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2018-08-01 11:49:05 +02:00
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DSpace Test had crashed at some point yesterday morning and I see the following in dmesg:
[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight
From the DSpace log I see that eventually Solr stopped responding, so I guess the java process that was OOM killed above was Tomcat&rsquo;s
I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;
Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core
The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;ll start starving the OS, PostgreSQL, and command line batch processes
I ran all system updates on DSpace Test and rebooted it
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2018-08-02 13:29:59 +02:00
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2018-08-01 11:49:05 +02:00
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DSpace Test had crashed at some point yesterday morning and I see the following in dmesg:
[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight
From the DSpace log I see that eventually Solr stopped responding, so I guess the java process that was OOM killed above was Tomcat&rsquo;s
I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;
Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core
The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;ll start starving the OS, PostgreSQL, and command line batch processes
I ran all system updates on DSpace Test and rebooted it
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2018-08-01 11:49:05 +02:00
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-08/">August, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54&#43;03:00">Wed Aug 01, 2018</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<li>DSpace Test had crashed at some point yesterday morning and I see the following in <code>dmesg</code>:</li>
</ul>
<pre><code>[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
</code></pre>
<ul>
<li>Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight</li>
<li>From the DSpace log I see that eventually Solr stopped responding, so I guess the <code>java</code> process that was OOM killed above was Tomcat&rsquo;s</li>
<li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</li>
<li>Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core</li>
<li>The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;ll start starving the OS, PostgreSQL, and command line batch processes</li>
<li>I ran all system updates on DSpace Test and rebooted it</li>
</ul>
<p></p>
2018-08-01 16:24:49 +02:00
<ul>
<li>I started looking over the latest round of IITA batch records from Sisay on DSpace Test: <a href="https://dspacetest.cgiar.org/handle/10568/103250">IITA July_30</a>
<ul>
<li>incorrect authorship types</li>
<li>dozens of inconsistencies, spelling mistakes, and white space in author affiliations</li>
<li>minor issues in countries (California is not a country)</li>
<li>minor issues in IITA subjects, ISBNs, languages, and AGROVOC subjects</li>
</ul></li>
</ul>
2018-08-02 13:29:59 +02:00
<h2 id="2018-08-02">2018-08-02</h2>
<ul>
<li>DSpace Test crashed again and I don&rsquo;t see the only error I see is this in <code>dmesg</code>:</li>
</ul>
<pre><code>[Thu Aug 2 00:00:12 2018] Out of memory: Kill process 1407 (java) score 787 or sacrifice child
[Thu Aug 2 00:00:12 2018] Killed process 1407 (java) total-vm:18876328kB, anon-rss:6323836kB, file-rss:0kB, shmem-rss:0kB
</code></pre>
<ul>
<li>I am still assuming that this is the Tomcat process that is dying, so maybe actually we need to reduce its memory instead of increasing it?</li>
<li>The risk we run there is that we&rsquo;ll start getting OutOfMemory errors from Tomcat</li>
<li>So basically we need a new test server with more RAM very soon&hellip;</li>
<li>Abenet asked about the workflow statistics in the Atmire CUA module again</li>
<li>Last year Atmire told me that it&rsquo;s disabled by default but you can enable it with <code>workflow.stats.enabled = true</code> in the CUA configuration file</li>
<li>There was a bug with adding users so they sent a patch, but I didn&rsquo;t merge it because it was <a href="https://github.com/ilri/DSpace/pull/319">very dirty</a> and I wasn&rsquo;t sure it actually fixed the problem</li>
<li>I just tried to enable the stats again on DSpace Test now that we&rsquo;re on DSpace 5.8 with updated Atmire modules, but every user I search for shows &ldquo;No data available&rdquo;</li>
<li>As a test I submitted a new item and I was able to see it in the workflow statistics &ldquo;data&rdquo; tab, but not in the graph</li>
</ul>
2018-08-01 11:49:05 +02:00
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<li><a href="/cgspace-notes/2018-08/">August, 2018</a></li>
<li><a href="/cgspace-notes/2018-07/">July, 2018</a></li>
<li><a href="/cgspace-notes/2018-06/">June, 2018</a></li>
<li><a href="/cgspace-notes/2018-05/">May, 2018</a></li>
<li><a href="/cgspace-notes/2018-04/">April, 2018</a></li>
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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