/Documentation/html/searchindex.js
+++ b/Documentation/html/searchindex.js
@@ -1 +1 @@
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the documentation","Auto-generated documentation for the Fortran programme","Auto-generated documentation for the Python scripts","CONTROL file changes","The compilation job script <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 for <code class=\"docutils literal notranslate\"><span class=\"pre\">calc_etadot</span></code>","The job script <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 wind","Access modes","Link collection","Hints for data set selection","Available data sets for member-state users","Available data sets for public users","Metrics","Static code analysis","Test cases","Gateway mode installation","Local mode installation","Remote mode installation","FAQ - Frequently asked questions","Known Bugs and Issues","Developer Team","Changelog","Developer Guide","Code-Level Documentation","ECMWF Data","Evaluation","Welcome to the <code class=\"docutils literal notranslate\"><span class=\"pre\">flex_extract</span></code> Documentation!","Installation","Usage","Support","ToDos"],titleterms:{"case":29,"class":2,"long":19,"new":[19,36],"public":[26,42,43],"static":28,CDS:[31,34],The:[4,5,6,9,10,11,12],accept:42,access:22,addit:[0,6,19],adjust:43,agreement:[],analysi:28,api:[31,34],applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calc_etadot:[9,19,34],calc_etadot_nml:13,calcul:21,can:[24,33],cera:43,certain:43,chang:[3,36],changelog:36,check:2,code:[28,34,38],collect:23,combin:[42,43],comparison:29,compil:4,compilejob:4,content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert:[],coordin:[],credenti:7,data:[6,17,18,19,24,25,26,34,39,43],dataset:[42,43],definit:43,depend:[30,31,32,42],destin:34,develop:[35,37],diagramm:0,differ:15,disaggreg:[2,17,19],distribut:33,document:[0,1,2,16,38,41],doe:[4,10],domain:6,download:42,eccod:34,ecflexpart:2,ecmwf:[7,31,39,42],ecmwf_env:[7,13],ensembl:19,environ:[30,31,32],equat:21,era5:34,era:43,error:34,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:[],fix:36,flex_extract:[41,42],flexpart:[19,42],flow:15,flux:[6,17,19],forecast:19,format:5,fort:19,fortran:[1,9,19,34,42],frequent:33,from:[21,33],full:42,gatewai:[30,34,43],gener:[1,2,6,15,16],get_mars_data:2,grib:[19,29],gributil:2,guid:37,hint:[24,43],horizont:21,how:24,index:19,input:[18,19],instal:[2,12,30,31,32,33,34,42],installscript:13,interim:43,issu:[34,44],job:[4,10,43],jobscript:13,known:[34,44],ksh:[4,10],level:[25,38],librari:33,licenc:42,line:0,link:23,list:44,local:[15,31,43],mail:44,makefil:9,mar:[19,21,29],marsretriev:2,member:[15,25],metric:27,mode:[14,15,22,30,31,32,43],model:25,modul:2,older:17,onlin:[],oper:43,option:[11,12],other:17,out:24,output:[19,21],overview:20,packag:33,paramet:[6,11,12,21,34,43],parti:33,pre:21,precipit:[17,19],predict:19,prepar:[21,30,31,32,43],prepare_flexpart:2,problem:34,program:[2,15,19,34,42],programm:1,proper:43,pure:[],python:2,question:33,quick:[],registr:42,releas:[34,36],remot:[32,43],report:44,request:[19,29],rest:[],retriev:[],run:11,script:[2,4,10,11,12],section:6,select:[24,43],sequenc:0,set:[15,24,25,26],setup:12,softwar:0,some:[],specif:43,specifi:[],sphinx:0,standard:19,start:[],state:25,submiss:11,submit:[2,11],submitscript:13,support:44,surfac:25,system:[31,44],team:35,temp:[],templat:13,temporari:19,test:[29,30,31,42],testcas:[],third:33,ticket:44,time:6,todo:45,tool:2,uiofil:2,updat:0,usag:[11,12,43],user:[6,7,15,25,26],using:21,veloc:21,version:17,vertic:[6,21],web:31,welcom:41,what:[4,10,24,33],wind:[6,21],workflow:15}})
\ No newline at end of file
diff --git a/For_developers/InstallationParameter.xls b/For_developers/InstallationParameter.xls
index 5a7ab0dd2d436c1fe93ee25269ed51865f8e6f8a..d60c2aa0647c33f84231d42b64c3e0bd90b336ab 100644
Binary files a/For_developers/InstallationParameter.xls and b/For_developers/InstallationParameter.xls differ
diff --git a/For_developers/Sphinx/Source/Documentation/Input/setup.rst b/For_developers/Sphinx/Source/Documentation/Input/setup.rst
index ee4469db9cd5714bf31c3a16b20a16a90e1cfcc8..3ef2879177ba5fb22698bf2898df8d1e0f822c85 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/setup.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/setup.rst
@@ -164,6 +164,7 @@ we see again all possible command line parameters.
usage: install.py [-h] [--target INSTALL_TARGET] [--makefile MAKEFILE]
[--ecuid ECUID] [--ecgid ECGID] [--gateway GATEWAY]
[--destination DESTINATION] [--installdir INSTALLDIR]
+ [--sysinstalldir SYSINSTALLDIR]
[--job_template JOB_TEMPLATE] [--controlfile CONTROLFILE]
Install flex_extract software locally or on ECMWF machines
@@ -171,7 +172,7 @@ we see again all possible command line parameters.
optional arguments:
-h, --help show this help message and exit
--target INSTALL_TARGET
- Valid targets: local | ecgate | cca , the latter two
+ Valid targets: syslocal | local | ecgate | cca , the latter two
are at ECMWF (default: None)
--makefile MAKEFILE Name of makefile to compile the Fortran
code. (default depends on `target`: local - makefile_local_gfortran,
@@ -185,6 +186,9 @@ we see again all possible command line parameters.
--installdir INSTALLDIR
Root directory where flex_extract will be installed
to. (default: None)
+ --sysinstalldir SYSINSTALLDIR
+ System installation path; where executables are
+ stored. (default: None)
--job_template JOB_TEMPLATE
The rudimentary template file to create a batch job
template for submission to ECMWF servers. (default:
@@ -197,6 +201,7 @@ we see again all possible command line parameters.
+
.. toctree::
:hidden:
:maxdepth: 2
diff --git a/For_developers/Sphinx/Source/Installation/local.rst b/For_developers/Sphinx/Source/Installation/local.rst
index 879a974aa189fee86182db257e2526924a972e28..6874a05a8dc6fc1a1ba9723a51a36dedf4d785bd 100644
--- a/For_developers/Sphinx/Source/Installation/local.rst
+++ b/For_developers/Sphinx/Source/Installation/local.rst
@@ -265,20 +265,20 @@ Local installation
The Fortran program called ``calc_etadot`` will be compiled during the
installation process. A suitable makefile (``makefile_local_gfortran``) for the compilation is set by default.
-This may be overwritten by the ``MAKEFILE`` parameter in ``setup.sh``.
+This may be overwritten by the ``MAKEFILE`` parameter in ``setup_local.sh``.
-However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup.sh``
+However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup_local.sh``
For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`.
-In the root directory of ``flex_extract``, open the ``setup.sh`` script
+In the root directory of ``flex_extract``, open the ``setup_local.sh`` script
with an editor and adapt the installation parameters in the section labelled with
"AVAILABLE COMMANDLINE ARGUMENTS TO SET" as shown below:
.. code-block:: bash
:caption: 'Example settings for a local installation.'
- :name: setup.sh
+ :name: setup_local.sh
...
# -----------------------------------------------------------------
@@ -293,6 +293,7 @@ with an editor and adapt the installation parameters in the section labelled wit
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
+ SYSINSTALLDIR=None
JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
@@ -302,14 +303,14 @@ Afterwards, type:
.. code-block:: bash
- $ ./setup.sh
+ $ ./setup_local.sh
to start the installation. You should see the following standard output.
.. code-block:: bash
- # Output of setup.sh
+ # Output of setup_local.sh
WARNING: installdir has not been specified
flex_extract will be installed in here by compiling the Fortran source in <path-to-flex_extract>/flex_extract_v7.1/Source/Fortran
Install flex_extract_v7.1 software at local in directory <path-to-flex_extract>/flex_extract_v7.1
@@ -326,3 +327,65 @@ to start the installation. You should see the following standard output.
lrwxrwxrwx. 1 <username> tmc 20 Aug 12 10:59 ./calc_etadot -> calc_etadot_fast.out
+
+Local system installation
+=========================
+
+There is also the possibility to separate the software executables from the user application files. For doing so, the ``TARGET`` parameter can be set to "syslocal" and the additional parameter ``SYSINSTALLDIR`` in the ``setup_local.sh`` has to be specified. This new path will contain the Fortran and Python executables of ``flex_extract``. If you chose to set a system path for this, please start the script as root.
+The user directory for ``flex_extract``, which basically consists of everything except the ``Source`` directory, will be installed into ``INSTALLDIR``.
+In this installation mode, an extra (hidden) ``.setup.rc`` file will be generated in the ``Run`` directory. It contains the necessary settings for running the local system mode.
+
+Despite the change in the ``TARGET`` parameter, the meaning of ``INSTALLDIR`` and the additional ``SYSINSTALLDIR``, the steps for installation are the same as in the local installation mentioned above. For example, modify the ``setup_local.sh`` file as follows:
+
+
+.. code-block:: bash
+ :caption: 'Example settings for a local system installation.'
+ :name: setup_local.sh
+
+ ...
+ # -----------------------------------------------------------------
+ # AVAILABLE COMMANDLINE ARGUMENTS TO SET
+ #
+ # THE USER HAS TO SPECIFY THESE PARAMETER
+ #
+ TARGET='syslocal'
+ MAKEFILE=<name_of_your_makefile>
+ ECUID=None
+ ECGID=None
+ GATEWAY=None
+ DESTINATION=None
+ INSTALLDIR=$HOME
+ SYSINSTALLDIR=/usr/bin/
+ JOB_TEMPLATE=''
+ CONTROLFILE='CONTROL_EA5'
+ ...
+
+
+Afterwards, type:
+
+.. code-block:: bash
+
+ $ sudo ./setup_local.sh
+
+to start the installation. You should see the following standard output.
+
+.. code-block:: bash
+
+ Flex_extract will be installed in <$HOME>
+ Install flex_extract_v7.1.2 software as syslocal in directory /usr/bin/flex_extract_v7.1.2
+
+ Using makefile: makefile_local_gfortran
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./rwgrib2.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./phgrreal.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./grphreal.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./ftrafo.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./calc_etadot.f90
+ /usr/local/bin/gfortran -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -I. -I/usr/local/include/ -fdefault-real-8 -fopenmp -fconvert=big-endian -c ./posnam.f90
+ /usr/local/bin/gfortran rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out -O3 -march=native -L/usr/local/lib64/ -leccodes_f90 -leccodes -lm -lemosR64 -fopenmp
+ ln -sf calc_etadot_fast.out calc_etadot
+
+ lrwxrwxrwx. 1 <username> tmc 20 27. Okt 23:25 ./calc_etadot -> calc_etadot_fast.out
+ SUCCESS: INSTALLATION FINISHED!
+
+
+You can now change into the user directory specified in ``INSTALLDIR`` and find a ``flex_extract_vX.X`` directory there.
diff --git a/README.md b/README.md
index 27fbaaf14450b205eebbc60bd5faa0afd177a11b..086848155008bf907b250c78462a52649a3c4d69 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
`flex_extract` is a software package to support retrieving meteorological fields from the European Centre for Medium-Range Weather Forecasts' (ECMWF) Meteorological Archival and Retrieval System (MARS) as input for the `FLEXTRA`/`FLEXPART` Atmospheric Transport Modelling system.
-`FLEXPART` (“FLEXible PARTicle dispersion model”, http://flexpart.eu) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes.
+`FLEXPART` ("FLEXible PARTicle dispersion model", http://flexpart.eu) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes.
## Installation and Usage
@@ -16,10 +16,10 @@ https://www.flexpart.eu/wiki/FpInputMetEcmwf
## Authors
-Anne Philipp, Leopold Haimberger and Petra Seibert
+Anne Tipka (formerly Philipp), Leopold Haimberger and Petra Seibert
## License
- (C) Copyright 2014-2019.
+ (C) Copyright 2014-2020.
SPDX-License-Identifier: CC-BY-4.0
@@ -27,3 +27,4 @@ Anne Philipp, Leopold Haimberger and Petra Seibert
International License. To view a copy of this license, visit
http://creativecommons.org/licenses/by/4.0/ or send a letter to
Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
+
diff --git a/Run/run_local.sh b/Run/run_local.sh
index 1c8243a585d923963812da8681dde76ab9df92c0..b1d4260c963a519bd0bc8a207ec57c8e2f28827c 100755
--- a/Run/run_local.sh
+++ b/Run/run_local.sh
@@ -11,7 +11,7 @@
# guarantee necessary parameters were set and consistent.
#
# @Licence:
-# (C) Copyright 2014-2019.
+# (C) Copyright 2014-2020.
#
# SPDX-License-Identifier: CC-BY-4.0
#
diff --git a/Source/Python/Classes/ControlFile.py b/Source/Python/Classes/ControlFile.py
index 8ffff5aa0bd248fa926ce53b9d8d75641d6f6b25..5783535188a05eb1a78a8b1ec314f72f09505f5f 100644
--- a/Source/Python/Classes/ControlFile.py
+++ b/Source/Python/Classes/ControlFile.py
@@ -20,6 +20,8 @@
# - outsourced the commandline argument assignments to control attributes
# June 2020 - Anne Philipp
# - update default makefile to None
+# August 2020 - Leopold Haimberger
+# - added a class parameter for system installation path
#
# @License:
# (C) Copyright 2014-2020.
@@ -403,6 +405,7 @@ class ControlFile(object):
self.flexextractdir = _config.PATH_FLEXEXTRACT_DIR
self.exedir = _config.PATH_FORTRAN_SRC
self.installdir = None
+ self.sysinstalldir = None
self.makefile = None
self.destination = None
self.gateway = None
diff --git a/Source/Python/Mods/tools.py b/Source/Python/Mods/tools.py
index 0286555e38617a01a78fdff51f94f6575d02ab7f..254af508229892094157d362400b77203b5f92c5 100644
--- a/Source/Python/Mods/tools.py
+++ b/Source/Python/Mods/tools.py
@@ -22,6 +22,10 @@
# put_file_to_ecserver, submit_job_to_ecserver, get_informations,
# get_dimensions, execute_subprocess, none_or_int, none_or_str
#
+# August 2020 - Leopold Haimberger (University of Vienna)
+# - added function to check if a specific string is in a file
+# - added function to overwrite lines in a file which contain specific string
+#
# @License:
# (C) Copyright 2014-2020.
# Anne Philipp, Leopold Haimberger
@@ -248,7 +252,7 @@ def get_cmdline_args():
parser.add_argument("--queue", dest="queue",
type=none_or_str, default=None,
help='The name of the ECMWF server name where the'
- 'job script is to be submitted '
+ 'job script is to be submitted '
'(e.g. ecgate | cca | ccb)')
args = parser.parse_args()
@@ -623,7 +627,7 @@ def get_list_as_string(list_obj, concatenate_sign=', '):
def make_dir(directory):
'''Creates a directory.
- If the directory already exists, an information is printed and the creation
+ If the directory already exists, an information is printed and the creation
skipped. The program stops only if there is another problem.
Parameters
@@ -855,8 +859,8 @@ def execute_subprocess(cmd_list, error_msg='SUBPROCESS FAILED!'):
Parameters
----------
cmd_list : list of str
- A list of the components for the command line execution.
- They will be concatenated with blank space for the command
+ A list of the components for the command line execution.
+ They will be concatenated with blank space for the command
to be submitted, like ['mv', file1, file2] for mv file1 file2.
Return
@@ -909,3 +913,59 @@ def generate_retrieval_period_boundary(c):
return start_period, end_period
+
+
+def check_for_string_in_file(filepath, search_string):
+ """
+ Search for a specific string in a file and return True if
+ the string was found.
+
+ Parameters
+ ----------
+ filepath : str
+ The full file path which is to be examined.
+
+ search_string : str
+ The string which is looked up for in the file.
+
+ Return
+ ------
+ Boolean :
+ True : String was found
+ False : String was not found
+ """
+ with open(filepath, 'r') as fio:
+ for line in fio:
+ if search_string in line:
+ return True
+ return False
+
+
+def overwrite_lines_in_file(filepath, search_string, sub_string):
+ """
+ Overwrites lines which contain the given search string with the
+ substitution string.
+
+ Parameters
+ ----------
+ search_string : str
+ The string which is looked up for in the file.
+
+ sub_string : str
+ The string which overwrites the search string.
+
+ Return
+ ------
+ """
+ with open(filepath, 'r') as fio:
+ data = fio.readlines()
+
+ with open(filepath, 'w') as fio:
+ for line in data:
+ if search_string in line:
+ fio.write(sub_string)
+ else:
+ fio.write(line)
+
+ return
+
diff --git a/Source/Python/_config.py b/Source/Python/_config.py
index dae1de931aac4124e1a5246dbc9c93a2663c15fa..49877e7198f8f9a82957338295b9a94bd21b2d00 100644
--- a/Source/Python/_config.py
+++ b/Source/Python/_config.py
@@ -8,6 +8,11 @@
# @Change History:
# June 2020 - Anne Philipp
# - changed template filenames to .template
+# August 2020 - Leopold Haimberger
+# - added another target for installation
+# - added filename which will contain paths for system version
+# - checks if software runs in normal local mode or system local mode
+# and defines paths to user directory and executable paths
#
# @License:
# (C) Copyright 2014-2020.
@@ -37,13 +42,13 @@ import platform
# PARAMETERS
# ------------------------------------------------------------------------------
-_VERSION_STR = '7.1.2'
+_VERSION_STR = '7.1.2_ctbto'
FLAG_ON_ECMWFSERVER = 'ecgb' in platform.node()
QUEUES_LIST = ['ecgate', 'cca', 'ccb']
-INSTALL_TARGETS = ['local', 'ecgate', 'cca', 'ccb']
+INSTALL_TARGETS = ['local', 'syslocal', 'ecgate', 'cca', 'ccb']
CDS_DATASET_ML = 'reanalysis-era5-complete'
CDS_DATASET_SFC = 'reanalysis-era5-single-levels'
@@ -69,6 +74,7 @@ TEMPFILE_NAMELIST = 'calc_etadot_nml.template'
FILE_NAMELIST = 'fort.4'
FILE_GRIB_INDEX = 'date_time_stepRange.idx'
FILE_GRIBTABLE = 'ecmwf_grib1_table_128'
+FILE_SYS_CONFIG = '.setup.rc'
# ------------------------------------------------------------------------------
# DIRECTORY NAMES
@@ -78,7 +84,7 @@ FLEXEXTRACT_DIRNAME = 'flex_extract_v' + _VERSION_STR
INPUT_DIRNAME_DEFAULT = 'Workspace'
# ------------------------------------------------------------------------------
-# PATHES
+# LOAD ENVIRONMENT VARIABLES FOR SYS VERSION; IF NECESSARRY
# ------------------------------------------------------------------------------
# path to the local python source files
@@ -88,15 +94,33 @@ PATH_LOCAL_PYTHON = os.path.dirname(os.path.abspath(
# add path to pythonpath
if PATH_LOCAL_PYTHON not in sys.path:
sys.path.append(PATH_LOCAL_PYTHON)
+
+# ------------------------------------------------------------------------------
+# PATHES
+# ------------------------------------------------------------------------------
+
PATH_FLEXEXTRACT_DIR = os.path.normpath(os.path.dirname(os.path.abspath(
inspect.getfile(inspect.currentframe()))) + '/../../')
+if not os.path.isdir(os.path.join(PATH_FLEXEXTRACT_DIR,'Run')):
+ # if it does not exist, we have a system installation in place
+ # we need to have a sys and user path
+ # configure correct system path
+ PATH_SYSTEM_DIR = os.path.join(PATH_FLEXEXTRACT_DIR, FLEXEXTRACT_DIRNAME)
+ # configure correct user path
+ PATH_FLEXEXTRACT_DIR = os.environ.get('FLEXEXTRACT_USER_DIR')
+else:
+ PATH_SYSTEM_DIR = PATH_FLEXEXTRACT_DIR
+
PATH_RUN_DIR = os.path.join(PATH_FLEXEXTRACT_DIR, 'Run')
-PATH_SOURCES = os.path.join(PATH_FLEXEXTRACT_DIR, 'Source')
+PATH_SOURCES = os.path.join(PATH_SYSTEM_DIR, 'Source')
PATH_TEMPLATES = os.path.join(PATH_FLEXEXTRACT_DIR, 'Templates')
PATH_ECMWF_ENV = os.path.join(PATH_RUN_DIR, FILE_USER_ENVVARS)
PATH_GRIBTABLE = os.path.join(PATH_TEMPLATES, FILE_GRIBTABLE)
PATH_JOBSCRIPTS = os.path.join(PATH_RUN_DIR, 'Jobscripts')
-PATH_FORTRAN_SRC = os.path.join(PATH_SOURCES, 'Fortran')
+if os.path.isdir(os.path.join(PATH_SYSTEM_DIR,'Fortran')):
+ PATH_FORTRAN_SRC = PATH_SYSTEM_DIR
+else:
+ PATH_FORTRAN_SRC = os.path.join(PATH_SOURCES, 'Fortran')
PATH_PYTHONTEST_SRC = os.path.join(PATH_SOURCES, 'Pythontest')
PATH_INPUT_DIR = os.path.join(PATH_RUN_DIR, INPUT_DIRNAME_DEFAULT)
PATH_TEST = os.path.join(PATH_FLEXEXTRACT_DIR, 'Testing')
diff --git a/Source/Python/install.py b/Source/Python/install.py
index 18170696c177e116c3b5028a8976f8d40e082c72..0488ee0cbcc046d0f3faf39b2bb561e82467c586 100755
--- a/Source/Python/install.py
+++ b/Source/Python/install.py
@@ -18,9 +18,14 @@
# - use of tarfile package in python
# June 2020 - Anne Philipp
# - renamed "convert" functions to "fortran" functions
-# - reconfigured mk_tarball to select *.template files instead
+# - reconfigured mk_tarball to select *.template files instead
# of *.nl and *.temp
# - added check for makefile settings
+# August 2020 - Leopold Haimberger
+# - added a new installation section for system installation (if-else block)
+# - read new argument from command line
+# - write .setup.rc for a system installation into Run directory
+# - copy executables to system path and user files to user path
#
# @License:
# (C) Copyright 2014-2020.
@@ -74,6 +79,7 @@ import os
import sys
import subprocess
import tarfile
+import shutil
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
# software specific classes and modules from flex_extract
@@ -81,7 +87,8 @@ import _config
from Classes.ControlFile import ControlFile
from Classes.UioFiles import UioFiles
from Mods.tools import (make_dir, put_file_to_ecserver, submit_job_to_ecserver,
- silent_remove, execute_subprocess, none_or_str)
+ silent_remove, execute_subprocess, none_or_str,
+ overwrite_lines_in_file, check_for_string_in_file)
# ------------------------------------------------------------------------------
# FUNCTIONS
@@ -102,11 +109,13 @@ def main():
c.assign_args_to_control(args)
check_install_conditions(c)
- if c.install_target.lower() != 'local': # ecgate or cca
+ if c.install_target.lower() not in ['local', 'syslocal']: # ecgate or cca
install_via_gateway(c)
else: # local
install_local(c)
+ print("SUCCESS: INSTALLATION FINISHED!")
+
return
def get_install_cmdline_args():
@@ -127,7 +136,7 @@ def get_install_cmdline_args():
parser.add_argument('--target', dest='install_target',
type=none_or_str, default=None,
- help="Valid targets: local | ecgate | cca , \
+ help="Valid targets: syslocal | local | ecgate | cca , \
the latter two are at ECMWF")
parser.add_argument("--makefile", dest="makefile",
type=none_or_str, default=None,
@@ -149,8 +158,12 @@ def get_install_cmdline_args():
parser.add_argument("--installdir", dest="installdir",
type=none_or_str, default=None,
- help='Root directory of the '
+ help='Root (user) directory of the '
'flex_extract installation')
+ parser.add_argument("--sysinstalldir", dest="sysinstalldir",
+ type=none_or_str, default=None,
+ help='System installation path; where '
+ 'executables are stored.')
# arguments for job submission to ECMWF, only needed by submit.py
parser.add_argument("--job_template", dest='job_template',
@@ -227,16 +240,24 @@ def install_local(c):
tar_file = os.path.join(_config.PATH_FLEXEXTRACT_DIR,
_config.FLEXEXTRACT_DIRNAME + '.tar')
- if c.installdir == _config.PATH_FLEXEXTRACT_DIR:
- print('WARNING: installdir has not been specified')
- print('flex_extract will be installed in here by compiling the ' +
- 'Fortran source in ' + _config.PATH_FORTRAN_SRC)
- os.chdir(_config.PATH_FORTRAN_SRC)
- else: # creates the target working directory for flex_extract
- c.installdir = os.path.expandvars(os.path.expanduser(
- c.installdir))
- if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) != \
- os.path.abspath(c.installdir):
+ c.installdir = os.path.abspath(os.path.expandvars(os.path.expanduser(
+ c.installdir)))
+ c.sysinstalldir = os.path.abspath(os.path.expandvars(os.path.expanduser(
+ c.sysinstalldir)))
+
+ # this is standard installation into a single directory
+ if c.install_target == 'local':
+
+ # installation into the current directory
+ if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.installdir:
+ print('WARNING: installdir has not been specified')
+ print('flex_extract will be installed in current dir by compiling the ' +
+ 'Fortran source in ' + _config.PATH_FORTRAN_SRC)
+ os.chdir(_config.PATH_FORTRAN_SRC)
+ # installation into a different path
+ elif os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) != c.installdir :
+
+ # creates the target working directory for flex_extract
mk_tarball(tar_file, c.install_target)
make_dir(os.path.join(c.installdir,
_config.FLEXEXTRACT_DIRNAME))
@@ -247,13 +268,92 @@ def install_local(c):
_config.FLEXEXTRACT_DIRNAME,
_config.PATH_REL_FORTRAN_SRC))
- # Create Fortran executable
- print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software at ' +
- c.install_target + ' in directory ' +
- os.path.abspath(c.installdir) + '\n')
-
- del_fortran_build('.')
- mk_fortran_build('.', c.makefile)
+ # Create Fortran executable
+ print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software at ' +
+ c.install_target + ' in directory ' + c.installdir + '\n')
+
+ del_fortran_build('.')
+ mk_fortran_build('.', c.makefile)
+ os.chdir('../../')
+ # make sure that the correct calling of submit.py script is in run_local.sh
+ overwrite_lines_in_file('Run/run_local.sh',
+ 'pyscript=', 'pyscript=../Source/Python/submit.py\n')
+
+ # this is system installation were executables and user files are separated
+ elif c.install_target == 'syslocal':
+ if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.sysinstalldir :
+ sys.exit('ERROR: System installation path is equal to user '
+ 'installation path.\n Please change either the system '
+ 'installation path or use installation target "local".')
+ if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) == c.installdir :
+ print('Flex_extract will be installed in current directory!')
+ else: # install user part in different dir
+ print('Flex_extract will be installed in ' + c.installdir )
+
+ c.installdir = os.path.join(c.installdir,_config.FLEXEXTRACT_DIRNAME)
+ if os.path.isdir(c.installdir):
+ shutil.rmtree(c.installdir)
+
+ # copy all files except Python and Fortranfiles to this dir
+ shutil.copytree(_config.PATH_FLEXEXTRACT_DIR,
+ c.installdir, symlinks=True)
+ shutil.rmtree(os.path.join(c.installdir,'Source'))
+ shutil.rmtree(os.path.join(c.installdir,'.git'))
+ for x in UioFiles(c.installdir, '*~').files:
+ silent_remove(x)
+
+ os.remove(os.path.join(c.installdir,'setup.sh'))
+ os.remove(os.path.join(c.installdir,'setup_local.sh'))
+
+ # configure run_local script correctly
+ # check if source of system config file is already in run_local.sh,
+ # if not, add it
+ if not check_for_string_in_file(os.path.join(c.installdir,'Run/run_local.sh'),
+ 'source .setup.rc'):
+ overwrite_lines_in_file(os.path.join(c.installdir,'Run/run_local.sh'),
+ '# PATH TO SUBMISSION SCRIPT',
+ '# PATH TO SUBMISSION SCRIPT\nsource '+_config.FILE_SYS_CONFIG+'\n')
+ # make sure that the correct calling of submit.py script is in run_local.sh
+ overwrite_lines_in_file(os.path.join(c.installdir,'Run/run_local.sh'),
+ 'pyscript=', 'pyscript=submit.py\n')
+
+ # change permission for file to executable
+ execute_subprocess(['chmod', '0775',
+ os.path.join(os.path.abspath(c.installdir),'Run/run_local.sh')])
+
+
+ # create systemdir
+ c.sysinstalldir = os.path.join(c.sysinstalldir,_config.FLEXEXTRACT_DIRNAME)
+ if os.path.isdir(c.sysinstalldir):
+ shutil.rmtree(c.sysinstalldir)
+
+ # create setup file for running flex_extract with system installation
+ with open(os.path.join(os.path.abspath(c.installdir),'Run/.setup.rc'),'w') as fio:
+ fio.write('#!/bin/bash \n')
+ fio.write('export FLEXEXTRACT_USER_DIR='+os.path.abspath(c.installdir)+'\n')
+ fio.write('export PATH='+os.path.abspath(c.sysinstalldir)+'/Python:${PATH}\n')
+ fio.write('export PATH='+os.path.abspath(c.sysinstalldir)+':${PATH}\n')
+
+ # copy all Python and Fortranfiles to this dir
+ shutil.copytree(_config.PATH_SOURCES, c.sysinstalldir, symlinks=True)
+
+ os.chdir(os.path.join(c.sysinstalldir,'Fortran'))
+ # Create Fortran executable
+ print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software as ' +
+ c.install_target + ' in directory ' +
+ os.path.abspath(c.sysinstalldir) + '\n')
+
+ del_fortran_build('.')
+ mk_fortran_build('.', c.makefile)
+
+ outfile = [x for x in UioFiles('.','*.out').files]
+ test=os.path.join(c.sysinstalldir,'calc_etadot')
+ if len(outfile) != 1:
+ print('WARNING: Multiple executables for Fortran code are available!')
+ # move executable one dir up and delete Fortran dir
+ os.chdir('..')
+ shutil.move(outfile[0], os.path.join(c.sysinstalldir,'calc_etadot'))
+ shutil.rmtree(os.path.join(os.path.abspath(c.sysinstalldir),'Fortran'))
os.chdir(_config.PATH_FLEXEXTRACT_DIR)
if os.path.isfile(tar_file):
@@ -288,7 +388,7 @@ def check_install_conditions(c):
print('use -h or --help for help')
sys.exit(1)
- if c.install_target and c.install_target != 'local':
+ if c.install_target and c.install_target not in ['local', 'syslocal']:
if not c.ecgid or not c.ecuid:
print('Please enter your ECMWF user id and group id '
' with command line options --ecuid --ecgid')
@@ -304,9 +404,16 @@ def check_install_conditions(c):
'local gateway server possible!')
if not c.installdir:
c.installdir = '${HOME}'
- else: # local
+ elif c.install_target == 'local':
if not c.installdir:
c.installdir = _config.PATH_FLEXEXTRACT_DIR
+ elif c.install_target == 'syslocal':
+ if not c.installdir:
+ c.installdir = _config.PATH_FLEXEXTRACT_DIR
+ if not c.sysinstalldir:
+ print('ERROR: System installation was selected but '
+ 'no system installation path was defined.')
+ sys.exit()
if not c.makefile:
print('WARNING: no makefile was specified.')
@@ -322,7 +429,7 @@ def check_install_conditions(c):
print('WARNING: default makefile selected: makefile_cray')
else:
pass
-
+
return
@@ -714,7 +821,7 @@ def mk_fortran_build(src_path, makefile):
print('ERROR: makefile call failed:')
print(e)
else:
- execute_subprocess(['ls', '-l',
+ execute_subprocess(['ls', '-l',
os.path.join(src_path, _config.FORTRAN_EXECUTABLE)],
error_msg='FORTRAN EXECUTABLE COULD NOT BE FOUND!')
diff --git a/Source/Python/submit.py b/Source/Python/submit.py
index 5265a433cc79c51f0363b46159df3839bbcaab8e..6d5eb8b6d2dded1a25bb3cbd6fcaf3bd703af0b2 100755
--- a/Source/Python/submit.py
+++ b/Source/Python/submit.py
@@ -113,7 +113,7 @@ def main():
# send files to ECMWF server
else:
submit(job_template, c, queue)
- exit_message = 'FLEX_EXTRACT JOB SCRIPT IS SUBMITED!'
+ exit_message = 'FLEX_EXTRACT JOB SCRIPT IS SUBMITTED!'
normal_exit(exit_message)
diff --git a/setup_local.sh b/setup_local.sh
index 8f9d0a2f020ec222c266792cee2a3ad26a8498c2..776e482a5a9ff51739bcba5ef07ac06e6725d76b 100755
--- a/setup_local.sh
+++ b/setup_local.sh
@@ -10,6 +10,11 @@
# python installation script. It also does some checks to
# guarantee necessary parameters were set.
#
+# @History:
+# Leopold Haimberger; Aug 2020
+# added new parameter for a system installation
+# (seperate executable and user directories)
+#
# @Licence:
# (C) Copyright 2014-2020.
#
@@ -32,6 +37,7 @@ ECGID='<groupID>'
GATEWAY='<gatewayname>'
DESTINATION='<name>@genericSftp'
INSTALLDIR=None
+SYSINSTALLDIR=None
JOB_TEMPLATE=''
CONTROLFILE='CONTROL_CERA'
# -----------------------------------------------------------------
@@ -75,8 +81,11 @@ fi
if [ -n "$MAKEFILE" ]; then
parameterlist+=" --makefile=$MAKEFILE"
fi
-if [ -n "$FLEXPARTDIR" ]; then # not empty
- parameterlist+=" --flexpartdir=$FLEXPARTDIR"
+if [ -n "$INSTALLDIR" ]; then
+ parameterlist+=" --installdir=$INSTALLDIR"
+fi
+if [ -n "$SYSINSTALLDIR" ]; then
+ parameterlist+=" --sysinstalldir=$SYSINSTALLDIR"
fi
if [ -n "$JOB_TEMPLATE" ]; then
parameterlist+=" --job_template=$JOB_TEMPLATE"
@@ -90,3 +99,5 @@ fi
$script $parameterlist
+
+