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<h1 id="using-pmodules">Using PModules<a class="headerlink" href="#using-pmodules" title="Permanent link"></a></h1>
<h2 id="environment-modules">Environment Modules<a class="headerlink" href="#environment-modules" title="Permanent link"></a></h2>
<p>On top of the operating system stack we provide different software using the PSI developed PModule system.</p>
<p>PModules is the official supported way and each package is deployed by a specific expert. Usually, in PModules
software which is used by many people will be found.</p>
<p>If you miss any package/versions or a software with a specific missing feature, contact us. We will study if is feasible or not to install it.</p>
<h2 id="module-release-stages">Module release stages<a class="headerlink" href="#module-release-stages" title="Permanent link"></a></h2>
<p>Three different <strong>release stages</strong> are available in Pmodules, ensuring proper software life cycling. These are the following: <strong><code>unstable</code></strong>, <strong><code>stable</code></strong> and <strong><code>deprecated</code></strong></p>
<h3 id="unstable-release-stage">Unstable release stage<a class="headerlink" href="#unstable-release-stage" title="Permanent link"></a></h3>
<p>The <strong><code>unstable</code></strong> release stage contains <em>unstable</em> releases of software. Software compilations here are usually under development or are not fully production ready.</p>
<p>This release stage is <strong>not directly visible</strong> by the end users, and needs to be explicitly invoked as follows:</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>module<span class="w"> </span>use<span class="w"> </span>unstable
</span></code></pre></div>
<p>Once software is validated and considered production ready, this is moved to the <code>stable</code> release stage.</p>
<h3 id="stable-release-stage">Stable release stage<a class="headerlink" href="#stable-release-stage" title="Permanent link"></a></h3>
<p>The <strong><code>stable</code></strong> release stage contains <em>stable</em> releases of software, which have been deeply tested and are fully supported.</p>
<p>This is the <strong><em>default</em></strong> release stage, and is visible by default. Whenever possible, users are strongly advised to use packages from this release stage.</p>
<h3 id="deprecated-release-stage">Deprecated release stage<a class="headerlink" href="#deprecated-release-stage" title="Permanent link"></a></h3>
<p>The <strong><code>deprecated</code></strong> release stage contains <em>deprecated</em> releases of software. Software in this release stage is usually deprecated or discontinued by their developers.
Also, minor versions or redundant compilations are moved here as long as there is a valid copy in the <em>stable</em> repository.</p>
<p>This release stage is <strong>not directly visible</strong> by the users, and needs to be explicitly invoked as follows:</p>
<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>module<span class="w"> </span>use<span class="w"> </span>deprecated
</span></code></pre></div>
<p>However, software moved to this release stage can be directly loaded without the need of invoking it. This ensure proper life cycling of the software, and making it transparent for the end users.</p>
<h2 id="module-overlays">Module overlays<a class="headerlink" href="#module-overlays" title="Permanent link"></a></h2>
<p>Recent Pmodules releases contain a feature called <strong>Pmodules overlays</strong>. In Merlin, overlays are used to source software from a different location.
In that way, we can have custom private versions of software in the cluster installed on high performance storage accessed over a low latency network.</p>
<p><strong>Pmodules overlays</strong> are still <strong><em>under development</em></strong>, therefore consider that <em>some features may not work or do not work as expected</em>.</p>
<p>Pmodule overlays can be used from Pmodules <code>v1.1.5</code>. However, Merlin is running Pmodules <code>v1.0.0rc10</code> as the default version.
Therefore, one needs to load first a newer version of it: this is available in the repositories and can be loaded with <strong><code>module load Pmodules/$version</code></strong> command.</p>
<p>Once running the proper Pmodules version, <strong>overlays</strong> are added (or invoked) with the <strong><code>module use $overlay_name</code></strong> command.</p>
<h3 id="overlay_merlin">overlay_merlin<a class="headerlink" href="#overlay_merlin" title="Permanent link"></a></h3>
<p>Some Merlin software is already provided through <strong>PModule overlays</strong> and has been validated for using and running it in that way.
Therefore, Melin contains an overlay called <strong><code>overlay_merlin</code></strong>. In this overlay, the software is installed in the Merlin high performance storage,
specifically in the <code>/data/software/pmodules</code> directory. In general, if another copy exists in the standard repository, we strongly recommend to use
the replica in the <code>overlay_merlin</code> overlay instead, as it provides faster access and it may also provide some customizations for the Merlin6 cluster.</p>
<p>For loading the <code>overlay_merlin</code>, please run:
</p><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>module<span class="w"> </span>load<span class="w"> </span>Pmodules/1.1.6<span class="w"> </span><span class="c1"># Or newer version</span>
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>module<span class="w"> </span>use<span class="w"> </span>overlay_merlin
</span></code></pre></div><p></p>
<p>Then, once <code>overlay_merlin</code> is invoked, it will disable central software installations with the same version (if exist), and will be replaced
by the local ones in Merlin. Releases from the central Pmodules repository which do not have a copy in the Merlin overlay will remain
visible. In example, for each ANSYS release, one can identify where it is installed by searching ANSYS in PModules with the <code>--verbose</code>
option. This will show the location of the different ANSYS releases as follows:
* For ANSYS releases installed in the central repositories, the path starts with <code>/opt/psi</code>
* For ANSYS releases installed in the Merlin6 repository (and/or overwritting the central ones), the path starts with <code>/data/software/pmodules</code></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><span class="o">(</span>base<span class="o">)</span><span class="w"> </span>❄<span class="w"> </span><span class="o">[</span>caubet_m@merlin-l-001:/data/user/caubet_m<span class="o">]</span><span class="c1"># module load Pmodules/1.1.6</span>
</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>module<span class="w"> </span>load:<span class="w"> </span>unstable<span class="w"> </span>module<span class="w"> </span>has<span class="w"> </span>been<span class="w"> </span>loaded<span class="w"> </span>--<span class="w"> </span>Pmodules/1.1.6
</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>
</span><span id="__span-3-4"><a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="o">(</span>base<span class="o">)</span><span class="w"> </span>❄<span class="w"> </span><span class="o">[</span>caubet_m@merlin-l-001:/data/user/caubet_m<span class="o">]</span><span class="c1"># module use merlin_overlay</span>
</span><span id="__span-3-5"><a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>
</span><span id="__span-3-6"><a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a><span class="o">(</span>base<span class="o">)</span><span class="w"> </span>❄<span class="w"> </span><span class="o">[</span>caubet_m@merlin-l-001:/data/user/caubet_m<span class="o">]</span><span class="c1"># module search ANSYS --verbose</span>
</span><span id="__span-3-7"><a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a>
</span><span id="__span-3-8"><a id="__codelineno-3-8" name="__codelineno-3-8" href="#__codelineno-3-8"></a>Module<span class="w"> </span>Rel.stage<span class="w"> </span>Group<span class="w"> </span>Dependencies/Modulefile
</span><span id="__span-3-9"><a id="__codelineno-3-9" name="__codelineno-3-9" href="#__codelineno-3-9"></a>-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
</span><span id="__span-3-10"><a id="__codelineno-3-10" name="__codelineno-3-10" href="#__codelineno-3-10"></a>ANSYS/2019R3<span class="w"> </span>stable<span class="w"> </span>Tools<span class="w"> </span>dependencies:
</span><span id="__span-3-11"><a id="__codelineno-3-11" name="__codelineno-3-11" href="#__codelineno-3-11"></a><span class="w"> </span>modulefile:<span class="w"> </span>/data/software/pmodules/Tools/modulefiles/ANSYS/2019R3
</span><span id="__span-3-12"><a id="__codelineno-3-12" name="__codelineno-3-12" href="#__codelineno-3-12"></a>ANSYS/2020R1<span class="w"> </span>stable<span class="w"> </span>Tools<span class="w"> </span>dependencies:
</span><span id="__span-3-13"><a id="__codelineno-3-13" name="__codelineno-3-13" href="#__codelineno-3-13"></a><span class="w"> </span>modulefile:<span class="w"> </span>/opt/psi/Tools/modulefiles/ANSYS/2020R1
</span><span id="__span-3-14"><a id="__codelineno-3-14" name="__codelineno-3-14" href="#__codelineno-3-14"></a>ANSYS/2020R1-1<span class="w"> </span>stable<span class="w"> </span>Tools<span class="w"> </span>dependencies:
</span><span id="__span-3-15"><a id="__codelineno-3-15" name="__codelineno-3-15" href="#__codelineno-3-15"></a><span class="w"> </span>modulefile:<span class="w"> </span>/opt/psi/Tools/modulefiles/ANSYS/2020R1-1
</span><span id="__span-3-16"><a id="__codelineno-3-16" name="__codelineno-3-16" href="#__codelineno-3-16"></a>ANSYS/2020R2<span class="w"> </span>stable<span class="w"> </span>Tools<span class="w"> </span>dependencies:
</span><span id="__span-3-17"><a id="__codelineno-3-17" name="__codelineno-3-17" href="#__codelineno-3-17"></a><span class="w"> </span>modulefile:<span class="w"> </span>/data/software/pmodules/Tools/modulefiles/ANSYS/2020R2
</span><span id="__span-3-18"><a id="__codelineno-3-18" name="__codelineno-3-18" href="#__codelineno-3-18"></a>ANSYS/2021R1<span class="w"> </span>stable<span class="w"> </span>Tools<span class="w"> </span>dependencies:
</span><span id="__span-3-19"><a id="__codelineno-3-19" name="__codelineno-3-19" href="#__codelineno-3-19"></a><span class="w"> </span>modulefile:<span class="w"> </span>/data/software/pmodules/Tools/modulefiles/ANSYS/2021R1
</span><span id="__span-3-20"><a id="__codelineno-3-20" name="__codelineno-3-20" href="#__codelineno-3-20"></a>ANSYS/2021R2<span class="w"> </span>stable<span class="w"> </span>Tools<span class="w"> </span>dependencies:
</span><span id="__span-3-21"><a id="__codelineno-3-21" name="__codelineno-3-21" href="#__codelineno-3-21"></a><span class="w"> </span>modulefile:<span class="w"> </span>/data/software/pmodules/Tools/modulefiles/ANSYS/2021R2
</span></code></pre></div>
<h2 id="pmodules-commands">PModules commands<a class="headerlink" href="#pmodules-commands" title="Permanent link"></a></h2>
<p>Below is listed a summary of all available commands:</p>
<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>module<span class="w"> </span>use<span class="w"> </span><span class="c1"># show all available PModule Software Groups as well as Release Stages</span>
</span><span id="__span-4-2"><a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>module<span class="w"> </span>avail<span class="w"> </span><span class="c1"># to see the list of available software packages provided via pmodules</span>
</span><span id="__span-4-3"><a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>module<span class="w"> </span>use<span class="w"> </span>unstable<span class="w"> </span><span class="c1"># to get access to a set of packages not fully tested by the community</span>
</span><span id="__span-4-4"><a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>module<span class="w"> </span>load<span class="w"> </span>&lt;package&gt;/&lt;version&gt;<span class="w"> </span><span class="c1"># to load specific software package with a specific version</span>
</span><span id="__span-4-5"><a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>module<span class="w"> </span>search<span class="w"> </span>&lt;string&gt;<span class="w"> </span><span class="c1"># to search for a specific software package and its dependencies.</span>
</span><span id="__span-4-6"><a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a>module<span class="w"> </span>list<span class="w"> </span><span class="c1"># to list which software is loaded in your environment</span>
</span><span id="__span-4-7"><a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a>module<span class="w"> </span>purge<span class="w"> </span><span class="c1"># unload all loaded packages and cleanup the environment</span>
</span></code></pre></div>
<h3 id="module-useunuse">module use/unuse<a class="headerlink" href="#module-useunuse" title="Permanent link"></a></h3>
<p>Without any parameter, <code>use</code> <strong>lists</strong> all available PModule <strong>Software Groups and Release Stages</strong>.</p>
<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>module<span class="w"> </span>use
</span></code></pre></div>
<p>When followed by a parameter, <code>use</code>/<code>unuse</code> invokes/uninvokes a PModule <strong>Software Group</strong> or <strong>Release Stage</strong>.</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>EM<span class="w"> </span><span class="c1"># Invokes the 'EM' software group</span>
</span><span id="__span-6-2"><a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>module<span class="w"> </span>unuse<span class="w"> </span>EM<span class="w"> </span><span class="c1"># Uninvokes the 'EM' software group</span>
</span><span id="__span-6-3"><a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>module<span class="w"> </span>use<span class="w"> </span>unstable<span class="w"> </span><span class="c1"># Invokes the 'unstable' Release stable</span>
</span><span id="__span-6-4"><a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a>module<span class="w"> </span>unuse<span class="w"> </span>unstable<span class="w"> </span><span class="c1"># Uninvokes the 'unstable' Release stable</span>
</span></code></pre></div>
<h3 id="module-avail">module avail<a class="headerlink" href="#module-avail" title="Permanent link"></a></h3>
<p>This option <strong>lists</strong> all available PModule <strong>Software Groups and their packages</strong>.</p>
<p>Please run <code>module avail --help</code> for further listing options.</p>
<h3 id="module-search">module search<a class="headerlink" href="#module-search" title="Permanent link"></a></h3>
<p>This is used to <strong>search</strong> for <strong>software packages</strong>. By default, if no <strong>Release Stage</strong> or <strong>Software Group</strong> is specified
in the options of the <code>module search</code> command, it will search from the already invoked <em>Software Groups</em> and <em>Release Stages</em>.
Direct package dependencies will be also showed.</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><span class="o">(</span>base<span class="o">)</span><span class="w"> </span><span class="o">[</span>caubet_m@merlin-l-001<span class="w"> </span>caubet_m<span class="o">]</span>$<span class="w"> </span>module<span class="w"> </span>search<span class="w"> </span>openmpi/4.0.5_slurm
</span><span id="__span-7-2"><a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>
</span><span id="__span-7-3"><a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>Module<span class="w"> </span>Release<span class="w"> </span>Group<span class="w"> </span>Requires
</span><span id="__span-7-4"><a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a>---------------------------------------------------------------------------
</span><span id="__span-7-5"><a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>openmpi/4.0.5_slurm<span class="w"> </span>stable<span class="w"> </span>Compiler<span class="w"> </span>gcc/8.4.0
</span><span id="__span-7-6"><a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>openmpi/4.0.5_slurm<span class="w"> </span>stable<span class="w"> </span>Compiler<span class="w"> </span>gcc/9.2.0
</span><span id="__span-7-7"><a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a>openmpi/4.0.5_slurm<span class="w"> </span>stable<span class="w"> </span>Compiler<span class="w"> </span>gcc/9.3.0
</span><span id="__span-7-8"><a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>openmpi/4.0.5_slurm<span class="w"> </span>stable<span class="w"> </span>Compiler<span class="w"> </span>intel/20.4
</span><span id="__span-7-9"><a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a>
</span><span id="__span-7-10"><a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a><span class="o">(</span>base<span class="o">)</span><span class="w"> </span><span class="o">[</span>caubet_m@merlin-l-001<span class="w"> </span>caubet_m<span class="o">]</span>$<span class="w"> </span>module<span class="w"> </span>load<span class="w"> </span>intel/20.4<span class="w"> </span>openmpi/4.0.5_slurm
</span></code></pre></div>
<p>Please run <code>module search --help</code> for further search options.</p>
<h3 id="module-loadunload">module load/unload<a class="headerlink" href="#module-loadunload" title="Permanent link"></a></h3>
<p>This loads/unloads specific software packages. Packages might have direct dependencies that need to be loaded first. Other dependencies
will be automatically loaded.</p>
<p>In the example below, the <code>openmpi/4.0.5_slurm</code> package will be loaded, however <code>gcc/9.3.0</code> must be loaded as well as this is a strict dependency. Direct dependencies must be loaded in advance. Users can load multiple packages one by one or at once. This can be useful for instance when loading a package with direct dependencies.</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-8-1"><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="c1"># Single line</span>
</span><span id="__span-8-2"><a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/9.3.0<span class="w"> </span>openmpi/4.0.5_slurm
</span><span id="__span-8-3"><a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>
</span><span id="__span-8-4"><a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="c1"># Multiple line</span>
</span><span id="__span-8-5"><a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/9.3.0
</span><span id="__span-8-6"><a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>module<span class="w"> </span>load<span class="w"> </span>openmpi/4.0.5_slurm
</span></code></pre></div>
<h4 id="module-purge">module purge<a class="headerlink" href="#module-purge" title="Permanent link"></a></h4>
<p>This command is an alternative to <code>module unload</code>, which can be used to unload <strong>all</strong> loaded module files.</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-9-1"><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>module<span class="w"> </span>purge
</span></code></pre></div>
<h2 id="when-to-request-for-new-pmodules-packages">When to request for new PModules packages<a class="headerlink" href="#when-to-request-for-new-pmodules-packages" title="Permanent link"></a></h2>
<h3 id="missing-software">Missing software<a class="headerlink" href="#missing-software" title="Permanent link"></a></h3>
<p>If you don't find a specific software and you know from other people interesing on it, it can be installed in PModules. Please contact us
and we will try to help with that. Deploying new software in PModules may take few days.</p>
<p>Usually installation of new software are possible as long as few users will use it. If you are insterested in to maintain this software,
please let us know.</p>
<h3 id="missing-version">Missing version<a class="headerlink" href="#missing-version" title="Permanent link"></a></h3>
<p>If the existing PModules versions for a specific package do not fit to your needs, is possible to ask for a new version.</p>
<p>Usually installation of newer versions will be supported, as long as few users will use it. Installation of intermediate versions can
be supported if this is strictly justified.</p>
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