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ESMCI · Oct 17, 2024 · 1b4bd19 · 1b4bd19
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diff --git a/branch/update-mvk-config/html/Tools_user/case.submit.html b/branch/update-mvk-config/html/Tools_user/case.submit.html
@@ -180,7 +180,9 @@
                         Only this job will be run, workflow and RESUBMIT are ignored.  Default is case.run.
   --no-batch            Do not submit jobs to batch system, run locally.
   --prereq PREREQ       Specify a prerequisite job id, this job will not start until the
-                        job with this id is completed (batch mode only).
+                        job with this id is completed (batch mode only). This feature overrides the
+                        CONTINUE_RUN=TRUE check for the existance of restart files and assumes that the
+                        files will be present when the case starts.
   --prereq-allow-failure
                         Allows starting the run even if the prerequisite fails.
                         This also allows resubmits to run if the original failed and the
@@ -199,6 +201,7 @@
                         You can specify multiple types with either comma-separated args or multiple -M flags.
   -a BATCH_ARGS, --batch-args BATCH_ARGS
                         Used to pass additional arguments to batch system.
+                        Do not use this feature to specify job prerequisites, use the --prereq feature instead.
   --chksum              Verifies input data checksums.
 
 Logging options:

diff --git a/branch/update-mvk-config/html/_modules/CIME/XML/env_batch.html b/branch/update-mvk-config/html/_modules/CIME/XML/env_batch.html
@@ -333,12 +333,35 @@ <h1>Source code for CIME.XML.env_batch</h1><div class="highlight"><pre>
             <span class="n">overrides</span><span class="p">[</span><span class="s2">&quot;tasks_per_node&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">tasks_per_node</span>
             <span class="k">if</span> <span class="n">thread_count</span><span class="p">:</span>
                 <span class="n">overrides</span><span class="p">[</span><span class="s2">&quot;thread_count&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">thread_count</span>
+                <span class="n">total_tasks</span> <span class="o">=</span> <span class="n">total_tasks</span> <span class="o">*</span> <span class="n">thread_count</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">total_tasks</span> <span class="o">=</span> <span class="n">total_tasks</span> <span class="o">*</span> <span class="n">case</span><span class="o">.</span><span class="n">thread_count</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="n">total_tasks</span> <span class="o">=</span> <span class="n">case</span><span class="o">.</span><span class="n">get_value</span><span class="p">(</span><span class="s2">&quot;TOTALPES&quot;</span><span class="p">)</span> <span class="o">*</span> <span class="nb">int</span><span class="p">(</span><span class="n">case</span><span class="o">.</span><span class="n">thread_count</span><span class="p">)</span>
+            <span class="c1"># Total PES accounts for threads as well as mpi tasks</span>
+            <span class="n">total_tasks</span> <span class="o">=</span> <span class="n">case</span><span class="o">.</span><span class="n">get_value</span><span class="p">(</span><span class="s2">&quot;TOTALPES&quot;</span><span class="p">)</span>
             <span class="n">thread_count</span> <span class="o">=</span> <span class="n">case</span><span class="o">.</span><span class="n">thread_count</span>
-        <span class="k">if</span> <span class="nb">int</span><span class="p">(</span><span class="n">total_tasks</span><span class="p">)</span> <span class="o">*</span> <span class="nb">int</span><span class="p">(</span><span class="n">thread_count</span><span class="p">)</span> <span class="o">&lt;</span> <span class="n">case</span><span class="o">.</span><span class="n">get_value</span><span class="p">(</span><span class="s2">&quot;MAX_TASKS_PER_NODE&quot;</span><span class="p">):</span>
+        <span class="k">if</span> <span class="nb">int</span><span class="p">(</span><span class="n">total_tasks</span><span class="p">)</span> <span class="o">&lt;</span> <span class="n">case</span><span class="o">.</span><span class="n">get_value</span><span class="p">(</span><span class="s2">&quot;MAX_TASKS_PER_NODE&quot;</span><span class="p">):</span>
             <span class="n">overrides</span><span class="p">[</span><span class="s2">&quot;max_tasks_per_node&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">total_tasks</span><span class="p">)</span>
 
+        <span class="c1"># when developed this variable was only needed on derecho, but I have tried to</span>
+        <span class="c1"># make it general enough that it can be used on other systems by defining MEM_PER_TASK and MAX_MEM_PER_NODE in config_machines.xml</span>
+        <span class="c1"># and adding {{ mem_per_node }} in config_batch.xml</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">mem_per_task</span> <span class="o">=</span> <span class="n">case</span><span class="o">.</span><span class="n">get_value</span><span class="p">(</span><span class="s2">&quot;MEM_PER_TASK&quot;</span><span class="p">)</span>
+            <span class="n">max_mem_per_node</span> <span class="o">=</span> <span class="n">case</span><span class="o">.</span><span class="n">get_value</span><span class="p">(</span><span class="s2">&quot;MAX_MEM_PER_NODE&quot;</span><span class="p">)</span>
+            <span class="n">mem_per_node</span> <span class="o">=</span> <span class="n">total_tasks</span>
+
+            <span class="k">if</span> <span class="n">mem_per_node</span> <span class="o">&lt;</span> <span class="n">mem_per_task</span><span class="p">:</span>
+                <span class="n">mem_per_node</span> <span class="o">=</span> <span class="n">mem_per_task</span>
+            <span class="k">elif</span> <span class="n">mem_per_node</span> <span class="o">&gt;</span> <span class="n">max_mem_per_node</span><span class="p">:</span>
+                <span class="n">mem_per_node</span> <span class="o">=</span> <span class="n">max_mem_per_node</span>
+            <span class="n">overrides</span><span class="p">[</span><span class="s2">&quot;mem_per_node&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">mem_per_node</span>
+        <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>
+            <span class="c1"># ignore this, the variables are not defined for this machine</span>
+            <span class="k">pass</span>
+        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">error</span><span class="p">:</span>
+            <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;An exception occured:&quot;</span><span class="p">,</span> <span class="n">error</span><span class="p">)</span>
+
         <span class="n">overrides</span><span class="p">[</span><span class="s2">&quot;ngpus_per_node&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ngpus_per_node</span>
         <span class="n">overrides</span><span class="p">[</span><span class="s2">&quot;mpirun&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">case</span><span class="o">.</span><span class="n">get_mpirun_cmd</span><span class="p">(</span><span class="n">job</span><span class="o">=</span><span class="n">job</span><span class="p">,</span> <span class="n">overrides</span><span class="o">=</span><span class="n">overrides</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">overrides</span></div>

diff --git a/branch/update-mvk-config/html/_sources/users_guide/testing.rst.txt b/branch/update-mvk-config/html/_sources/users_guide/testing.rst.txt
@@ -395,7 +395,6 @@ For this case the default ``evv_test_config`` and ``generate_namelist`` function
   component = "eam"
   # components = [] can be omitted when modifying a single component
   ninst = 10
-  critical = 21
 
 .. _MVK Complex:
 
@@ -417,6 +416,7 @@ Note; this is a toy example, no scientific usage.
   import os
   from CIME.SystemTests.mvk import EVV_LIB_DIR
   from CIME.namelist import Namelist
+  from CIME.utils import safe_copy
   from CIME.utils import run_cmd
 
   component "eam"
@@ -438,15 +438,18 @@ Note; this is a toy example, no scientific usage.
     if component in ["eam", "clm"]:
       with namelist(filename) as nml:
         if component == "eam":
-          nml.set_variable_value("eam_specific", f"perturn-{i}")
+          # arguments group, key, value
+          nml.set_variable_value("", "eam_specific", f"perturn-{i}")
         elif component == "clm":
           if i % 2 == 0:
-            nml.set_variable_value("clm_specific", "even")
+            nml.set_variable_value("", "clm_specific", "even")
           else:
-            nml.set_variable_value("clm_specific", "odd")
+            nml.set_variable_value("", "clm_specific", "odd")
     else:
       stat, output, err = run_cmd(f"atmchange initial_conditions::perturbation_random_seed = {i*32}")
 
+      safe_copy("namelist_scream.xml", f"namelist_scream_{i:04}.xml")
+
 
 ========================
 Test progress and output

diff --git a/branch/update-mvk-config/html/searchindex.js b/branch/update-mvk-config/html/searchindex.js
diff --git a/branch/update-mvk-config/html/users_guide/testing.html b/branch/update-mvk-config/html/users_guide/testing.html
@@ -602,7 +602,6 @@ <h5><span class="section-number">10.1.3.4.1. </span>MVK<a class="headerlink" hre
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">component</span> <span class="o">=</span> <span class="s2">&quot;eam&quot;</span>
 <span class="c1"># components = [] can be omitted when modifying a single component</span>
 <span class="n">ninst</span> <span class="o">=</span> <span class="mi">10</span>
-<span class="n">critical</span> <span class="o">=</span> <span class="mi">21</span>
 </pre></div>
 </div>
 <p id="mvk-complex">If more control over the evv4esm configuration file or the per instance configuration is desired then
@@ -617,6 +616,7 @@ <h5><span class="section-number">10.1.3.4.1. </span>MVK<a class="headerlink" hre
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">from</span> <span class="nn">CIME.SystemTests.mvk</span> <span class="kn">import</span> <span class="n">EVV_LIB_DIR</span>
 <span class="kn">from</span> <span class="nn">CIME.namelist</span> <span class="kn">import</span> <span class="n">Namelist</span>
+<span class="kn">from</span> <span class="nn">CIME.utils</span> <span class="kn">import</span> <span class="n">safe_copy</span>
 <span class="kn">from</span> <span class="nn">CIME.utils</span> <span class="kn">import</span> <span class="n">run_cmd</span>
 
 <span class="n">component</span> <span class="s2">&quot;eam&quot;</span>
@@ -638,14 +638,17 @@ <h5><span class="section-number">10.1.3.4.1. </span>MVK<a class="headerlink" hre
   <span class="k">if</span> <span class="n">component</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;eam&quot;</span><span class="p">,</span> <span class="s2">&quot;clm&quot;</span><span class="p">]:</span>
     <span class="k">with</span> <span class="n">namelist</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">nml</span><span class="p">:</span>
       <span class="k">if</span> <span class="n">component</span> <span class="o">==</span> <span class="s2">&quot;eam&quot;</span><span class="p">:</span>
-        <span class="n">nml</span><span class="o">.</span><span class="n">set_variable_value</span><span class="p">(</span><span class="s2">&quot;eam_specific&quot;</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;perturn-</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="c1"># arguments group, key, value</span>
+        <span class="n">nml</span><span class="o">.</span><span class="n">set_variable_value</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="s2">&quot;eam_specific&quot;</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;perturn-</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
       <span class="k">elif</span> <span class="n">component</span> <span class="o">==</span> <span class="s2">&quot;clm&quot;</span><span class="p">:</span>
         <span class="k">if</span> <span class="n">i</span> <span class="o">%</span> <span class="mi">2</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-          <span class="n">nml</span><span class="o">.</span><span class="n">set_variable_value</span><span class="p">(</span><span class="s2">&quot;clm_specific&quot;</span><span class="p">,</span> <span class="s2">&quot;even&quot;</span><span class="p">)</span>
+          <span class="n">nml</span><span class="o">.</span><span class="n">set_variable_value</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="s2">&quot;clm_specific&quot;</span><span class="p">,</span> <span class="s2">&quot;even&quot;</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
-          <span class="n">nml</span><span class="o">.</span><span class="n">set_variable_value</span><span class="p">(</span><span class="s2">&quot;clm_specific&quot;</span><span class="p">,</span> <span class="s2">&quot;odd&quot;</span><span class="p">)</span>
+          <span class="n">nml</span><span class="o">.</span><span class="n">set_variable_value</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="s2">&quot;clm_specific&quot;</span><span class="p">,</span> <span class="s2">&quot;odd&quot;</span><span class="p">)</span>
   <span class="k">else</span><span class="p">:</span>
     <span class="n">stat</span><span class="p">,</span> <span class="n">output</span><span class="p">,</span> <span class="n">err</span> <span class="o">=</span> <span class="n">run_cmd</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;atmchange initial_conditions::perturbation_random_seed = </span><span class="si">{</span><span class="n">i</span><span class="o">*</span><span class="mi">32</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+
+    <span class="n">safe_copy</span><span class="p">(</span><span class="s2">&quot;namelist_scream.xml&quot;</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;namelist_scream_</span><span class="si">{</span><span class="n">i</span><span class="si">:</span><span class="s2">04</span><span class="si">}</span><span class="s2">.xml&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
 </section>