[ci skip] Autodoc commit for 1f067ab.

latest/_sources/installation/resource-manager/slurm.rst.txt

@@ -6,26 +6,38 @@ Slurm
 A YAML cluster configuration file for a Slurm resource manager on an HPC
 cluster looks like:
 
+.. warning::
+  Open OnDemand's Slurm support defaults to issuing CLI commands with
+  the ``--export`` flag set to ``NONE``, when Slurms default is ``ALL``.
+  This can cause issues with jobs that require ``srun``.
+
+  Work arounds are currently to ``export SLURM_EXPORT_ENV=ALL``
+  in a :ref:`script_wrapper <script_wrapper>` before any job scripts run.
+
+  Alternatively, you can use ``copy_enviornment`` below with the caveat
+  that the PUNs environment is very different from regular shell sessions.
+
 .. code-block:: yaml
    :emphasize-lines: 8-
 
    # /etc/ood/config/clusters.d/my_cluster.yml
    ---
    v2:
-     metadata:
-       title: "My Cluster"
-     login:
-       host: "my_cluster.my_center.edu"
-     job:
-       adapter: "slurm"
-       cluster: "my_cluster"
-       bin: "/path/to/slurm/bin"
-       conf: "/path/to/slurm.conf"
-       # bin_overrides:
-         # sbatch: "/usr/local/bin/sbatch"
-         # squeue: ""
-         # scontrol: ""
-         # scancel: ""
+      metadata:
+        title: "My Cluster"
+      login:
+        host: "my_cluster.my_center.edu"
+      job:
+        adapter: "slurm"
+        cluster: "my_cluster"
+        bin: "/path/to/slurm/bin"
+        conf: "/path/to/slurm.conf"
+        # bin_overrides:
+          # sbatch: "/usr/local/bin/sbatch"
+          # squeue: ""
+          # scontrol: ""
+          # scancel: ""
+        copy_enviornment: false
 
 with the following configuration options:
 
@@ -36,7 +48,7 @@ cluster
 
   .. warning::
     Using the ``cluster`` option is discouraged. This is because maintenance
-    outages on the Slurm DB will propogate to Open OnDemand.  Instead sites
+    outages on the Slurm database will propogate to Open OnDemand.  Instead sites
     should use different ``conf`` files for each cluster to limit maintenance outages.
 bin
   The path to the Slurm client installation binaries.
@@ -54,6 +66,12 @@ bin_overrides
   - `scontrol`
   - `scancel`
 
+copy_enviornment
+  Copies the enviornment of the PUN when issuing CLI commands. Default behaviour
+  for Open OnDemand is to use ``--export=NONE`` flag. Setting this to true will
+  cause Open OnDemand to issue CLI commands with ``--export=ALL``. Though this may
+  cause issues as the PUN's environment is very different than a regular shell session.
+
 .. note::
 
    If you do not have a multi-cluster Slurm setup you can remove the ``cluster:

latest/_sources/reference/files/submit-yml/basic-bc-options.rst.txt

@@ -119,20 +119,22 @@ Basic Batch Connect Options
 
         header: 'echo "all done at $(date)"'
 
+.. _script_wrapper:
+
 .. describe:: script_wrapper (String, "%s")
 
-    wrap the script ('%s' being the script content) with commands before
-    and after
+    Wrap the script (``%s`` being the script content) with commands before
+    and after.
 
     Default
-      the script has no wrapper
+      The script has no wrapper.
 
       .. code-block:: yaml
 
         script_wrapper: "%s"
 
     Example
-      load a module before the script and echo a statement after it
+      Load a module before the script and echo a statement after it.
 
       .. code-block:: yaml
 

latest/installation/resource-manager/slurm.html

@@ -215,23 +215,34 @@
 <span id="resource-manager-slurm"></span><h1>Slurm<a class="headerlink" href="#slurm" title="Permalink to this headline">¶</a></h1>
 <p>A YAML cluster configuration file for a Slurm resource manager on an HPC
 cluster looks like:</p>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>Open OnDemand’s Slurm support defaults to issuing CLI commands with
+the <code class="docutils literal notranslate"><span class="pre">--export</span></code> flag set to <code class="docutils literal notranslate"><span class="pre">NONE</span></code>, when Slurms default is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>.
+This can cause issues with jobs that require <code class="docutils literal notranslate"><span class="pre">srun</span></code>.</p>
+<p>Work arounds are currently to <code class="docutils literal notranslate"><span class="pre">export</span> <span class="pre">SLURM_EXPORT_ENV=ALL</span></code>
+in a <a class="reference internal" href="../../reference/files/submit-yml/basic-bc-options.html#script-wrapper"><span class="std std-ref">script_wrapper</span></a> before any job scripts run.</p>
+<p>Alternatively, you can use <code class="docutils literal notranslate"><span class="pre">copy_enviornment</span></code> below with the caveat
+that the PUNs environment is very different from regular shell sessions.</p>
+</div>
 <div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="c1"># /etc/ood/config/clusters.d/my_cluster.yml</span><span class="w"></span>
 <span class="nn">---</span><span class="w"></span>
 <span class="nt">v2</span><span class="p">:</span><span class="w"></span>
-<span class="w">  </span><span class="nt">metadata</span><span class="p">:</span><span class="w"></span>
-<span class="w">    </span><span class="nt">title</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;My</span><span class="nv"> </span><span class="s">Cluster&quot;</span><span class="w"></span>
-<span class="w">  </span><span class="nt">login</span><span class="p">:</span><span class="w"></span>
-<span class="w">    </span><span class="nt">host</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;my_cluster.my_center.edu&quot;</span><span class="w"></span>
-<span class="hll"><span class="w">  </span><span class="nt">job</span><span class="p">:</span><span class="w"></span>
-</span><span class="hll"><span class="w">    </span><span class="nt">adapter</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;slurm&quot;</span><span class="w"></span>
-</span><span class="hll"><span class="w">    </span><span class="nt">cluster</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;my_cluster&quot;</span><span class="w"></span>
-</span><span class="hll"><span class="w">    </span><span class="nt">bin</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;/path/to/slurm/bin&quot;</span><span class="w"></span>
-</span><span class="hll"><span class="w">    </span><span class="nt">conf</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;/path/to/slurm.conf&quot;</span><span class="w"></span>
-</span><span class="hll"><span class="w">    </span><span class="c1"># bin_overrides:</span><span class="w"></span>
-</span><span class="hll"><span class="w">      </span><span class="c1"># sbatch: &quot;/usr/local/bin/sbatch&quot;</span><span class="w"></span>
-</span><span class="hll"><span class="w">      </span><span class="c1"># squeue: &quot;&quot;</span><span class="w"></span>
-</span><span class="hll"><span class="w">      </span><span class="c1"># scontrol: &quot;&quot;</span><span class="w"></span>
-</span><span class="hll"><span class="w">      </span><span class="c1"># scancel: &quot;&quot;</span><span class="w"></span>
+<span class="w">   </span><span class="nt">metadata</span><span class="p">:</span><span class="w"></span>
+<span class="w">     </span><span class="nt">title</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;My</span><span class="nv"> </span><span class="s">Cluster&quot;</span><span class="w"></span>
+<span class="w">   </span><span class="nt">login</span><span class="p">:</span><span class="w"></span>
+<span class="w">     </span><span class="nt">host</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;my_cluster.my_center.edu&quot;</span><span class="w"></span>
+<span class="hll"><span class="w">   </span><span class="nt">job</span><span class="p">:</span><span class="w"></span>
+</span><span class="hll"><span class="w">     </span><span class="nt">adapter</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;slurm&quot;</span><span class="w"></span>
+</span><span class="hll"><span class="w">     </span><span class="nt">cluster</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;my_cluster&quot;</span><span class="w"></span>
+</span><span class="hll"><span class="w">     </span><span class="nt">bin</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;/path/to/slurm/bin&quot;</span><span class="w"></span>
+</span><span class="hll"><span class="w">     </span><span class="nt">conf</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;/path/to/slurm.conf&quot;</span><span class="w"></span>
+</span><span class="hll"><span class="w">     </span><span class="c1"># bin_overrides:</span><span class="w"></span>
+</span><span class="hll"><span class="w">       </span><span class="c1"># sbatch: &quot;/usr/local/bin/sbatch&quot;</span><span class="w"></span>
+</span><span class="hll"><span class="w">       </span><span class="c1"># squeue: &quot;&quot;</span><span class="w"></span>
+</span><span class="hll"><span class="w">       </span><span class="c1"># scontrol: &quot;&quot;</span><span class="w"></span>
+</span><span class="hll"><span class="w">       </span><span class="c1"># scancel: &quot;&quot;</span><span class="w"></span>
+</span><span class="hll"><span class="w">     </span><span class="nt">copy_enviornment</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span><span class="w"></span>
 </span></pre></div>
 </div>
 <p>with the following configuration options:</p>
@@ -242,7 +253,7 @@
 <div class="admonition warning">
 <p class="admonition-title">Warning</p>
 <p>Using the <code class="docutils literal notranslate"><span class="pre">cluster</span></code> option is discouraged. This is because maintenance
-outages on the Slurm DB will propogate to Open OnDemand.  Instead sites
+outages on the Slurm database will propogate to Open OnDemand.  Instead sites
 should use different <code class="docutils literal notranslate"><span class="pre">conf</span></code> files for each cluster to limit maintenance outages.</p>
 </div>
 </dd>
@@ -261,6 +272,11 @@
 <li><p><cite>scancel</cite></p></li>
 </ul>
 </dd>
+<dt>copy_enviornment</dt><dd><p>Copies the enviornment of the PUN when issuing CLI commands. Default behaviour
+for Open OnDemand is to use <code class="docutils literal notranslate"><span class="pre">--export=NONE</span></code> flag. Setting this to true will
+cause Open OnDemand to issue CLI commands with <code class="docutils literal notranslate"><span class="pre">--export=ALL</span></code>. Though this may
+cause issues as the PUN’s environment is very different than a regular shell session.</p>
+</dd>
 </dl>
 <div class="admonition note">
 <p class="admonition-title">Note</p>

latest/reference/files/submit-yml/basic-bc-options.html

@@ -334,18 +334,18 @@
 </dl>
 </dd></dl>
 
-<dl class="describe">
+<span class="target" id="script-wrapper"></span><dl class="describe">
 <dt>
 <code class="sig-name descname">script_wrapper (String, &quot;%s&quot;)</code></dt>
-<dd><p>wrap the script (‘%s’ being the script content) with commands before
-and after</p>
+<dd><p>Wrap the script (<code class="docutils literal notranslate"><span class="pre">%s</span></code> being the script content) with commands before
+and after.</p>
 <dl>
-<dt>Default</dt><dd><p>the script has no wrapper</p>
+<dt>Default</dt><dd><p>The script has no wrapper.</p>
 <div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="nt">script_wrapper</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;%s&quot;</span><span class="w"></span>
 </pre></div>
 </div>
 </dd>
-<dt>Example</dt><dd><p>load a module before the script and echo a statement after it</p>
+<dt>Example</dt><dd><p>Load a module before the script and echo a statement after it.</p>
 <div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="nt">script_wrapper</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">|</span><span class="w"></span>
 <span class="w">  </span><span class="no">module load vnc</span><span class="w"></span>
 <span class="w">  </span><span class="no">%s</span><span class="w"></span>