Changeset b1674ed in flex_extract.git for Documentation/html/Installation/local.html


Ignore:
Timestamp:
Apr 1, 2020, 5:03:13 PM (4 years ago)
Author:
Anne Philipp <anne.philipp@…>
Branches:
master, ctbto, dev
Children:
d78851d, e0005c9
Parents:
50f9ca6
Message:

updated online documentation FIX for tickets #265 and #262

File:
1 edited

Legend:

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  • Documentation/html/Installation/local.html

    rd720895 rb1674ed  
    2222   
    2323      <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
    24         <script type="text/javascript" src="../_static/jquery.js"></script>
    25         <script type="text/javascript" src="../_static/underscore.js"></script>
    26         <script type="text/javascript" src="../_static/doctools.js"></script>
    27         <script type="text/javascript" src="../_static/language_data.js"></script>
    28         <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
     24        <script src="../_static/jquery.js"></script>
     25        <script src="../_static/underscore.js"></script>
     26        <script src="../_static/doctools.js"></script>
     27        <script src="../_static/language_data.js"></script>
     28        <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
    2929   
    3030    <script type="text/javascript" src="../_static/js/theme.js"></script>
    … …  
    195195<p>The environment on your local system has to provide these software packages
    196196and libraries, since the preparation of the extraction and the post-processing is done on the local machine:</p>
    197 <table border="1" class="docutils">
     197<table class="docutils align-default">
    198198<colgroup>
    199 <col width="74%" />
    200 <col width="26%" />
     199<col style="width: 74%" />
     200<col style="width: 26%" />
    201201</colgroup>
    202 <tbody valign="top">
    203 <tr class="row-odd"><td>Python part</td>
    204 <td>Fortran part</td>
     202<tbody>
     203<tr class="row-odd"><td><p>Python part</p></td>
     204<td><p>Fortran part</p></td>
    205205</tr>
    206 <tr class="row-even"><td><ul class="first last simple">
    207 <li><a class="reference external" href="https://www.python.org/downloads/">Python3</a></li>
    208 <li><a class="reference external" href="http://www.numpy.org/">numpy</a></li>
    209 <li><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></li>
    210 <li><a class="reference external" href="https://packages.debian.org/sid/python3-eccodes">eccodes for python</a></li>
    211 <li><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ecmwf-api-client</a> (everything except ERA5)</li>
    212 <li><a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> (just for ERA5)</li>
     206<tr class="row-even"><td><ul class="simple">
     207<li><p><a class="reference external" href="https://www.python.org/downloads/">Python3</a></p></li>
     208<li><p><a class="reference external" href="http://www.numpy.org/">numpy</a></p></li>
     209<li><p><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></p></li>
     210<li><p><a class="reference external" href="https://packages.debian.org/sid/python3-eccodes">eccodes for python</a></p></li>
     211<li><p><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ecmwf-api-client</a> (everything except ERA5)</p></li>
     212<li><p><a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> (just for ERA5 and member user)</p></li>
    213213</ul>
    214214</td>
    215 <td><ul class="first last simple">
    216 <li><a class="reference external" href="https://gcc.gnu.org/wiki/GFortran">gfortran</a></li>
    217 <li><a class="reference external" href="http://www.fftw.org">fftw3</a></li>
    218 <li><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">eccodes</a></li>
    219 <li><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">emoslib</a></li>
     215<td><ul class="simple">
     216<li><p><a class="reference external" href="https://gcc.gnu.org/wiki/GFortran">gfortran</a></p></li>
     217<li><p><a class="reference external" href="http://www.fftw.org">fftw3</a></p></li>
     218<li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/ECC">eccodes</a></p></li>
     219<li><p><a class="reference external" href="https://software.ecmwf.int/wiki/display/EMOS/Emoslib">emoslib</a></p></li>
    220220</ul>
    221221</td>
    … …  
    248248</div>
    249249<div class="admonition note">
    250 <p class="first admonition-title">Note</p>
     250<p class="admonition-title">Note</p>
    251251<p>In case you would like to use Anaconda Python we recommend you follow the installation instructions of
    252252<a class="reference external" href="https://docs.anaconda.com/anaconda/install/linux/">Anaconda Python Installation for Linux</a> and then install the
    253253<code class="docutils literal notranslate"><span class="pre">eccodes</span></code> package from <code class="docutils literal notranslate"><span class="pre">conda</span></code> with:</p>
    254 <div class="last highlight-bash notranslate"><div class="highlight"><pre><span></span>conda install conda-forge::python-eccodes
     254<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda install conda-forge::python-eccodes
    255255</pre></div>
    256256</div>
    … …  
    258258<p>The CDS API (cdsapi) is required for ERA5 data and the ECMWF Web API (ecmwf-api-client) for all other public datasets.</p>
    259259<div class="admonition note">
    260 <p class="first admonition-title">Note</p>
    261 <p class="last">Since <strong>public users</strong> currently don’t have access to the full <em>ERA5</em> dataset they can skip the installation of the <code class="docutils literal notranslate"><span class="pre">CDS</span> <span class="pre">API</span></code>.</p>
     260<p class="admonition-title">Note</p>
     261<p>Since <strong>public users</strong> currently don’t have access to the full <em>ERA5</em> dataset they can skip the installation of the <code class="docutils literal notranslate"><span class="pre">CDS</span> <span class="pre">API</span></code>.</p>
    262262</div>
    263263<p>Both user groups have to provide keys with their credentials for the Web API’s in their home directory. Therefore, follow these instructions:</p>
    264 <dl class="docutils">
    265 <dt>ECMWF Web API:</dt>
    266 <dd>Go to <a class="reference external" href="https://confluence.ecmwf.int//display/WEBAPI/Access+MARS">MARS access</a> website and log in with your credentials. Afterwards, on this site in section “Install ECMWF KEY” the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file <cite>.ecmwfapirc</cite> in your home directory).</dd>
    267 <dt>CDS API:</dt>
    268 <dd>Go to ‘CDS API registration’_ and register there too. Log in at the <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> website and follow the instructions at section “Install the CDS API key” to save your credentials in a <cite>.cdsapirc</cite> file.</dd>
     264<dl class="simple">
     265<dt>ECMWF Web API:</dt><dd><p>Go to <a class="reference external" href="https://confluence.ecmwf.int//display/WEBAPI/Access+MARS">MARS access</a> website and log in with your credentials. Afterwards, on this site in section “Install ECMWF KEY” the key for the ECMWF Web API should be listed. Please follow the instructions in this section under 1 (save the key in a file <cite>.ecmwfapirc</cite> in your home directory).</p>
     266</dd>
     267<dt>CDS API:</dt><dd><p>Go to <a class="reference external" href="https://cds.climate.copernicus.eu/user/register">CDS API registration</a> and register there too. Log in at the <a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> website and follow the instructions at section “Install the CDS API key” to save your credentials in a <cite>.cdsapirc</cite> file.</p>
     268</dd>
    269269</dl>
    270270</div>
    … …  
    285285<div class="section" id="ecmwf-web-api">
    286286<h4>ECMWF Web API<a class="headerlink" href="#ecmwf-web-api" title="Permalink to this headline">¶</a></h4>
    287 <table border="1" class="docutils">
     287<table class="docutils align-default">
    288288<colgroup>
    289 <col width="50%" />
    290 <col width="50%" />
     289<col style="width: 50%" />
     290<col style="width: 50%" />
    291291</colgroup>
    292 <tbody valign="top">
    293 <tr class="row-odd"><td>Please use this piece of Python code for <strong>Member user</strong>:</td>
    294 <td>Please use this piece of Python code for <strong>Public user</strong>:</td>
     292<tbody>
     293<tr class="row-odd"><td><p>Please use this piece of Python code for <strong>Member user</strong>:</p></td>
     294<td><p>Please use this piece of Python code for <strong>Public user</strong>:</p></td>
    295295</tr>
    296 <tr class="row-even"><td><div class="first last highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ecmwfapi</span> <span class="kn">import</span> <span class="n">ECMWFService</span>
     296<tr class="row-even"><td><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ecmwfapi</span> <span class="kn">import</span> <span class="n">ECMWFService</span>
    297297
    298298<span class="n">server</span> <span class="o">=</span> <span class="n">ECMWFService</span><span class="p">(</span><span class="s1">&#39;mars&#39;</span><span class="p">)</span>
    … …  
    314314</div>
    315315</td>
    316 <td><div class="first last highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ecmwfapi</span> <span class="kn">import</span> <span class="n">ECMWFDataServer</span>
     316<td><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ecmwfapi</span> <span class="kn">import</span> <span class="n">ECMWFDataServer</span>
    317317
    318318<span class="n">server</span> <span class="o">=</span> <span class="n">ECMWFDataServer</span><span class="p">()</span>
    … …  
    389389<div class="section" id="local-installation">
    390390<span id="ref-install-local"></span><h2>Local installation<a class="headerlink" href="#local-installation" title="Permalink to this headline">¶</a></h2>
    391 <p>First prepare the Fortran <code class="docutils literal notranslate"><span class="pre">makefile</span></code> for your environment and set it in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script. (See section <span class="xref std std-ref">ref-convert</span> for information on the Fortran program.)
    392 <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> comes with two <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> prepared for the <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> and
    393 the <code class="docutils literal notranslate"><span class="pre">ifort</span></code> compiler. The <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> version assumes that <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> and <code class="docutils literal notranslate"><span class="pre">emoslib</span></code> are installed as distribution packages.</p>
    394 <blockquote>
    395 <div><ul class="simple">
    396 <li>makefile.local.gfortran</li>
    397 <li>makefile.local.ifort</li>
    398 </ul>
    399 </div></blockquote>
    400 <p>They can be found at <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Fortran</span></code>, where
    401 <code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted with the current version number.</p>
     391<p>First prepare the Fortran <code class="docutils literal notranslate"><span class="pre">makefile</span></code> for your environment and set it in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script. (See section <a class="reference internal" href="../Documentation/Input/fortran_makefile.html#ref-convert"><span class="std std-ref">Fortran Makefile</span></a> for more information.)
     392<code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> comes with two <code class="docutils literal notranslate"><span class="pre">makefiles</span></code> prepared for the <code class="docutils literal notranslate"><span class="pre">gfortran</span></code> compiler. One for the normal use <code class="docutils literal notranslate"><span class="pre">makefile_fast</span></code> and one for debugging <code class="docutils literal notranslate"><span class="pre">makefile_debug</span></code> which is usually only resonable for developers.</p>
     393<p>They assume that <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> and <code class="docutils literal notranslate"><span class="pre">emoslib</span></code> are installed as distribution packages and can be found at <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Source/Fortran</span></code>, where <code class="docutils literal notranslate"><span class="pre">vX.X</span></code> should be substituted with the current version number.</p>
    402394<div class="admonition caution">
    403 <p class="first admonition-title">Caution</p>
    404 <p class="last">It is necessary to adapt <strong>ECCODES_INCLUDE_DIR</strong> and <strong>ECCODES_LIB</strong> in these
     395<p class="admonition-title">Caution</p>
     396<p>It is necessary to adapt <strong>ECCODES_INCLUDE_DIR</strong> and <strong>ECCODES_LIB</strong> in these
    405397<code class="docutils literal notranslate"><span class="pre">makefiles</span></code> if other than standard paths are used.</p>
    406398</div>
    … …  
    409401choice to modify with an editor of your choice. We use the <code class="docutils literal notranslate"><span class="pre">nedit</span></code> in this case.</p>
    410402<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> flex_extract_vX.X/Source/Fortran
    411 nedit makefile.local.gfortran
     403nedit makefile_fast
    412404</pre></div>
    413405</div>
    414406<p>Edit the paths to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library on your local machine.</p>
    415407<div class="admonition caution">
    416 <p class="first admonition-title">Caution</p>
     408<p class="admonition-title">Caution</p>
    417409<p>This can vary from system to system.
    418410It is suggested to use a command like</p>
    … …  
    423415</pre></div>
    424416</div>
    425 <p class="last">to find out the path to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library.</p>
     417<p>to find out the path to the <code class="docutils literal notranslate"><span class="pre">eccodes</span></code> library.</p>
    426418</div>
    427419<p>Substitute these paths in the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> for parameters <strong>ECCODES_INCLUDE_DIR</strong>
    … …  
    432424</pre></div>
    433425</div>
    434 <p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code> will be compiled during the
     426<p>The Fortran program called <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> will be compiled during the
    435427installation process.Therefore the name of the <code class="docutils literal notranslate"><span class="pre">makefile</span></code> to be used needs to be given in  <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>.</p>
    436428<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
    … …  
    446438<span class="c1">#</span>
    447439<span class="nv">TARGET</span><span class="o">=</span><span class="s1">&#39;local&#39;</span>
    448 <span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">&#39;makefile.local.gfortran&#39;</span>
     440<span class="nv">MAKEFILE</span><span class="o">=</span><span class="s1">&#39;makefile_fast&#39;</span>
    449441<span class="nv">ECUID</span><span class="o">=</span>None
    450442<span class="nv">ECGID</span><span class="o">=</span>None
    … …  
    464456<p>to start the installation. You should see the following standard output.</p>
    465457<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
    466 WARNING: installdir has not been specified
    467 flex_extract will be installed in here by compiling the Fortran <span class="nb">source</span> in /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/source/fortran
    468 Install flex_extract_v7.1 software at <span class="nb">local</span> in directory /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1
    469 
    470 Using makefile: Makefile.local.gfortran
    471 gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -c -g -O3 -fopenmp phgrreal.f
    472 gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -c -g -O3 -fopenmp grphreal.f
    473 gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -c -g -O3 -fopenmp ftrafo.f
    474 gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 rwGRIB2.f90
    475 gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 posnam.f
    476 gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -c -O3 -fopenmp -I. -I/usr/local/gcc-4.9.3/grib_api-1.14.3/include -O3 preconvert.f90
    477 gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -O3 -O3 -fopenmp -o ./CONVERT2 ftrafo.o phgrreal.o grphreal.o rwGRIB2.o posnam.o preconvert.o -L/usr/local/gcc-4.9.3/grib_api-1.14.3/lib -Bstatic  -lgrib_api_f77 -lgrib_api_f90 -lgrib_api -Bdynamic  -lm  -ljasper -lemosR64
    478 
    479 -rwxrwxr-x. <span class="m">1</span> philipa8 tmc <span class="m">282992</span> May <span class="m">23</span> <span class="m">22</span>:27 ./CONVERT2
     458    WARNING: installdir has not been specified
     459    flex_extract will be installed in here by compiling the Fortran <span class="nb">source</span> in &lt;path-to-flex_extract&gt;/flex_extract_v7.1/Source/Fortran
     460    Install flex_extract_v7.1 software at <span class="nb">local</span> in directory &lt;path-to-flex_extract&gt;/flex_extract_v7.1
     461
     462    Using makefile: makefile_fast
     463    gfortran   -O3 -march<span class="o">=</span>native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian   -c     ./rwgrib2.f90
     464    gfortran   -O3 -march<span class="o">=</span>native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian   -c     ./phgrreal.f90
     465    gfortran   -O3 -march<span class="o">=</span>native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian   -c     ./grphreal.f90
     466    gfortran   -O3 -march<span class="o">=</span>native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian   -c     ./ftrafo.f90
     467    gfortran   -O3 -march<span class="o">=</span>native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian   -c     ./calc_etadot.f90
     468    gfortran   -O3 -march<span class="o">=</span>native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert<span class="o">=</span>big-endian   -c     ./posnam.f90
     469    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 -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -fopenmp
     470    ln -sf calc_etadot_fast.out calc_etadot
     471
     472    lrwxrwxrwx. <span class="m">1</span> &lt;username&gt; tmc <span class="m">20</span> <span class="m">15</span>. Mär <span class="m">13</span>:31 ./calc_etadot -&gt; calc_etadot_fast.out
    480473</pre></div>
    481474</div>
    … …  
    503496  <div role="contentinfo">
    504497    <p>
    505         &copy; Copyright 2019, Anne Philipp and Leopold Haimberger
     498        &copy; Copyright 2020, Anne Philipp and Leopold Haimberger
    506499
    507500    </p>
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