<!DOCTYPE html> <html lang="en-us"> <head prefix="og: http://ogp.me/ns#"> <meta charset="utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1" /> <meta property="og:title" content=" December, 2015 · CGSpace Notes" /> <meta property="og:site_name" content="CGSpace Notes" /> <meta property="og:url" content="/cgspace-notes/2015-12/" /> <meta property="og:type" content="article" /> <meta property="og:article:published_time" content="2015-12-02T13:18:00+03:00" /> <meta property="og:article:tag" content="notes" /> <title> December, 2015 · CGSpace Notes </title> <link rel="stylesheet" href="/cgspace-notes/css/bootstrap.min.css" /> <link rel="stylesheet" href="/cgspace-notes/css/main.css" /> <link rel="stylesheet" href="/cgspace-notes/css/font-awesome.min.css" /> <link rel="stylesheet" href="/cgspace-notes/css/github.css" /> <link rel="stylesheet" href="//fonts.googleapis.com/css?family=Source+Sans+Pro:200,300,400" type="text/css"> <link rel="shortcut icon" href="/cgspace-notes/images/favicon.ico" /> <link rel="apple-touch-icon" href="/cgspace-notes/images/apple-touch-icon.png" /> </head> <body> <header class="global-header" style="background-image:url(../images/bg.jpg )"> <section class="header-text"> <h1><a href="/cgspace-notes/">CGSpace Notes</a></h1> <div class="sns-links hidden-print"> </div> <a href="/cgspace-notes/" class="btn-header btn-back hidden-xs"> <i class="fa fa-angle-left" aria-hidden="true"></i> Home </a> </section> </header> <main class="container"> <article> <header> <h1 class="text-primary">December, 2015</h1> <div class="post-meta clearfix"> <div class="post-date pull-left"> Posted on <time datetime="2015-12-02T13:18:00+03:00"> Dec 2, 2015 </time> </div> <div class="pull-right"> <span class="post-tag small"><a href="/cgspace-notes//tags/notes">#notes</a></span> </div> </div> </header> <section> <h2 id="2015-12-02:012a628feed6d64ae1151cbd6151ccd6">2015-12-02</h2> <ul> <li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li> </ul> <pre><code># cd /home/dspacetest.cgiar.org/log # ls -lh dspace.log.2015-11-18* -rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18 -rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo -rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz </code></pre> <ul> <li>I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper</li> <li>Need to remember to go check if everything is ok in a few days and then change CGSpace</li> <li>CGSpace went down again (due to PostgreSQL idle connections of course)</li> <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> </ul> <pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle 39 </code></pre> <ul> <li>I restarted PostgreSQL and Tomcat and it’s back</li> <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> </ul> <pre><code># apt-get install pgtune # pgtune -i /etc/postgresql/9.3/main/postgresql.conf -o postgresql.conf-pgtune # mv /etc/postgresql/9.3/main/postgresql.conf /etc/postgresql/9.3/main/postgresql.conf.orig # mv postgresql.conf-pgtune /etc/postgresql/9.3/main/postgresql.conf </code></pre> <ul> <li>It introduced the following new settings:</li> </ul> <pre><code>default_statistics_target = 50 maintenance_work_mem = 480MB constraint_exclusion = on checkpoint_completion_target = 0.9 effective_cache_size = 5632MB work_mem = 48MB wal_buffers = 8MB checkpoint_segments = 16 shared_buffers = 1920MB max_connections = 80 </code></pre> <ul> <li>Now I need to go read PostgreSQL docs about these options, and watch memory settings in munin etc</li> <li>For what it’s worth, now the REST API should be faster (because of these PostgreSQL tweaks):</li> </ul> <pre><code>$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 1.474 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 2.141 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 1.685 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 1.995 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 1.786 </code></pre> <ul> <li>Last week it was an average of 8 seconds… now this is <sup>1</sup>⁄<sub>4</sub> of that</li> <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> </ul> <p><img src="../images/2015/12/ccafs-item-no-metadata.png" alt="CCAFS item" /></p> <ul> <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> <li>I filed a ticket on Atmire’s issue tracker</li> <li>I also filed a ticket on Atmire’s issue tracker for the PostgreSQL stuff</li> </ul> <h2 id="2015-12-03:012a628feed6d64ae1151cbd6151ccd6">2015-12-03</h2> <ul> <li>CGSpace very slow, and monitoring emailing me to say its down, even though I can load the page (very slowly)</li> <li>Idle postgres connections look like this (with no change in DSpace db settings lately):</li> </ul> <pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle 29 </code></pre> <ul> <li>I restarted Tomcat and postgres…</li> <li>Atmire commented that we should raise the JVM heap size by ~500M, so it is now <code>-Xms3584m -Xmx3584m</code></li> <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> <li>A possible side effect is that I see that the REST API is twice as fast for the request above now:</li> </ul> <pre><code>$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 1.368 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.968 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 1.006 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.849 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.806 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.854 </code></pre> <h2 id="2015-12-05:012a628feed6d64ae1151cbd6151ccd6">2015-12-05</h2> <ul> <li>CGSpace has been up and down all day and REST API is completely unresponsive</li> <li>PostgreSQL idle connections are currently:</li> </ul> <pre><code>postgres@linode01:~$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle 28 </code></pre> <ul> <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> <li>The PostgreSQL stats from Munin all point to something database-related with the DSpace 5 upgrade around mid–late November</li> </ul> <p><img src="../images/2015/12/postgres_bgwriter-year.png" alt="PostgreSQL bgwriter (year)" /> <img src="../images/2015/12/postgres_cache_cgspace-year.png" alt="PostgreSQL cache (year)" /> <img src="../images/2015/12/postgres_locks_cgspace-year.png" alt="PostgreSQL locks (year)" /> <img src="../images/2015/12/postgres_scans_cgspace-year.png" alt="PostgreSQL scans (year)" /></p> <h2 id="2015-12-07:012a628feed6d64ae1151cbd6151ccd6">2015-12-07</h2> <ul> <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> <li>After deploying the fix to CGSpace the REST API is consistently faster:</li> </ul> <pre><code>$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.675 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.599 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.588 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.566 $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all 0.497 </code></pre> <h2 id="2015-12-08:012a628feed6d64ae1151cbd6151ccd6">2015-12-08</h2> <ul> <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> <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> </ul> </section> <footer> <section class="author-info row"> <div class="author-avatar col-md-2"> </div> <div class="author-meta col-md-6"> <h1 class="author-name text-primary">Alan Orth</h1> </div> </section> <ul class="pager"> <li class="previous"><a href="/cgspace-notes/2015-11/"><span aria-hidden="true">←</span> Older</a></li> <li class="next"><a href="/cgspace-notes/2016-01/">Newer <span aria-hidden="true">→</span></a></li> </ul> </footer> </article> </main> <footer class="container global-footer"> <div class="copyright-note pull-left"> </div> <div class="sns-links hidden-print"> </div> </footer> <script src="/cgspace-notes/js/highlight.pack.js"></script> <script> hljs.initHighlightingOnLoad(); </script> </body> </html>