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December, 2015 · CGSpace Notes
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<h1><a href="/cgspace-notes/">CGSpace Notes</a></h1>
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<h1 class="text-primary">December, 2015</h1>
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Posted on
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<time datetime="2015-12-02T13:18:00+03:00">
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Dec 2, 2015
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<span class="post-tag small"><a href="/cgspace-notes//tags/notes">#notes</a></span>
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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’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’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… now this is <sup>1</sup>⁄<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’t see any errors in dspace.log when browsing that item</li>
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<li>I filed a ticket on Atmire’s issue tracker</li>
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<li>I also filed a ticket on Atmire’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…</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’t out of heap yet, but it’s probably fair enough that the DSpace 5 upgrade (and new Atmire modules) requires more memory so it’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’t fix the stability issues, so I’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’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
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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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0.599
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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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0.588
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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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0.566
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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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0.497
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</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’t as good, but it’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’s crawl rate to the “Let Google optimize” setting</li>
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