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href="https://alanorth.github.io/cgspace-notes/posts/index.xml" title="CGSpace Notes" /> </head> <body> <div class="blog-masthead"> <div class="container"> <nav class="nav blog-nav"> <a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1> <p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 01, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-11-01">2018-11-01</h2> <ul> <li>Finalize AReS Phase I and Phase II ToRs</li> <li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li> </ul> <h2 id="2018-11-03">2018-11-03</h2> <ul> <li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li> <li>Today these are the top 10 IPs:</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-11/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-10/">October, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-10-01T22:31:54+03:00">Mon Oct 01, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-10-01">2018-10-01</h2> <ul> <li>Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items</li> <li>I created a GitHub issue to track this <a href="https://github.com/ilri/DSpace/issues/389">#389</a>, because I’m super busy in Nairobi right now</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-10/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-09/">September, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-09-02T09:55:54+03:00">Sun Sep 02, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-09-02">2018-09-02</h2> <ul> <li>New <a href="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5">PostgreSQL JDBC driver version 42.2.5</a></li> <li>I’ll update the DSpace role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li> <li>Also, I’ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month</li> <li>I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-09/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><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+03:00">Wed Aug 01, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <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’s</li> <li>I’m not sure why Tomcat didn’t crash with an OutOfMemoryError…</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’ll eventually need to upgrade to a larger one because we’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> <a href='https://alanorth.github.io/cgspace-notes/2018-08/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-07/">July, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-07-01T12:56:54+03:00">Sun Jul 01, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-07-01">2018-07-01</h2> <ul> <li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li> </ul> <pre><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace </code></pre><ul> <li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li> </ul> <pre><code>There is insufficient memory for the Java Runtime Environment to continue. </code></pre> <a href='https://alanorth.github.io/cgspace-notes/2018-07/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-06/">June, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-06-04T19:49:54-07:00">Mon Jun 04, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-06-04">2018-06-04</h2> <ul> <li>Test the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 module upgrades from Atmire</a> (<a href="https://github.com/ilri/DSpace/pull/378">#378</a>) <ul> <li>There seems to be a problem with the CUA and L&R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn’t build</li> </ul> </li> <li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li> <li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li> </ul> <pre><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n </code></pre><ul> <li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></li> <li>Time to index ~70,000 items on CGSpace:</li> </ul> <pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b real 74m42.646s user 8m5.056s sys 2m7.289s </code></pre> <a href='https://alanorth.github.io/cgspace-notes/2018-06/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-05/">May, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-05-01T16:43:54+03:00">Tue May 01, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-05-01">2018-05-01</h2> <ul> <li>I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface: <ul> <li>http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E</li> <li>http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E</li> </ul> </li> <li>Then I reduced the JVM heap size from 6144 back to 5120m</li> <li>Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> to support hosts choosing which distribution they want to use</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-05/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-04/">April, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-04-01T16:13:54+02:00">Sun Apr 01, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-04-01">2018-04-01</h2> <ul> <li>I tried to test something on DSpace Test but noticed that it’s down since god knows when</li> <li>Catalina logs at least show some memory errors yesterday:</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-04/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-03/">March, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-03-02T16:07:54+02:00">Fri Mar 02, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-03-02">2018-03-02</h2> <ul> <li>Export a CSV of the IITA community metadata for Martin Mueller</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-03/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-02/">February, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-02-01T16:28:54+02:00">Thu Feb 01, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-02-01">2018-02-01</h2> <ul> <li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li> <li>We don’t need to distinguish between internal and external works, so that makes it just a simple list</li> <li>Yesterday I figured out how to monitor DSpace sessions using JMX</li> <li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu’s <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="/cgspace-notes/2018-01/">in 2018-01</a></li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-02/'>Read more →</a> </article> <nav class="blog-pagination"> <a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/3/" 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