Changeset d720895 in flex_extract.git for Documentation/html/Installation/remote.html


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

updated online docu

File:
1 edited

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  • Documentation/html/Installation/remote.html

    r30f7911 rd720895  
    9494<li class="toctree-l2"><a class="reference internal" href="../installation.html#licence-agreement-for-public-datasets">Licence agreement for public datasets</a></li>
    9595<li class="toctree-l2"><a class="reference internal" href="../installation.html#download-flex-extract">Download <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a></li>
    96 <li class="toctree-l2"><a class="reference internal" href="../installation.html#environment-requirements">Environment requirements</a></li>
     96<li class="toctree-l2"><a class="reference internal" href="../installation.html#dependencies">Dependencies</a></li>
    9797<li class="toctree-l2 current"><a class="reference internal" href="../installation.html#installation-of-flex-extract">Installation of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code></a><ul class="current">
    9898<li class="toctree-l3 current"><a class="current reference internal" href="#">Remote mode installation</a><ul>
    99 <li class="toctree-l4"><a class="reference internal" href="#remote-environment-requirements">Remote environment requirements</a></li>
     99<li class="toctree-l4"><a class="reference internal" href="#remote-mode-dependencies">Remote mode - dependencies</a></li>
    100100<li class="toctree-l4"><a class="reference internal" href="#prepare-remote-environment">Prepare remote environment</a></li>
    101101<li class="toctree-l4"><a class="reference internal" href="#remote-installation">Remote installation</a></li>
    … …  
    189189<div class="toctree-wrapper compound">
    190190</div>
    191 <div class="section" id="remote-environment-requirements">
    192 <span id="ref-req-remote"></span><span id="ref-remote-mode"></span><h2>Remote environment requirements<a class="headerlink" href="#remote-environment-requirements" title="Permalink to this headline">¶</a></h2>
    193 <p>The environment for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> on ECMWF servers has to provide these
    194 software packages and libraries:</p>
     191<div class="section" id="remote-mode-dependencies">
     192<span id="ref-req-remote"></span><span id="ref-remote-mode"></span><h2>Remote mode - dependencies<a class="headerlink" href="#remote-mode-dependencies" title="Permalink to this headline">¶</a></h2>
     193<p>The following software is required, and already available at the ECMWF servers:</p>
    195194<table border="1" class="docutils">
    196195<colgroup>
    … …  
    222221<div class="section" id="prepare-remote-environment">
    223222<span id="ref-prep-remote"></span><h2>Prepare remote environment<a class="headerlink" href="#prepare-remote-environment" title="Permalink to this headline">¶</a></h2>
    224 <p>The environment on the ECMWF server (such as <em>ecgate</em> or <em>cca</em>) is already
    225 prepared. ECMWF server provide all libraries via a module system which is
    226 going to be selected by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> automatically.</p>
     223<p>ECMWF servers provide all libraries via a module system. Loading the required modules is already built into <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> and no user action is needed.</p>
    227224</div>
    228225<div class="section" id="remote-installation">
    229226<span id="ref-install-remote"></span><h2>Remote installation<a class="headerlink" href="#remote-installation" title="Permalink to this headline">¶</a></h2>
    230 <p>First, log in on one of the ECMWF Linux server, such as <em>ecgate</em> or <em>cca/ccb</em>.
     227<p>First, log in on one of the ECMWF servers, such as <em>ecgate</em> or <em>cca/ccb</em>.
    231228Substitute <em>&lt;ecuid&gt;</em> with your ECMWF user name:</p>
    232229<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ssh -X &lt;ecuid&gt;@ecaccess.ecmwf.int
    … …  
    251248***************************************************************
    252249
    253 &lt;ecuid&gt;@131.130.157.5&#39;s password: ***
     250&lt;ecuid&gt;@&lt;ipname/address&gt;&#39;s password: ***
    254251Select hostname (ecgate, cca, ccb) [ecgate]: ecgate
    255252
    … …  
    257254</pre></div>
    258255</div>
    259 <p>Then, copy the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> tar ball (from section <a class="reference internal" href="../installation.html#ref-download"><span class="std std-ref">Download flex_extract</span></a>)
    260 to the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory of the ECMWF Linux server via <code class="docutils literal notranslate"><span class="pre">scp</span></code>.
    261 Substitute the <em>&lt;localuser&gt;</em> and <em>&lt;server.edu&gt;</em> placeholders with your credentials.
     256<p>Substitute the <em>&lt;localuser&gt;</em> and <em>&lt;localmachine.tld&gt;</em> placeholders with your local user name and the IP name or address of your local machine.
    262257Untar the file and change into the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory.</p>
    263 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp &lt;localuser&gt;@&lt;server.edu&gt;:/path/to/tarfile/flex_extract_vX.X.tar.gz  <span class="nv">$HOME</span>/
     258<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>scp &lt;localuser&gt;@&lt;localmachine.tld&gt;:&lt;/path/to/tarfile/&gt;flex_extract_vX.X.tar.gz  <span class="nv">$HOME</span>/
    264259<span class="nb">cd</span> <span class="nv">$HOME</span>
    265260tar xvf flex_extract_vX.X.tar.gz
    … …  
    267262</pre></div>
    268263</div>
    269 <p>On these ECMWF servers, it is not necessary to prepare the environment or the
    270 <code class="docutils literal notranslate"><span class="pre">Makefile</span></code> for the Fortran program (<code class="docutils literal notranslate"><span class="pre">CONVERT2</span></code>) as described above.
    271 All third party libraries are available from a module system. The <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>
    272 is optimized for ECMWF servers and the compilation
    273 script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code>, which will be submitted by <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> to the
    274 batch job queue at ECMWF, does load all relevant modules from the ECMWF’s module system.</p>
    275 <p>So there is just the need to execute the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script from the
    276 <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory for installation.
     264<p>Execute the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> script from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>’s root directory.
    277265Before executing it, it is necessary to adapt some parameters from <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code>
    278266described in <span class="xref std std-doc">Documentation/Input/setup</span>.</p>
    279 <p>Open <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> with your editor and adapt the values:</p>
     267<p>Open <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> with your preferred editor (e.g., <a href="#id1"><span class="problematic" id="id2">``</span></a>nano’‘) and adapt the values:</p>
    280268<table border="1" class="docutils">
    281269<colgroup>
    … …  
    284272</colgroup>
    285273<tbody valign="top">
    286 <tr class="row-odd"><td>Take this for target = <strong>ectrans</strong></td>
    287 <td>Take this for target = <strong>cca</strong></td>
     274<tr class="row-odd"><td>Use this for target = <strong>ectrans</strong></td>
     275<td>Use this for target = <strong>cca</strong></td>
    288276</tr>
    289277<tr class="row-even"><td><div class="first last highlight-bash notranslate"><div class="highlight"><pre><span></span>...
    … …  
    329317</table>
    330318<p><span class="underline">Please substitute the values of ECUID and ECGID
    331 with your own credentials and settings.</span></p>
     319with your own ones (look at any of your files with ``ls -l’’ to see uid and gid).</span></p>
    332320<div class="admonition note">
    333321<p class="first admonition-title">Note</p>
    334 <p class="last">If a local gateway server is available the transfer of files could be done
    335 via the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. Therefore a valid <em>GATEWAY</em> and <em>DESTINATION</em>
    336 have to be present and should be set in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file.</p>
     322<p class="last">If a local gateway server is available, files can be transferred with <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. In that case, a valid <em>GATEWAY</em> and <em>DESTINATION</em> have to be present in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file (even if not used, the lines must not be deleted).</p>
    337323</div>
    338324<p>Afterwards, type:</p>
    … …  
    341327</pre></div>
    342328</div>
    343 <p>to start the installation. You should see the following output at the command line.</p>
     329<p>to start the installation. You should see the following on standard output.</p>
    344330<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Output of setup.sh</span>
    345331Create tarball ...
    … …  
    348334</pre></div>
    349335</div>
    350 <p>The email content should look like this with a “SUCCESS” statement in the last line:</p>
     336<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the email address connectd to the user account on ECMWF servers. The email content should look like this with a “SUCCESS” statement in the last line:</p>
    351337<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -c -g -O3 -fopenmp phgrreal.f
    352338gfortran   -m64 -fdefault-real-8 -fcray-pointer -fno-second-underscore  -ffixed-line-length-132 -fopenmp  -fconvert<span class="o">=</span>big-endian  -c -g -O3 -fopenmp grphreal.f
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