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<h1 id="openmpi">OpenMPI<a class="headerlink" href="#openmpi" title="Permanent link"></a></h1>
<p>This document describes which set of OpenMPI versions in PModules are supported
in the Merlin6 cluster.</p>
<h2 id="usage">Usage<a class="headerlink" href="#usage" title="Permanent link"></a></h2>
<h3 id="srun">srun<a class="headerlink" href="#srun" title="Permanent link"></a></h3>
<p>We strongly recommend the use of <strong><code>srun</code></strong> over <strong><code>mpirun</code></strong> or <strong><code>mpiexec</code></strong>.
Using <strong><code>srun</code></strong> would properly bind tasks in to cores and less customization
is needed, while <strong><code>mpirun</code></strong> and '<strong>mpiexec</strong>' might need more advanced
configuration and should be only used by advanced users. Please, <strong><em>always</em></strong>
adapt your scripts for using <strong><code>srun</code></strong> before opening a support ticket. Also,
please contact us on any problem when using a module.</p>
<p>Example:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>srun<span class="w"> </span>./app
</span></code></pre></div>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
<p>Always run OpenMPI with the <strong><code>srun</code></strong> command. The only exception is for
advanced users, however <strong><code>srun</code></strong> is still recommended.</p>
</div>
<h3 id="openmpi-with-ucx">OpenMPI with UCX<a class="headerlink" href="#openmpi-with-ucx" title="Permanent link"></a></h3>
<p><strong>OpenMPI</strong> supports <strong>UCX</strong> starting from version 3.0, but it’s recommended to
use version 4.0 or higher due to stability and performance improvements.
<strong>UCX</strong> should be used only by advanced users, as it requires to run it with
<strong><code>mpirun</code></strong> (needs advanced knowledge) and is an exception for running MPI
without <strong><code>srun</code></strong> (<strong>UCX</strong> is not integrated at PSI within <strong><code>srun</code></strong>).</p>
<p>For running UCX, one should:</p>
<ul>
<li>add the following options to <strong><code>mpirun</code></strong>:</li>
</ul>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>-mca<span class="w"> </span>pml<span class="w"> </span>ucx<span class="w"> </span>--mca<span class="w"> </span>btl<span class="w"> </span>^vader,tcp,openib,uct<span class="w"> </span>-x<span class="w"> </span><span class="nv">UCX_NET_DEVICES</span><span class="o">=</span>mlx5_0:1
</span></code></pre></div>
<ul>
<li>or alternatively, add the following options <strong>before</strong> <strong><code>mpirun</code></strong>:</li>
</ul>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="nb">export</span><span class="w"> </span><span class="nv">OMPI_MCA_pml</span><span class="o">=</span><span class="s2">"ucx"</span>
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nb">export</span><span class="w"> </span><span class="nv">OMPI_MCA_btl</span><span class="o">=</span><span class="s2">"^vader,tcp,openib,uct"</span>
</span><span id="__span-2-3"><a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nb">export</span><span class="w"> </span><span class="nv">UCX_NET_DEVICES</span><span class="o">=</span>mlx5_0:1
</span></code></pre></div>
<p>In addition, one can add the following options for debugging purposes (visit
<a href="https://github.com/openucx/ucx/wiki/Logging">UCX Logging</a> for possible
<code>UCX_LOG_LEVEL</code> values):</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>-x<span class="w"> </span><span class="nv">UCX_LOG_LEVEL</span><span class="o">=</span>&lt;data<span class="p">|</span>debug<span class="p">|</span>warn<span class="p">|</span>info<span class="p">|</span>...&gt;<span class="w"> </span>-x<span class="w"> </span><span class="nv">UCX_LOG_FILE</span><span class="o">=</span>&lt;filename&gt;
</span></code></pre></div>
<p>This can be also added externally before the <strong><code>mpirun</code></strong> call (see below
example). Full example:</p>
<ul>
<li>Within the <strong><code>mpirun</code></strong> command:</li>
</ul>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>mpirun<span class="w"> </span>-np<span class="w"> </span><span class="nv">$SLURM_NTASKS</span><span class="w"> </span>-mca<span class="w"> </span>pml<span class="w"> </span>ucx<span class="w"> </span>--mca<span class="w"> </span>btl<span class="w"> </span>^vader,tcp,openib,uct<span class="w"> </span>-x<span class="w"> </span><span class="nv">UCX_NET_DEVICES</span><span class="o">=</span>mlx5_0:1<span class="w"> </span>-x<span class="w"> </span><span class="nv">UCX_LOG_LEVEL</span><span class="o">=</span>data<span class="w"> </span>-x<span class="w"> </span><span class="nv">UCX_LOG_FILE</span><span class="o">=</span>UCX-<span class="nv">$SLURM_JOB_ID</span>.log<span class="w"> </span>./app
</span></code></pre></div>
<ul>
<li>Outside the <strong><code>mpirun</code></strong> command:</li>
</ul>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-5-1"><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="nb">export</span><span class="w"> </span><span class="nv">OMPI_MCA_pml</span><span class="o">=</span><span class="s2">"ucx"</span>
</span><span id="__span-5-2"><a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a><span class="nb">export</span><span class="w"> </span><span class="nv">OMPI_MCA_btl</span><span class="o">=</span><span class="s2">"^vader,tcp,openib,uct"</span>
</span><span id="__span-5-3"><a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a><span class="nb">export</span><span class="w"> </span><span class="nv">UCX_NET_DEVICES</span><span class="o">=</span>mlx5_0:1
</span><span id="__span-5-4"><a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="nb">export</span><span class="w"> </span><span class="nv">UCX_LOG_LEVEL</span><span class="o">=</span>data
</span><span id="__span-5-5"><a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a><span class="nb">export</span><span class="w"> </span><span class="nv">UCX_LOG_FILE</span><span class="o">=</span>UCX-<span class="nv">$SLURM_JOB_ID</span>.log
</span><span id="__span-5-6"><a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a>
</span><span id="__span-5-7"><a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a>mpirun<span class="w"> </span>-np<span class="w"> </span><span class="nv">$SLURM_NTASKS</span><span class="w"> </span>./app
</span></code></pre></div>
<h2 id="supported-openmpi-versions">Supported OpenMPI versions<a class="headerlink" href="#supported-openmpi-versions" title="Permanent link"></a></h2>
<p>For running OpenMPI properly in a Slurm batch system, <strong><em>OpenMPI and Slurm must
be compiled accordingly</em></strong>.</p>
<p>We can find a large number of compilations of OpenMPI modules in the PModules
central repositories. However, only some of them are suitable for running in a
Slurm cluster: <strong><em>any OpenMPI versions with suffixes <code>_slurm</code> are suitable for
running in the Merlin6 cluster</em></strong>. Also, OpenMPI with suffix <code>_merlin6</code> can be
used, but these will be fully replaced by the <code>_slurm</code> series in the future (so
it can be used on any Slurm cluster at PSI). Please, <strong><em>avoid using any other
OpenMPI releases</em></strong>.</p>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
<p>Suitable <strong>OpenMPI</strong> versions for running in the Merlin6 cluster:</p>
<ul>
<li><code>openmpi/&lt;version&gt;_slurm</code> <em>[Recommended]</em></li>
<li><code>openmpi/&lt;version&gt;_merlin6</code></li>
</ul>
</div>
<h3 id="unstable-repository">'unstable' repository<a class="headerlink" href="#unstable-repository" title="Permanent link"></a></h3>
<p>New OpenMPI versions that need to be tested will be compiled first in the
<strong><code>unstable</code></strong> repository, and once validated will be moved to
<strong><code>stable</code></strong>. We can not ensure that modules in that repository are
production ready, but you can use it <em>at your own risk</em>.</p>
<p>For using <em>unstable</em> modules, you might need to load the <strong><code>unstable</code></strong>
PModules repository as follows:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-6-1"><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>module<span class="w"> </span>use<span class="w"> </span>unstable
</span></code></pre></div>
<h3 id="stable-repository">'stable' repository<a class="headerlink" href="#stable-repository" title="Permanent link"></a></h3>
<p>Officially supported <a href="https://www.open-mpi.org/software/ompi">OpenMPI versions</a>
will be available in the <strong><code>stable</code></strong> repository (which is the <em>default</em> loaded
repository).</p>
<p>For further information, please check <a href="https://www.open-mpi.org/software/ompi/"><em>Current</em> and <em>still
supported</em></a> versions in the left-hand
sidebar.</p>
<p>Usually, not more than 2 minor update releases will be present in the
<strong><code>stable</code></strong> repository. Older minor update releases will be moved to
<strong><code>deprecated</code></strong> despite are officially supported. This will ensure that
users compile new software with the latest stable versions, but we keep
available the old versions for software which was compiled with it.</p>
<h4 id="deprecated-repository">'deprecated' repository<a class="headerlink" href="#deprecated-repository" title="Permanent link"></a></h4>
<p>Old OpenMPI versions (it is, any official OpenMPI version which has been moved
to <strong>retired</strong> or <strong>ancient</strong>) will be moved to the <strong><em><code>deprecated</code></em></strong> PModules
repository. For further information, please check <a href="https://www.open-mpi.org/software/ompi/"><em>Older
versions</em></a> in the left-hand sidebar.
versions.</p>
<p>Also, as mentioned in <a href="#stable-repository">before</a>, older official supported
OpenMPI releases (minor updates) will be moved to <code>deprecated</code>.</p>
<p>For using <em>deprecated</em> modules, you might need to load the <strong><code>deprecated</code></strong>
PModules repository as follows:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-7-1"><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a>module<span class="w"> </span>use<span class="w"> </span>deprecated
</span></code></pre></div>
<p>However, this is usually not needed: when loading directly a specific version
in the <code>deprecated</code> repository, if this is not found in <code>stable</code> it try to
search and to fallback to other repositories (<code>deprecated</code> or <code>unstable</code>).</p>
<h3 id="about-missing-versions">About missing versions<a class="headerlink" href="#about-missing-versions" title="Permanent link"></a></h3>
<h4 id="missing-openmpi-versions">Missing OpenMPI versions<a class="headerlink" href="#missing-openmpi-versions" title="Permanent link"></a></h4>
<p>For legacy software, some users might require a different OpenMPI version. <strong>We
always encourage</strong> users to try one of the existing stable versions (<em>OpenMPI
always with suffix <code>_slurm</code> or <code>_merlin6</code>!</em>), as they will contain the latest
bug fixes and they usually should work. In the worst case, you can also try
with the ones in the deprecated repository (again, <em>OpenMPI always with suffix
<code>_slurm</code> or <code>_merlin6</code>!</em>), or for very old software which was based on OpenMPI
v1 you can follow the guide <a href="https://www.open-mpi.org/faq/?category=mpi-removed">FAQ: Removed MPI
constructs</a>, which provides
some easy steps for migrating from OpenMPI v1 to v2 or superior or also is
useful to find out why your code does not compile properly.</p>
<p>When, after trying the mentioned versions and guide, you are still facing
problems, please contact us. Also, please contact us if you require a newer
version with a different <code>gcc</code> or <code>intel</code> compiler (in example, Intel v19).</p>
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