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<h1 id="hardware-and-software-description">Hardware And Software Description<a class="headerlink" href="#hardware-and-software-description" title="Permanent link"></a></h1>
<h2 id="hardware">Hardware<a class="headerlink" href="#hardware" title="Permanent link"></a></h2>
<h3 id="computing-nodes">Computing Nodes<a class="headerlink" href="#computing-nodes" title="Permanent link"></a></h3>
<p>The new Merlin6 cluster contains a solution based on <strong>four</strong> <a href="https://h20195.www2.hpe.com/v2/getdocument.aspx?docname=a00016641enw"><strong>HPE Apollo k6000 Chassis</strong></a></p>
<ul>
<li><em>Three</em> of them contain 24 x <a href="https://h20195.www2.hpe.com/v2/GetDocument.aspx?docname=a00016634enw"><strong>HP Apollo XL230K Gen10</strong></a> blades.</li>
<li>A <em>fourth</em> chassis was purchased on 2021 with <a href="https://h20195.www2.hpe.com/v2/GetDocument.aspx?docname=a00016634enw"><strong>HP Apollo XL230K Gen10</strong></a> blades dedicated to few experiments. Blades have slighly different components depending on specific project requirements.</li>
</ul>
<p>The connectivity for the Merlin6 cluster is based on <strong>ConnectX-5 EDR-100Gbps</strong>, and each chassis contains:</p>
<ul>
<li>1 x <a href="https://h20195.www2.hpe.com/v2/getdocument.aspx?docname=a00016643enw">HPE Apollo InfiniBand EDR 36-port Unmanaged Switch</a><ul>
<li>24 internal EDR-100Gbps ports (1 port per blade for internal low latency connectivity)</li>
<li>12 external EDR-100Gbps ports (for external for internal low latency connectivity)</li>
</ul>
</li>
</ul>
<table>
<thead>
<tr>
<th scope="colgroup" style="vertical-align:middle;text-align:center;" colspan="8">Merlin6 CPU Computing Nodes</th>
</tr>
<tr>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Chassis</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Node</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Processor</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Sockets</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Cores</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Threads</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Scratch</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Memory</th>
</tr>
</thead>
<tbody>
<tr style="vertical-align:middle;text-align:center;" ralign="center">
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>#0</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>merlin-c-0[01-24]</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><a href="https://ark.intel.com/content/www/us/en/ark/products/120491/intel-xeon-gold-6152-processor-30-25m-cache-2-10-ghz.html">Intel Xeon Gold 6152</a></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">44</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">1.2TB</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">384GB</td>
</tr>
<tr style="vertical-align:middle;text-align:center;" ralign="center">
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>#1</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>merlin-c-1[01-24]</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><a href="https://ark.intel.com/content/www/us/en/ark/products/120491/intel-xeon-gold-6152-processor-30-25m-cache-2-10-ghz.html">Intel Xeon Gold 6152</a></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">44</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">1.2TB</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">384GB</td>
</tr>
<tr style="vertical-align:middle;text-align:center;" ralign="center">
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>#2</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>merlin-c-2[01-24]</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><a href="https://ark.intel.com/content/www/us/en/ark/products/120491/intel-xeon-gold-6152-processor-30-25m-cache-2-10-ghz.html">Intel Xeon Gold 6152</a></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">44</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">1.2TB</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">384GB</td>
</tr>
<tr style="vertical-align:middle;text-align:center;" ralign="center">
<td style="vertical-align:middle;text-align:center;" rowspan="3"><b>#3</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>merlin-c-3[01-12]</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="3"><a href="https://ark.intel.com/content/www/us/en/ark/products/199343/intel-xeon-gold-6240r-processor-35-75m-cache-2-40-ghz.html">Intel Xeon Gold 6240R</a></td>
<td style="vertical-align:middle;text-align:center;" rowspan="3">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="3">48</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="3">1.2TB</td>
<td style="vertical-align:middle;text-align:center;" rowspan="2">768GB</td>
</tr>
<tr style="vertical-align:middle;text-align:center;" ralign="center">
<td rowspan="1"><b>merlin-c-3[03-18]</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">1</td>
</tr>
<tr style="vertical-align:middle;text-align:center;" ralign="center">
<td rowspan="1"><b>merlin-c-3[19-24]</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">384GB</td>
</tr>
</tbody>
</table>
<p>Each blade contains a NVMe disk, where up to 300TB are dedicated to the O.S., and ~1.2TB are reserved for local <code>/scratch</code>.</p>
<h3 id="login-nodes">Login Nodes<a class="headerlink" href="#login-nodes" title="Permanent link"></a></h3>
<p><em>One old login node</em> (<code>merlin-l-01.psi.ch</code>) is inherit from the previous Merlin5 cluster. Its mainly use is for running some BIO services (<code>cryosparc</code>) and for submitting jobs.
<em>Two new login nodes</em> (<code>merlin-l-001.psi.ch</code>,<code>merlin-l-002.psi.ch</code>) with similar configuration to the Merlin6 computing nodes are available for the users. The mainly use
is for compiling software and submitting jobs.</p>
<p>The connectivity is based on <strong>ConnectX-5 EDR-100Gbps</strong> for the new login nodes, and <strong>ConnectIB FDR-56Gbps</strong> for the old one.</p>
<table>
<thead>
<tr>
<th scope="colgroup" style="vertical-align:middle;text-align:center;" colspan="8">Merlin6 CPU Computing Nodes</th>
</tr>
<tr>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Hardware</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Node</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Processor</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Sockets</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Cores</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Threads</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Scratch</th>
<th scope="col" style="vertical-align:middle;text-align:center;" colspan="1">Memory</th>
</tr>
</thead>
<tbody>
<tr style="vertical-align:middle;text-align:center;" ralign="center">
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>Old</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>merlin-l-01</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><a href="https://ark.intel.com/products/91768/Intel-Xeon-Processor-E5-2697A-v4-40M-Cache-2-60-GHz-">Intel Xeon E5-2697AV4</a></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">16</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">100GB</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">512GB</td>
</tr>
<tr style="vertical-align:middle;text-align:center;" ralign="center">
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>New</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><b>merlin-l-00[1,2]</b></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1"><a href="https://ark.intel.com/content/www/us/en/ark/products/120491/intel-xeon-gold-6152-processor-30-25m-cache-2-10-ghz.html">Intel Xeon Gold 6152</a></td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">44</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">2</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">1.8TB</td>
<td style="vertical-align:middle;text-align:center;" rowspan="1">384GB</td>
</tr>
</tbody>
</table>
<h3 id="storage">Storage<a class="headerlink" href="#storage" title="Permanent link"></a></h3>
<p>The storage node is based on the <a href="https://lenovopress.com/lp0626-lenovo-distributed-storage-solution-for-ibm-spectrum-scale-x3650-m5">Lenovo Distributed Storage Solution for IBM Spectrum Scale</a>.</p>
<ul>
<li>2 x <strong>Lenovo DSS G240</strong> systems, each one composed by 2 IO Nodes <strong>ThinkSystem SR650</strong> mounting 4 x <strong>Lenovo Storage D3284 High Density Expansion</strong> enclosures.</li>
<li>Each IO node has a connectivity of 400Gbps (4 x EDR 100Gbps ports, 2 of them are <strong>ConnectX-5</strong> and 2 are <strong>ConnectX-4</strong>).</li>
</ul>
<p>The storage solution is connected to the HPC clusters through 2 x <strong>Mellanox SB7800 InfiniBand 1U Switches</strong> for high availability and load balancing.</p>
<h3 id="network">Network<a class="headerlink" href="#network" title="Permanent link"></a></h3>
<p>Merlin6 cluster connectivity is based on the <a href="https://en.wikipedia.org/wiki/InfiniBand"><strong>Infiniband</strong></a> technology. This allows fast access with very low latencies to the data as well as running
extremely efficient MPI-based jobs:</p>
<ul>
<li>Connectivity amongst different computing nodes on different chassis ensures up to 1200Gbps of aggregated bandwidth.</li>
<li>Inter connectivity (communication amongst computing nodes in the same chassis) ensures up to 2400Gbps of aggregated bandwidth.</li>
<li>Communication to the storage ensures up to 800Gbps of aggregated bandwidth.</li>
</ul>
<p>Merlin6 cluster currently contains 5 Infiniband Managed switches and 3 Infiniband Unmanaged switches (one per HP Apollo chassis):</p>
<ul>
<li>1 x <strong>MSX6710</strong> (FDR) for connecting old GPU nodes, old login nodes and MeG cluster to the Merlin6 cluster (and storage). No High Availability mode possible.</li>
<li>2 x <strong>MSB7800</strong> (EDR) for connecting Login Nodes, Storage and other nodes in High Availability mode.</li>
<li>3 x <strong>HP EDR Unmanaged</strong> switches, each one embedded to each HP Apollo k6000 chassis solution.</li>
<li>2 x <strong>MSB7700</strong> (EDR) are the top switches, interconnecting the Apollo unmanaged switches and the managed switches (MSX6710, MSB7800).</li>
</ul>
<h2 id="software">Software<a class="headerlink" href="#software" title="Permanent link"></a></h2>
<p>In Merlin6, we try to keep the latest software stack release to get the latest features and improvements. Due to this, <strong>Merlin6</strong> runs:</p>
<ul>
<li><a href="https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/7/html/7.9_release_notes/index"><strong>RedHat Enterprise Linux 7</strong></a></li>
<li><a href="https://slurm.schedmd.com/"><strong>Slurm</strong></a>, we usually try to keep it up to date with the most recent versions.</li>
<li><a href="https://www.ibm.com/support/knowledgecenter/en/STXKQY_5.0.2/ibmspectrumscale502_welcome.html"><strong>GPFS v5</strong></a></li>
<li><a href="https://www.mellanox.com/products/infiniband-drivers/linux/mlnx_ofed"><strong>MLNX_OFED LTS v.5.2-2.2.0.0 or newer</strong></a> for all <strong>ConnectX-5</strong> or superior cards.<ul>
<li><a href="https://www.mellanox.com/products/infiniband-drivers/linux/mlnx_ofed">MLNX_OFED LTS v.4.9-2.2.4.0</a> is installed for remaining <strong>ConnectX-3</strong> and <strong>ConnectIB</strong> cards.</li>
</ul>
</li>
</ul>
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