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<meta name="description" content=" Using Host libraries: GPU drivers and OpenMPI BTLs May 9, 2017 / Singularity does a fantastic job of isolating you from the host so you don’thave to muck about with LD_LIBRARY_PATH, you just get exactly the libraryversions you want. However, in some situations you need to use libraryversions that match host exactly. Two common ones are NVIDIA gpudriver user-space libraries, and OpenMPI transport drivers for high performancenetworking. There are many ways to solve these problems. Some people build a container andcopy the version of the libs (installed on the host) into the container.What We will learn todayThis document describes how to use a bind mount, symlinks and ldconfig so that when the hostlibraries are updated the container does not need to be rebuilt.Note this tutorial is tested with Singularity commit 945c6ee343a1e6101e22396a90dfdb5944f442b6, which is part of the (current) development branch, and thus it should work with version 2.3 when that is released. The version of OpenMPI used is 2.1.0 (versions above 2.1 should work).EnvironmentIn our environment we run CentOS 7 hosts with: slurm located on /opt/slurm-<version> and the slurm user slurm Mellanox network cards with drivers installed to /opt/mellanox ( Specifically we run a RoCEv1 network for Lustre and MPI communications) NVIDIA GPUs with drivers installed to /lib64 OpenMPI (by default) for MPI processesCreating your imageSince we are building an ubuntu image, it may be easier to create an ubuntu VMto create the image. Alternatively you can follow the recipe here.Use the following def file to create the image.The mysterious wget line gets a list of all the libraries that the CentOS hosthas in /lib64 that we think its safe to use in the container. Specificallythese are things like nvidia drivers.Also note: in hostlibs.def we create a slurm user. Obviously if your SlurmUser is different you should change this name. We make directories for /opt and /usr/local/openmpi. We’re going to bindmount these from the host so we get all the bits of OpenMPI and Mellanox and Slurm that we need.Executing your imageOn our system we do:SINGULARITYENV_LD_LIBRARY_PATH=/usr/local/openmpi/2.1.0-gcc4/lib:/opt/munge-0.5.11/lib:/opt/slurm-16.05.4/lib:/opt/slurm-16.05.4/lib/slurm:/desired_hostlibs:/opt/mellanox/mxm/lib/export SINGULARITYENV_LD_LIBRARY_PATHthensrun singularity exec -B /usr/local/openmpi:/usr/local/openmpi -B /opt:/opt -B /lib64:/all_hostlibs hostlibs.img <path to binary> Please enable JavaScript to view the comments powered by Disqus. Site last generated: Jul 26, 2017 ">
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<h1 class="post-title" itemprop="name headline">Using Host libraries: GPU drivers and OpenMPI BTLs</h1>
<p class="post-meta"><time datetime="2017-05-09T00:00:00-04:00" itemprop="datePublished">May 9, 2017</time> /
</p>
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<div class="post-content" itemprop="articleBody">
<p>Singularity does a fantastic job of isolating you from the host so you don’t
have to muck about with <code class="highlighter-rouge">LD_LIBRARY_PATH</code>, you just get exactly the library
versions you want. However, in some situations you need to use library
versions that match host exactly. Two common ones are NVIDIA gpu
driver user-space libraries, and OpenMPI transport drivers for high performance
networking. There are many ways to solve these problems. Some people build a container and
copy the version of the libs (installed on the host) into the container.</p>
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<div id="toc"></div>
<h2 id="what-we-will-learn-today">What We will learn today</h2>
<p>This document describes how to use a bind mount, symlinks and ldconfig so that when the host
libraries are updated the container does not need to be rebuilt.</p>
<p><strong>Note</strong> this tutorial is tested with Singularity <a href="https://github.com/singularityware/singularity/commit/945c6ee343a1e6101e22396a90dfdb5944f442b6" target="_blank">commit 945c6ee343a1e6101e22396a90dfdb5944f442b6</a>,
which is part of the (current) development branch, and thus it should work with version 2.3
when that is released. The version of OpenMPI used is 2.1.0 (versions above 2.1 should work).</p>
<h2 id="environment">Environment</h2>
<p>In our environment we run CentOS 7 hosts with:</p>
<ol>
<li>slurm located on <code class="highlighter-rouge">/opt/slurm-<version></code> and the slurm user <code class="highlighter-rouge">slurm</code></li>
<li>Mellanox network cards with drivers installed to <code class="highlighter-rouge">/opt/mellanox</code> (
Specifically we run a RoCEv1 network for Lustre and MPI communications)</li>
<li>NVIDIA GPUs with drivers installed to <code class="highlighter-rouge">/lib64</code></li>
<li>OpenMPI (by default) for MPI processes</li>
</ol>
<h2 id="creating-your-image">Creating your image</h2>
<p>Since we are building an ubuntu image, it may be easier to create an ubuntu VM
to create the image. Alternatively you can follow the recipe
<a href="/building-ubuntu-rhel-host" target="_blank"> here</a>.</p>
<p>Use the following def file to create the image.</p>
<style>
/* Better styles for embedding GitHub Gists */
.gist{font-size:13px;line-height:20px;margin-bottom:20px;width:100%}
.gist pre{font-family:Menlo,Monaco,'Bitstream Vera Sans Mono','Courier New',monospace !important}
.gist-meta{font-family:Helvetica,Arial,sans-serif;font-size:13px !important}
.gist-meta a{color:#26a !important;text-decoration:none}
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</style>
<script src="https://gist.github.com/l1ll1/89b3f067d5b790ace6e6767be5ea2851.js?file=hostlibs.def"></script>
<p>The mysterious <code class="highlighter-rouge">wget</code> line gets a list of all the libraries that the CentOS host
has in <code class="highlighter-rouge">/lib64</code> that <em>we</em> think its safe to use in the container. Specifically
these are things like nvidia drivers.</p>
<style>
/* Better styles for embedding GitHub Gists */
.gist{font-size:13px;line-height:20px;margin-bottom:20px;width:100%}
.gist pre{font-family:Menlo,Monaco,'Bitstream Vera Sans Mono','Courier New',monospace !important}
.gist-meta{font-family:Helvetica,Arial,sans-serif;font-size:13px !important}
.gist-meta a{color:#26a !important;text-decoration:none}
.gist-meta a:hover{color:#0e4071 !important}
</style>
<script src="https://gist.github.com/l1ll1/89b3f067d5b790ace6e6767be5ea2851.js?file=desired_hostlibs.txt"></script>
<p>Also note:</p>
<ol>
<li>in <code class="highlighter-rouge">hostlibs.def</code> we create a slurm user. Obviously if your <code class="highlighter-rouge">SlurmUser</code> is different you should change this name.</li>
<li>We make directories for <code class="highlighter-rouge">/opt</code> and <code class="highlighter-rouge">/usr/local/openmpi</code>. We’re going to bindmount these from the host so we get all the bits of OpenMPI and Mellanox and Slurm that we need.</li>
</ol>
<h2 id="executing-your-image">Executing your image</h2>
<p>On our system we do:</p>
<div class="highlighter-rouge"><pre class="highlight"><code>SINGULARITYENV_LD_LIBRARY_PATH=/usr/local/openmpi/2.1.0-gcc4/lib:/opt/munge-0.5.11/lib:/opt/slurm-16.05.4/lib:/opt/slurm-16.05.4/lib/slurm:/desired_hostlibs:/opt/mellanox/mxm/lib/
export SINGULARITYENV_LD_LIBRARY_PATH
</code></pre>
</div>
<p>then</p>
<div class="highlighter-rouge"><pre class="highlight"><code>srun singularity exec -B /usr/local/openmpi:/usr/local/openmpi -B /opt:/opt -B /lib64:/all_hostlibs hostlibs.img <path to binary>
</code></pre>
</div>
</div>
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