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2019-06-02 10:57:51 +03:00
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70
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@ -10,7 +10,7 @@
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2019-05-01T07:37:43&#43;03:00"/>
<meta property="og:updated_time" content="2019-05-06T10:30:43&#43;03:00"/>
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -29,7 +29,7 @@
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"description": "Documenting day-to-day work on the [CGSpace](https:\/\/cgspace.cgiar.org) repository."
}
@ -89,6 +89,29 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-05/">May, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-05-06T10:30:43&#43;03:00">Mon May 06, 2019</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>
</p>
</header>
<h2 id="2019-06-02">2019-06-02</h2>
<ul>
<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-05/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-05/">May, 2019</a></h2>
@ -399,45 +422,6 @@ sys 0m1.979s
<article class="blog-post">
<header>
<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>
</p>
</header>
<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<li><p>DSpace Test had crashed at some point yesterday morning and I see the following in <code>dmesg</code>:</p>
<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></li>
<li><p>Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight</p></li>
<li><p>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</p></li>
<li><p>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</p></li>
<li><p>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</p></li>
<li><p>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</p></li>
<li><p>I ran all system updates on DSpace Test and rebooted it</p></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-08/'>Read more →</a>
</article>
<nav class="blog-pagination">
@ -466,12 +450,12 @@ sys 0m1.979s
<li><a href="/cgspace-notes/posts/">Posts</a></li>
<li><a href="/cgspace-notes/2019-05/">May, 2019</a></li>
<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
<li><a href="/cgspace-notes/2019-02/">February, 2019</a></li>
</ol>
</section>

16
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@ -6,11 +6,25 @@
<description>Recent content in Posts on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Wed, 01 May 2019 07:37:43 +0300</lastBuildDate>
<lastBuildDate>Mon, 06 May 2019 10:30:43 +0300</lastBuildDate>
<atom:link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>May, 2019</title>
<link>https://alanorth.github.io/cgspace-notes/2019-05/</link>
<pubDate>Mon, 06 May 2019 10:30:43 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2019-05/</guid>
<description>&lt;h2 id=&#34;2019-06-02&#34;&gt;2019-06-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Merge the &lt;a href=&#34;https://github.com/ilri/DSpace/pull/425&#34;&gt;Solr filterCache&lt;/a&gt; and &lt;a href=&#34;https://github.com/ilri/DSpace/pull/426&#34;&gt;XMLUI ISI journal&lt;/a&gt; changes to the &lt;code&gt;5_x-prod&lt;/code&gt; branch and deploy on CGSpace&lt;/li&gt;
&lt;li&gt;Run system updates on CGSpace (linode18) and reboot it&lt;/li&gt;
&lt;/ul&gt;</description>
</item>
<item>
<title>May, 2019</title>
<link>https://alanorth.github.io/cgspace-notes/2019-05/</link>

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@ -10,7 +10,7 @@
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2019-05-01T07:37:43&#43;03:00"/>
<meta property="og:updated_time" content="2019-05-06T10:30:43&#43;03:00"/>
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -29,7 +29,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2019-05-01T07:37:43\x2b03:00",
"dateModified": "2019-05-06T10:30:43\x2b03:00",
"keywords": "notes,notes,",
"description": "Documenting day-to-day work on the [CGSpace](https:\/\/cgspace.cgiar.org) repository."
}
@ -89,6 +89,45 @@
<article class="blog-post">
<header>
<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>
</p>
</header>
<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<li><p>DSpace Test had crashed at some point yesterday morning and I see the following in <code>dmesg</code>:</p>
<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></li>
<li><p>Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight</p></li>
<li><p>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</p></li>
<li><p>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</p></li>
<li><p>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</p></li>
<li><p>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</p></li>
<li><p>I ran all system updates on DSpace Test and rebooted it</p></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"><a href="https://alanorth.github.io/cgspace-notes/2018-07/">July, 2018</a></h2>
@ -415,35 +454,6 @@ COPY 54701
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54&#43;03:00">Sun Oct 01, 2017</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>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li><p>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</p>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre></li>
<li><p>There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</p></li>
<li><p>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</p></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/" rel="prev" role="button">Previous page</a>
@ -472,12 +482,12 @@ COPY 54701
<li><a href="/cgspace-notes/posts/">Posts</a></li>
<li><a href="/cgspace-notes/2019-05/">May, 2019</a></li>
<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
<li><a href="/cgspace-notes/2019-02/">February, 2019</a></li>
</ol>
</section>

61
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@ -10,7 +10,7 @@
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2019-05-01T07:37:43&#43;03:00"/>
<meta property="og:updated_time" content="2019-05-06T10:30:43&#43;03:00"/>
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -29,7 +29,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2019-05-01T07:37:43\x2b03:00",
"dateModified": "2019-05-06T10:30:43\x2b03:00",
"keywords": "notes,notes,",
"description": "Documenting day-to-day work on the [CGSpace](https:\/\/cgspace.cgiar.org) repository."
}
@ -89,6 +89,35 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54&#43;03:00">Sun Oct 01, 2017</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>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li><p>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</p>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre></li>
<li><p>There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</p></li>
<li><p>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</p></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></h2>
@ -352,30 +381,6 @@ DELETE 1
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00&#43;03:00">Mon Jan 02, 2017</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>
</p>
</header>
<h2 id="2017-01-02">2017-01-02</h2>
<ul>
<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
<li>I asked on the dspace-tech mailing list because it seems to be broken, and actually now I&rsquo;m not sure if we&rsquo;ve ever had the sharding task run successfully over all these years</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-01/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/2/" rel="prev" role="button">Previous page</a>
@ -404,12 +409,12 @@ DELETE 1
<li><a href="/cgspace-notes/posts/">Posts</a></li>
<li><a href="/cgspace-notes/2019-05/">May, 2019</a></li>
<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
<li><a href="/cgspace-notes/2019-02/">February, 2019</a></li>
</ol>
</section>

56
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@ -10,7 +10,7 @@
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2019-05-01T07:37:43&#43;03:00"/>
<meta property="og:updated_time" content="2019-05-06T10:30:43&#43;03:00"/>
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -29,7 +29,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2019-05-01T07:37:43\x2b03:00",
"dateModified": "2019-05-06T10:30:43\x2b03:00",
"keywords": "notes,notes,",
"description": "Documenting day-to-day work on the [CGSpace](https:\/\/cgspace.cgiar.org) repository."
}
@ -89,6 +89,30 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00&#43;03:00">Mon Jan 02, 2017</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>
</p>
</header>
<h2 id="2017-01-02">2017-01-02</h2>
<ul>
<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
<li>I asked on the dspace-tech mailing list because it seems to be broken, and actually now I&rsquo;m not sure if we&rsquo;ve ever had the sharding task run successfully over all these years</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-01/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2>
@ -360,30 +384,6 @@ text_value
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-03/">March, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-03-02T16:50:00&#43;03:00">Wed Mar 02, 2016</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>
</p>
</header>
<h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
<li>For some reason we still have the <code>index-lucene-update</code> cron job active on CGSpace, but I&rsquo;m pretty sure we don&rsquo;t need it as of the latest few versions of Atmire&rsquo;s Listings and Reports module</li>
<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-03/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/3/" rel="prev" role="button">Previous page</a>
@ -412,12 +412,12 @@ text_value
<li><a href="/cgspace-notes/posts/">Posts</a></li>
<li><a href="/cgspace-notes/2019-05/">May, 2019</a></li>
<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
<li><a href="/cgspace-notes/2019-02/">February, 2019</a></li>
</ol>
</section>

32
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@ -10,7 +10,7 @@
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2019-05-01T07:37:43&#43;03:00"/>
<meta property="og:updated_time" content="2019-05-06T10:30:43&#43;03:00"/>
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -29,7 +29,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2019-05-01T07:37:43\x2b03:00",
"dateModified": "2019-05-06T10:30:43\x2b03:00",
"keywords": "notes,notes,",
"description": "Documenting day-to-day work on the [CGSpace](https:\/\/cgspace.cgiar.org) repository."
}
@ -89,6 +89,30 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-03/">March, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-03-02T16:50:00&#43;03:00">Wed Mar 02, 2016</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>
</p>
</header>
<h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
<li>For some reason we still have the <code>index-lucene-update</code> cron job active on CGSpace, but I&rsquo;m pretty sure we don&rsquo;t need it as of the latest few versions of Atmire&rsquo;s Listings and Reports module</li>
<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-02/">February, 2016</a></h2>
@ -229,12 +253,12 @@
<li><a href="/cgspace-notes/posts/">Posts</a></li>
<li><a href="/cgspace-notes/2019-05/">May, 2019</a></li>
<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
<li><a href="/cgspace-notes/2019-02/">February, 2019</a></li>
</ol>
</section>