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<h1 id="known-problems">Known Problems<a class="headerlink" href="#known-problems" title="Permanent link"></a></h1>
<h2 id="common-errors">Common errors<a class="headerlink" href="#common-errors" title="Permanent link"></a></h2>
<h3 id="illegal-instruction-error">Illegal instruction error<a class="headerlink" href="#illegal-instruction-error" title="Permanent link"></a></h3>
<p>It may happened that your code, compiled on one machine will not be executed on another throwing exception like <strong>"(Illegal instruction)"</strong>.
This is usually because the software was compiled with a set of instructions newer than the ones available in the node where the software runs,
and it mostly depends on the processor generation.</p>
<p>In example, <code>merlin-l-001</code> and <code>merlin-l-002</code> contain a newer generation of processors than the old GPUs nodes, or than the Merlin5 cluster.
Hence, unless one compiles the software with compatibility with set of instructions from older processors, it will not run on old nodes.
Sometimes, this is properly set by default at the compilation time, but sometimes is not.</p>
<p>For GCC, please refer to <a href="https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html">GCC x86 Options</a> for compiling options. In case of doubts, contact us.</p>
<h2 id="slurm">Slurm<a class="headerlink" href="#slurm" title="Permanent link"></a></h2>
<h3 id="sbatch-using-one-core-despite-setting-c-cpus-per-task">sbatch using one core despite setting -c/--cpus-per-task<a class="headerlink" href="#sbatch-using-one-core-despite-setting-c-cpus-per-task" title="Permanent link"></a></h3>
<p>From <strong>Slurm v22.05.6</strong>, the behavior of <code>srun</code> has changed. Merlin has been updated to this version since <em>Tuesday 13.12.2022</em>.</p>
<p><code>srun</code> will no longer read in <code>SLURM_CPUS_PER_TASK</code>, which is typically set when defining <code>-c/--cpus-per-task</code> in the <code>sbatch</code> command.
This means you will implicitly have to specify <code>-c\--cpus-per-task</code> also on your <code>srun</code> calls, or set the new <code>SRUN_CPUS_PER_TASK</code> environment variable to accomplish the same thing.
Therefore, unless this is implicitly specified, <code>srun</code> will use only one Core per task (resulting in 2 CPUs per task when multithreading is enabled)</p>
<p>An example for setting up <code>srun</code> with <code>-c\--cpus-per-task</code>:</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><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"># cat mysbatch_method1</span>
</span><span id="__span-0-2"><a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="c1">#!/bin/bash</span>
</span><span id="__span-0-3"><a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="c1">#SBATCH -n 1</span>
</span><span id="__span-0-4"><a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="c1">#SBATCH --cpus-per-task=8</span>
</span><span id="__span-0-5"><a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a>
</span><span id="__span-0-6"><a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="nb">echo</span><span class="w"> </span><span class="s1">'From Slurm v22.05.8 srun does not inherit $SLURM_CPUS_PER_TASK'</span>
</span><span id="__span-0-7"><a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>srun<span class="w"> </span>python<span class="w"> </span>-c<span class="w"> </span><span class="s2">"import os; print(os.sched_getaffinity(0))"</span>
</span><span id="__span-0-8"><a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a>
</span><span id="__span-0-9"><a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a><span class="nb">echo</span><span class="w"> </span><span class="s1">'One has to implicitly specify $SLURM_CPUS_PER_TASK'</span>
</span><span id="__span-0-10"><a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a><span class="nb">echo</span><span class="w"> </span><span class="s1">'In this example, by setting -c/--cpus-per-task in srun'</span>
</span><span id="__span-0-11"><a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a>srun<span class="w"> </span>--cpus-per-task<span class="o">=</span><span class="nv">$SLURM_CPUS_PER_TASK</span><span class="w"> </span>python<span class="w"> </span>-c<span class="w"> </span><span class="s2">"import os; print(os.sched_getaffinity(0))"</span>
</span><span id="__span-0-12"><a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a>
</span><span id="__span-0-13"><a id="__codelineno-0-13" name="__codelineno-0-13" href="#__codelineno-0-13"></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"># sbatch mysbatch_method1</span>
</span><span id="__span-0-14"><a id="__codelineno-0-14" name="__codelineno-0-14" href="#__codelineno-0-14"></a>Submitted<span class="w"> </span>batch<span class="w"> </span>job<span class="w"> </span><span class="m">8000813</span>
</span><span id="__span-0-15"><a id="__codelineno-0-15" name="__codelineno-0-15" href="#__codelineno-0-15"></a>
</span><span id="__span-0-16"><a id="__codelineno-0-16" name="__codelineno-0-16" href="#__codelineno-0-16"></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"># cat slurm-8000813.out</span>
</span><span id="__span-0-17"><a id="__codelineno-0-17" name="__codelineno-0-17" href="#__codelineno-0-17"></a>From<span class="w"> </span>Slurm<span class="w"> </span>v22.05.8<span class="w"> </span>srun<span class="w"> </span>does<span class="w"> </span>not<span class="w"> </span>inherit<span class="w"> </span><span class="nv">$SLURM_CPUS_PER_TASK</span>
</span><span id="__span-0-18"><a id="__codelineno-0-18" name="__codelineno-0-18" href="#__codelineno-0-18"></a><span class="o">{</span><span class="m">1</span>,<span class="w"> </span><span class="m">45</span><span class="o">}</span>
</span><span id="__span-0-19"><a id="__codelineno-0-19" name="__codelineno-0-19" href="#__codelineno-0-19"></a>One<span class="w"> </span>has<span class="w"> </span>to<span class="w"> </span>implicitly<span class="w"> </span>specify<span class="w"> </span><span class="nv">$SLURM_CPUS_PER_TASK</span>
</span><span id="__span-0-20"><a id="__codelineno-0-20" name="__codelineno-0-20" href="#__codelineno-0-20"></a>In<span class="w"> </span>this<span class="w"> </span>example,<span class="w"> </span>by<span class="w"> </span>setting<span class="w"> </span>-c/--cpus-per-task<span class="w"> </span><span class="k">in</span><span class="w"> </span>srun
</span><span id="__span-0-21"><a id="__codelineno-0-21" name="__codelineno-0-21" href="#__codelineno-0-21"></a><span class="o">{</span><span class="m">1</span>,<span class="w"> </span><span class="m">2</span>,<span class="w"> </span><span class="m">3</span>,<span class="w"> </span><span class="m">4</span>,<span class="w"> </span><span class="m">45</span>,<span class="w"> </span><span class="m">46</span>,<span class="w"> </span><span class="m">47</span>,<span class="w"> </span><span class="m">48</span><span class="o">}</span>
</span></code></pre></div>
<p>An example to accomplish the same thing with the <code>SRUN_CPUS_PER_TASK</code> environment variable:</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><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"># cat mysbatch_method2</span>
</span><span id="__span-1-2"><a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="c1">#!/bin/bash</span>
</span><span id="__span-1-3"><a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="c1">#SBATCH -n 1</span>
</span><span id="__span-1-4"><a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="c1">#SBATCH --cpus-per-task=8</span>
</span><span id="__span-1-5"><a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>
</span><span id="__span-1-6"><a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a><span class="nb">echo</span><span class="w"> </span><span class="s1">'From Slurm v22.05.8 srun does not inherit $SLURM_CPUS_PER_TASK'</span>
</span><span id="__span-1-7"><a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a>srun<span class="w"> </span>python<span class="w"> </span>-c<span class="w"> </span><span class="s2">"import os; print(os.sched_getaffinity(0))"</span>
</span><span id="__span-1-8"><a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>
</span><span id="__span-1-9"><a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a><span class="nb">echo</span><span class="w"> </span><span class="s1">'One has to implicitly specify $SLURM_CPUS_PER_TASK'</span>
</span><span id="__span-1-10"><a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a><span class="nb">echo</span><span class="w"> </span><span class="s1">'In this example, by setting an environment variable SRUN_CPUS_PER_TASK'</span>
</span><span id="__span-1-11"><a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a><span class="nb">export</span><span class="w"> </span><span class="nv">SRUN_CPUS_PER_TASK</span><span class="o">=</span><span class="nv">$SLURM_CPUS_PER_TASK</span>
</span><span id="__span-1-12"><a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a>srun<span class="w"> </span>python<span class="w"> </span>-c<span class="w"> </span><span class="s2">"import os; print(os.sched_getaffinity(0))"</span>
</span><span id="__span-1-13"><a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>
</span><span id="__span-1-14"><a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></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"># sbatch mysbatch_method2</span>
</span><span id="__span-1-15"><a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>Submitted<span class="w"> </span>batch<span class="w"> </span>job<span class="w"> </span><span class="m">8000815</span>
</span><span id="__span-1-16"><a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a>
</span><span id="__span-1-17"><a id="__codelineno-1-17" name="__codelineno-1-17" href="#__codelineno-1-17"></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"># cat slurm-8000815.out</span>
</span><span id="__span-1-18"><a id="__codelineno-1-18" name="__codelineno-1-18" href="#__codelineno-1-18"></a>From<span class="w"> </span>Slurm<span class="w"> </span>v22.05.8<span class="w"> </span>srun<span class="w"> </span>does<span class="w"> </span>not<span class="w"> </span>inherit<span class="w"> </span><span class="nv">$SLURM_CPUS_PER_TASK</span>
</span><span id="__span-1-19"><a id="__codelineno-1-19" name="__codelineno-1-19" href="#__codelineno-1-19"></a><span class="o">{</span><span class="m">1</span>,<span class="w"> </span><span class="m">45</span><span class="o">}</span>
</span><span id="__span-1-20"><a id="__codelineno-1-20" name="__codelineno-1-20" href="#__codelineno-1-20"></a>One<span class="w"> </span>has<span class="w"> </span>to<span class="w"> </span>implicitly<span class="w"> </span>specify<span class="w"> </span><span class="nv">$SLURM_CPUS_PER_TASK</span>
</span><span id="__span-1-21"><a id="__codelineno-1-21" name="__codelineno-1-21" href="#__codelineno-1-21"></a>In<span class="w"> </span>this<span class="w"> </span>example,<span class="w"> </span>by<span class="w"> </span>setting<span class="w"> </span>an<span class="w"> </span>environment<span class="w"> </span>variable<span class="w"> </span>SRUN_CPUS_PER_TASK
</span><span id="__span-1-22"><a id="__codelineno-1-22" name="__codelineno-1-22" href="#__codelineno-1-22"></a><span class="o">{</span><span class="m">1</span>,<span class="w"> </span><span class="m">2</span>,<span class="w"> </span><span class="m">3</span>,<span class="w"> </span><span class="m">4</span>,<span class="w"> </span><span class="m">45</span>,<span class="w"> </span><span class="m">46</span>,<span class="w"> </span><span class="m">47</span>,<span class="w"> </span><span class="m">48</span><span class="o">}</span>
</span></code></pre></div>
<h2 id="general-topics">General topics<a class="headerlink" href="#general-topics" title="Permanent link"></a></h2>
<h3 id="default-shell">Default SHELL<a class="headerlink" href="#default-shell" title="Permanent link"></a></h3>
<p>In general, <strong><code>/bin/bash</code> is the recommended default user's SHELL</strong> when working in Merlin.</p>
<p>Some users might notice that BASH is not the default SHELL when logging in to Merlin systems, or they might need to run a different SHELL.
This is probably because when the PSI account was requested, no SHELL description was specified or a different one was requested explicitly by the requestor.
Users can check which is the default SHELL specified in the PSI account with the following command:</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>getent<span class="w"> </span>passwd<span class="w"> </span><span class="nv">$USER</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>awk<span class="w"> </span>-F:<span class="w"> </span><span class="s1">'{print $NF}'</span>
</span></code></pre></div>
<p>If SHELL does not correspond to the one you need to use, you should request a central change for it.
This is because Merlin accounts are central PSI accounts. Hence, <strong>change must be requested</strong> via <a href="index.md#psi-service-now">PSI Service Now</a>.</p>
<p>Alternatively, if you work on other PSI Linux systems but for Merlin you need a different SHELL type, a temporary change can be performed during login startup.
You can update one of the following files:</p>
<ul>
<li><code>~/.login</code></li>
<li><code>~/.profile</code></li>
<li>Any <code>rc</code> or <code>profile</code> file in your home directory (i.e. <code>.cshrc</code>, <code>.bashrc</code>, <code>.bash_profile</code>, etc.)</li>
</ul>
<p>with the following lines:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># Replace MY_SHELL with the bash type you need</span>
</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="nv">MY_SHELL</span><span class="o">=</span>/bin/bash
</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="nb">exec</span><span class="w"> </span><span class="nv">$MY_SHELL</span><span class="w"> </span>-l
</span></code></pre></div>
<p>Notice that available <em>shells</em> can be found in the following file:</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>cat<span class="w"> </span>/etc/shells
</span></code></pre></div>
<h3 id="3d-acceleration-opengl-vs-mesa">3D acceleration: OpenGL vs Mesa<a class="headerlink" href="#3d-acceleration-opengl-vs-mesa" title="Permanent link"></a></h3>
<p>Some applications can run with OpenGL support. This is only possible when the node contains a GPU card.</p>
<p>In general, X11 with Mesa Driver is the recommended method as it will work in all cases (no need of GPUs). In example, for ParaView:</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>load<span class="w"> </span>paraview
</span><span id="__span-5-2"><a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>paraview-mesa<span class="w"> </span>paraview<span class="w"> </span><span class="c1"># 'paraview --mesa' for old releases</span>
</span></code></pre></div>
<p>However, if one needs to run with OpenGL support, this is still possible by running <code>vglrun</code>. In example, for running Paraview:</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>load<span class="w"> </span>paraview
</span><span id="__span-6-2"><a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>vglrun<span class="w"> </span>paraview
</span></code></pre></div>
<p>Officially, the supported method for running <code>vglrun</code> is by using the <a href="../../merlin7/02-How-To-Use-Merlin/nomachine/">NoMachine remote desktop</a>.
Running <code>vglrun</code> it's also possible using SSH with X11 Forwarding. However, it's very slow and it's only recommended when running
in Slurm (from <a href="../../merlin7/02-How-To-Use-Merlin/nomachine/">NoMachine</a>). Please, avoid running <code>vglrun</code> over SSH from a desktop or laptop.</p>
<h2 id="software">Software<a class="headerlink" href="#software" title="Permanent link"></a></h2>
<h3 id="ansys">ANSYS<a class="headerlink" href="#ansys" title="Permanent link"></a></h3>
<p>Sometimes, running ANSYS/Fluent requires X11 support. For that, one should run fluent 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>load<span class="w"> </span>ANSYS
</span><span id="__span-7-2"><a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>fluent<span class="w"> </span>-driver<span class="w"> </span>x11
</span></code></pre></div>
<h3 id="paraview">Paraview<a class="headerlink" href="#paraview" title="Permanent link"></a></h3>
<p>For running Paraview, one can run it with Mesa support or OpenGL support. Please refer to <a href="#3d-acceleration-opengl-vs-mesa">OpenGL vs Mesa</a> for
further information about how to run it.</p>
<h3 id="module-command-not-found">Module command not found<a class="headerlink" href="#module-command-not-found" title="Permanent link"></a></h3>
<p>In some circumstances the module command may not be initialized properly. For instance, you may see the following error upon logon:</p>
<div class="language-text highlight"><span class="filename">Text Only</span><pre><span></span><code><span id="__span-8-1"><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>bash: module: command not found
</span></code></pre></div>
<p>The most common cause for this is a custom <code>.bashrc</code> file which fails to source the global <code>/etc/bashrc</code> responsible for setting up PModules in some OS versions. To fix this, add the following to <code>$HOME/.bashrc</code>:</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><span class="k">if</span><span class="w"> </span><span class="o">[</span><span class="w"> </span>-f<span class="w"> </span>/etc/bashrc<span class="w"> </span><span class="o">]</span><span class="p">;</span><span class="w"> </span><span class="k">then</span>
</span><span id="__span-9-2"><a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="w"> </span>.<span class="w"> </span>/etc/bashrc
</span><span id="__span-9-3"><a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="k">fi</span>
</span></code></pre></div>
<p>It can also be fixed temporarily in an existing terminal by running <code>. /etc/bashrc</code> manually.</p>
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