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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2">
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<div class="md-nav__link md-nav__container">
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<a href="../../../news/" class="md-nav__link ">
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<span class="md-ellipsis">
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News
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</span>
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</a>
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<label class="md-nav__link " for="__nav_2" id="__nav_2_label" tabindex="0">
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<span class="md-nav__icon md-icon"></span>
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</div>
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_2">
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<span class="md-nav__icon md-icon"></span>
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News
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2_2">
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<label class="md-nav__link" for="__nav_2_2" id="__nav_2_2_label" tabindex="0">
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<span class="md-ellipsis">
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Archive
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</span>
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_2_2_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_2_2">
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<span class="md-nav__icon md-icon"></span>
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Archive
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../../news/archive/2026/" class="md-nav__link">
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<span class="md-ellipsis">
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2026
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../../news/archive/2024/" class="md-nav__link">
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<span class="md-ellipsis">
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2024
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../../news/archive/2019/" class="md-nav__link">
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<span class="md-ellipsis">
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2019
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</span>
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</a>
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</ul>
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</nav>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3">
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<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
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<span class="md-ellipsis">
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Merlin 7
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</span>
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_3">
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<span class="md-nav__icon md-icon"></span>
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Merlin 7
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3_1">
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<label class="md-nav__link" for="__nav_3_1" id="__nav_3_1_label" tabindex="0">
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<span class="md-ellipsis">
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Quick Start Guide
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</span>
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_3_1_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_3_1">
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<span class="md-nav__icon md-icon"></span>
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Quick Start Guide
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<a href="../../../merlin7/01-Quick-Start-Guide/introduction/" class="md-nav__link">
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<span class="md-ellipsis">
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Introduction
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../../merlin7/01-Quick-Start-Guide/code-of-conduct/" class="md-nav__link">
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<span class="md-ellipsis">
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Code Of Conduct
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../../merlin7/01-Quick-Start-Guide/requesting-accounts/" class="md-nav__link">
|
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|
|
<span class="md-ellipsis">
|
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|
Requesting Merlin Accounts
|
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</span>
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</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../../merlin7/01-Quick-Start-Guide/requesting-projects/" class="md-nav__link">
|
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|
<span class="md-ellipsis">
|
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|
Requesting a Merlin Project
|
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</span>
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</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../../merlin7/01-Quick-Start-Guide/accessing-interactive-nodes/" class="md-nav__link">
|
|
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|
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|
|
<span class="md-ellipsis">
|
|
|
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|
|
Accessing Interactive Nodes
|
|
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|
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|
|
</span>
|
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|
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</a>
|
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</li>
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<li class="md-nav__item">
|
|
<a href="../../../merlin7/01-Quick-Start-Guide/accessing-slurm/" class="md-nav__link">
|
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|
|
<span class="md-ellipsis">
|
|
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|
|
Accessing Slurm Cluster
|
|
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|
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|
|
</span>
|
|
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|
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|
|
|
</a>
|
|
</li>
|
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</ul>
|
|
</nav>
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</li>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3_2">
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<label class="md-nav__link" for="__nav_3_2" id="__nav_3_2_label" tabindex="0">
|
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|
|
<span class="md-ellipsis">
|
|
|
|
|
|
How To Use Merlin7
|
|
|
|
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|
|
</span>
|
|
|
|
|
|
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
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|
|
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_3_2_label" aria-expanded="false">
|
|
<label class="md-nav__title" for="__nav_3_2">
|
|
<span class="md-nav__icon md-icon"></span>
|
|
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|
How To Use Merlin7
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|
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</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/connect-from-linux/" class="md-nav__link">
|
|
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|
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|
|
<span class="md-ellipsis">
|
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|
|
Connecting from a Linux Client
|
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|
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</span>
|
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</a>
|
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</li>
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|
<li class="md-nav__item">
|
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<a href="../../../merlin7/02-How-To-Use-Merlin/connect-from-windows/" class="md-nav__link">
|
|
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|
|
<span class="md-ellipsis">
|
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|
|
Connecting from a Windows Client
|
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|
|
</span>
|
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|
</a>
|
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</li>
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|
<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/connect-from-macos/" class="md-nav__link">
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|
|
<span class="md-ellipsis">
|
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|
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|
|
Connecting from a MacOS Client
|
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|
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</span>
|
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</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/storage/" class="md-nav__link">
|
|
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|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Merlin7 Storage
|
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|
|
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|
|
</span>
|
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|
|
</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/transfer-data/" class="md-nav__link">
|
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|
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|
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|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Transferring Data
|
|
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|
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</span>
|
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|
</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../../merlin7/02-How-To-Use-Merlin/archive/" class="md-nav__link">
|
|
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|
<span class="md-ellipsis">
|
|
|
|
|
|
Archive & PSI Data Catalog
|
|
|
|
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|
|
</span>
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</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/nomachine/" class="md-nav__link">
|
|
|
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|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Remote Desktop Access to Merlin7
|
|
|
|
|
|
|
|
</span>
|
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|
|
</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/merlin-rmount/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Using merlin_rmount
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
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|
|
</a>
|
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</li>
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|
|
<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/merlin_tools/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Merlin7 Tools
|
|
|
|
|
|
|
|
</span>
|
|
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|
|
</a>
|
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</li>
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|
<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/ssh-keys/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Configuring SSH Keys in Merlin
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
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|
|
<li class="md-nav__item">
|
|
<a href="../../../merlin7/02-How-To-Use-Merlin/kerberos/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Kerberos and AFS authentication
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
|
</li>
|
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<a href="../../quick-start-guide/code-of-conduct/" class="md-nav__link">
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<span class="md-ellipsis">
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Code Of Conduct
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../quick-start-guide/requesting-accounts/" class="md-nav__link">
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<span class="md-ellipsis">
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Requesting Merlin Accounts
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../quick-start-guide/requesting-projects/" class="md-nav__link">
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<span class="md-ellipsis">
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Requesting a Merlin Project
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../quick-start-guide/accessing-interactive-nodes/" class="md-nav__link">
|
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<span class="md-ellipsis">
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Accessing Interactive Nodes
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</span>
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</a>
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</li>
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<li class="md-nav__item">
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<a href="../../quick-start-guide/accessing-slurm/" class="md-nav__link">
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<span class="md-ellipsis">
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Accessing Slurm Cluster
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</span>
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</a>
|
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</li>
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</ul>
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</nav>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2">
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<label class="md-nav__link" for="__nav_4_2" id="__nav_4_2_label" tabindex="">
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<span class="md-ellipsis">
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How To Use Merlin
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</span>
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
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<label class="md-nav__title" for="__nav_4_2">
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<span class="md-nav__icon md-icon"></span>
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How To Use Merlin
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</label>
|
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
|
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<a href="../../how-to-use-merlin/connect-from-linux/" class="md-nav__link">
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<span class="md-ellipsis">
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Connecting from a Linux Client
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</span>
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</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../how-to-use-merlin/connect-from-windows/" class="md-nav__link">
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<span class="md-ellipsis">
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Connecting from a Windows Client
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</span>
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</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../how-to-use-merlin/connect-from-macos/" class="md-nav__link">
|
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<span class="md-ellipsis">
|
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Connecting from a MacOS Client
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</span>
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</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../how-to-use-merlin/storage/" class="md-nav__link">
|
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<span class="md-ellipsis">
|
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|
Merlin6 Storage
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</span>
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</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../how-to-use-merlin/transfer-data/" class="md-nav__link">
|
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|
|
<span class="md-ellipsis">
|
|
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|
|
Transferring Data
|
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</span>
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</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../how-to-use-merlin/archive/" class="md-nav__link">
|
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|
|
<span class="md-ellipsis">
|
|
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|
|
Archive & PSI Data Catalog
|
|
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|
|
|
|
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</span>
|
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</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../how-to-use-merlin/ssh-keys/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Configuring SSH Keys in Merlin
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
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</li>
|
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<li class="md-nav__item">
|
|
<a href="../../how-to-use-merlin/kerberos/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Kerberos and AFS authentication
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
</a>
|
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</li>
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<li class="md-nav__item">
|
|
<a href="../../how-to-use-merlin/using-modules/" class="md-nav__link">
|
|
|
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|
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|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Using PModules
|
|
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|
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</span>
|
|
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|
|
</a>
|
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3">
|
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<label class="md-nav__link" for="__nav_4_3" id="__nav_4_3_label" tabindex="">
|
|
|
|
|
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|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Slurm General Documentation
|
|
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|
|
|
</span>
|
|
|
|
|
|
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
|
|
|
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
|
|
<label class="md-nav__title" for="__nav_4_3">
|
|
<span class="md-nav__icon md-icon"></span>
|
|
|
|
|
|
Slurm General Documentation
|
|
|
|
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</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
|
|
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<li class="md-nav__item">
|
|
<a href="../../slurm-general-docs/slurm-basic-commands/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Slurm Basic Commands
|
|
|
|
|
|
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</span>
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</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../slurm-general-docs/running-jobs/" class="md-nav__link">
|
|
|
|
|
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|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Running Slurm Scripts
|
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</span>
|
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</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../slurm-general-docs/interactive-jobs/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Running Interactive Jobs
|
|
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|
|
|
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</span>
|
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</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../slurm-general-docs/slurm-examples/" class="md-nav__link">
|
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|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Slurm Examples
|
|
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|
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</span>
|
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</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../slurm-general-docs/monitoring/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Monitoring
|
|
|
|
|
|
|
|
</span>
|
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|
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|
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</a>
|
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</li>
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</ul>
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</nav>
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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|
|
|
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|
|
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4">
|
|
|
|
|
|
<label class="md-nav__link" for="__nav_4_4" id="__nav_4_4_label" tabindex="">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
GPU Cluster
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
|
|
|
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
|
|
<label class="md-nav__title" for="__nav_4_4">
|
|
<span class="md-nav__icon md-icon"></span>
|
|
|
|
|
|
GPU Cluster
|
|
|
|
|
|
</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../../gmerlin6/cluster-introduction/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Introduction
|
|
|
|
|
|
|
|
</span>
|
|
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|
|
|
|
|
</a>
|
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</li>
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<li class="md-nav__item">
|
|
<a href="../../../gmerlin6/hardware-and-software-description/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Hardware And Software Description
|
|
|
|
|
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|
|
</span>
|
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</a>
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</li>
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<li class="md-nav__item">
|
|
<a href="../../../gmerlin6/slurm-configuration/" class="md-nav__link">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Slurm cluster 'gmerlin6'
|
|
|
|
|
|
|
|
</span>
|
|
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|
|
</a>
|
|
</li>
|
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</ul>
|
|
</nav>
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_5">
|
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|
|
<label class="md-nav__link" for="__nav_4_5" id="__nav_4_5_label" tabindex="">
|
|
|
|
|
|
|
|
<span class="md-ellipsis">
|
|
|
|
|
|
Jupyterhub
|
|
|
|
|
|
|
|
</span>
|
|
|
|
|
|
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
|
|
|
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_5_label" aria-expanded="false">
|
|
<label class="md-nav__title" for="__nav_4_5">
|
|
<span class="md-nav__icon md-icon"></span>
|
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Jupyterhub
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|
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</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
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<li class="md-nav__item">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M10 20H6V4h7v5h5v3.1l2-2V8l-6-6H6c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h4zm10.2-7c.1 0 .3.1.4.2l1.3 1.3c.2.2.2.6 0 .8l-1 1-2.1-2.1 1-1c.1-.1.2-.2.4-.2m0 3.9L14.1 23H12v-2.1l6.1-6.1z"></path></svg>
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<h1 id="gothic">GOTHIC<a class="headerlink" href="#gothic" title="Permanent link">¶</a></h1>
|
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<h2 id="installation">Installation<a class="headerlink" href="#installation" title="Permanent link">¶</a></h2>
|
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<p>Gothic is locally installed in Merlin in the following directory:</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>/data/project/general/software/gothic
|
|
</span></code></pre></div>
|
|
<p>Multiple versions are available. As of August 22, 2022, the latest installed
|
|
version is <strong>Gothic 8.3 QA</strong>.</p>
|
|
<p>Future releases will be placed in the PSI Modules system, therefore, loading it
|
|
through PModules will be possible at some point. However, in the meantime one
|
|
has to use the existing installations present in
|
|
<code>/data/project/general/software/gothic</code>.</p>
|
|
<h2 id="running-gothic">Running Gothic<a class="headerlink" href="#running-gothic" title="Permanent link">¶</a></h2>
|
|
<h3 id="general-requirements">General requirements<a class="headerlink" href="#general-requirements" title="Permanent link">¶</a></h3>
|
|
<p>When running Gothic in interactive or batch mode, one has to consider
|
|
the following requirements:</p>
|
|
<ul>
|
|
<li><strong>Use always one node only</strong>: Gothic runs a single instance.
|
|
Therefore, it can not run on multiple nodes. Adding option <code>--nodes=1-1</code> or
|
|
<code>-N 1-1</code> is strongly recommended: this will prevent Slurm to allocate
|
|
multiple nodes if the Slurm allocation definition is ambiguous.</li>
|
|
<li><strong>Use one task only</strong>: Gothic spawns one main process, which then will
|
|
spawn multiple threads depending on the number of available cores.
|
|
Therefore, one has to specify 1 task (<code>--ntasks=1</code> or <code>-n 1</code>).</li>
|
|
<li><strong>Use multiple CPUs</strong>: since Gothic will spawn multiple threads, then
|
|
multiple CPUs can be used. Adding <code>--cpus-per-task=<num_cpus></code> or <code>-c
|
|
<num_cpus></code> is in general recommended. Notice that <code><num_cpus></code> must never
|
|
exceed the maximum number of CPUS in a compute node (usually <em>88</em>).</li>
|
|
<li><strong>Use multithread</strong>: Gothic is an OpenMP based software, therefore,
|
|
running in hyper-threading mode is strongly recommended. Use the option
|
|
<code>--hint=multithread</code> for enforcing hyper-threading.</li>
|
|
<li><strong>[Optional]</strong> <em>Memory setup</em>: The default memory per CPU (4000MB)
|
|
is usually enough for running Gothic. If you require more memory, you can
|
|
always set the <code>--mem=<mem_in_MB></code> option. This is in general <em>not
|
|
necessary</em>.</li>
|
|
</ul>
|
|
<h3 id="interactive">Interactive<a class="headerlink" href="#interactive" title="Permanent link">¶</a></h3>
|
|
<p><strong>Is not allowed to run CPU intensive interactive jobs in the login nodes</strong>.
|
|
Only applications capable to limit the number of cores are allowed to run for
|
|
longer time. Also, <strong>running in the login nodes is not efficient</strong>, since
|
|
resources are shared with other processes and users.</p>
|
|
<p>Is possible to submit interactive jobs to the cluster by allocating a full
|
|
compute node, or even by allocating a few cores only. This will grant dedicated
|
|
CPUs and resources and in general it will not affect other users.</p>
|
|
<p>For interactive jobs, is strongly recommended to use the <code>hourly</code> partition,
|
|
which usually has a good availability of nodes.</p>
|
|
<p>For longer runs, one should use the <code>daily</code> (or <code>general</code>) partition. However,
|
|
getting interactive access to nodes on these partitions is sometimes more
|
|
difficult if the cluster is pretty full.</p>
|
|
<p>To submit an interactive job, consider the following requirements:</p>
|
|
<ul>
|
|
<li><strong>X11 forwarding must be enabled</strong>: Gothic spawns an interactive
|
|
window which requires X11 forwarding when using it remotely, therefore
|
|
using the Slurm option <code>--x11</code> is necessary.</li>
|
|
<li><strong>Ensure that the scratch area is accessible</strong>: For running Gothic,
|
|
one has to define a scratch area with the <code>GTHTMP</code> environment variable.
|
|
There are two options:</li>
|
|
<li>
|
|
<p><strong>Use local scratch</strong>: Each compute node has its own <code>/scratch</code> area.
|
|
This area is independent to any other node, therefore not visible by other
|
|
nodes. Using the top directory <code>/scratch</code> for interactive jobs is the
|
|
simplest way, and it can be defined before or after the allocation
|
|
creation, 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><span class="c1"># Example 1: Define GTHTMP before the allocation</span>
|
|
</span><span id="__span-1-2"><a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GTHTMP</span><span class="o">=</span>/scratch
|
|
</span><span id="__span-1-3"><a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>salloc<span class="w"> </span>...
|
|
</span><span id="__span-1-4"><a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a>
|
|
</span><span id="__span-1-5"><a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a><span class="c1"># Example 2: Define GTHTMP after the allocation</span>
|
|
</span><span id="__span-1-6"><a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>salloc<span class="w"> </span>...
|
|
</span><span id="__span-1-7"><a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GTHTMP</span><span class="o">=</span>/scratch
|
|
</span></code></pre></div>
|
|
<p>Notice that if you want to create a custom sub-directory (i.e.
|
|
<code>/scratch/$USER</code>, one has to create the sub-directory on every new
|
|
allocation! In example:</p>
|
|
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># Example 1:</span>
|
|
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GTHTMP</span><span class="o">=</span>/scratch/<span class="nv">$USER</span>
|
|
</span><span id="__span-2-3"><a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>salloc<span class="w"> </span>...
|
|
</span><span id="__span-2-4"><a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>mkdir<span class="w"> </span>-p<span class="w"> </span><span class="nv">$GTHTMP</span>
|
|
</span><span id="__span-2-5"><a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>
|
|
</span><span id="__span-2-6"><a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a><span class="c1"># Example 2:</span>
|
|
</span><span id="__span-2-7"><a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>salloc<span class="w"> </span>...
|
|
</span><span id="__span-2-8"><a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GTHTMP</span><span class="o">=</span>/scratch/<span class="nv">$USER</span>
|
|
</span><span id="__span-2-9"><a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>mkdir<span class="w"> </span>-p<span class="w"> </span><span class="nv">$GTHTMP</span>
|
|
</span></code></pre></div>
|
|
<p>Creating sub-directories makes the process more complex, therefore using
|
|
just <code>/scratch</code> is simpler and recommended.
|
|
2. <strong>Shared scratch</strong>: Using shared scratch allows to have a directory
|
|
visible from all compute nodes and login nodes. Therefore, one can use
|
|
<code>/shared-scratch</code> to achieve the same as in <strong>1.</strong>, but creating a
|
|
sub-directory needs to be done just once.</p>
|
|
<p>Please, consider that <code>/scratch</code> usually provides better performance and,
|
|
in addition, will offload the main storage. Therefore, using <strong>local
|
|
scratch</strong> is strongly recommended. Use the shared scratch only when
|
|
strongly necessary.</p>
|
|
</li>
|
|
<li>
|
|
<p><strong>Use the <code>hourly</code> partition</strong>: Using the <code>hourly</code> partition is
|
|
recommended for running interactive jobs (latency is in general lower).
|
|
However, <code>daily</code> and <code>general</code> are also available if you expect longer
|
|
runs, but in these cases you should expect longer waiting times.</p>
|
|
</li>
|
|
</ul>
|
|
<p>These requirements are in addition to the requirements previously described in
|
|
the <a href="#general-requirements">General requirements</a> section.</p>
|
|
<h4 id="interactive-allocations-examples">Interactive allocations: examples<a class="headerlink" href="#interactive-allocations-examples" title="Permanent link">¶</a></h4>
|
|
<ul>
|
|
<li>Requesting a full node:</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>salloc<span class="w"> </span>--partition<span class="o">=</span>hourly<span class="w"> </span>-N<span class="w"> </span><span class="m">1</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1</span><span class="w"> </span>-c<span class="w"> </span><span class="m">88</span><span class="w"> </span>--hint<span class="o">=</span>multithread<span class="w"> </span>--x11<span class="w"> </span>--exclusive<span class="w"> </span>--mem<span class="o">=</span><span class="m">0</span>
|
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</span></code></pre></div>
|
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<ul>
|
|
<li>Requesting 22 CPUs from a node, with default memory per CPU (4000MB/CPU):</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="nv">num_cpus</span><span class="o">=</span><span class="m">22</span>
|
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</span><span id="__span-4-2"><a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>salloc<span class="w"> </span>--partition<span class="o">=</span>hourly<span class="w"> </span>-N<span class="w"> </span><span class="m">1</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1</span><span class="w"> </span>-c<span class="w"> </span><span class="nv">$num_cpus</span><span class="w"> </span>--hint<span class="o">=</span>multithread<span class="w"> </span>--x11
|
|
</span></code></pre></div>
|
|
<h3 id="batch-job">Batch job<a class="headerlink" href="#batch-job" title="Permanent link">¶</a></h3>
|
|
<p>The Slurm cluster is mainly used by non interactive batch jobs: Users submit a
|
|
job, which goes into a queue, and waits until Slurm can assign resources to it.
|
|
In general, the longer the job, the longer the waiting time, unless there are
|
|
enough free resources to inmediately start running it.</p>
|
|
<p>Running Gothic in a Slurm batch script is pretty simple. One has to mainly
|
|
consider the requirements described in the <a href="#general-requirements">General
|
|
requirements</a> section, and:</p>
|
|
<ul>
|
|
<li><strong>Use local scratch</strong> for running batch jobs. In general, defining
|
|
<code>GTHTMP</code> in a batch script is simpler than on an allocation. If you plan to
|
|
run multiple jobs in the same node, you can even create a second
|
|
sub-directory level based on the Slurm Job ID:</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>mkdir<span class="w"> </span>-p<span class="w"> </span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</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">GTHTMP</span><span class="o">=</span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</span>
|
|
</span><span id="__span-5-3"><a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>...<span class="w"> </span><span class="c1"># Run Gothic here</span>
|
|
</span><span id="__span-5-4"><a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a>rm<span class="w"> </span>-rf<span class="w"> </span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</span>
|
|
</span></code></pre></div>
|
|
<p>Temporary data generated by the job in <code>GTHTMP</code> must be removed at the end of
|
|
the job, as showed above.</p>
|
|
<h4 id="batch-script-examples">Batch script: examples<a class="headerlink" href="#batch-script-examples" title="Permanent link">¶</a></h4>
|
|
<ul>
|
|
<li>Requesting a full node:</li>
|
|
</ul>
|
|
<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 -l</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 --job-name=Gothic</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 --time=3-00:00:00</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 --partition=general</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 --nodes=1</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 --ntasks=1</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 --cpus-per-task=88</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 --hint=multithread</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 --exclusive</span>
|
|
</span><span id="__span-6-10"><a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="c1">#SBATCH --mem=0</span>
|
|
</span><span id="__span-6-11"><a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a><span class="c1">#SBATCH --clusters=merlin6</span>
|
|
</span><span id="__span-6-12"><a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a>
|
|
</span><span id="__span-6-13"><a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a><span class="nv">INPUT_FILE</span><span class="o">=</span><span class="s1">'MY_INPUT.SIN'</span>
|
|
</span><span id="__span-6-14"><a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></a>
|
|
</span><span id="__span-6-15"><a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a>mkdir<span class="w"> </span>-p<span class="w"> </span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</span>
|
|
</span><span id="__span-6-16"><a id="__codelineno-6-16" name="__codelineno-6-16" href="#__codelineno-6-16"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GTHTMP</span><span class="o">=</span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</span>
|
|
</span><span id="__span-6-17"><a id="__codelineno-6-17" name="__codelineno-6-17" href="#__codelineno-6-17"></a>
|
|
</span><span id="__span-6-18"><a id="__codelineno-6-18" name="__codelineno-6-18" href="#__codelineno-6-18"></a>/data/project/general/software/gothic/gothic8.3qa/bin/gothic_s.sh<span class="w"> </span><span class="nv">$INPUT_FILE</span><span class="w"> </span>-m<span class="w"> </span>-np<span class="w"> </span><span class="nv">$SLURM_CPUS_PER_TASK</span>
|
|
</span><span id="__span-6-19"><a id="__codelineno-6-19" name="__codelineno-6-19" href="#__codelineno-6-19"></a><span class="nv">gth_exit_code</span><span class="o">=</span><span class="nv">$?</span>
|
|
</span><span id="__span-6-20"><a id="__codelineno-6-20" name="__codelineno-6-20" href="#__codelineno-6-20"></a>
|
|
</span><span id="__span-6-21"><a id="__codelineno-6-21" name="__codelineno-6-21" href="#__codelineno-6-21"></a><span class="c1"># Clean up data in /scratch</span>
|
|
</span><span id="__span-6-22"><a id="__codelineno-6-22" name="__codelineno-6-22" href="#__codelineno-6-22"></a>rm<span class="w"> </span>-rf<span class="w"> </span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</span>
|
|
</span><span id="__span-6-23"><a id="__codelineno-6-23" name="__codelineno-6-23" href="#__codelineno-6-23"></a>
|
|
</span><span id="__span-6-24"><a id="__codelineno-6-24" name="__codelineno-6-24" href="#__codelineno-6-24"></a><span class="c1"># Return exit code from GOTHIC</span>
|
|
</span><span id="__span-6-25"><a id="__codelineno-6-25" name="__codelineno-6-25" href="#__codelineno-6-25"></a><span class="nb">exit</span><span class="w"> </span><span class="nv">$gth_exit_code</span>
|
|
</span></code></pre></div>
|
|
<ul>
|
|
<li>Requesting 22 CPUs from a node, with default memory per CPU (4000MB/CPU):</li>
|
|
</ul>
|
|
<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 -l</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 --job-name=Gothic</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 --time=3-00:00:00</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 --partition=general</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 --nodes=1</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 --ntasks=1</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 --cpus-per-task=22</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 --hint=multithread</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 --clusters=merlin6</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="nv">INPUT_FILE</span><span class="o">=</span><span class="s1">'MY_INPUT.SIN'</span>
|
|
</span><span id="__span-7-12"><a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a>
|
|
</span><span id="__span-7-13"><a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a>mkdir<span class="w"> </span>-p<span class="w"> </span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</span>
|
|
</span><span id="__span-7-14"><a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GTHTMP</span><span class="o">=</span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</span>
|
|
</span><span id="__span-7-15"><a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a>
|
|
</span><span id="__span-7-16"><a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a>/data/project/general/software/gothic/gothic8.3qa/bin/gothic_s.sh<span class="w"> </span><span class="nv">$INPUT_FILE</span><span class="w"> </span>-m<span class="w"> </span>-np<span class="w"> </span><span class="nv">$SLURM_CPUS_PER_TASK</span>
|
|
</span><span id="__span-7-17"><a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a><span class="nv">gth_exit_code</span><span class="o">=</span><span class="nv">$?</span>
|
|
</span><span id="__span-7-18"><a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a>
|
|
</span><span id="__span-7-19"><a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a><span class="c1"># Clean up data in /scratch</span>
|
|
</span><span id="__span-7-20"><a id="__codelineno-7-20" name="__codelineno-7-20" href="#__codelineno-7-20"></a>rm<span class="w"> </span>-rf<span class="w"> </span>/scratch/<span class="nv">$USER</span>/<span class="nv">$SLURM_JOB_ID</span>
|
|
</span><span id="__span-7-21"><a id="__codelineno-7-21" name="__codelineno-7-21" href="#__codelineno-7-21"></a>
|
|
</span><span id="__span-7-22"><a id="__codelineno-7-22" name="__codelineno-7-22" href="#__codelineno-7-22"></a><span class="c1"># Return exit code from GOTHIC</span>
|
|
</span><span id="__span-7-23"><a id="__codelineno-7-23" name="__codelineno-7-23" href="#__codelineno-7-23"></a><span class="nb">exit</span><span class="w"> </span><span class="nv">$gth_exit_code</span>
|
|
</span></code></pre></div>
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