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377 lines
20 KiB
XML
<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
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<title>CGSpace Notes</title>
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<link>/cgspace-notes/</link>
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<description>Recent content on CGSpace Notes</description>
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<generator>Hugo -- gohugo.io</generator>
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<language>en-us</language>
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<lastBuildDate>Wed, 13 Jan 2016 13:18:00 +0300</lastBuildDate>
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<atom:link href="/cgspace-notes/index.xml" rel="self" type="application/rss+xml" />
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<item>
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<title>January, 2016</title>
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<link>/cgspace-notes/2016-01/</link>
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<pubDate>Wed, 13 Jan 2016 13:18:00 +0300</pubDate>
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<guid>/cgspace-notes/2016-01/</guid>
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<description>
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<h2 id="2016-01-13:3846b7fcbca60cdedafd373cb39cd76d">2016-01-13</h2>
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<ul>
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<li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li>
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<li>I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.</li>
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<li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li>
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</ul>
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<h2 id="2016-01-14:3846b7fcbca60cdedafd373cb39cd76d">2016-01-14</h2>
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<ul>
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<li>Update CCAFS project identifiers in input-forms.xml</li>
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<li>Run system updates and restart the server</li>
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</ul>
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<h2 id="2016-01-18:3846b7fcbca60cdedafd373cb39cd76d">2016-01-18</h2>
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<ul>
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<li>Change &ldquo;Extension material&rdquo; to &ldquo;Extension Material&rdquo; in input-forms.xml (a mistake that fell through the cracks when we fixed the others in DSpace 4 era)</li>
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</ul>
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<h2 id="2016-01-19:3846b7fcbca60cdedafd373cb39cd76d">2016-01-19</h2>
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<ul>
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<li>Work on tweaks and updates for the social sharing icons on item pages: add Delicious and Mendeley (from Academicons), make links open in new windows, and set the icon color to the theme&rsquo;s primary color (<a href="https://github.com/ilri/DSpace/issues/157">#157</a>)</li>
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<li>Tweak date-based facets to show more values in drill-down ranges (<a href="https://github.com/ilri/DSpace/issues/162">#162</a>)</li>
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<li>Need to remember to clear the Cocoon cache after deployment or else you don&rsquo;t see the new ranges immediately</li>
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</ul>
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</description>
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</item>
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<item>
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<title>December, 2015</title>
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<link>/cgspace-notes/2015-12/</link>
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<pubDate>Wed, 02 Dec 2015 13:18:00 +0300</pubDate>
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<guid>/cgspace-notes/2015-12/</guid>
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<description>
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<h2 id="2015-12-02:012a628feed6d64ae1151cbd6151ccd6">2015-12-02</h2>
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<ul>
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<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
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</ul>
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<pre><code># cd /home/dspacetest.cgiar.org/log
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# ls -lh dspace.log.2015-11-18*
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-rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18
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-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
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-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
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</code></pre>
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<ul>
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<li>I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper</li>
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<li>Need to remember to go check if everything is ok in a few days and then change CGSpace</li>
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<li>CGSpace went down again (due to PostgreSQL idle connections of course)</li>
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<li>Current database settings for DSpace are <code>db.maxconnections = 30</code> and <code>db.maxidle = 8</code>, yet idle connections are exceeding this:</li>
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</ul>
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<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
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39
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</code></pre>
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<ul>
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<li>I restarted PostgreSQL and Tomcat and it&rsquo;s back</li>
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<li>On a related note of why CGSpace is so slow, I decided to finally try the <code>pgtune</code> script to tune the postgres settings:</li>
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</ul>
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<pre><code># apt-get install pgtune
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# pgtune -i /etc/postgresql/9.3/main/postgresql.conf -o postgresql.conf-pgtune
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# mv /etc/postgresql/9.3/main/postgresql.conf /etc/postgresql/9.3/main/postgresql.conf.orig
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# mv postgresql.conf-pgtune /etc/postgresql/9.3/main/postgresql.conf
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</code></pre>
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<ul>
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<li>It introduced the following new settings:</li>
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</ul>
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<pre><code>default_statistics_target = 50
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maintenance_work_mem = 480MB
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constraint_exclusion = on
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checkpoint_completion_target = 0.9
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effective_cache_size = 5632MB
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work_mem = 48MB
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wal_buffers = 8MB
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checkpoint_segments = 16
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shared_buffers = 1920MB
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max_connections = 80
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</code></pre>
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<ul>
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<li>Now I need to go read PostgreSQL docs about these options, and watch memory settings in munin etc</li>
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<li>For what it&rsquo;s worth, now the REST API should be faster (because of these PostgreSQL tweaks):</li>
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</ul>
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<pre><code>$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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1.474
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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2.141
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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1.685
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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1.995
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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1.786
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</code></pre>
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<ul>
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<li>Last week it was an average of 8 seconds&hellip; now this is <sup>1</sup>&frasl;<sub>4</sub> of that</li>
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<li>CCAFS noticed that one of their items displays only the Atmire statlets: <a href="https://cgspace.cgiar.org/handle/10568/42445">https://cgspace.cgiar.org/handle/10568/42445</a></li>
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</ul>
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<p><img src="../images/2015/12/ccafs-item-no-metadata.png" alt="CCAFS item" /></p>
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<ul>
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<li>The authorizations for the item are all public READ, and I don&rsquo;t see any errors in dspace.log when browsing that item</li>
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<li>I filed a ticket on Atmire&rsquo;s issue tracker</li>
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<li>I also filed a ticket on Atmire&rsquo;s issue tracker for the PostgreSQL stuff</li>
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</ul>
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<h2 id="2015-12-03:012a628feed6d64ae1151cbd6151ccd6">2015-12-03</h2>
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<ul>
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<li>CGSpace very slow, and monitoring emailing me to say its down, even though I can load the page (very slowly)</li>
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<li>Idle postgres connections look like this (with no change in DSpace db settings lately):</li>
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</ul>
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<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
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29
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</code></pre>
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<ul>
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<li>I restarted Tomcat and postgres&hellip;</li>
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<li>Atmire commented that we should raise the JVM heap size by ~500M, so it is now <code>-Xms3584m -Xmx3584m</code></li>
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<li>We weren&rsquo;t out of heap yet, but it&rsquo;s probably fair enough that the DSpace 5 upgrade (and new Atmire modules) requires more memory so it&rsquo;s ok</li>
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<li>A possible side effect is that I see that the REST API is twice as fast for the request above now:</li>
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</ul>
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<pre><code>$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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1.368
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.968
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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1.006
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.849
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.806
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$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.854
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</code></pre>
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<h2 id="2015-12-05:012a628feed6d64ae1151cbd6151ccd6">2015-12-05</h2>
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<ul>
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<li>CGSpace has been up and down all day and REST API is completely unresponsive</li>
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<li>PostgreSQL idle connections are currently:</li>
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</ul>
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<pre><code>postgres@linode01:~$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
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28
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</code></pre>
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<ul>
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<li>I have reverted all the pgtune tweaks from the other day, as they didn&rsquo;t fix the stability issues, so I&rsquo;d rather not have them introducing more variables into the equation</li>
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<li>The PostgreSQL stats from Munin all point to something database-related with the DSpace 5 upgrade around mid–late November</li>
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</ul>
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<p><img src="../images/2015/12/postgres_bgwriter-year.png" alt="PostgreSQL bgwriter (year)" />
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<img src="../images/2015/12/postgres_cache_cgspace-year.png" alt="PostgreSQL cache (year)" />
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<img src="../images/2015/12/postgres_locks_cgspace-year.png" alt="PostgreSQL locks (year)" />
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<img src="../images/2015/12/postgres_scans_cgspace-year.png" alt="PostgreSQL scans (year)" /></p>
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<h2 id="2015-12-07:012a628feed6d64ae1151cbd6151ccd6">2015-12-07</h2>
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<ul>
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<li>Atmire sent <a href="https://github.com/ilri/DSpace/pull/161">some fixes</a> to DSpace&rsquo;s REST API code that was leaving contexts open (causing the slow performance and database issues)</li>
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<li>After deploying the fix to CGSpace the REST API is consistently faster:</li>
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||
</ul>
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<pre><code>$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.675
|
||
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.599
|
||
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.588
|
||
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.566
|
||
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
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0.497
|
||
</code></pre>
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<h2 id="2015-12-08:012a628feed6d64ae1151cbd6151ccd6">2015-12-08</h2>
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<ul>
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<li>Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn&rsquo;t as good, but it&rsquo;s much faster and causes less IO/CPU load</li>
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<li>Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot&rsquo;s crawl rate to the &ldquo;Let Google optimize&rdquo; setting</li>
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</ul>
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</description>
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</item>
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<item>
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<title>November, 2015</title>
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<link>/cgspace-notes/2015-11/</link>
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<pubDate>Mon, 23 Nov 2015 17:00:57 +0300</pubDate>
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||
<guid>/cgspace-notes/2015-11/</guid>
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<description>
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<h2 id="2015-11-22:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-22</h2>
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<ul>
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<li>CGSpace went down</li>
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<li>Looks like DSpace exhausted its PostgreSQL connection pool</li>
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<li>Last week I had increased the limit from 30 to 60, which seemed to help, but now there are many more idle connections:</li>
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</ul>
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<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
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78
|
||
</code></pre>
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<ul>
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<li>For now I have increased the limit from 60 to 90, run updates, and rebooted the server</li>
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</ul>
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<h2 id="2015-11-24:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-24</h2>
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<ul>
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<li>CGSpace went down again</li>
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<li>Getting emails from uptimeRobot and uptimeButler that it&rsquo;s down, and Google Webmaster Tools is sending emails that there is an increase in crawl errors</li>
|
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<li>Looks like there are still a bunch of idle PostgreSQL connections:</li>
|
||
</ul>
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<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
|
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96
|
||
</code></pre>
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<ul>
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<li>For some reason the number of idle connections is very high since we upgraded to DSpace 5</li>
|
||
</ul>
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<h2 id="2015-11-25:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-25</h2>
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<ul>
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<li>Troubleshoot the DSpace 5 OAI breakage caused by nginx routing config</li>
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<li>The OAI application requests stylesheets and javascript files with the path <code>/oai/static/css</code>, which gets matched here:</li>
|
||
</ul>
|
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<pre><code># static assets we can load from the file system directly with nginx
|
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location ~ /(themes|static|aspects/ReportingSuite) {
|
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try_files $uri @tomcat;
|
||
...
|
||
</code></pre>
|
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<ul>
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<li>The document root is relative to the xmlui app, so this gets a 404—I&rsquo;m not sure why it doesn&rsquo;t pass to <code>@tomcat</code></li>
|
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<li>Anyways, I can&rsquo;t find any URIs with path <code>/static</code>, and the more important point is to handle all the static theme assets, so we can just remove <code>static</code> from the regex for now (who cares if we can&rsquo;t use nginx to send Etags for OAI CSS!)</li>
|
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<li>Also, I noticed we aren&rsquo;t setting CSP headers on the static assets, because in nginx headers are inherited in child blocks, but if you use <code>add_header</code> in a child block it doesn&rsquo;t inherit the others</li>
|
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<li>We simply need to add <code>include extra-security.conf;</code> to the above location block (but research and test first)</li>
|
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<li>We should add WOFF assets to the list of things to set expires for:</li>
|
||
</ul>
|
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|
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<pre><code>location ~* \.(?:ico|css|js|gif|jpe?g|png|woff)$ {
|
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</code></pre>
|
||
|
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<ul>
|
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<li>We should also add <code>aspects/Statistics</code> to the location block for static assets (minus <code>static</code> from above):</li>
|
||
</ul>
|
||
|
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<pre><code>location ~ /(themes|aspects/ReportingSuite|aspects/Statistics) {
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Need to check <code>/about</code> on CGSpace, as it&rsquo;s blank on my local test server and we might need to add something there</li>
|
||
<li>CGSpace has been up and down all day due to PostgreSQL idle connections (current DSpace pool is 90):</li>
|
||
</ul>
|
||
|
||
<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
|
||
93
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>I looked closer at the idle connections and saw that many have been idle for hours (current time on server is <code>2015-11-25T20:20:42+0000</code>):</li>
|
||
</ul>
|
||
|
||
<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | less -S
|
||
datid | datname | pid | usesysid | usename | application_name | client_addr | client_hostname | client_port | backend_start | xact_start |
|
||
-------+----------+-------+----------+----------+------------------+-------------+-----------------+-------------+-------------------------------+-------------------------------+---
|
||
20951 | cgspace | 10966 | 18205 | cgspace | | 127.0.0.1 | | 37731 | 2015-11-25 13:13:02.837624+00 | | 20
|
||
20951 | cgspace | 10967 | 18205 | cgspace | | 127.0.0.1 | | 37737 | 2015-11-25 13:13:03.069421+00 | | 20
|
||
...
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>There is a relevant Jira issue about this: <a href="https://jira.duraspace.org/browse/DS-1458">https://jira.duraspace.org/browse/DS-1458</a></li>
|
||
<li>It seems there is some sense changing DSpace&rsquo;s default <code>db.maxidle</code> from unlimited (-1) to something like 8 (Tomcat default) or 10 (Confluence default)</li>
|
||
<li>Change <code>db.maxidle</code> from -1 to 10, reduce <code>db.maxconnections</code> from 90 to 50, and restart postgres and tomcat7</li>
|
||
<li>Also redeploy DSpace Test with a clean sync of CGSpace and mirror these database settings there as well</li>
|
||
<li>Also deploy the nginx fixes for the <code>try_files</code> location block as well as the expires block</li>
|
||
</ul>
|
||
|
||
<h2 id="2015-11-26:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-26</h2>
|
||
|
||
<ul>
|
||
<li>CGSpace behaving much better since changing <code>db.maxidle</code> yesterday, but still two up/down notices from monitoring this morning (better than 50!)</li>
|
||
<li>CCAFS colleagues mentioned that the REST API is very slow, 24 seconds for one item</li>
|
||
<li>Not as bad for me, but still unsustainable if you have to get many:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
|
||
8.415
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Monitoring e-mailed in the evening to say CGSpace was down</li>
|
||
<li>Idle connections in PostgreSQL again:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
|
||
66
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>At the time, the current DSpace pool size was 50&hellip;</li>
|
||
<li>I reduced the pool back to the default of 30, and reduced the <code>db.maxidle</code> settings from 10 to 8</li>
|
||
</ul>
|
||
|
||
<h2 id="2015-11-29:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-29</h2>
|
||
|
||
<ul>
|
||
<li>Still more alerts that CGSpace has been up and down all day</li>
|
||
<li>Current database settings for DSpace:</li>
|
||
</ul>
|
||
|
||
<pre><code>db.maxconnections = 30
|
||
db.maxwait = 5000
|
||
db.maxidle = 8
|
||
db.statementpool = true
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>And idle connections:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
|
||
49
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace&rsquo;s thirst can ever be quenched</li>
|
||
<li>On another note, SUNScholar&rsquo;s notes suggest adjusting some other postgres variables: <a href="http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database">http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database</a></li>
|
||
<li>This might help with REST API speed (which I mentioned above and still need to do real tests)</li>
|
||
</ul>
|
||
</description>
|
||
</item>
|
||
|
||
</channel>
|
||
</rss> |