HPCE/gitea-pages
0
0
Fork 0
Code Issues 3 Pull Requests Actions Packages Projects Activity
Files
0630bafb43cc9b996f31220bdd9f09ea6b5f90e4
gitea-pages/merlin7/05-Software-Support/lammps/index.html
Gitea Actions 0630bafb43 Deployed acde833 with MkDocs version: 1.6.1
2026-02-10 11:25:50 +00:00

4758 lines
84 KiB
HTML
Raw Blame History

<!DOCTYPE html><html lang="en" class="no-js"><head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<link rel="canonical" href="https://hpce.pages.psi.ch/merlin7/05-Software-Support/lammps/">
<link rel="prev" href="../quantum-espresso/">
<link rel="next" href="../gromacs/">
<link rel="icon" href="../../../images/favicon.ico">
<meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.7.0">
<title>LAMMPS - HPCE User Documentation</title>
<link rel="stylesheet" href="../../../assets/stylesheets/main.618322db.min.css">
<link rel="stylesheet" href="../../../assets/stylesheets/palette.ab4e12ef.min.css">
<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&amp;display=fallback">
<style>:root{--md-text-font:"Roboto";--md-code-font:"Roboto Mono"}</style>
<link rel="stylesheet" href="../../../css/custom-nav.css">
<script>__md_scope=new URL("../../..",location),__md_hash=e=>[...e].reduce(((e,_)=>(e<<5)-e+_.charCodeAt(0)),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
<link href="../../../assets/stylesheets/glightbox.min.css" rel="stylesheet"><script src="../../../assets/javascripts/glightbox.min.js"></script><style id="glightbox-style">
html.glightbox-open { overflow: initial; height: 100%; }
.gslide-title { margin-top: 0px; user-select: text; }
.gslide-desc { color: #666; user-select: text; }
.gslide-image img { background: white; }
.gscrollbar-fixer { padding-right: 15px; }
.gdesc-inner { font-size: 0.75rem; }
body[data-md-color-scheme="slate"] .gdesc-inner { background: var(--md-default-bg-color); }
body[data-md-color-scheme="slate"] .gslide-title { color: var(--md-default-fg-color); }
body[data-md-color-scheme="slate"] .gslide-desc { color: var(--md-default-fg-color); }
</style></head>
<body dir="ltr" data-md-color-scheme="default" data-md-color-primary="indigo" data-md-color-accent="indigo">
<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
<input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
<label class="md-overlay" for="__drawer"></label>
<div data-md-component="skip">
<a href="#lammps" class="md-skip">
Skip to content
</a>
</div>
<div data-md-component="announce">
</div>
<header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
<nav class="md-header__inner md-grid" aria-label="Header">
<a href="../../.." title="HPCE User Documentation" class="md-header__button md-logo" aria-label="HPCE User Documentation" data-md-component="logo">
<img src="../../../images/hpce_logo.png" alt="logo">
</a>
<label class="md-header__button md-icon" for="__drawer">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z"></path></svg>
</label>
<div class="md-header__title" data-md-component="header-title">
<div class="md-header__ellipsis">
<div class="md-header__topic">
<span class="md-ellipsis">
HPCE User Documentation
</span>
</div>
<div class="md-header__topic" data-md-component="header-topic">
<span class="md-ellipsis">
LAMMPS
</span>
</div>
</div>
</div>
<form class="md-header__option" data-md-component="palette">
<input class="md-option" data-md-color-media="(prefers-color-scheme)" data-md-color-scheme="default" data-md-color-primary="indigo" data-md-color-accent="indigo" aria-label="Switch to light mode" type="radio" name="__palette" id="__palette_0">
<label class="md-header__button md-icon" title="Switch to light mode" for="__palette_1" hidden>
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3.9 12c0-1.71 1.39-3.1 3.1-3.1h4V7H7a5 5 0 0 0-5 5 5 5 0 0 0 5 5h4v-1.9H7c-1.71 0-3.1-1.39-3.1-3.1M8 13h8v-2H8zm9-6h-4v1.9h4c1.71 0 3.1 1.39 3.1 3.1s-1.39 3.1-3.1 3.1h-4V17h4a5 5 0 0 0 5-5 5 5 0 0 0-5-5"></path></svg>
</label>
<input class="md-option" data-md-color-media="(prefers-color-scheme: light)" data-md-color-scheme="default" data-md-color-primary="indigo" data-md-color-accent="indigo" aria-label="Switch to dark mode" type="radio" name="__palette" id="__palette_1">
<label class="md-header__button md-icon" title="Switch to dark mode" for="__palette_2" hidden>
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M17 7H7a5 5 0 0 0-5 5 5 5 0 0 0 5 5h10a5 5 0 0 0 5-5 5 5 0 0 0-5-5m0 8a3 3 0 0 1-3-3 3 3 0 0 1 3-3 3 3 0 0 1 3 3 3 3 0 0 1-3 3"></path></svg>
</label>
<input class="md-option" data-md-color-media="(prefers-color-scheme: dark)" data-md-color-scheme="slate" data-md-color-primary="indigo" data-md-color-accent="indigo" aria-label="Switch to system preference" type="radio" name="__palette" id="__palette_2">
<label class="md-header__button md-icon" title="Switch to system preference" for="__palette_0" hidden>
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M17 7H7a5 5 0 0 0-5 5 5 5 0 0 0 5 5h10a5 5 0 0 0 5-5 5 5 0 0 0-5-5M7 15a3 3 0 0 1-3-3 3 3 0 0 1 3-3 3 3 0 0 1 3 3 3 3 0 0 1-3 3"></path></svg>
</label>
</form>
<script>var palette=__md_get("__palette");if(palette&&palette.color){if("(prefers-color-scheme)"===palette.color.media){var media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']");palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent")}for(var[key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script>
<label class="md-header__button md-icon" for="__search">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.52 6.52 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5"></path></svg>
</label>
<div class="md-search" data-md-component="search" role="dialog">
<label class="md-search__overlay" for="__search"></label>
<div class="md-search__inner" role="search">
<form class="md-search__form" name="search">
<input type="text" class="md-search__input" name="query" aria-label="Search" placeholder="Search" autocapitalize="off" autocorrect="off" autocomplete="off" spellcheck="false" data-md-component="search-query" required>
<label class="md-search__icon md-icon" for="__search">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.52 6.52 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5"></path></svg>
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11z"></path></svg>
</label>
<nav class="md-search__options" aria-label="Search">
<button type="reset" class="md-search__icon md-icon" title="Clear" aria-label="Clear" tabindex="-1">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"></path></svg>
</button>
</nav>
</form>
<div class="md-search__output">
<div class="md-search__scrollwrap" tabindex="0" data-md-scrollfix>
<div class="md-search-result" data-md-component="search-result">
<div class="md-search-result__meta">
Initializing search
</div>
<ol class="md-search-result__list" role="presentation"></ol>
</div>
</div>
</div>
</div>
</div>
<div class="md-header__source">
<a href="https://gitea.psi.ch/hpce/gitea-pages" title="Go to repository" class="md-source" data-md-component="source">
<div class="md-source__icon md-icon">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 7.1.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2025 Fonticons, Inc.--><path d="M439.6 236.1 244 40.5c-5.4-5.5-12.8-8.5-20.4-8.5s-15 3-20.4 8.4L162.5 81l51.5 51.5c27.1-9.1 52.7 16.8 43.4 43.7l49.7 49.7c34.2-11.8 61.2 31 35.5 56.7-26.5 26.5-70.2-2.9-56-37.3L240.3 199v121.9c25.3 12.5 22.3 41.8 9.1 55-6.4 6.4-15.2 10.1-24.3 10.1s-17.8-3.6-24.3-10.1c-17.6-17.6-11.1-46.9 11.2-56v-123c-20.8-8.5-24.6-30.7-18.6-45L142.6 101 8.5 235.1C3 240.6 0 247.9 0 255.5s3 15 8.5 20.4l195.6 195.7c5.4 5.4 12.7 8.4 20.4 8.4s15-3 20.4-8.4l194.7-194.7c5.4-5.4 8.4-12.8 8.4-20.4s-3-15-8.4-20.4"></path></svg>
</div>
<div class="md-source__repository">
User Documentation Repository
</div>
</a>
</div>
</nav>
<nav class="md-tabs" aria-label="Tabs" data-md-component="tabs">
<div class="md-grid">
<ul class="md-tabs__list">
<li class="md-tabs__item">
<a href="../../.." class="md-tabs__link">
Home
</a>
</li>
<li class="md-tabs__item">
<a href="../../../news/" class="md-tabs__link">
News
</a>
</li>
<li class="md-tabs__item md-tabs__item--active">
<a href="../../01-Quick-Start-Guide/introduction/" class="md-tabs__link">
Merlin 7
</a>
</li>
<li class="md-tabs__item">
<a href="../../../merlin6/introduction/" class="md-tabs__link">
Merlin 6
</a>
</li>
<li class="md-tabs__item">
<a href="../../../meg/introduction/" class="md-tabs__link">
MeG
</a>
</li>
<li class="md-tabs__item">
<a href="../../../cscs-userlab/introduction/" class="md-tabs__link">
PSI@CSCS
</a>
</li>
<li class="md-tabs__item">
<a href="../../../support/introduction/" class="md-tabs__link">
Support
</a>
</li>
</ul>
</div>
</nav>
</header>
<div class="md-container" data-md-component="container">
<main class="md-main" data-md-component="main">
<div class="md-main__inner md-grid">
<div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation">
<div class="md-sidebar__scrollwrap">
<div class="md-sidebar__inner">
<nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
<label class="md-nav__title" for="__drawer">
<a href="../../.." title="HPCE User Documentation" class="md-nav__button md-logo" aria-label="HPCE User Documentation" data-md-component="logo">
<img src="../../../images/hpce_logo.png" alt="logo">
</a>
HPCE User Documentation
</label>
<div class="md-nav__source">
<a href="https://gitea.psi.ch/hpce/gitea-pages" title="Go to repository" class="md-source" data-md-component="source">
<div class="md-source__icon md-icon">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 7.1.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2025 Fonticons, Inc.--><path d="M439.6 236.1 244 40.5c-5.4-5.5-12.8-8.5-20.4-8.5s-15 3-20.4 8.4L162.5 81l51.5 51.5c27.1-9.1 52.7 16.8 43.4 43.7l49.7 49.7c34.2-11.8 61.2 31 35.5 56.7-26.5 26.5-70.2-2.9-56-37.3L240.3 199v121.9c25.3 12.5 22.3 41.8 9.1 55-6.4 6.4-15.2 10.1-24.3 10.1s-17.8-3.6-24.3-10.1c-17.6-17.6-11.1-46.9 11.2-56v-123c-20.8-8.5-24.6-30.7-18.6-45L142.6 101 8.5 235.1C3 240.6 0 247.9 0 255.5s3 15 8.5 20.4l195.6 195.7c5.4 5.4 12.7 8.4 20.4 8.4s15-3 20.4-8.4l194.7-194.7c5.4-5.4 8.4-12.8 8.4-20.4s-3-15-8.4-20.4"></path></svg>
</div>
<div class="md-source__repository">
User Documentation Repository
</div>
</a>
</div>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../.." class="md-nav__link">
<span class="md-ellipsis">
Home
</span>
</a>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2">
<div class="md-nav__link md-nav__container">
<a href="../../../news/" class="md-nav__link ">
<span class="md-ellipsis">
News
</span>
</a>
<label class="md-nav__link " for="__nav_2" id="__nav_2_label" tabindex="0">
<span class="md-nav__icon md-icon"></span>
</label>
</div>
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_2">
<span class="md-nav__icon md-icon"></span>
News
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2_2">
<label class="md-nav__link" for="__nav_2_2" id="__nav_2_2_label" tabindex="0">
<span class="md-ellipsis">
Archive
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_2_2_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_2_2">
<span class="md-nav__icon md-icon"></span>
Archive
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../news/archive/2026/" class="md-nav__link">
<span class="md-ellipsis">
2026
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../news/archive/2024/" class="md-nav__link">
<span class="md-ellipsis">
2024
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../news/archive/2019/" class="md-nav__link">
<span class="md-ellipsis">
2019
</span>
</a>
</li>
</ul>
</nav>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="">
<span class="md-ellipsis">
Merlin 7
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
<label class="md-nav__title" for="__nav_3">
<span class="md-nav__icon md-icon"></span>
Merlin 7
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3_1">
<label class="md-nav__link" for="__nav_3_1" id="__nav_3_1_label" tabindex="">
<span class="md-ellipsis">
Quick Start Guide
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_3_1_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_3_1">
<span class="md-nav__icon md-icon"></span>
Quick Start Guide
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../01-Quick-Start-Guide/introduction/" class="md-nav__link">
<span class="md-ellipsis">
Introduction
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../01-Quick-Start-Guide/code-of-conduct/" class="md-nav__link">
<span class="md-ellipsis">
Code Of Conduct
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../01-Quick-Start-Guide/requesting-accounts/" class="md-nav__link">
<span class="md-ellipsis">
Requesting Merlin Accounts
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../01-Quick-Start-Guide/requesting-projects/" class="md-nav__link">
<span class="md-ellipsis">
Requesting a Merlin Project
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../01-Quick-Start-Guide/accessing-interactive-nodes/" class="md-nav__link">
<span class="md-ellipsis">
Accessing Interactive Nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../01-Quick-Start-Guide/accessing-slurm/" class="md-nav__link">
<span class="md-ellipsis">
Accessing Slurm Cluster
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3_2">
<label class="md-nav__link" for="__nav_3_2" id="__nav_3_2_label" tabindex="">
<span class="md-ellipsis">
How To Use Merlin7
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<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>
How To Use Merlin7
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/connect-from-linux/" class="md-nav__link">
<span class="md-ellipsis">
Connecting from a Linux Client
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/connect-from-windows/" class="md-nav__link">
<span class="md-ellipsis">
Connecting from a Windows Client
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/connect-from-macos/" class="md-nav__link">
<span class="md-ellipsis">
Connecting from a MacOS Client
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/storage/" class="md-nav__link">
<span class="md-ellipsis">
Merlin7 Storage
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/transfer-data/" class="md-nav__link">
<span class="md-ellipsis">
Transferring Data
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/archive/" class="md-nav__link">
<span class="md-ellipsis">
Archive &amp; PSI Data Catalog
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/nomachine/" class="md-nav__link">
<span class="md-ellipsis">
Remote Desktop Access to Merlin7
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/merlin-rmount/" class="md-nav__link">
<span class="md-ellipsis">
Using merlin_rmount
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/merlin_tools/" class="md-nav__link">
<span class="md-ellipsis">
Merlin7 Tools
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/ssh-keys/" class="md-nav__link">
<span class="md-ellipsis">
Configuring SSH Keys in Merlin
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/kerberos/" class="md-nav__link">
<span class="md-ellipsis">
Kerberos and AFS authentication
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../02-How-To-Use-Merlin/software-repositories/" class="md-nav__link">
<span class="md-ellipsis">
Software repositories
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3_3">
<label class="md-nav__link" for="__nav_3_3" id="__nav_3_3_label" tabindex="">
<span class="md-ellipsis">
Slurm General Documentation
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_3_3_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_3_3">
<span class="md-nav__icon md-icon"></span>
Slurm General Documentation
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../03-Slurm-General-Documentation/merlin7-configuration/" class="md-nav__link">
<span class="md-ellipsis">
Slurm cluster 'merlin7'
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../03-Slurm-General-Documentation/slurm-configuration/" class="md-nav__link">
<span class="md-ellipsis">
Slurm merlin7 Configuration
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../03-Slurm-General-Documentation/interactive-jobs/" class="md-nav__link">
<span class="md-ellipsis">
Running Interactive Jobs
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../03-Slurm-General-Documentation/slurm-examples/" class="md-nav__link">
<span class="md-ellipsis">
Slurm Examples
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3_4">
<label class="md-nav__link" for="__nav_3_4" id="__nav_3_4_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_3_4_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_3_4">
<span class="md-nav__icon md-icon"></span>
Jupyterhub
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../04-Jupyterhub/jupyterhub/" class="md-nav__link">
<span class="md-ellipsis">
Jupyterhub on Merlin7
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3_5" checked>
<label class="md-nav__link" for="__nav_3_5" id="__nav_3_5_label" tabindex="">
<span class="md-ellipsis">
Software Support
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_3_5_label" aria-expanded="true">
<label class="md-nav__title" for="__nav_3_5">
<span class="md-nav__icon md-icon"></span>
Software Support
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../pmodules/" class="md-nav__link">
<span class="md-ellipsis">
PSI Modules
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../spack/" class="md-nav__link">
<span class="md-ellipsis">
Spack
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../openmpi/" class="md-nav__link">
<span class="md-ellipsis">
OpenMPI Support
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../ansys/" class="md-nav__link">
<span class="md-ellipsis">
ANSYS
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../ansys-rsm/" class="md-nav__link">
<span class="md-ellipsis">
ANSYS RSM (Remote Resolve Manager)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../cp2k/" class="md-nav__link">
<span class="md-ellipsis">
CP2k
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../quantum-espresso/" class="md-nav__link">
<span class="md-ellipsis">
Quantum Espresso
</span>
</a>
</li>
<li class="md-nav__item md-nav__item--active">
<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
<label class="md-nav__link md-nav__link--active" for="__toc">
<span class="md-ellipsis">
LAMMPS
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<a href="./" class="md-nav__link md-nav__link--active">
<span class="md-ellipsis">
LAMMPS
</span>
</a>
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
<label class="md-nav__title" for="__toc">
<span class="md-nav__icon md-icon"></span>
Table of contents
</label>
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
<li class="md-nav__item">
<a href="#lammps_1" class="md-nav__link">
<span class="md-ellipsis">
LAMMPS
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#licensing-terms-and-conditions" class="md-nav__link">
<span class="md-ellipsis">
Licensing Terms and Conditions
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#how-to-run-on-merlin7" class="md-nav__link">
<span class="md-ellipsis">
How to run on Merlin7
</span>
</a>
<nav class="md-nav" aria-label="How to run on Merlin7">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#cpu-nodes" class="md-nav__link">
<span class="md-ellipsis">
CPU nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#a100-nodes" class="md-nav__link">
<span class="md-ellipsis">
A100 nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#gh-nodes" class="md-nav__link">
<span class="md-ellipsis">
GH nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#sbatch-cpu-4-mpi-ranks-16-omp-threads" class="md-nav__link">
<span class="md-ellipsis">
SBATCH CPU, 4 MPI ranks, 16 OMP threads
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#sbatch-a100-4-gpu-16-omp-threads-4-mpi-ranks" class="md-nav__link">
<span class="md-ellipsis">
SBATCH A100, 4 GPU, 16 OMP threads, 4 MPI ranks
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#sbatch-gh-2-gpu-18-omp-threads-2-mpi-ranks" class="md-nav__link">
<span class="md-ellipsis">
SBATCH GH, 2 GPU, 18 OMP threads, 2 MPI ranks
</span>
</a>
</li>
</ul>
</nav>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="../gromacs/" class="md-nav__link">
<span class="md-ellipsis">
GROMACS
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../opal-x/" class="md-nav__link">
<span class="md-ellipsis">
OPAL-X
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../ippl/" class="md-nav__link">
<span class="md-ellipsis">
IPPL
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../cray-module.env/" class="md-nav__link">
<span class="md-ellipsis">
Cray Programming Environment
</span>
</a>
</li>
</ul>
</nav>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4">
<label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
<span class="md-ellipsis">
Merlin 6
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_4">
<span class="md-nav__icon md-icon"></span>
Merlin 6
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1">
<label class="md-nav__link" for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
<span class="md-ellipsis">
Quick Start Guide
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_4_1">
<span class="md-nav__icon md-icon"></span>
Quick Start Guide
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../merlin6/introduction/" class="md-nav__link">
<span class="md-ellipsis">
About Merlin6
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/quick-start-guide/code-of-conduct/" class="md-nav__link">
<span class="md-ellipsis">
Code Of Conduct
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/quick-start-guide/requesting-accounts/" class="md-nav__link">
<span class="md-ellipsis">
Requesting Merlin Accounts
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/quick-start-guide/requesting-projects/" class="md-nav__link">
<span class="md-ellipsis">
Requesting a Merlin Project
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/quick-start-guide/accessing-interactive-nodes/" class="md-nav__link">
<span class="md-ellipsis">
Accessing Interactive Nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/quick-start-guide/accessing-slurm/" class="md-nav__link">
<span class="md-ellipsis">
Accessing Slurm Cluster
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2">
<label class="md-nav__link" for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
<span class="md-ellipsis">
How To Use Merlin
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_4_2">
<span class="md-nav__icon md-icon"></span>
How To Use Merlin
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/connect-from-linux/" class="md-nav__link">
<span class="md-ellipsis">
Connecting from a Linux Client
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/connect-from-windows/" class="md-nav__link">
<span class="md-ellipsis">
Connecting from a Windows Client
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/connect-from-macos/" class="md-nav__link">
<span class="md-ellipsis">
Connecting from a MacOS Client
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/storage/" class="md-nav__link">
<span class="md-ellipsis">
Merlin6 Storage
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/transfer-data/" class="md-nav__link">
<span class="md-ellipsis">
Transferring Data
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/archive/" class="md-nav__link">
<span class="md-ellipsis">
Archive &amp; PSI Data Catalog
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/ssh-keys/" class="md-nav__link">
<span class="md-ellipsis">
Configuring SSH Keys in Merlin
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/kerberos/" class="md-nav__link">
<span class="md-ellipsis">
Kerberos and AFS authentication
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/how-to-use-merlin/using-modules/" class="md-nav__link">
<span class="md-ellipsis">
Using PModules
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3">
<label class="md-nav__link" for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
<span class="md-ellipsis">
Slurm General Documentation
</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
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../merlin6/slurm-general-docs/slurm-basic-commands/" class="md-nav__link">
<span class="md-ellipsis">
Slurm Basic Commands
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/slurm-general-docs/running-jobs/" class="md-nav__link">
<span class="md-ellipsis">
Running Slurm Scripts
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/slurm-general-docs/interactive-jobs/" class="md-nav__link">
<span class="md-ellipsis">
Running Interactive Jobs
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/slurm-general-docs/slurm-examples/" class="md-nav__link">
<span class="md-ellipsis">
Slurm Examples
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/slurm-general-docs/monitoring/" class="md-nav__link">
<span class="md-ellipsis">
Monitoring
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<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="0">
<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>
<li class="md-nav__item">
<a href="../../../gmerlin6/cluster-introduction/" class="md-nav__link">
<span class="md-ellipsis">
Introduction
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../gmerlin6/hardware-and-software-description/" class="md-nav__link">
<span class="md-ellipsis">
Hardware And Software Description
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../gmerlin6/slurm-configuration/" class="md-nav__link">
<span class="md-ellipsis">
Slurm cluster 'gmerlin6'
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_5">
<label class="md-nav__link" for="__nav_4_5" id="__nav_4_5_label" tabindex="0">
<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>
Jupyterhub
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../merlin6/jupyterhub/jupyterhub/" class="md-nav__link">
<span class="md-ellipsis">
Jupyterhub on Merlin
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/jupyterhub/jupyter-examples/" class="md-nav__link">
<span class="md-ellipsis">
Jupyter examples on merlin6
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/jupyterhub/jupytext/" class="md-nav__link">
<span class="md-ellipsis">
Jupytext - efficient editing
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/jupyterhub/jupyter-extensions/" class="md-nav__link">
<span class="md-ellipsis">
Jupyter Extensions
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/jupyterhub/jupyterlab/" class="md-nav__link">
<span class="md-ellipsis">
Jupyterlab User interface
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/jupyterhub/jupyterhub-trouble/" class="md-nav__link">
<span class="md-ellipsis">
Jupyterhub Troubleshooting
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_6">
<label class="md-nav__link" for="__nav_4_6" id="__nav_4_6_label" tabindex="0">
<span class="md-ellipsis">
Software Support
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_6_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_4_6">
<span class="md-nav__icon md-icon"></span>
Software Support
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/ansys/" class="md-nav__link">
<span class="md-ellipsis">
ANSYS
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/ansys-rsm/" class="md-nav__link">
<span class="md-ellipsis">
ANSYS - RSM
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/ansys-cfx/" class="md-nav__link">
<span class="md-ellipsis">
ANSYS - CFX
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/ansys-fluent/" class="md-nav__link">
<span class="md-ellipsis">
ANSYS - Fluent
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/ansys-mapdl/" class="md-nav__link">
<span class="md-ellipsis">
ANSYS - MAPDL
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/ansys-hfss/" class="md-nav__link">
<span class="md-ellipsis">
ANSYS HFSS (ElectroMagnetics)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/gothic/" class="md-nav__link">
<span class="md-ellipsis">
GOTHIC
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/merlin-rmount/" class="md-nav__link">
<span class="md-ellipsis">
merlin_rmount
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/impi/" class="md-nav__link">
<span class="md-ellipsis">
Intel MPI Support
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/openmpi/" class="md-nav__link">
<span class="md-ellipsis">
OpenMPI
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/paraview/" class="md-nav__link">
<span class="md-ellipsis">
ParaView
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../merlin6/software-support/python/" class="md-nav__link">
<span class="md-ellipsis">
Python
</span>
</a>
</li>
</ul>
</nav>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5">
<label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
<span class="md-ellipsis">
MeG
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_5">
<span class="md-nav__icon md-icon"></span>
MeG
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../meg/introduction/" class="md-nav__link">
<span class="md-ellipsis">
The MEG local HPC cluster
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../meg/contact/" class="md-nav__link">
<span class="md-ellipsis">
Support
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../meg/migration-to-merlin7/" class="md-nav__link">
<span class="md-ellipsis">
Meg to Merlin7 Migration Guide
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6">
<label class="md-nav__link" for="__nav_6" id="__nav_6_label" tabindex="0">
<span class="md-ellipsis">
PSI@CSCS
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_6">
<span class="md-nav__icon md-icon"></span>
PSI@CSCS
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../cscs-userlab/introduction/" class="md-nav__link">
<span class="md-ellipsis">
PSI HPC@CSCS
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../cscs-userlab/transfer-data/" class="md-nav__link">
<span class="md-ellipsis">
Transferring Data
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_7">
<label class="md-nav__link" for="__nav_7" id="__nav_7_label" tabindex="0">
<span class="md-ellipsis">
Support
</span>
<span class="md-nav__icon md-icon"></span>
</label>
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
<label class="md-nav__title" for="__nav_7">
<span class="md-nav__icon md-icon"></span>
Support
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../../../support/introduction/" class="md-nav__link">
<span class="md-ellipsis">
Getting Support
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../support/faq/" class="md-nav__link">
<span class="md-ellipsis">
FAQ
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../support/known-problems/" class="md-nav__link">
<span class="md-ellipsis">
Known Problems
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../../../support/troubleshooting/" class="md-nav__link">
<span class="md-ellipsis">
Troubleshooting
</span>
</a>
</li>
</ul>
</nav>
</li>
</ul>
</nav>
</div>
</div>
</div>
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc">
<div class="md-sidebar__scrollwrap">
<div class="md-sidebar__inner">
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
<label class="md-nav__title" for="__toc">
<span class="md-nav__icon md-icon"></span>
Table of contents
</label>
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
<li class="md-nav__item">
<a href="#lammps_1" class="md-nav__link">
<span class="md-ellipsis">
LAMMPS
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#licensing-terms-and-conditions" class="md-nav__link">
<span class="md-ellipsis">
Licensing Terms and Conditions
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#how-to-run-on-merlin7" class="md-nav__link">
<span class="md-ellipsis">
How to run on Merlin7
</span>
</a>
<nav class="md-nav" aria-label="How to run on Merlin7">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#cpu-nodes" class="md-nav__link">
<span class="md-ellipsis">
CPU nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#a100-nodes" class="md-nav__link">
<span class="md-ellipsis">
A100 nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#gh-nodes" class="md-nav__link">
<span class="md-ellipsis">
GH nodes
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#sbatch-cpu-4-mpi-ranks-16-omp-threads" class="md-nav__link">
<span class="md-ellipsis">
SBATCH CPU, 4 MPI ranks, 16 OMP threads
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#sbatch-a100-4-gpu-16-omp-threads-4-mpi-ranks" class="md-nav__link">
<span class="md-ellipsis">
SBATCH A100, 4 GPU, 16 OMP threads, 4 MPI ranks
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#sbatch-gh-2-gpu-18-omp-threads-2-mpi-ranks" class="md-nav__link">
<span class="md-ellipsis">
SBATCH GH, 2 GPU, 18 OMP threads, 2 MPI ranks
</span>
</a>
</li>
</ul>
</nav>
</li>
</ul>
</nav>
</div>
</div>
</div>
<div class="md-content" data-md-component="content">
<article class="md-content__inner md-typeset">
<a href="https://gitea.psi.ch/hpce/gitea-pages/_edit/master/docs/merlin7/05-Software-Support/lammps.md" title="Edit this page" class="md-content__button md-icon" rel="edit">
<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>
</a>
<h1 id="lammps">LAMMPS<a class="headerlink" href="#lammps" title="Permanent link"></a></h1>
<h2 id="lammps_1">LAMMPS<a class="headerlink" href="#lammps_1" title="Permanent link"></a></h2>
<p>LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. The current version of LAMMPS is written in C++.</p>
<h2 id="licensing-terms-and-conditions">Licensing Terms and Conditions<a class="headerlink" href="#licensing-terms-and-conditions" title="Permanent link"></a></h2>
<p>LAMMPS is an open-source code, available free-of-charge, and distributed under the terms of the GNU Public License Version 2 (GPLv2), which means you can use or modify the code however you wish for your own purposes, but have to adhere to certain rules when redistributing it - specifically in binary form - or are distributing software derived from it or that includes parts of it.</p>
<p>LAMMPS comes with no warranty of any kind.</p>
<p>As each source file states in its header, it is a copyrighted code, and thus not in the public domain. For more information about open-source software and open-source distribution, see www.gnu.org or www.opensource.org. The legal text of the GPL as it applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.</p>
<p>Here is a more specific summary of what the GPL means for LAMMPS users:</p>
<p>(1) Anyone is free to use, copy, modify, or extend LAMMPS in any way they choose, including for commercial purposes.</p>
<p>(2) If you distribute a modified version of LAMMPS, it must remain open-source, meaning you are required to distribute all of it under the terms of the GPLv2. You should clearly annotate such a modified code as a derivative version of LAMMPS. This is best done by changing the name (example: LIGGGHTS is such a modified and extended version of LAMMPS).</p>
<p>(3) If you release any code that includes or uses LAMMPS source code, then it must also be open-sourced, meaning you distribute it under the terms of the GPLv2. You may write code that interfaces LAMMPS to a differently licensed library. In that case the code that provides the interface must be licensed GPLv2, but not necessarily that library unless you are distributing binaries that require the library to run.</p>
<p>(4) If you give LAMMPS files to someone else, the GPLv2 LICENSE file and source file headers (including the copyright and GPLv2 notices) should remain part of the code.</p>
<h2 id="how-to-run-on-merlin7">How to run on Merlin7<a class="headerlink" href="#how-to-run-on-merlin7" title="Permanent link"></a></h2>
<h3 id="cpu-nodes">CPU nodes<a class="headerlink" href="#cpu-nodes" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-0-2"><a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.8-jsrx-A100-gpu<span class="w"> </span>lammps/20250722-37gs-omp
</span></code></pre></div>
<h3 id="a100-nodes">A100 nodes<a class="headerlink" href="#a100-nodes" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-1-2"><a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.8-jsrx-A100-gpu<span class="w"> </span>lammps/20250722-xcaf-A100-gpu-omp
</span></code></pre></div>
<h3 id="gh-nodes">GH nodes<a class="headerlink" href="#gh-nodes" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.8-fvlo-GH200-gpu<span class="w"> </span>lammps/20250722-3tfv-GH200-gpu-omp
</span></code></pre></div>
<h3 id="sbatch-cpu-4-mpi-ranks-16-omp-threads">SBATCH CPU, 4 MPI ranks, 16 OMP threads<a class="headerlink" href="#sbatch-cpu-4-mpi-ranks-16-omp-threads" title="Permanent link"></a></h3>
<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="ch">#!/bin/bash</span>
</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="c1">#SBATCH --time=00:10:00 # maximum execution time of 10 minutes</span>
</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="c1">#SBATCH --nodes=1 # requesting 1 compute node</span>
</span><span id="__span-3-4"><a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="c1">#SBATCH --ntasks=4 # use 4 MPI rank (task)</span>
</span><span id="__span-3-5"><a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a><span class="c1">#SBATCH --partition=hourly</span>
</span><span id="__span-3-6"><a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a><span class="c1">#SBATCH --cpus-per-task=16 # modify this number of CPU cores per MPI task</span>
</span><span id="__span-3-7"><a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a><span class="c1">#SBATCH --output=_scheduler-stdout.txt</span>
</span><span id="__span-3-8"><a id="__codelineno-3-8" name="__codelineno-3-8" href="#__codelineno-3-8"></a><span class="c1">#SBATCH --error=_scheduler-stderr.txt</span>
</span><span id="__span-3-9"><a id="__codelineno-3-9" name="__codelineno-3-9" href="#__codelineno-3-9"></a>
</span><span id="__span-3-10"><a id="__codelineno-3-10" name="__codelineno-3-10" href="#__codelineno-3-10"></a><span class="nb">unset</span><span class="w"> </span>PMODULES_ENV
</span><span id="__span-3-11"><a id="__codelineno-3-11" name="__codelineno-3-11" href="#__codelineno-3-11"></a>module<span class="w"> </span>purge
</span><span id="__span-3-12"><a id="__codelineno-3-12" name="__codelineno-3-12" href="#__codelineno-3-12"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-3-13"><a id="__codelineno-3-13" name="__codelineno-3-13" href="#__codelineno-3-13"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.8-jsrx-A100-gpu<span class="w"> </span>lammps/20250722-37gs-omp
</span><span id="__span-3-14"><a id="__codelineno-3-14" name="__codelineno-3-14" href="#__codelineno-3-14"></a>
</span><span id="__span-3-15"><a id="__codelineno-3-15" name="__codelineno-3-15" href="#__codelineno-3-15"></a><span class="nb">export</span><span class="w"> </span><span class="nv">FI_CXI_RX_MATCH_MODE</span><span class="o">=</span>software
</span><span id="__span-3-16"><a id="__codelineno-3-16" name="__codelineno-3-16" href="#__codelineno-3-16"></a><span class="nb">export</span><span class="w"> </span><span class="nv">OMP_NUM_THREADS</span><span class="o">=</span><span class="nv">$SLURM_CPUS_PER_TASK</span>
</span><span id="__span-3-17"><a id="__codelineno-3-17" name="__codelineno-3-17" href="#__codelineno-3-17"></a><span class="nb">export</span><span class="w"> </span><span class="nv">OMP_PROC_BIND</span><span class="o">=</span>spread
</span><span id="__span-3-18"><a id="__codelineno-3-18" name="__codelineno-3-18" href="#__codelineno-3-18"></a><span class="nb">export</span><span class="w"> </span><span class="nv">OMP_PLACES</span><span class="o">=</span>threads
</span><span id="__span-3-19"><a id="__codelineno-3-19" name="__codelineno-3-19" href="#__codelineno-3-19"></a>
</span><span id="__span-3-20"><a id="__codelineno-3-20" name="__codelineno-3-20" href="#__codelineno-3-20"></a>srun<span class="w"> </span>--cpu-bind<span class="o">=</span>cores<span class="w"> </span>lmp<span class="w"> </span>-k<span class="w"> </span>on<span class="w"> </span>t<span class="w"> </span><span class="nv">$OMP_NUM_THREADS</span><span class="w"> </span>-sf<span class="w"> </span>kk<span class="w"> </span>-in<span class="w"> </span>lj_kokkos.in
</span></code></pre></div>
<h3 id="sbatch-a100-4-gpu-16-omp-threads-4-mpi-ranks">SBATCH A100, 4 GPU, 16 OMP threads, 4 MPI ranks<a class="headerlink" href="#sbatch-a100-4-gpu-16-omp-threads-4-mpi-ranks" title="Permanent link"></a></h3>
<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="ch">#!/bin/bash</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 --time=00:10:00 # maximum execution time of 10 minutes</span>
</span><span id="__span-4-3"><a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a><span class="c1">#SBATCH --output=_scheduler-stdout.txt</span>
</span><span id="__span-4-4"><a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="c1">#SBATCH --error=_scheduler-stderr.txt</span>
</span><span id="__span-4-5"><a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a><span class="c1">#SBATCH --nodes=1 # number of GH200 nodes with each node having 4 CPU+GPU</span>
</span><span id="__span-4-6"><a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a><span class="c1">#SBATCH --ntasks-per-node=4 # 4 MPI ranks per node</span>
</span><span id="__span-4-7"><a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a><span class="c1">#SBATCH --cluster=gmerlin7</span>
</span><span id="__span-4-8"><a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a><span class="c1">#SBATCH --hint=nomultithread</span>
</span><span id="__span-4-9"><a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a><span class="c1">#SBATCH --partition=a100-hourly</span>
</span><span id="__span-4-10"><a id="__codelineno-4-10" name="__codelineno-4-10" href="#__codelineno-4-10"></a><span class="c1">#SBATCH --gpus-per-task=1</span>
</span><span id="__span-4-11"><a id="__codelineno-4-11" name="__codelineno-4-11" href="#__codelineno-4-11"></a>
</span><span id="__span-4-12"><a id="__codelineno-4-12" name="__codelineno-4-12" href="#__codelineno-4-12"></a><span class="nb">unset</span><span class="w"> </span>PMODULES_ENV
</span><span id="__span-4-13"><a id="__codelineno-4-13" name="__codelineno-4-13" href="#__codelineno-4-13"></a>module<span class="w"> </span>purge
</span><span id="__span-4-14"><a id="__codelineno-4-14" name="__codelineno-4-14" href="#__codelineno-4-14"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-4-15"><a id="__codelineno-4-15" name="__codelineno-4-15" href="#__codelineno-4-15"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.8-jsrx-A100-gpu<span class="w"> </span>lammps/20250722-xcaf-A100-gpu-omp
</span><span id="__span-4-16"><a id="__codelineno-4-16" name="__codelineno-4-16" href="#__codelineno-4-16"></a>
</span><span id="__span-4-17"><a id="__codelineno-4-17" name="__codelineno-4-17" href="#__codelineno-4-17"></a><span class="nb">export</span><span class="w"> </span><span class="nv">FI_CXI_RX_MATCH_MODE</span><span class="o">=</span>software
</span><span id="__span-4-18"><a id="__codelineno-4-18" name="__codelineno-4-18" href="#__codelineno-4-18"></a>
</span><span id="__span-4-19"><a id="__codelineno-4-19" name="__codelineno-4-19" href="#__codelineno-4-19"></a>srun<span class="w"> </span>lmp<span class="w"> </span>-in<span class="w"> </span>lj_kokkos.in<span class="w"> </span>-k<span class="w"> </span>on<span class="w"> </span>g<span class="w"> </span><span class="si">${</span><span class="nv">SLURM_GPUS_PER_TASK</span><span class="si">}</span><span class="w"> </span>-sf<span class="w"> </span>kk<span class="w"> </span>-pk<span class="w"> </span>kokkos<span class="w"> </span>gpu/aware<span class="w"> </span>on
</span></code></pre></div>
<h3 id="sbatch-gh-2-gpu-18-omp-threads-2-mpi-ranks">SBATCH GH, 2 GPU, 18 OMP threads, 2 MPI ranks<a class="headerlink" href="#sbatch-gh-2-gpu-18-omp-threads-2-mpi-ranks" title="Permanent link"></a></h3>
<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="ch">#!/bin/bash</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 --time=00:10:00 # maximum execution time of 10 minutes</span>
</span><span id="__span-5-3"><a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a><span class="c1">#SBATCH --output=_scheduler-stdout.txt</span>
</span><span id="__span-5-4"><a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="c1">#SBATCH --error=_scheduler-stderr.txt</span>
</span><span id="__span-5-5"><a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a><span class="c1">#SBATCH --nodes=1 # number of GH200 nodes with each node having 4 CPU+GPU</span>
</span><span id="__span-5-6"><a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a><span class="c1">#SBATCH --ntasks-per-node=2 # 2 MPI ranks per node</span>
</span><span id="__span-5-7"><a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a><span class="c1">#SBATCH --cluster=gmerlin7</span>
</span><span id="__span-5-8"><a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a><span class="c1">#SBATCH --hint=nomultithread</span>
</span><span id="__span-5-9"><a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></a><span class="c1">#SBATCH --partition=gh-hourly</span>
</span><span id="__span-5-10"><a id="__codelineno-5-10" name="__codelineno-5-10" href="#__codelineno-5-10"></a><span class="c1">#SBATCH --gpus-per-task=1</span>
</span><span id="__span-5-11"><a id="__codelineno-5-11" name="__codelineno-5-11" href="#__codelineno-5-11"></a>
</span><span id="__span-5-12"><a id="__codelineno-5-12" name="__codelineno-5-12" href="#__codelineno-5-12"></a><span class="nb">unset</span><span class="w"> </span>PMODULES_ENV
</span><span id="__span-5-13"><a id="__codelineno-5-13" name="__codelineno-5-13" href="#__codelineno-5-13"></a>module<span class="w"> </span>purge
</span><span id="__span-5-14"><a id="__codelineno-5-14" name="__codelineno-5-14" href="#__codelineno-5-14"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-5-15"><a id="__codelineno-5-15" name="__codelineno-5-15" href="#__codelineno-5-15"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.8-fvlo-GH200-gpu<span class="w"> </span>lammps/20250722-3tfv-GH200-gpu-omp
</span><span id="__span-5-16"><a id="__codelineno-5-16" name="__codelineno-5-16" href="#__codelineno-5-16"></a>
</span><span id="__span-5-17"><a id="__codelineno-5-17" name="__codelineno-5-17" href="#__codelineno-5-17"></a><span class="nb">export</span><span class="w"> </span><span class="nv">FI_CXI_RX_MATCH_MODE</span><span class="o">=</span>software
</span><span id="__span-5-18"><a id="__codelineno-5-18" name="__codelineno-5-18" href="#__codelineno-5-18"></a>
</span><span id="__span-5-19"><a id="__codelineno-5-19" name="__codelineno-5-19" href="#__codelineno-5-19"></a>srun<span class="w"> </span>lmp<span class="w"> </span>-in<span class="w"> </span>lj_kokkos.in<span class="w"> </span>-k<span class="w"> </span>on<span class="w"> </span>g<span class="w"> </span><span class="si">${</span><span class="nv">SLURM_GPUS_PER_TASK</span><span class="si">}</span><span class="w"> </span>-sf<span class="w"> </span>kk<span class="w"> </span>-pk<span class="w"> </span>kokkos<span class="w"> </span>gpu/aware<span class="w"> </span>on
</span></code></pre></div>
</article>
</div>
<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
</div>
</main>
<footer class="md-footer">
<div class="md-footer-meta md-typeset">
<div class="md-footer-meta__inner md-grid">
<div class="md-copyright">
<div class="md-copyright__highlight">
Copyright © 2025 HPC and Emerging Technologies Group/CSD @ Paul Scherrer Institut
</div>
Made with
<a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
Material for MkDocs
</a>
</div>
</div>
</div>
</footer>
</div>
<div class="md-dialog" data-md-component="dialog">
<div class="md-dialog__inner md-typeset"></div>
</div>
<script id="__config" type="application/json">{"annotate": null, "base": "../../..", "features": ["navigation.instant", "navigation.tabs", "navigation.tabs.sticky", "navigation.sections", "navigation.indexes", "toc.follow", "content.action.edit"], "search": "../../../assets/javascripts/workers/search.7a47a382.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
<script src="../../../assets/javascripts/bundle.e71a0d61.min.js"></script>
<script id="init-glightbox">const lightbox = GLightbox({"touchNavigation": true, "loop": false, "zoomable": true, "draggable": true, "openEffect": "zoom", "closeEffect": "zoom", "slideEffect": "slide"});
document$.subscribe(()=>{ lightbox.reload(); });
</script></body></html>
Reference in New Issue View Git Blame Copy Permalink