hacking-plotms-to-let-pipeline-run.html

<!DOCTYPE html>
<html lang="en">
<link rel="stylesheet" type="text/css" href="https://keflavich.github.io/blog/theme/css/style.css" />
<link rel="icon" type="image/gif" href="https://keflavich.github.io/blog/theme/favicon8.ico">
<head>
    <base href="https://keflavich.github.io/blog">
        <title>Adam Ginsburg's blog</title>
        <meta charset="utf-8" />
        <link href="https://keflavich.github.io/blog/feeds/all.atom.xml" type="application/atom+xml" rel="alternate" title="Adam Ginsburg's blog Full Atom Feed" />
        <link href="https://keflavich.github.io/blog/feeds/{slug}.atom.xml" type="application/atom+xml" rel="alternate" title="Adam Ginsburg's blog Categories Atom Feed" />
<!-- Using MathJax, with the delimiters $ -->
<!-- Conflict with pygments for the .mo and .mi -->
<script type="text/x-mathjax-config">
    MathJax.Hub.Config({
    "HTML-CSS": {
    styles: {
    ".MathJax .mo, .MathJax .mi": {color: "inherit !important"}},
    'div.typeset': { 'text-align': 'left'}
    },
    tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']],processEscapes: true}
    });
    TeX: {
        extensions: ["AMSmath.js", "AMSsymbols.js"]
    }
    MathJax.Hub.Register.StartupHook("HTML-CSS Jax Ready",function () {
    var VARIANT = MathJax.OutputJax["HTML-CSS"].FONTDATA.VARIANT;
    VARIANT["normal"].fonts.unshift("MathJax_SansSerif");
    VARIANT["bold"].fonts.unshift("MathJax_SansSerif-bold");
    VARIANT["italic"].fonts.unshift("MathJax_SansSerif-italic");
    VARIANT["-tex-mathit"].fonts.unshift("MathJax_SansSerif-italic");
    });
    MathJax.Hub.Register.StartupHook("SVG Jax Ready",function () {
    var VARIANT = MathJax.OutputJax.SVG.FONTDATA.VARIANT;
    VARIANT["normal"].fonts.unshift("MathJax_SansSerif");
    VARIANT["bold"].fonts.unshift("MathJax_SansSerif-bold");
    VARIANT["italic"].fonts.unshift("MathJax_SansSerif-italic");
    VARIANT["-tex-mathit"].fonts.unshift("MathJax_SansSerif-italic");
    });
</script>

<script type="text/javascript"
src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML">
</script>
        
</head>

<body id="base" class="home">


    <header id="banner" class="body" >
        <div id="header" style='background-image: url("https://keflavich.github.io/blog/images/GC_4096sq_bolo.png"); background-position:left; min-heigt: 200px;  background-repeat: no-repeat; max-width: 80%;'>
            <h1 style="color: #C4C4C4;"><a class="header" href="https://keflavich.github.io/blog">Adam Ginsburg's blog <strong></strong></a></h1>

            <nav id="menu"><ul id="menulist">
                <li><a href="https://www.adamgginsburg.com">Homepage</a></li>
                <li><a href="/blog//index.html">Blog Index</a></li>
                <li><a href="/blog//blog/category/bgps.html">BGPS Blog</a></li>
                <li><a href="/blog//blog/category/publications.html">Publications</a></li>
                <li><a href="/blog//blog/archives.html">Archives</a></li>
                <li><a href="/blog//blog/tags.html">Tags</a></li>
            </ul></nav><!-- /#menu -->
        </div>
    </header><!-- /#banner -->

  <div id="sidebar">
    <ul>
      <li>
        <h3 id='recent_header'>Recent Posts</h3>
        <ul>
              <li class="post">
                  2025/03/15
                  <br>
                  <a href="https://keflavich.github.io/blog/pushing-to-a-pull-request.html">Pushing to a pull request</a>
              </li>
              <li class="post">
                  2023/08/11
                  <br>
                  <a href="https://keflavich.github.io/blog/editing-metadata-in-measurement-sets.html">Editing metadata in measurement sets</a>
              </li>
              <li class="post">
                  2022/05/06
                  <br>
                  <a href="https://keflavich.github.io/blog/casa-mpi-debugging-contd.html">CASA MPI debugging cont'd</a>
              </li>
              <li class="post">
                  2022/05/01
                  <br>
                  <a href="https://keflavich.github.io/blog/co2-monitoring-at-conferences-update-in-2022.html">CO2 Monitoring at Conferences: Update in 2022</a>
              </li>
              <li class="post">
                  2022/04/14
                  <br>
                  <a href="https://keflavich.github.io/blog/alma-cycle-9-corrupted-zip-fix.html">ALMA Cycle 9 corrupted zip fix</a>
              </li>
        </ul>
      </li>
    
    </ul>
  </div><!-- end #sidebar -->

  <div id="content">
<section id="content" class="body">
  <header>
    <h2 class="entry-title">
      <a href="https://keflavich.github.io/blog/hacking-plotms-to-let-pipeline-run.html" rel="bookmark"
         title="Permalink to Hacking plotms to let pipeline run">Hacking plotms to let pipeline run</a></h2>
 
  </header>
  <footer class="post-info">
    <abbr class="published" title="2022-04-11T08:02:00-06:00">
      2022/04/11
    </abbr>
    <address class="vcard author">
      By <a class="url fn" href="https://keflavich.github.io/blog/author/adam-ginsburg-adamgginsburggmailcom.html">Adam Ginsburg (Adam.G.Ginsburg@gmail.com)</a>
    </address>
  </footer><!-- /.post-info -->
  <div class="entry-content">
    <p>For the ACES project, I'm re-running the ALMA pipeline using MPI.</p>
<p>However, this results in all runs crashing with the following error:</p>
<div class="highlight"><pre><span></span>2022-04-06 04:22:43 INFO: Executing plotms(vis=&#39;uid___A002_Xf512ae_X2626.ms&#39;, xaxis=&#39;azimuth&#39;, yaxis=&#39;elevation&#39;, spw=&#39;25:0~0,27:0~0,29:0~0,31:0~0,33:0~0,35:0~0&#39;, antenna=&#39;0&amp;&amp;*&#39;, avgchannel=&#39;9000&#39;, avgtime=&#39;10&#39;, coloraxis=&#39;field&#39;, customflaggedsymbol=True, flaggedsymbolshape=&#39;autoscaling&#39;, title=&#39;Elevation vs Azimuth for uid___A002_Xf512ae_X2626.ms&#39;, plotfile=&#39;azel.png&#39;, showgui=False, clearplots=True)
fuse: failed to exec fusermount: No such file or directory

Cannot mount AppImage, please check your FUSE setup.
You might still be able to extract the contents of this AppImage
if you run it with the --appimage-extract option.
See https://github.com/AppImage/AppImageKit/wiki/FUSE
for more information
open dir error: No such file or directory
</pre></div>
<p>This fails even if I set the global APPIMAGE_EXTRACT_AND_RUN as <a class="reference external" href="https://docs.appimage.org/user-guide/troubleshooting/fuse.html#extract-and-run-type-2-appimages">directed</a>
on the appimage.org docs.</p>
<p>This indicates that the appimage is older than the environmental variable.</p>
<p>Running the full command &quot;works&quot;:
<tt class="docutils literal"><span class="pre">/orange/adamginsburg/casa/casa-6.2.1-7-pipeline-2021.2.0.128/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage</span> <span class="pre">--appimage-extract</span></tt>
but <tt class="docutils literal"><span class="pre">--appimage-extract-and-run</span></tt> gives <tt class="docutils literal"><span class="pre">--appimage-extract-and-run</span> is not yet implemented in version <span class="pre">continuous-1-g6f3138f</span></tt></p>
<p>So to run plotms, we need to use the <tt class="docutils literal">AppRun</tt> executable in the extracted <tt class="docutils literal"><span class="pre">squashfs-root</span></tt> directory.</p>
<p>My original hack was to just tell plotms not to run at all, which I accomplished by editing the
<tt class="docutils literal">plotmstool.py</tt> file (<tt class="docutils literal"><span class="pre">lib/py/lib/python3.6/site-packages/casaplotms/private/plotmstool.py</span></tt>) to
just skip the <tt class="docutils literal">__launch</tt> command:</p>
<div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">__launch</span><span class="p">(</span> <span class="n">uri</span><span class="o">=</span><span class="kc">None</span> <span class="p">):</span>
    <span class="k">return</span>
</pre></div>
<p>However, in writing this post, I've changed to instead modifying the <tt class="docutils literal">app_path</tt> to this:</p>
<div class="highlight"><pre><span></span><span class="n">app_path</span> <span class="o">=</span> <span class="s2">&quot;/tmp/casaplotms/squashfs-root/AppRun&quot;</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">__os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">app_path</span><span class="p">):</span>
    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Did not find extracted path </span><span class="si">{</span><span class="n">app_path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
    <span class="n">app_path</span> <span class="o">=</span> <span class="n">__os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span> <span class="n">__os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span> <span class="n">__os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">__os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="vm">__file__</span><span class="p">),</span><span class="s2">&quot;..&quot;</span><span class="p">)</span> <span class="p">),</span> <span class="s1">&#39;__bin__/casaplotms-x86_64.AppImage&#39;</span><span class="p">)</span>
</pre></div>
<p>I haven't tried it but I'm slightly hopeful.</p>

  </div><!-- /.entry-content -->
</section>

  </div>

    <script type="text/javascript">
    var _gaq = _gaq || [];
    _gaq.push(['_setAccount', 'UA-37306139-1']);
    _gaq.push(['_trackPageview']);
    (function() {
        var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
        ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
        var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
    })();

    (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
    (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
    m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
    })(window,document,'script','//www.google-analytics.com/analytics.js','ga');

    ga('create', 'UA-37306139-1');
    ga('send', 'pageview');
</script>
<!-- Start of StatCounter Code for Default Guide -->
<script type="text/javascript">
var sc_project=9280906; 
var sc_invisible=1; 
var sc_security="7107d360"; 
var scJsHost = (("https:" == document.location.protocol) ?
"https://secure." : "http://www.");
document.write("<sc"+"ript type='text/javascript' src='" +
scJsHost+
"statcounter.com/counter/counter.js'></"+"script>");
</script>
<!--<noscript><div class="statcounter"><a title="hit counter"
href="http://statcounter.com/free-hit-counter/"
target="_blank"><img class="statcounter"
src="http://c.statcounter.com/9280906/0/7107d360/1/"
alt="hit counter"></a></div></noscript>-->
<!-- End of StatCounter Code for Default Guide -->
<script type="text/javascript">
  var disqus_shortname = 'adamginsburgsblog';
  var disqus_identifier = '/hacking-plotms-to-let-pipeline-run.html';
  var disqus_url = 'https://keflavich.github.io/blog/hacking-plotms-to-let-pipeline-run.html';
  var disqus_title = 'Hacking plotms to let pipeline run';
  (function() {
        var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
        dsq.src = 'https://' + disqus_shortname + '.disqus.com/embed.js';
        (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
   })();
</script>
</body>
</html>