posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS/index.html


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<!DOCTYPE html><html lang="en"><head><meta charset="UTF-8"/><meta name="og:site_name" content="Navan Chauhan"/><link rel="canonical" href="https://navanchauhan.github.io/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS"/><meta name="twitter:url" content="https://navanchauhan.github.io/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS"/><meta name="og:url" content="https://navanchauhan.github.io/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS"/><title>Fixing X11 Error on macOS Catalina for AmberTools 18/19 | Navan Chauhan</title><meta name="twitter:title" content="Fixing X11 Error on macOS Catalina for AmberTools 18/19 | Navan Chauhan"/><meta name="og:title" content="Fixing X11 Error on macOS Catalina for AmberTools 18/19 | Navan Chauhan"/><meta name="description" content="Fixing Could not find the X11 libraries; you may need to edit config.h, AmberTools macOS Catalina"/><meta name="twitter:description" content="Fixing Could not find the X11 libraries; you may need to edit config.h, AmberTools macOS Catalina"/><meta name="og:description" content="Fixing Could not find the X11 libraries; you may need to edit config.h, AmberTools macOS Catalina"/><meta name="twitter:card" content="summary"/><link rel="stylesheet" href="/styles.css" type="text/css"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><link rel="shortcut icon" href="/images/favicon.png" type="image/png"/><link rel="alternate" href="/feed.rss" type="application/rss+xml" title="Subscribe to Navan Chauhan"/><meta name="twitter:image" content="https://navanchauhan.github.io/images/logo.png"/><meta name="og:image" content="https://navanchauhan.github.io/images/logo.png"/></head><head><script src="https://www.googletagmanager.com/gtag/js?id=UA-108635191-1v"></script><script>window.dataLayer = window.dataLayer || [];function gtag(){dataLayer.push(arguments);}gtag('js', new Date());gtag('config', 'UA-108635191-1');</script></head><body class="item-page"><header><div class="wrapper"><a class="site-name" href="/">Navan Chauhan</a><nav><ul><li><a href="/about">About Me</a></li><li><a class="selected" href="/posts">Posts</a></li><li><a href="/publications">Publications</a></li><li><a href="/assets/résumé.pdf">Résumé</a></li><li><a href="https://navanchauhan.github.io/repo">Repo</a></li></ul></nav></div></header><div class="wrapper"><article><div class="content"><span class="reading-time">1 minute read</span><span class="reading-time">Created on April 13, 2020</span><h1>Fixing X11 Error on macOS Catalina for AmberTools 18/19</h1><p>I was trying to install AmberTools on my macOS Catalina Installation. Running <code>./configure -macAccelerate clang</code> gave me an error that it could not find X11 libraries, even though <code>locate libXt</code> showed that my installation was correct.</p><p>Error:</p><pre><code><div class="highlight"><span></span><span class="n">Could</span> <span class="n">not</span> <span class="bp">find</span> <span class="n">the</span> <span class="n">X11</span> <span class="n">libraries</span><span class="p">;</span> <span class="n">you</span> <span class="n">may</span> <span class="n">need</span> <span class="n">to</span> <span class="n">edit</span> <span class="n">config</span><span class="p">.</span><span class="n">h</span>
   <span class="n">to</span> <span class="kr">set</span> <span class="n">the</span> <span class="n">XHOME</span> <span class="n">and</span> <span class="n">XLIBS</span> <span class="n">variables</span><span class="p">.</span>
<span class="n">Error</span><span class="p">:</span> <span class="n">The</span> <span class="n">X11</span> <span class="n">libraries</span> <span class="n">are</span> <span class="n">not</span> <span class="k">in</span> <span class="n">the</span> <span class="n">usual</span> <span class="n">location</span> <span class="o">!</span>
       <span class="n">To</span> <span class="n">search</span> <span class="k">for</span> <span class="n">them</span> <span class="k">try</span> <span class="n">the</span> <span class="n">command</span><span class="p">:</span> <span class="n">locate</span> <span class="n">libXt</span>
       <span class="n">On</span> <span class="n">new</span> <span class="n">Fedora</span> <span class="n">OS</span><span class="err">&#39;</span><span class="n">s</span> <span class="n">install</span> <span class="n">the</span> <span class="n">libXt</span><span class="o">-</span><span class="n">devel</span> <span class="n">libXext</span><span class="o">-</span><span class="n">devel</span>
       <span class="n">libX11</span><span class="o">-</span><span class="n">devel</span> <span class="n">libICE</span><span class="o">-</span><span class="n">devel</span> <span class="n">libSM</span><span class="o">-</span><span class="n">devel</span> <span class="n">packages</span><span class="p">.</span>
       <span class="n">On</span> <span class="n">old</span> <span class="n">Fedora</span> <span class="n">OS</span><span class="err">&#39;</span><span class="n">s</span> <span class="n">install</span> <span class="n">the</span> <span class="n">xorg</span><span class="o">-</span><span class="n">x11</span><span class="o">-</span><span class="n">devel</span> <span class="n">package</span><span class="p">.</span>
       <span class="n">On</span> <span class="n">RedHat</span> <span class="n">OS</span><span class="err">&#39;</span><span class="n">s</span> <span class="n">install</span> <span class="n">the</span> <span class="n">XFree86</span><span class="o">-</span><span class="n">devel</span> <span class="n">package</span><span class="p">.</span>
       <span class="n">On</span> <span class="n">Ubuntu</span> <span class="n">OS</span><span class="err">&#39;</span><span class="n">s</span> <span class="n">install</span> <span class="n">the</span> <span class="n">xorg</span><span class="o">-</span><span class="n">dev</span> <span class="n">and</span> <span class="n">xserver</span><span class="o">-</span><span class="n">xorg</span> <span class="n">packages</span><span class="p">.</span>

          <span class="p">...</span><span class="n">more</span> <span class="n">info</span> <span class="k">for</span> <span class="n">various</span> <span class="n">linuxes</span> <span class="n">at</span> <span class="n">ambermd</span><span class="p">.</span><span class="n">org</span><span class="o">/</span><span class="n">ubuntu</span><span class="p">.</span><span class="n">html</span>

       <span class="n">To</span> <span class="n">build</span> <span class="n">Amber</span> <span class="n">without</span> <span class="n">XLEaP</span><span class="p">,</span> <span class="n">re</span><span class="o">-</span><span class="n">run</span> <span class="n">configure</span> <span class="n">with</span> <span class="err">&#39;</span><span class="o">-</span><span class="n">noX11</span><span class="p">:</span>
            <span class="p">.</span><span class="o">/</span><span class="n">configure</span> <span class="o">-</span><span class="n">noX11</span> <span class="o">--</span><span class="n">with</span><span class="o">-</span><span class="n">python</span> <span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">local</span><span class="o">/</span><span class="n">bin</span><span class="o">/</span><span class="n">python3</span> <span class="o">-</span><span class="n">macAccelerate</span> <span class="n">clang</span>
<span class="n">Configure</span> <span class="n">failed</span> <span class="n">due</span> <span class="n">to</span> <span class="n">the</span> <span class="n">errors</span> <span class="n">above</span><span class="p">!</span>
</div>

</code></pre><p>I searcehd on Google for a solution on their, sadly there was not even a single thread which had a solution about this error.</p><h2>The Fix</h2><p>Simply reinstalling XQuartz using homebrew fixed the error <code>brew cask reinstall xquartz</code></p><p>If you do not have xquartz installed, you need to run <code>brew cask install xquartz</code></p></div><span>Tagged with: </span><ul class="tag-list"><li><a href="/tags/moleculardynamics">molecular-dynamics</a></li><li><a href="/tags/macos">macOS</a></li></ul><div id="disqus_thread"></div><script src="/assets/disqus.js"></script><noscript>Please enable JavaScript to view the comments</noscript></article></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>