mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-24 15:40:17 +01:00
306 lines
11 KiB
HTML
306 lines
11 KiB
HTML
<!DOCTYPE html>
|
||
<html lang="en">
|
||
|
||
<head>
|
||
<meta charset="utf-8">
|
||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
||
<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
|
||
|
||
|
||
|
||
|
||
|
||
<meta name="description" content="">
|
||
<meta name="author" content="Alan Orth">
|
||
|
||
<!-- OpenGraph Metadata: http://ogp.me/ -->
|
||
<meta property="og:title" content="December, 2015">
|
||
<meta property="og:description" content="">
|
||
|
||
|
||
<meta property="og:type" content="article">
|
||
<meta property="article:published_time" content="2015-12-02T13:18:00+03:00">
|
||
<meta property="article:author" content="Alan Orth">
|
||
|
||
<meta property="og:image" content="https://alanorth.github.io/images/bg.jpg">
|
||
|
||
|
||
|
||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2015-12/">
|
||
|
||
<!-- Metadata for Twitter: https://dev.twitter.com/cards/markup -->
|
||
|
||
<meta property="twitter:card" content="summary_large_image">
|
||
<meta property="twitter:image" content="https://alanorth.github.io/images/bg.jpg">
|
||
|
||
|
||
<meta property="twitter:title" content="December, 2015">
|
||
<meta property="twitter:description" content="">
|
||
|
||
<meta name="generator" content="Hugo 0.16" />
|
||
|
||
|
||
<base href="https://alanorth.github.io/cgspace-notes/">
|
||
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2015-12/">
|
||
|
||
<title>December, 2015 | CGSpace Notes</title>
|
||
|
||
<!-- combined, minified CSS -->
|
||
<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet">
|
||
|
||
<!-- RSS 2.0 feed of posts -->
|
||
<link href="https://alanorth.github.io/cgspace-notes/post/index.xml" type="application/rss+xml" rel="alternate">
|
||
</head>
|
||
|
||
<body>
|
||
|
||
<div class="blog-masthead">
|
||
<div class="container">
|
||
<nav class="nav blog-nav">
|
||
<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
|
||
|
||
</nav>
|
||
</div>
|
||
</div>
|
||
|
||
<header class="blog-header">
|
||
<div class="container">
|
||
<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
|
||
|
||
</div>
|
||
</header>
|
||
|
||
<div class="container">
|
||
<div class="row">
|
||
<div class="col-sm-8 blog-main">
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2015-12/" title="December, 2015">December, 2015</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2015-12-02T13:18:00+03:00">Wed Dec 02, 2015</time> by <a href="#">Alan Orth</a></p>
|
||
</header>
|
||
|
||
|
||
<h2 id="2015-12-02">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="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">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">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="2015/12/postgres_bgwriter-year.png" alt="PostgreSQL bgwriter (year)" />
|
||
<img src="2015/12/postgres_cache_cgspace-year.png" alt="PostgreSQL cache (year)" />
|
||
<img src="2015/12/postgres_locks_cgspace-year.png" alt="PostgreSQL locks (year)" />
|
||
<img src="2015/12/postgres_scans_cgspace-year.png" alt="PostgreSQL scans (year)" /></p>
|
||
|
||
<h2 id="2015-12-07">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">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>
|
||
|
||
|
||
|
||
</article>
|
||
|
||
|
||
</div> <!-- /.blog-main -->
|
||
|
||
|
||
<aside class="col-sm-3 offset-sm-1 blog-sidebar">
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Recent Posts</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2016-07/">July, 2016</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2016-05/">May, 2016</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Links</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
||
|
||
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
||
|
||
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
</aside>
|
||
|
||
|
||
|
||
</div> <!-- /.row -->
|
||
</div> <!-- /.container -->
|
||
|
||
<footer class="blog-footer">
|
||
<p>
|
||
Blog template built by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
|
||
</p>
|
||
</footer>
|
||
|
||
</body>
|
||
|
||
</html>
|