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<h1 id="running-slurm-scripts">Running Slurm Scripts<a class="headerlink" href="#running-slurm-scripts" title="Permanent link"></a></h1>
<h2 id="the-rules">The rules<a class="headerlink" href="#the-rules" title="Permanent link"></a></h2>
<p>Before starting using the cluster, please read the following rules:</p>
<ol>
<li>To ease and improve <em>scheduling</em> and <em>backfilling</em>, always try to <strong>estimate and</strong> to <strong>define a proper run time</strong> of your jobs:<ul>
<li>Use <code>--time=&lt;D-HH:MM:SS&gt;</code> for that.</li>
<li>For very long runs, please consider using <strong><em><a href="#array-jobs-running-very-long-tasks-with-checkpoint-files">Job Arrays with Checkpointing</a></em></strong></li>
</ul>
</li>
<li>Try to optimize your jobs for running at most within <strong>one day</strong>. Please, consider the following:<ul>
<li>Some software can simply scale up by using more nodes while drastically reducing the run time.</li>
<li>Some software allow to save a specific state, and a second job can start from that state: <strong><em><a href="#array-jobs-running-very-long-tasks-with-checkpoint-files">Job Arrays with Checkpointing</a></em></strong> can help you with that.</li>
<li>Jobs submitted to <strong><code>hourly</code></strong> get more priority than jobs submitted to <strong><code>daily</code></strong>: always use <strong><code>hourly</code></strong> for jobs shorter than 1 hour.</li>
<li>Jobs submitted to <strong><code>daily</code></strong> get more priority than jobs submitted to <strong><code>general</code></strong>: always use <strong><code>daily</code></strong> for jobs shorter than 1 day.</li>
</ul>
</li>
<li>Is <strong>forbidden</strong> to run <strong>very short jobs</strong> as they cause a lot of overhead but also can cause severe problems to the main scheduler.<ul>
<li><strong><em>Question:</em></strong> Is my job a very short job? <strong><em>Answer:</em></strong> If it lasts in few seconds or very few minutes, yes.</li>
<li><strong><em>Question:</em></strong> How long should my job run? <strong><em>Answer:</em></strong> as the <em>Rule of Thumb</em>, from 5' would start being ok, from 15' would preferred.</li>
<li>Use <strong><em><a href="#packed-jobs-running-a-large-number-of-short-tasks">Packed Jobs</a></em></strong> for running a large number of short tasks.</li>
</ul>
</li>
<li>Do not submit hundreds of similar jobs!<ul>
<li>Use <strong><em><a href="#array-jobs-launching-a-large-number-of-related-jobs">Array Jobs</a></em></strong> for gathering jobs instead.</li>
</ul>
</li>
</ol>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
<p>Having a good estimation of the <em>time</em> needed by your jobs, a proper way for
running them, and optimizing the jobs to <em>run within one day</em> will contribute
to make the system fairly and efficiently used.</p>
</div>
<h2 id="basic-commands-for-running-batch-scripts">Basic commands for running batch scripts<a class="headerlink" href="#basic-commands-for-running-batch-scripts" title="Permanent link"></a></h2>
<ul>
<li>Use <strong><code>sbatch</code></strong> for submitting a batch script to Slurm.</li>
<li>Use <strong><code>srun</code></strong> for running parallel tasks.</li>
<li>Use <strong><code>squeue</code></strong> for checking jobs status.</li>
<li>Use <strong><code>scancel</code></strong> for cancelling/deleting a job from the queue.</li>
</ul>
<div class="admonition tip">
<p class="admonition-title">Tip</p>
<p>Use Linux <code>man</code> pages when needed (i.e. <code>man sbatch</code>), mostly for checking the available options for the above commands.</p>
</div>
<h2 id="basic-settings">Basic settings<a class="headerlink" href="#basic-settings" title="Permanent link"></a></h2>
<p>For a complete list of options and parameters available is recommended to use the <strong>man pages</strong> (i.e. <code>man sbatch</code>, <code>man srun</code>, <code>man salloc</code>).</p>
<p>Please, notice that behaviour for some parameters might change depending on the command used when running jobs (in example, <code>--exclusive</code> behaviour in <code>sbatch</code> differs from <code>srun</code>).</p>
<p>In this chapter we show the basic parameters which are usually needed in the Merlin cluster.</p>
<h3 id="common-settings">Common settings<a class="headerlink" href="#common-settings" title="Permanent link"></a></h3>
<p>The following settings are the minimum required for running a job in the Merlin CPU and GPU nodes. Please, consider taking a look to the <strong>man pages</strong> (i.e. <code>man sbatch</code>, <code>man salloc</code>, <code>man srun</code>) for more information about all possible options. Also, do not hesitate to contact us on any questions.</p>
<ul>
<li><strong>Clusters:</strong> For running jobs in the different Slurm clusters, users should to add the following option:</li>
</ul>
<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="c1">#SBATCH --clusters=&lt;cluster_name&gt; # Possible values: merlin6, gmerlin6</span>
</span></code></pre></div>
<p>Refer to the documentation of each cluster (<a href="../../slurm-configuration/"><strong><code>merlin6</code></strong></a>,<a href="../../../gmerlin6/slurm-configuration/"><strong><code>gmerlin6</code></strong></a> for further information.</p>
<ul>
<li><strong>Partitions:</strong> except when using the <em>default</em> partition for each cluster, one needs to specify the partition:</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><span class="c1">#SBATCH --partition=&lt;partition_name&gt; # Check each cluster documentation for possible values</span>
</span></code></pre></div>
<p>Refer to the documentation of each cluster (<a href="../../slurm-configuration/"><strong><code>merlin6</code></strong></a>,<a href="../../../gmerlin6/slurm-configuration/"><strong><code>gmerlin6</code></strong></a> for further information.</p>
<ul>
<li><strong>[Optional] Disabling shared nodes</strong>: by default, nodes are not exclusive. Hence, multiple users can run in the same node. One can request exclusive node usage with the following option:</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="c1">#SBATCH --exclusive # Only if you want a dedicated node</span>
</span></code></pre></div>
<ul>
<li><strong>Time</strong>: is important to define how long a job should run, according to the reality. This will help Slurm when <em>scheduling</em> and <em>backfilling</em>, and will let Slurm managing job queues in a more efficient way. This value can never exceed the <code>MaxTime</code> of the affected partition.</li>
</ul>
<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">#SBATCH --time=&lt;D-HH:MM:SS&gt; # Can not exceed the partition `MaxTime`</span>
</span></code></pre></div>
<p>Refer to the documentation of each cluster (<a href="../../slurm-configuration/"><strong><code>merlin6</code></strong></a>,<a href="../../../gmerlin6/slurm-configuration/"><strong><code>gmerlin6</code></strong></a> for further information about partition <code>MaxTime</code> values.</p>
<ul>
<li><strong>Output and error files</strong>: by default, Slurm script will generate standard output (<code>slurm-%j.out</code>, where <code>%j</code> is the job_id) and error (<code>slurm-%j.err</code>, where <code>%j</code> is the job_id) files in the directory from where the job was submitted. Users can change default name with the following options:</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><span class="c1">#SBATCH --output=&lt;filename&gt; # Can include path. Patterns accepted (i.e. %j)</span>
</span><span id="__span-4-2"><a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a><span class="c1">#SBATCH --error=&lt;filename&gt; # Can include path. Patterns accepted (i.e. %j)</span>
</span></code></pre></div>
<p>Use <strong>man sbatch</strong> (<code>man sbatch | grep -A36 '^filename pattern'</code>) for getting a list specification of <strong>filename patterns</strong>.</p>
<ul>
<li><strong>Enable/Disable Hyper-Threading</strong>: Whether a node has or not Hyper-Threading depends on the node configuration. By default, HT nodes have HT enabled, but one should specify it from the Slurm command as follows:</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="c1">#SBATCH --hint=multithread # Use extra threads with in-core multi-threading.</span>
</span><span id="__span-5-2"><a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a><span class="c1">#SBATCH --hint=nomultithread # Don't use extra threads with in-core multi-threading.</span>
</span></code></pre></div>
<p>Refer to the documentation of each cluster (<a href="../../slurm-configuration/"><strong><code>merlin6</code></strong></a>,<a href="../../../gmerlin6/slurm-configuration/"><strong><code>gmerlin6</code></strong></a> for further information about node configuration and Hyper-Threading.
Consider that, sometimes, depending on your job requirements, you might need also to setup how many <code>--ntasks-per-core</code> or <code>--cpus-per-task</code> (even other options) in addition to the <code>--hint</code> command. Please, contact us in case of doubts.</p>
<p>!!! tip
In general, for the cluster <code>merlin6</code> <span style="color:orange;"><strong>--hint=[no]multithread</strong></span> is a recommended
field. On the other hand, <span style="color:orange;"><strong>--ntasks-per-core</strong></span> is only needed when
one needs to define how a task should be handled within a core, and this
setting will not be generally used on Hybrid MPI/OpenMP jobs where
multiple cores are needed for single tasks.</p>
<h2 id="batch-script-templates">Batch script templates<a class="headerlink" href="#batch-script-templates" title="Permanent link"></a></h2>
<h3 id="cpu-based-jobs-templates">CPU-based jobs templates<a class="headerlink" href="#cpu-based-jobs-templates" title="Permanent link"></a></h3>
<p>The following examples apply to the <strong>Merlin6</strong> cluster.</p>
<h4 id="nomultithreaded-jobs-template">Nomultithreaded jobs template<a class="headerlink" href="#nomultithreaded-jobs-template" title="Permanent link"></a></h4>
<p>The following template should be used by any user submitting jobs to the Merlin6 CPU nodes:</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><span class="ch">#!/bin/bash</span>
</span><span id="__span-6-2"><a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="c1">#SBATCH --cluster=merlin6 # Cluster name</span>
</span><span id="__span-6-3"><a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="c1">#SBATCH --partition=general,daily,hourly # Specify one or multiple partitions</span>
</span><span id="__span-6-4"><a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="c1">#SBATCH --time=&lt;D-HH:MM:SS&gt; # Strongly recommended</span>
</span><span id="__span-6-5"><a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="c1">#SBATCH --output=&lt;output_file&gt; # Generate custom output file</span>
</span><span id="__span-6-6"><a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="c1">#SBATCH --error=&lt;error_file&gt; # Generate custom error file</span>
</span><span id="__span-6-7"><a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="c1">#SBATCH --hint=nomultithread # Mandatory for multithreaded jobs</span>
</span><span id="__span-6-8"><a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="c1">##SBATCH --exclusive # Uncomment if you need exclusive node usage</span>
</span><span id="__span-6-9"><a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="c1">##SBATCH --ntasks-per-core=1 # Only mandatory for multithreaded single tasks</span>
</span><span id="__span-6-10"><a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a>
</span><span id="__span-6-11"><a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a><span class="c1">## Advanced options example</span>
</span><span id="__span-6-12"><a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a><span class="c1">##SBATCH --nodes=1 # Uncomment and specify #nodes to use</span>
</span><span id="__span-6-13"><a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a><span class="c1">##SBATCH --ntasks=44 # Uncomment and specify #nodes to use</span>
</span><span id="__span-6-14"><a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></a><span class="c1">##SBATCH --ntasks-per-node=44 # Uncomment and specify #tasks per node</span>
</span><span id="__span-6-15"><a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a><span class="c1">##SBATCH --cpus-per-task=44 # Uncomment and specify the number of cores per task</span>
</span></code></pre></div>
<h4 id="multithreaded-jobs-template">Multithreaded jobs template<a class="headerlink" href="#multithreaded-jobs-template" title="Permanent link"></a></h4>
<p>The following template should be used by any user submitting jobs to the Merlin6 CPU nodes:</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="ch">#!/bin/bash</span>
</span><span id="__span-7-2"><a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1">#SBATCH --cluster=merlin6 # Cluster name</span>
</span><span id="__span-7-3"><a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="c1">#SBATCH --partition=general,daily,hourly # Specify one or multiple partitions</span>
</span><span id="__span-7-4"><a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1">#SBATCH --time=&lt;D-HH:MM:SS&gt; # Strongly recommended</span>
</span><span id="__span-7-5"><a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="c1">#SBATCH --output=&lt;output_file&gt; # Generate custom output file</span>
</span><span id="__span-7-6"><a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a><span class="c1">#SBATCH --error=&lt;error_file&gt; # Generate custom error file</span>
</span><span id="__span-7-7"><a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a><span class="c1">#SBATCH --hint=multithread # Mandatory for multithreaded jobs</span>
</span><span id="__span-7-8"><a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a><span class="c1">##SBATCH --exclusive # Uncomment if you need exclusive node usage</span>
</span><span id="__span-7-9"><a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a><span class="c1">##SBATCH --ntasks-per-core=2 # Only mandatory for multithreaded single tasks</span>
</span><span id="__span-7-10"><a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a>
</span><span id="__span-7-11"><a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a><span class="c1">## Advanced options example</span>
</span><span id="__span-7-12"><a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a><span class="c1">##SBATCH --nodes=1 # Uncomment and specify #nodes to use</span>
</span><span id="__span-7-13"><a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a><span class="c1">##SBATCH --ntasks=88 # Uncomment and specify #nodes to use</span>
</span><span id="__span-7-14"><a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a><span class="c1">##SBATCH --ntasks-per-node=88 # Uncomment and specify #tasks per node</span>
</span><span id="__span-7-15"><a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a><span class="c1">##SBATCH --cpus-per-task=88 # Uncomment and specify the number of cores per task</span>
</span></code></pre></div>
<h3 id="gpu-based-jobs-templates">GPU-based jobs templates<a class="headerlink" href="#gpu-based-jobs-templates" title="Permanent link"></a></h3>
<p>The following template should be used by any user submitting jobs to GPU nodes:</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="ch">#!/bin/bash</span>
</span><span id="__span-8-2"><a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="c1">#SBATCH --cluster=gmerlin6 # Cluster name</span>
</span><span id="__span-8-3"><a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="c1">#SBATCH --partition=gpu,gpu-short # Specify one or multiple partitions, or</span>
</span><span id="__span-8-4"><a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="c1">#SBATCH --partition=gwendolen,gwendolen-long # Only for Gwendolen users</span>
</span><span id="__span-8-5"><a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="c1">#SBATCH --gpus="&lt;type&gt;:&lt;num_gpus&gt;" # &lt;type&gt; is optional, &lt;num_gpus&gt; is mandatory</span>
</span><span id="__span-8-6"><a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a><span class="c1">#SBATCH --time=&lt;D-HH:MM:SS&gt; # Strongly recommended</span>
</span><span id="__span-8-7"><a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="c1">#SBATCH --output=&lt;output_file&gt; # Generate custom output file</span>
</span><span id="__span-8-8"><a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="c1">#SBATCH --error=&lt;error_file&gt; # Generate custom error file</span>
</span><span id="__span-8-9"><a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="c1">##SBATCH --exclusive # Uncomment if you need exclusive node usage</span>
</span><span id="__span-8-10"><a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a>
</span><span id="__span-8-11"><a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="c1">## Advanced options example</span>
</span><span id="__span-8-12"><a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a><span class="c1">##SBATCH --nodes=1 # Uncomment and specify number of nodes to use</span>
</span><span id="__span-8-13"><a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a><span class="c1">##SBATCH --ntasks=1 # Uncomment and specify number of nodes to use</span>
</span><span id="__span-8-14"><a id="__codelineno-8-14" name="__codelineno-8-14" href="#__codelineno-8-14"></a><span class="c1">##SBATCH --cpus-per-gpu=5 # Uncomment and specify the number of cores per task</span>
</span><span id="__span-8-15"><a id="__codelineno-8-15" name="__codelineno-8-15" href="#__codelineno-8-15"></a><span class="c1">##SBATCH --mem-per-gpu=16000 # Uncomment and specify the number of cores per task</span>
</span><span id="__span-8-16"><a id="__codelineno-8-16" name="__codelineno-8-16" href="#__codelineno-8-16"></a><span class="c1">##SBATCH --gpus-per-node=&lt;type&gt;:2 # Uncomment and specify the number of GPUs per node</span>
</span><span id="__span-8-17"><a id="__codelineno-8-17" name="__codelineno-8-17" href="#__codelineno-8-17"></a><span class="c1">##SBATCH --gpus-per-socket=&lt;type&gt;:2 # Uncomment and specify the number of GPUs per socket</span>
</span><span id="__span-8-18"><a id="__codelineno-8-18" name="__codelineno-8-18" href="#__codelineno-8-18"></a><span class="c1">##SBATCH --gpus-per-task=&lt;type&gt;:1 # Uncomment and specify the number of GPUs per task</span>
</span></code></pre></div>
<h2 id="advanced-configurations">Advanced configurations<a class="headerlink" href="#advanced-configurations" title="Permanent link"></a></h2>
<h3 id="array-jobs-launching-a-large-number-of-related-jobs">Array Jobs: launching a large number of related jobs<a class="headerlink" href="#array-jobs-launching-a-large-number-of-related-jobs" title="Permanent link"></a></h3>
<p>If you need to run a large number of jobs based on the same executable with systematically varying inputs,
e.g. for a parameter sweep, you can do this most easily in form of a <strong>simple array job</strong>.</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="ch">#!/bin/bash</span>
</span><span id="__span-9-2"><a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="c1">#SBATCH --job-name=test-array</span>
</span><span id="__span-9-3"><a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="c1">#SBATCH --partition=daily</span>
</span><span id="__span-9-4"><a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="c1">#SBATCH --ntasks=1</span>
</span><span id="__span-9-5"><a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a><span class="c1">#SBATCH --time=08:00:00</span>
</span><span id="__span-9-6"><a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a><span class="c1">#SBATCH --array=1-8</span>
</span><span id="__span-9-7"><a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>
</span><span id="__span-9-8"><a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a><span class="nb">echo</span><span class="w"> </span><span class="k">$(</span>date<span class="k">)</span><span class="w"> </span><span class="s2">"I am job number </span><span class="si">${</span><span class="nv">SLURM_ARRAY_TASK_ID</span><span class="si">}</span><span class="s2">"</span>
</span><span id="__span-9-9"><a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a>srun<span class="w"> </span>myprogram<span class="w"> </span>config-file-<span class="si">${</span><span class="nv">SLURM_ARRAY_TASK_ID</span><span class="si">}</span>.dat
</span></code></pre></div>
<p>This will run 8 independent jobs, where each job can use the counter
variable <code>SLURM_ARRAY_TASK_ID</code> defined by Slurm inside of the job's
environment to feed the correct input arguments or configuration file
to the "myprogram" executable. Each job will receive the same set of
configurations (e.g. time limit of 8h in the example above).</p>
<p>The jobs are independent, but they will run in parallel (if the cluster resources allow for
it). The jobs will get JobIDs like {some-number}_0 to {some-number}_7, and they also will each
have their own output file.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<ul>
<li>Do not use such jobs if you have very short tasks, since each array sub job will incur the full overhead for launching an independent Slurm job. For such cases you should used a <strong>packed job</strong> (see below).</li>
<li>If you want to control how many of these jobs can run in parallel, you can use the <code>#SBATCH --array=1-100%5</code> syntax. The <code>%5</code> will define
that only 5 sub jobs may ever run in parallel.</li>
</ul>
</div>
<p>You also can use an array job approach to run over all files in a directory, substituting the payload with</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-10-1"><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="nv">FILES</span><span class="o">=(</span>/path/to/data/*<span class="o">)</span>
</span><span id="__span-10-2"><a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>srun<span class="w"> </span>./myprogram<span class="w"> </span><span class="si">${</span><span class="nv">FILES</span><span class="p">[</span><span class="nv">$SLURM_ARRAY_TASK_ID</span><span class="p">]</span><span class="si">}</span>
</span></code></pre></div>
<p>Or for a trivial case you could supply the values for a parameter scan in form
of a argument list that gets fed to the program using the counter variable.</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-11-1"><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="nv">ARGS</span><span class="o">=(</span><span class="m">0</span>.05<span class="w"> </span><span class="m">0</span>.25<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="m">100</span><span class="o">)</span>
</span><span id="__span-11-2"><a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>srun<span class="w"> </span>./my_program.exe<span class="w"> </span><span class="si">${</span><span class="nv">ARGS</span><span class="p">[</span><span class="nv">$SLURM_ARRAY_TASK_ID</span><span class="p">]</span><span class="si">}</span>
</span></code></pre></div>
<h3 id="array-jobs-running-very-long-tasks-with-checkpoint-files">Array jobs: running very long tasks with checkpoint files<a class="headerlink" href="#array-jobs-running-very-long-tasks-with-checkpoint-files" title="Permanent link"></a></h3>
<p>If you need to run a job for much longer than the queues (partitions) permit, and
your executable is able to create checkpoint files, you can use this
strategy:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-12-1"><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="ch">#!/bin/bash</span>
</span><span id="__span-12-2"><a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="c1">#SBATCH --job-name=test-checkpoint</span>
</span><span id="__span-12-3"><a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="c1">#SBATCH --partition=general</span>
</span><span id="__span-12-4"><a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="c1">#SBATCH --ntasks=1</span>
</span><span id="__span-12-5"><a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="c1">#SBATCH --time=7-00:00:00 # each job can run for 7 days</span>
</span><span id="__span-12-6"><a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="c1">#SBATCH --cpus-per-task=1</span>
</span><span id="__span-12-7"><a id="__codelineno-12-7" name="__codelineno-12-7" href="#__codelineno-12-7"></a><span class="c1">#SBATCH --array=1-10%1 # Run a 10-job array, one job at a time.</span>
</span><span id="__span-12-8"><a id="__codelineno-12-8" name="__codelineno-12-8" href="#__codelineno-12-8"></a><span class="k">if</span><span class="w"> </span><span class="nb">test</span><span class="w"> </span>-e<span class="w"> </span>checkpointfile<span class="p">;</span><span class="w"> </span><span class="k">then</span>
</span><span id="__span-12-9"><a id="__codelineno-12-9" name="__codelineno-12-9" href="#__codelineno-12-9"></a><span class="w"> </span><span class="c1"># There is a checkpoint file;</span>
</span><span id="__span-12-10"><a id="__codelineno-12-10" name="__codelineno-12-10" href="#__codelineno-12-10"></a><span class="w"> </span>myprogram<span class="w"> </span>--read-checkp<span class="w"> </span>checkpointfile
</span><span id="__span-12-11"><a id="__codelineno-12-11" name="__codelineno-12-11" href="#__codelineno-12-11"></a><span class="k">else</span>
</span><span id="__span-12-12"><a id="__codelineno-12-12" name="__codelineno-12-12" href="#__codelineno-12-12"></a><span class="w"> </span><span class="c1"># There is no checkpoint file, start a new simulation.</span>
</span><span id="__span-12-13"><a id="__codelineno-12-13" name="__codelineno-12-13" href="#__codelineno-12-13"></a><span class="w"> </span>myprogram
</span><span id="__span-12-14"><a id="__codelineno-12-14" name="__codelineno-12-14" href="#__codelineno-12-14"></a><span class="k">fi</span>
</span></code></pre></div>
<p>The <code>%1</code> in the <code>#SBATCH --array=1-10%1</code> statement defines that only 1 subjob can ever run in parallel, so
this will result in subjob n+1 only being started when job n has finished. It will read the checkpoint file
if it is present.</p>
<h3 id="packed-jobs-running-a-large-number-of-short-tasks">Packed jobs: running a large number of short tasks<a class="headerlink" href="#packed-jobs-running-a-large-number-of-short-tasks" title="Permanent link"></a></h3>
<p>Since the launching of a Slurm job incurs some overhead, you should not submit each short task as a separate
Slurm job. Use job packing, i.e. you run the short tasks within the loop of a single Slurm job.</p>
<p>You can launch the short tasks using <code>srun</code> with the <code>--exclusive</code> switch (not to be confused with the
switch of the same name used in the SBATCH commands). This switch will ensure that only a specified
number of tasks can run in parallel.</p>
<p>As an example, the following job submission script will ask Slurm for
44 cores (threads), then it will run the =myprog= program 1000 times with
arguments passed from 1 to 1000. But with the =-N1 -n1 -c1
--exclusive= option, it will control that at any point in time only 44
instances are effectively running, each being allocated one CPU. You
can at this point decide to allocate several CPUs or tasks by adapting
the corresponding parameters.</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-13-1"><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="ch">#! /bin/bash</span>
</span><span id="__span-13-2"><a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="c1">#SBATCH --job-name=test-checkpoint</span>
</span><span id="__span-13-3"><a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="c1">#SBATCH --partition=general</span>
</span><span id="__span-13-4"><a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="c1">#SBATCH --ntasks=1</span>
</span><span id="__span-13-5"><a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="c1">#SBATCH --time=7-00:00:00</span>
</span><span id="__span-13-6"><a id="__codelineno-13-6" name="__codelineno-13-6" href="#__codelineno-13-6"></a><span class="c1">#SBATCH --ntasks=44 # defines the number of parallel tasks</span>
</span><span id="__span-13-7"><a id="__codelineno-13-7" name="__codelineno-13-7" href="#__codelineno-13-7"></a><span class="k">for</span><span class="w"> </span>i<span class="w"> </span><span class="k">in</span><span class="w"> </span><span class="o">{</span><span class="m">1</span>..1000<span class="o">}</span>
</span><span id="__span-13-8"><a id="__codelineno-13-8" name="__codelineno-13-8" href="#__codelineno-13-8"></a><span class="k">do</span>
</span><span id="__span-13-9"><a id="__codelineno-13-9" name="__codelineno-13-9" href="#__codelineno-13-9"></a><span class="w"> </span>srun<span class="w"> </span>-N1<span class="w"> </span>-n1<span class="w"> </span>-c1<span class="w"> </span>--exclusive<span class="w"> </span>./myprog<span class="w"> </span><span class="nv">$i</span><span class="w"> </span><span class="p">&amp;</span>
</span><span id="__span-13-10"><a id="__codelineno-13-10" name="__codelineno-13-10" href="#__codelineno-13-10"></a><span class="k">done</span>
</span><span id="__span-13-11"><a id="__codelineno-13-11" name="__codelineno-13-11" href="#__codelineno-13-11"></a><span class="nb">wait</span>
</span></code></pre></div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The <code>&amp;</code> at the end of the <code>srun</code> line is needed to not have the script waiting (blocking).
The <code>wait</code> command waits for all such background tasks to finish and returns the exit code.</p>
</div>
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