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zingale committed Feb 22, 2025
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6 changes: 6 additions & 0 deletions _sources/nersc-workflow.rst.txt
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Expand Up @@ -7,6 +7,9 @@ Managing Jobs at NERSC
Perlmutter
----------

GPU jobs
^^^^^^^^

Perlmutter has 1536 GPU nodes, each with 4 NVIDIA A100 GPUs -- therefore it is best to use
4 MPI tasks per node.

Expand Down Expand Up @@ -36,6 +39,9 @@ includes the restart logic to allow for job chaining.
warning signal and the end of the allocation by adjusting the
``#SBATCH --signal=B:URG@<n>`` line at the top of the script.

CPU jobs
^^^^^^^^

Below is an example that runs on CPU-only nodes. Here ``ntasks-per-node``
refers to number of MPI processes (used for distributed parallelism) per node,
and ``cpus-per-task`` refers to number of hyper threads used per task
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8 changes: 0 additions & 8 deletions _static/basic.css
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pre {
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66 changes: 33 additions & 33 deletions _static/pygments.css
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13 changes: 8 additions & 5 deletions _static/searchtools.js
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Expand Up @@ -513,9 +513,11 @@ const Search = {
// perform the search on the required terms
searchTerms.forEach((word) => {
const files = [];
// find documents, if any, containing the query word in their text/title term indices
// use Object.hasOwnProperty to avoid mismatching against prototype properties
const arr = [
{ files: terms[word], score: Scorer.term },
{ files: titleTerms[word], score: Scorer.title },
{ files: terms.hasOwnProperty(word) ? terms[word] : undefined, score: Scorer.term },
{ files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, score: Scorer.title },
];
// add support for partial matches
if (word.length > 2) {
Expand Down Expand Up @@ -547,8 +549,9 @@ const Search = {

// set score for the word in each file
recordFiles.forEach((file) => {
if (!scoreMap.has(file)) scoreMap.set(file, {});
scoreMap.get(file)[word] = record.score;
if (!scoreMap.has(file)) scoreMap.set(file, new Map());
const fileScores = scoreMap.get(file);
fileScores.set(word, record.score);
});
});

Expand Down Expand Up @@ -587,7 +590,7 @@ const Search = {
break;

// select one (max) score for the file.
const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
const score = Math.max(...wordList.map((w) => scoreMap.get(file).get(w)));
// add result to the result list
results.push([
docNames[file],
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2 changes: 1 addition & 1 deletion alcf.html
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Expand Up @@ -7,7 +7,7 @@

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Working at ALCF &mdash; AMReX-Astro 1.0 documentation</title>
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2 changes: 1 addition & 1 deletion genindex.html
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<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Index &mdash; AMReX-Astro 1.0 documentation</title>
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2 changes: 1 addition & 1 deletion iacs.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Working at IACS &mdash; AMReX-Astro 1.0 documentation</title>
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2 changes: 1 addition & 1 deletion index.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>AMReX Astrophysics Suite &mdash; AMReX-Astro 1.0 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
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2 changes: 1 addition & 1 deletion nersc-compilers.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Compiling at NERSC &mdash; AMReX-Astro 1.0 documentation</title>
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2 changes: 1 addition & 1 deletion nersc-hpss.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Archiving Data to HPSS &mdash; AMReX-Astro 1.0 documentation</title>
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<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
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2 changes: 1 addition & 1 deletion nersc-visualization.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Visualization at NERSC &mdash; AMReX-Astro 1.0 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
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12 changes: 10 additions & 2 deletions nersc-workflow.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Managing Jobs at NERSC &mdash; AMReX-Astro 1.0 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
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Expand Down Expand Up @@ -53,6 +53,8 @@
<li class="toctree-l2"><a class="reference internal" href="nersc-compilers.html">Compiling at NERSC</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Managing Jobs at NERSC</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#perlmutter">Perlmutter</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#gpu-jobs">GPU jobs</a></li>
<li class="toctree-l4"><a class="reference internal" href="#cpu-jobs">CPU jobs</a></li>
<li class="toctree-l4"><a class="reference internal" href="#filesystems">Filesystems</a></li>
<li class="toctree-l4"><a class="reference internal" href="#chaining">Chaining</a></li>
</ul>
Expand Down Expand Up @@ -97,6 +99,8 @@
<h1>Managing Jobs at NERSC<a class="headerlink" href="#managing-jobs-at-nersc" title="Link to this heading"></a></h1>
<section id="perlmutter">
<h2>Perlmutter<a class="headerlink" href="#perlmutter" title="Link to this heading"></a></h2>
<section id="gpu-jobs">
<h3>GPU jobs<a class="headerlink" href="#gpu-jobs" title="Link to this heading"></a></h3>
<p>Perlmutter has 1536 GPU nodes, each with 4 NVIDIA A100 GPUs – therefore it is best to use
4 MPI tasks per node.</p>
<div class="admonition note">
Expand All @@ -118,7 +122,7 @@ <h2>Perlmutter<a class="headerlink" href="#perlmutter" title="Link to this headi
<span class="c1">#SBATCH -N 16</span>
<span class="c1">#SBATCH --ntasks-per-node=4</span>
<span class="c1">#SBATCH --gpus-per-task=1</span>
<span class="c1">#SBATCH --gpu-bind=map_gpu:0,1,2,3</span>
<span class="c1">#SBATCH --gpu-bind=none</span>
<span class="c1">#SBATCH --signal=B:URG@120</span>

<span class="nb">export</span><span class="w"> </span><span class="nv">CASTRO_EXEC</span><span class="o">=</span>./Castro2d.gnu.MPI.CUDA.SMPLSDC.ex
Expand Down Expand Up @@ -213,6 +217,9 @@ <h2>Perlmutter<a class="headerlink" href="#perlmutter" title="Link to this headi
warning signal and the end of the allocation by adjusting the
<code class="docutils literal notranslate"><span class="pre">#SBATCH</span> <span class="pre">--signal=B:URG&#64;&lt;n&gt;</span></code> line at the top of the script.</p>
</div>
</section>
<section id="cpu-jobs">
<h3>CPU jobs<a class="headerlink" href="#cpu-jobs" title="Link to this heading"></a></h3>
<p>Below is an example that runs on CPU-only nodes. Here <code class="docutils literal notranslate"><span class="pre">ntasks-per-node</span></code>
refers to number of MPI processes (used for distributed parallelism) per node,
and <code class="docutils literal notranslate"><span class="pre">cpus-per-task</span></code> refers to number of hyper threads used per task
Expand Down Expand Up @@ -336,6 +343,7 @@ <h2>Perlmutter<a class="headerlink" href="#perlmutter" title="Link to this headi
</pre></div></div><p>and an estimate of the start time can be found via:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span class="prompt1">squeue<span class="w"> </span>--me<span class="w"> </span>--start</span>
</pre></div></div><p>to cancel a job, you would use <code class="docutils literal notranslate"><span class="pre">scancel</span></code>.</p>
</section>
<section id="filesystems">
<h3>Filesystems<a class="headerlink" href="#filesystems" title="Link to this heading"></a></h3>
<p>We can run on the common filesystem, CFS, to share files with everyone
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4 changes: 3 additions & 1 deletion nersc.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Working at NERSC &mdash; AMReX-Astro 1.0 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
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Expand Down Expand Up @@ -99,6 +99,8 @@ <h1>Working at NERSC<a class="headerlink" href="#working-at-nersc" title="Link t
</li>
<li class="toctree-l1"><a class="reference internal" href="nersc-workflow.html">Managing Jobs at NERSC</a><ul>
<li class="toctree-l2"><a class="reference internal" href="nersc-workflow.html#perlmutter">Perlmutter</a><ul>
<li class="toctree-l3"><a class="reference internal" href="nersc-workflow.html#gpu-jobs">GPU jobs</a></li>
<li class="toctree-l3"><a class="reference internal" href="nersc-workflow.html#cpu-jobs">CPU jobs</a></li>
<li class="toctree-l3"><a class="reference internal" href="nersc-workflow.html#filesystems">Filesystems</a></li>
<li class="toctree-l3"><a class="reference internal" href="nersc-workflow.html#chaining">Chaining</a></li>
</ul>
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Batch Visualization on Andes &mdash; AMReX-Astro 1.0 documentation</title>
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Compiling at OLCF &mdash; AMReX-Astro 1.0 documentation</title>
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