deploy: 1c1d0be

_sources/nersc-compilers.rst.txt

@@ -34,7 +34,7 @@ Build, e.g. the Castro Sedov hydro test problem
 
 .. prompt:: bash
 
-   make -j COMP=gnu TINY_PROFILE=TRUE USE_MPI=TRUE USE_OMP=FALSE USE_CUDA=TRUE -j 4
+   make COMP=gnu TINY_PROFILE=TRUE USE_MPI=TRUE USE_OMP=FALSE USE_CUDA=TRUE -j 4
 
 Hypre
 ^^^^^

_sources/nersc-workflow.rst.txt

@@ -39,6 +39,9 @@ each OpenMP thread per physical core, so it is best to set ``OMP_NUM_THREADS`` t
    Jobs should be run in your ``$SCRATCH`` directory. By default,
    SLURM will change directory into the submission directory.
 
+   Alternately, you can run in the common file system, ``$CFS/m3018``,
+   which everyone in the project has access to.
+
 Jobs are submitted as:
 
 .. prompt:: bash
@@ -57,6 +60,8 @@ and an estimate of the start time can be found via:
 
    squeue --me --start
 
+to cancel a job, you would use ``scancel``.
+
 
 Chaining
 ^^^^^^^^

_static/basic.css

@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

_static/documentation_options.js

@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,

_static/pygments.css

@@ -17,6 +17,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
 .highlight .gr { color: #FF0000 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */

_static/searchtools.js

@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**

_static/sphinx_highlight.js

@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});

alcf.html

@@ -13,11 +13,11 @@
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-        <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
-        <script src="_static/clipboard.min.js"></script>
-        <script src="_static/copybutton.js"></script>
+        <script src="_static/documentation_options.js?v=f2a433a1"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/clipboard.min.js?v=a7894cd8"></script>
+        <script src="_static/copybutton.js?v=f281be69"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -90,11 +90,11 @@
            <div itemprop="articleBody">
 
   <section id="working-at-alcf">
-<h1>Working at ALCF<a class="headerlink" href="#working-at-alcf" title="Permalink to this heading">¶</a></h1>
+<h1>Working at ALCF<a class="headerlink" href="#working-at-alcf" title="Link to this heading">¶</a></h1>
 <p>Polaris has 560 nodes each with 4 NVIDIA A100 GPUs.</p>
 <p>The PBS scheduler is used.</p>
 <section id="logging-in">
-<h2>Logging In<a class="headerlink" href="#logging-in" title="Permalink to this heading">¶</a></h2>
+<h2>Logging In<a class="headerlink" href="#logging-in" title="Link to this heading">¶</a></h2>
 <p>ssh into:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>polaris.alcf.ornl.gov
 </pre></div>
@@ -103,7 +103,7 @@ <h2>Logging In<a class="headerlink" href="#logging-in" title="Permalink to this
 there.  This is read at the end of <code class="docutils literal notranslate"><span class="pre">/etc/bash.bashrc</span></code></p>
 </section>
 <section id="compiling">
-<h2>Compiling<a class="headerlink" href="#compiling" title="Permalink to this heading">¶</a></h2>
+<h2>Compiling<a class="headerlink" href="#compiling" title="Link to this heading">¶</a></h2>
 <p>Load the modules:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><style type="text/css">
 span.prompt1:before {
@@ -115,11 +115,11 @@ <h2>Compiling<a class="headerlink" href="#compiling" title="Permalink to this he
 <div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">make<span class="w"> </span><span class="nv">COMP</span><span class="o">=</span>gnu<span class="w"> </span><span class="nv">USE_CUDA</span><span class="o">=</span>TRUE</span>
 </pre></div></div></section>
 <section id="disks">
-<h2>Disks<a class="headerlink" href="#disks" title="Permalink to this heading">¶</a></h2>
+<h2>Disks<a class="headerlink" href="#disks" title="Link to this heading">¶</a></h2>
 <p>Project workspace is at: <code class="docutils literal notranslate"><span class="pre">/lus/grand/projects/AstroExplosions/</span></code></p>
 </section>
 <section id="queues">
-<h2>Queues<a class="headerlink" href="#queues" title="Permalink to this heading">¶</a></h2>
+<h2>Queues<a class="headerlink" href="#queues" title="Link to this heading">¶</a></h2>
 <p><a class="reference external" href="https://www.alcf.anl.gov/support/user-guides/polaris/queueing-and-running-jobs/job-and-queue-scheduling/index.html">https://www.alcf.anl.gov/support/user-guides/polaris/queueing-and-running-jobs/job-and-queue-scheduling/index.html</a></p>
 <p>For production jobs, you submit to the <code class="docutils literal notranslate"><span class="pre">prod</span></code> queue.</p>
 <div class="admonition note">
@@ -128,7 +128,7 @@ <h2>Queues<a class="headerlink" href="#queues" title="Permalink to this heading"
 </div>
 </section>
 <section id="submitting">
-<h2>Submitting<a class="headerlink" href="#submitting" title="Permalink to this heading">¶</a></h2>
+<h2>Submitting<a class="headerlink" href="#submitting" title="Link to this heading">¶</a></h2>
 <p>Clone the <code class="docutils literal notranslate"><span class="pre">GettingStarted</span></code> repo:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">git<span class="w"> </span>clone<span class="w"> </span>git@github.com:argonne-lcf/GettingStarted.git</span>
 </pre></div></div><p>you’ll want to use the examples in
@@ -137,7 +137,7 @@ <h2>Submitting<a class="headerlink" href="#submitting" title="Permalink to this
 <code class="docutils literal notranslate"><span class="pre">set_affinity_gpu_polaris.sh</span></code> copied into your run directory.</p>
 <p>Here’s a submission script that will run on 2 nodes with 4 GPUs / node:</p>
 <div class="literal-block-wrapper docutils container" id="id1">
-<div class="code-block-caption"><span class="caption-text"><code class="docutils literal notranslate"><span class="pre">polaris.submit</span></code></span><a class="headerlink" href="#id1" title="Permalink to this code">¶</a></div>
+<div class="code-block-caption"><span class="caption-text"><code class="docutils literal notranslate"><span class="pre">polaris.submit</span></code></span><a class="headerlink" href="#id1" title="Link to this code">¶</a></div>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/sh</span>
 <span class="c1">#PBS -l select=2:system=polaris</span>
 <span class="c1">#PBS -l place=scatter</span>
@@ -173,11 +173,11 @@ <h2>Submitting<a class="headerlink" href="#submitting" title="Permalink to this
 <div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">qstat<span class="w"> </span>-u<span class="w"> </span>username</span>
 </pre></div></div></section>
 <section id="automatic-restarting">
-<h2>Automatic Restarting<a class="headerlink" href="#automatic-restarting" title="Permalink to this heading">¶</a></h2>
+<h2>Automatic Restarting<a class="headerlink" href="#automatic-restarting" title="Link to this heading">¶</a></h2>
 <p>A version of the submission script that automatically restarts from
 the last checkpoint is:</p>
 <div class="literal-block-wrapper docutils container" id="id2">
-<div class="code-block-caption"><span class="caption-text"><code class="docutils literal notranslate"><span class="pre">polaris.submit</span></code></span><a class="headerlink" href="#id2" title="Permalink to this code">¶</a></div>
+<div class="code-block-caption"><span class="caption-text"><code class="docutils literal notranslate"><span class="pre">polaris.submit</span></code></span><a class="headerlink" href="#id2" title="Link to this code">¶</a></div>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/sh</span>
 <span class="c1">#PBS -l select=2:system=polaris</span>
 <span class="c1">#PBS -l place=scatter</span>
@@ -254,10 +254,10 @@ <h2>Automatic Restarting<a class="headerlink" href="#automatic-restarting" title
 </div>
 </section>
 <section id="job-chaining">
-<h2>Job Chaining<a class="headerlink" href="#job-chaining" title="Permalink to this heading">¶</a></h2>
+<h2>Job Chaining<a class="headerlink" href="#job-chaining" title="Link to this heading">¶</a></h2>
 <p>A script that can be used to chain jobs with PBS is:</p>
 <div class="literal-block-wrapper docutils container" id="id3">
-<div class="code-block-caption"><span class="caption-text"><code class="docutils literal notranslate"><span class="pre">chainqsub.sh</span></code></span><a class="headerlink" href="#id3" title="Permalink to this code">¶</a></div>
+<div class="code-block-caption"><span class="caption-text"><code class="docutils literal notranslate"><span class="pre">chainqsub.sh</span></code></span><a class="headerlink" href="#id3" title="Link to this code">¶</a></div>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/sh -f</span>
 
 <span class="k">if</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>!<span class="w"> </span><span class="s2">&quot;</span><span class="nv">$1</span><span class="s2">&quot;</span><span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span>

genindex.html

@@ -12,11 +12,11 @@
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-        <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
-        <script src="_static/clipboard.min.js"></script>
-        <script src="_static/copybutton.js"></script>
+        <script src="_static/documentation_options.js?v=f2a433a1"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/clipboard.min.js?v=a7894cd8"></script>
+        <script src="_static/copybutton.js?v=f281be69"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" /> 

iacs.html

@@ -13,11 +13,11 @@
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-        <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
-        <script src="_static/clipboard.min.js"></script>
-        <script src="_static/copybutton.js"></script>
+        <script src="_static/documentation_options.js?v=f2a433a1"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/clipboard.min.js?v=a7894cd8"></script>
+        <script src="_static/copybutton.js?v=f281be69"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -92,21 +92,21 @@
            <div itemprop="articleBody">
 
   <section id="working-at-iacs">
-<h1>Working at IACS<a class="headerlink" href="#working-at-iacs" title="Permalink to this heading">¶</a></h1>
+<h1>Working at IACS<a class="headerlink" href="#working-at-iacs" title="Link to this heading">¶</a></h1>
 <section id="ookami">
-<h2>Ookami<a class="headerlink" href="#ookami" title="Permalink to this heading">¶</a></h2>
+<h2>Ookami<a class="headerlink" href="#ookami" title="Link to this heading">¶</a></h2>
 <p>Ookami seems to have 48 compute cores grouped into 4 pools of 12
 threads (there is actually a 13th core on each for OS stuff).  So an
 ideal config would be running 4 MPI each with 12 threads.</p>
 <p>Log-in to <code class="docutils literal notranslate"><span class="pre">login.ookami.stonybrook.edu</span></code></p>
 <section id="amrex-setup">
-<h3>AMReX setup<a class="headerlink" href="#amrex-setup" title="Permalink to this heading">¶</a></h3>
+<h3>AMReX setup<a class="headerlink" href="#amrex-setup" title="Link to this heading">¶</a></h3>
 <p>We need to tell AMReX about the machine.  Put the following <code class="docutils literal notranslate"><span class="pre">Make.local</span></code> file
 in <code class="docutils literal notranslate"><span class="pre">amrex/Tools/GNUmake</span></code>:</p>
 <p><a class="reference external" href="https://raw.githubusercontent.com/AMReX-Astro/workflow/main/job_scripts/iacs/Make.local">https://raw.githubusercontent.com/AMReX-Astro/workflow/main/job_scripts/iacs/Make.local</a></p>
 </section>
 <section id="cray-compilers">
-<h3>Cray compilers<a class="headerlink" href="#cray-compilers" title="Permalink to this heading">¶</a></h3>
+<h3>Cray compilers<a class="headerlink" href="#cray-compilers" title="Link to this heading">¶</a></h3>
 <p>You can only access the Cray environment on a compute note:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>srun<span class="w"> </span>-p<span class="w"> </span>short<span class="w"> </span>-N<span class="w"> </span><span class="m">1</span><span class="w"> </span>-n<span class="w"> </span><span class="m">48</span><span class="w"> </span>--pty<span class="w"> </span>bash
 </pre></div>
@@ -144,9 +144,9 @@ <h3>Cray compilers<a class="headerlink" href="#cray-compilers" title="Permalink
 </div>
 </section>
 <section id="gcc">
-<h3>GCC<a class="headerlink" href="#gcc" title="Permalink to this heading">¶</a></h3>
+<h3>GCC<a class="headerlink" href="#gcc" title="Link to this heading">¶</a></h3>
 <section id="gcc-10-2">
-<h4>GCC 10.2<a class="headerlink" href="#gcc-10-2" title="Permalink to this heading">¶</a></h4>
+<h4>GCC 10.2<a class="headerlink" href="#gcc-10-2" title="Link to this heading">¶</a></h4>
 <p>This needs to be done on the compute notes.</p>
 <p>Load modules as:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>module<span class="w"> </span>load<span class="w"> </span>slurm