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96<li class="toctree-l2"><a class="reference internal" href="../overview.html">Overview</a></li>
97<li class="toctree-l2 current"><a class="reference internal" href="../input.html">Control &amp; input data</a><ul class="current">
98<li class="toctree-l3"><a class="reference internal" href="setup.html">The installation script - <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></a></li>
99<li class="toctree-l3 current"><a class="current reference internal" href="#">The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a><ul>
100<li class="toctree-l4"><a class="reference internal" href="#what-does-the-compilation-script-do">What does the compilation script do?</a></li>
101<li class="toctree-l4"><a class="reference internal" href="#example-compilejob-ksh">Example <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code></a></li>
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104<li class="toctree-l3"><a class="reference internal" href="fortran_makefile.html">The Fortran makefile for <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></a></li>
105<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
106<li class="toctree-l3"><a class="reference internal" href="jobscript.html">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
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195  <div class="section" id="the-compilation-job-script-compilejob-ksh">
196<h1>The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code><a class="headerlink" href="#the-compilation-job-script-compilejob-ksh" title="Permalink to this headline"></a></h1>
197<p>The compile job is a Korn-shell script which will be created during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong> from a template called <code class="docutils literal notranslate"><span class="pre">installscript.template</span></code> in the template directory.</p>
198<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
199the Korn-shell script from the template files by substituting the individual parameters.
200These individual parameters are marked by a doubled <code class="docutils literal notranslate"><span class="pre">$</span></code> sign in <code class="docutils literal notranslate"><span class="pre">installscript.template</span></code>.</p>
201<p>The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
202server system to load the necessary modules for the environment when submitted to the batch queue.</p>
203<p>The submission is done by the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> tool from within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-job-submit</span></code>.</p>
204<div class="section" id="what-does-the-compilation-script-do">
205<h2>What does the compilation script do?<a class="headerlink" href="#what-does-the-compilation-script-do" title="Permalink to this headline"></a></h2>
206<blockquote>
207<div><ol class="arabic simple">
208<li><p>It sets the necessary batch-system parameters</p></li>
209<li><p>It prepares the job environment at the ECMWF servers by loading the necessary library modules</p></li>
210<li><p>It sets some environment variables for the single session</p></li>
211<li><p>It creates the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> path of the user</p></li>
212<li><p>It untars the tarball into the root directory.</p></li>
213<li><p>It compiles the Fortran program using <code class="docutils literal notranslate"><span class="pre">makefile</span></code>.</p></li>
214<li><p>At the end, it checks whether the script has returned an error or not, and emails the log file to the user.</p></li>
215</ol>
216</div></blockquote>
217</div>
218<div class="section" id="example-compilejob-ksh">
219<h2>Example <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code><a class="headerlink" href="#example-compilejob-ksh" title="Permalink to this headline"></a></h2>
220<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
221
222<span class="c1"># ON ECGB:</span>
223<span class="c1"># start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE  on gateway server</span>
224<span class="c1"># start with sbatch NAME_OF_THIS_FILE directly on machine</span>
225
226<span class="c1">#SBATCH --workdir=/scratch/ms/at/km4a</span>
227<span class="c1">#SBATCH --qos=normal</span>
228<span class="c1">#SBATCH --job-name=flex_ecmwf</span>
229<span class="c1">#SBATCH --output=flex_ecmwf.%j.out</span>
230<span class="c1">#SBATCH --error=flex_ecmwf.%j.out</span>
231<span class="c1">#SBATCH --mail-type=FAIL</span>
232<span class="c1">#SBATCH --time=12:00:00</span>
233
234<span class="c1">## CRAY specific batch requests</span>
235<span class="c1">##PBS -N flex_ecmwf</span>
236<span class="c1">##PBS -q ns</span>
237<span class="c1">##PBS -S /usr/bin/ksh</span>
238<span class="c1">##PBS -o /scratch/ms/at/km4a/flex_ecmwf.${Jobname}.${Job_ID}.out</span>
239<span class="c1"># job output is in .ecaccess_DO_NOT_REMOVE</span>
240<span class="c1">##PBS -j oe</span>
241<span class="c1">##PBS -V</span>
242<span class="c1">##PBS -l EC_threads_per_task=1</span>
243<span class="c1">##PBS -l EC_memory_per_task=3200MB</span>
244
245<span class="nb">set</span> -x
246<span class="nb">export</span> <span class="nv">VERSION</span><span class="o">=</span><span class="m">7</span>.1
247<span class="k">case</span> <span class="si">${</span><span class="nv">HOST</span><span class="si">}</span> in
248  *ecg*<span class="o">)</span>
249  module unload grib_api
250  module unload emos
251  module load python3
252  module load eccodes
253  module load emos/455-r64
254  <span class="nb">export</span> <span class="nv">FLEXPART_ROOT_SCRIPTS</span><span class="o">=</span><span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>
255  <span class="nb">export</span> <span class="nv">MAKEFILE</span><span class="o">=</span>makefile_ecgate
256  <span class="p">;;</span>
257  *cca*<span class="o">)</span>
258  module switch PrgEnv-cray PrgEnv-intel
259  module load python3
260  module load eccodes
261  module load emos/455-r64
262  <span class="nb">echo</span> <span class="si">${</span><span class="nv">GROUP</span><span class="si">}</span>
263  <span class="nb">echo</span> <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>
264  <span class="nb">echo</span> <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span> <span class="p">|</span> awk -F / <span class="s1">&#39;{print $1, $2, $3, $4}&#39;</span>
265  <span class="nb">export</span> <span class="nv">GROUP</span><span class="o">=</span><span class="sb">`</span><span class="nb">echo</span> <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span> <span class="p">|</span> awk -F / <span class="s1">&#39;{print $4}&#39;</span><span class="sb">`</span>
266  <span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span>/scratch/ms/<span class="si">${</span><span class="nv">GROUP</span><span class="si">}</span>/<span class="si">${</span><span class="nv">USER</span><span class="si">}</span>
267  <span class="nb">export</span> <span class="nv">FLEXPART_ROOT_SCRIPTS</span><span class="o">=</span><span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>
268  <span class="nb">export</span> <span class="nv">MAKEFILE</span><span class="o">=</span>makefile_ecgate
269  <span class="p">;;</span>
270<span class="k">esac</span>
271
272mkdir -p <span class="si">${</span><span class="nv">FLEXPART_ROOT_SCRIPTS</span><span class="si">}</span>/flex_extract_v<span class="si">${</span><span class="nv">VERSION</span><span class="si">}</span>
273<span class="nb">cd</span> <span class="si">${</span><span class="nv">FLEXPART_ROOT_SCRIPTS</span><span class="si">}</span>/flex_extract_v<span class="si">${</span><span class="nv">VERSION</span><span class="si">}</span>   <span class="c1"># if FLEXPART_ROOT is not set this means cd to the home directory</span>
274tar -xvf <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v<span class="si">${</span><span class="nv">VERSION</span><span class="si">}</span>.tar
275<span class="nb">cd</span> Source/Fortran
276<span class="se">\r</span>m *.o *.mod calc_etadot
277make -f <span class="si">${</span><span class="nv">MAKEFILE</span><span class="si">}</span> &gt;flexcompile <span class="m">2</span>&gt;flexcompile
278
279ls -l calc_etadot &gt;&gt;flexcompile
280<span class="k">if</span> <span class="o">[</span> <span class="nv">$?</span> -eq <span class="m">0</span> <span class="o">]</span><span class="p">;</span> <span class="k">then</span>
281  <span class="nb">echo</span> <span class="s1">&#39;SUCCESS!&#39;</span> &gt;&gt;flexcompile
282  mail -s flexcompile.<span class="si">${</span><span class="nv">HOST</span><span class="si">}</span>.<span class="nv">$$</span> <span class="si">${</span><span class="nv">USER</span><span class="si">}</span> &lt;flexcompile
283<span class="k">else</span>
284  <span class="nb">echo</span> Environment: &gt;&gt;flexcompile
285  env &gt;&gt; flexcompile
286  mail -s <span class="s2">&quot;ERROR! flexcompile.</span><span class="si">${</span><span class="nv">HOST</span><span class="si">}</span><span class="s2">.</span><span class="nv">$$</span><span class="s2">&quot;</span> <span class="si">${</span><span class="nv">USER</span><span class="si">}</span> &lt;flexcompile
287<span class="k">fi</span>
288</pre></div>
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