1
0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2024-12-23 21:44:30 +01:00
cgspace-notes/docs/2015-12/index.html

350 lines
12 KiB
HTML
Raw Normal View History

2018-02-11 17:28:23 +01:00
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta property="og:title" content="December, 2015" />
<meta property="og:description" content="2015-12-02
Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less space:
# 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
" />
<meta property="og:type" content="article" />
2019-02-02 13:12:57 +01:00
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2015-12/" />
<meta property="article:published_time" content="2015-12-02T13:18:00&#43;03:00"/>
2018-03-09 21:16:20 +01:00
<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
2018-09-30 07:23:48 +02:00
2018-02-11 17:28:23 +01:00
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="December, 2015"/>
<meta name="twitter:description" content="2015-12-02
Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less space:
# 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
"/>
2019-04-21 14:31:15 +02:00
<meta name="generator" content="Hugo 0.55.3" />
2018-02-11 17:28:23 +01:00
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "BlogPosting",
"headline": "December, 2015",
2019-04-13 11:15:55 +02:00
"url": "https:\/\/alanorth.github.io\/cgspace-notes\/2015-12\/",
2018-04-30 18:05:39 +02:00
"wordCount": "753",
2019-04-13 11:15:55 +02:00
"datePublished": "2015-12-02T13:18:00\x2b03:00",
"dateModified": "2018-03-09T22:10:33\x2b02:00",
2018-02-11 17:28:23 +01:00
"author": {
"@type": "Person",
"name": "Alan Orth"
},
"keywords": "Notes"
}
</script>
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2015-12/">
<title>December, 2015 | CGSpace Notes</title>
<!-- combined, minified CSS -->
2019-02-13 17:47:17 +01:00
<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
2018-02-11 17:28:23 +01:00
2019-04-14 15:59:47 +02:00
<!-- RSS 2.0 feed -->
2018-02-11 17:28:23 +01:00
</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>
2018-12-19 12:20:39 +01:00
2018-02-11 17:28:23 +01:00
<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>
<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
</div>
</header>
2018-12-19 12:20:39 +01:00
2018-02-11 17:28:23 +01:00
<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/">December, 2015</a></h2>
<p class="blog-post-meta"><time datetime="2015-12-02T13:18:00&#43;03:00">Wed Dec 02, 2015</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</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&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="/cgspace-notes/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">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">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 midlate November</li>
</ul>
<p><img src="/cgspace-notes/2015/12/postgres_bgwriter-year.png" alt="PostgreSQL bgwriter (year)" />
<img src="/cgspace-notes/2015/12/postgres_cache_cgspace-year.png" alt="PostgreSQL cache (year)" />
<img src="/cgspace-notes/2015/12/postgres_locks_cgspace-year.png" alt="PostgreSQL locks (year)" />
<img src="/cgspace-notes/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&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>
<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&rsquo;t as good, but it&rsquo;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&rsquo;s crawl rate to the &ldquo;Let Google optimize&rdquo; setting</li>
</ul>
</article>
</div> <!-- /.blog-main -->
<aside class="col-sm-3 ml-auto blog-sidebar">
<section class="sidebar-module">
<h4>Recent Posts</h4>
<ol class="list-unstyled">
2019-04-01 08:02:18 +02:00
<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
2019-04-13 11:15:55 +02:00
<li><a href="/cgspace-notes/posts/">Posts</a></li>
2019-03-01 12:17:17 +01:00
<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
2019-02-01 20:45:50 +01:00
<li><a href="/cgspace-notes/2019-02/">February, 2019</a></li>
2019-01-02 08:59:01 +01:00
<li><a href="/cgspace-notes/2019-01/">January, 2019</a></li>
2018-02-11 17:28:23 +01:00
</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 created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
</p>
<p>
<a href="#">Back to top</a>
</p>
</footer>
</body>
</html>