alanorth/cgspace-notes
1
0
Fork 0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2024-11-22 22:55:04 +01:00
Code Issues Projects Releases Wiki Activity
9243ef93ae
cgspace-notes/public/2015-12/index.html
Alan Orth 9243ef93ae
Add notes for 2015-12-07 
Signed-off-by: Alan Orth <alan.orth@gmail.com>
2015-12-07 19:10:54 +02:00

289 lines
9.9 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

<!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 &middot; 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&#43;03:00" />
<meta property="og:article:tag" content="notes" />
<title>
December, 2015 &middot; 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>
&nbsp;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&#43;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&rsquo;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&rsquo;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&hellip; now this is <sup>1</sup>&frasl;<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&rsquo;t see any errors in dspace.log when browsing that item</li>
<li>I filed a ticket on Atmire&rsquo;s issue tracker</li>
<li>I also filed a ticket on Atmire&rsquo;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&hellip;</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&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>
<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&rsquo;t fix the stability issues, so I&rsquo;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&rsquo;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>
</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">&larr;</span> Older</a></li>
<li class="next disabled"><a href="#">Newer <span aria-hidden="true">&rarr;</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>
Reference in New Issue View Git Blame Copy Permalink