deploy: 2fd5f0a

C2SM · Feb 27, 2024 · 2237e5e · 2237e5e
1 parent 0fae5ff
commit 2237e5e
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Showing 10 changed files with 633 additions and 17 deletions.
diff --git a/latest/.doctrees/environment.pickle b/latest/.doctrees/environment.pickle
diff --git a/latest/.doctrees/howtorun.doctree b/latest/.doctrees/howtorun.doctree
diff --git a/latest/_modules/index.html b/latest/_modules/index.html
@@ -176,6 +176,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="jobs/tools/write_cosmo_input_ghg.html">jobs.tools.write_cosmo_input_ghg</a></li>
 <li><a href="jobs/tools/write_int2lm_input_art.html">jobs.tools.write_int2lm_input_art</a></li>
 <li><a href="jobs/verify_chain.html">jobs.verify_chain</a></li>
+<li><a href="run_chain.html">run_chain</a></li>
 </ul>
 
            </div>

diff --git a/latest/_modules/jobs/post_cosmo.html b/latest/_modules/jobs/post_cosmo.html
@@ -158,7 +158,7 @@ <h1>Source code for jobs.post_cosmo</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">tools</span><span class="p">,</span> <span class="n">prepare_cosmo</span>
 
-<span class="n">BASIC_PYTHON_JOB</span> <span class="o">=</span> <span class="kc">False</span>
+<span class="n">BASIC_PYTHON_JOB</span> <span class="o">=</span> <span class="kc">True</span>
 
 
 <span class="k">def</span> <span class="nf">logfile_header_template</span><span class="p">():</span>
@@ -190,10 +190,10 @@ <h1>Source code for jobs.post_cosmo</h1><div class="highlight"><pre>
     <span class="n">commands</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
 
     <span class="k">return</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
-        <span class="s2">&quot;srun cp -Raf </span><span class="si">{int2lm_run_src}</span><span class="s2">/. </span><span class="si">{int2lm_run_dest}</span><span class="s2">/&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;srun cp -Raf </span><span class="si">{cosmo_run_src}</span><span class="s2">/. </span><span class="si">{cosmo_run_dest}</span><span class="s2">/&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;srun cp -Raf </span><span class="si">{cosmo_output_src}</span><span class="s2">/. </span><span class="si">{cosmo_output_dest}</span><span class="s2">/&quot;</span><span class="p">,</span>
-        <span class="s2">&quot;srun cp -Raf </span><span class="si">{logs_src}</span><span class="s2">/. </span><span class="si">{logs_dest}</span><span class="s2">/&quot;</span>
+        <span class="s2">&quot;srun cp -Rafv </span><span class="si">{int2lm_run_src}</span><span class="s2">/. </span><span class="si">{int2lm_run_dest}</span><span class="s2">/&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;srun cp -Rafv </span><span class="si">{cosmo_run_src}</span><span class="s2">/. </span><span class="si">{cosmo_run_dest}</span><span class="s2">/&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;srun cp -Rafv </span><span class="si">{cosmo_output_src}</span><span class="s2">/. </span><span class="si">{cosmo_output_dest}</span><span class="s2">/&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;srun cp -Rafv </span><span class="si">{logs_src}</span><span class="s2">/. </span><span class="si">{logs_dest}</span><span class="s2">/&quot;</span><span class="p">,</span> <span class="s2">&quot;unset SLURM_MEM_PER_CPU&quot;</span>
     <span class="p">])</span>
 
 

diff --git a/latest/_modules/jobs/prepare_icon.html b/latest/_modules/jobs/prepare_icon.html
@@ -229,15 +229,27 @@ <h1>Source code for jobs.prepare_icon</h1><div class="highlight"><pre>
 
     <span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">&#39;Copy ICON input data (IC/BC) to working directory&#39;</span><span class="p">)</span>
     <span class="c1"># Copy input files to scratch</span>
-    <span class="n">script_lines</span> <span class="o">=</span> <span class="p">[</span>
-        <span class="s1">&#39;#!/usr/bin/env bash&#39;</span><span class="p">,</span>
-        <span class="sa">f</span><span class="s1">&#39;#SBATCH --job-name=&quot;copy_input_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">casename</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">startdate_sim_yyyymmddhh</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">enddate_sim_yyyymmddhh</span><span class="si">}</span><span class="s1">&quot;&#39;</span><span class="p">,</span>
-        <span class="sa">f</span><span class="s1">&#39;#SBATCH --account=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">compute_account</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;#SBATCH --time=00:10:00&#39;</span><span class="p">,</span>
-        <span class="sa">f</span><span class="s1">&#39;#SBATCH --partition=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">compute_queue</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span>
-        <span class="sa">f</span><span class="s1">&#39;#SBATCH --constraint=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">constraint</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;#SBATCH --nodes=1&#39;</span><span class="p">,</span>
-        <span class="sa">f</span><span class="s1">&#39;#SBATCH --output=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">logfile</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;#SBATCH --open-mode=append&#39;</span><span class="p">,</span>
-        <span class="sa">f</span><span class="s1">&#39;#SBATCH --chdir=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">icon_work</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span>
-    <span class="p">]</span>
+    <span class="k">if</span> <span class="n">cfg</span><span class="o">.</span><span class="n">machine</span> <span class="o">==</span> <span class="s1">&#39;daint&#39;</span><span class="p">:</span>
+        <span class="n">script_lines</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;#!/usr/bin/env bash&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --job-name=&quot;copy_input_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">casename</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">startdate_sim_yyyymmddhh</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">enddate_sim_yyyymmddhh</span><span class="si">}</span><span class="s1">&quot;&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --account=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">compute_account</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;#SBATCH --time=00:10:00&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --partition=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">compute_queue</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --constraint=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">constraint</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;#SBATCH --nodes=1&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --output=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">logfile</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;#SBATCH --open-mode=append&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --chdir=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">icon_work</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span>
+        <span class="p">]</span>
+    <span class="k">elif</span> <span class="n">cfg</span><span class="o">.</span><span class="n">machine</span> <span class="o">==</span> <span class="s1">&#39;euler&#39;</span><span class="p">:</span>
+        <span class="n">script_lines</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;#!/usr/bin/env bash&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --job-name=&quot;copy_input_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">casename</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">startdate_sim_yyyymmddhh</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">enddate_sim_yyyymmddhh</span><span class="si">}</span><span class="s1">&quot;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;#SBATCH --time=00:10:00&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --partition=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">compute_queue</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --constraint=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">constraint</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;#SBATCH --ntasks=1&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --output=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">logfile</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;#SBATCH --open-mode=append&#39;</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;#SBATCH --chdir=</span><span class="si">{</span><span class="n">cfg</span><span class="o">.</span><span class="n">icon_work</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span>
+        <span class="p">]</span>
     <span class="k">for</span> <span class="n">target</span><span class="p">,</span> <span class="n">destination</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">cfg</span><span class="o">.</span><span class="n">input_files</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span>
                                    <span class="n">cfg</span><span class="o">.</span><span class="n">input_files_scratch</span><span class="o">.</span><span class="n">values</span><span class="p">()):</span>
         <span class="n">script_lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;rsync -av </span><span class="si">{</span><span class="n">target</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">destination</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>