mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-12-25 14:34:30 +01:00
322 lines
15 KiB
HTML
322 lines
15 KiB
HTML
<!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="September, 2024" />
|
||
<meta property="og:description" content="2024-09-01
|
||
|
||
Upgrade CGSpace to DSpace 7.6.2
|
||
" />
|
||
<meta property="og:type" content="article" />
|
||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2024-09/" />
|
||
<meta property="article:published_time" content="2024-09-01T21:16:00-07:00" />
|
||
<meta property="article:modified_time" content="2024-09-30T07:56:53+03:00" />
|
||
|
||
|
||
|
||
<meta name="twitter:card" content="summary"/>
|
||
<meta name="twitter:title" content="September, 2024"/>
|
||
<meta name="twitter:description" content="2024-09-01
|
||
|
||
Upgrade CGSpace to DSpace 7.6.2
|
||
"/>
|
||
<meta name="generator" content="Hugo 0.133.1">
|
||
|
||
|
||
|
||
<script type="application/ld+json">
|
||
{
|
||
"@context": "http://schema.org",
|
||
"@type": "BlogPosting",
|
||
"headline": "September, 2024",
|
||
"url": "https://alanorth.github.io/cgspace-notes/2024-09/",
|
||
"wordCount": "769",
|
||
"datePublished": "2024-09-01T21:16:00-07:00",
|
||
"dateModified": "2024-09-30T07:56:53+03:00",
|
||
"author": {
|
||
"@type": "Person",
|
||
"name": "Alan Orth"
|
||
},
|
||
"keywords": "Notes"
|
||
}
|
||
</script>
|
||
|
||
|
||
|
||
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2024-09/">
|
||
|
||
<title>September, 2024 | CGSpace Notes</title>
|
||
|
||
|
||
<!-- combined, minified CSS -->
|
||
|
||
<link href="https://alanorth.github.io/cgspace-notes/css/style.c6ba80bc50669557645abe05f86b73cc5af84408ed20f1551a267bc19ece8228.css" rel="stylesheet" integrity="sha256-xrqAvFBmlVdkWr4F+GtzzFr4RAjtIPFVGiZ7wZ7Ogig=" crossorigin="anonymous">
|
||
|
||
|
||
<!-- minified Font Awesome for SVG icons -->
|
||
|
||
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script>
|
||
|
||
<!-- RSS 2.0 feed -->
|
||
|
||
|
||
|
||
|
||
</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" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
|
||
<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
|
||
</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" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2024-09/">September, 2024</a></h2>
|
||
<p class="blog-post-meta">
|
||
<time datetime="2024-09-01T21:16:00-07:00">Sun Sep 01, 2024</time>
|
||
in
|
||
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
||
|
||
|
||
</p>
|
||
</header>
|
||
<h2 id="2024-09-01">2024-09-01</h2>
|
||
<ul>
|
||
<li>Upgrade CGSpace to DSpace 7.6.2</li>
|
||
</ul>
|
||
<h2 id="2024-09-05">2024-09-05</h2>
|
||
<ul>
|
||
<li>Finalize work on migrating DSpace Angular from Yarn to NPM</li>
|
||
</ul>
|
||
<h2 id="2024-09-06">2024-09-06</h2>
|
||
<ul>
|
||
<li>This morning Tomcat crashed due to an OOM kill:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>Sep 06 00:00:24 server systemd[1]: tomcat9.service: A process of this unit has been killed by the OOM killer.
|
||
Sep 06 00:00:25 server systemd[1]: tomcat9.service: Main process exited, code=killed, status=9/KILL
|
||
Sep 06 00:00:25 server systemd[1]: tomcat9.service: Failed with result 'oom-kill'.
|
||
</code></pre><ul>
|
||
<li>According to the system journal, it was a Node.js dspace-angular process that tried to allocate memory and failed, thus invoking the OOM killer</li>
|
||
<li>Currently I see high memory usage in those processes:</li>
|
||
</ul>
|
||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ pm2 status
|
||
</span></span><span style="display:flex;"><span>┌────┬──────────────┬─────────────┬─────────┬─────────┬──────────┬────────┬──────┬───────────┬──────────┬──────────┬──────────┬──────────┐
|
||
</span></span><span style="display:flex;"><span>│ id │ name │ namespace │ version │ mode │ pid │ uptime │ ↺ │ status │ cpu │ mem │ user │ watching │
|
||
</span></span><span style="display:flex;"><span>├────┼──────────────┼─────────────┼─────────┼─────────┼──────────┼────────┼──────┼───────────┼──────────┼──────────┼──────────┼──────────┤
|
||
</span></span><span style="display:flex;"><span>│ 0 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 994 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
|
||
</span></span><span style="display:flex;"><span>│ 1 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1015 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
|
||
</span></span><span style="display:flex;"><span>│ 2 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1029 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
|
||
</span></span><span style="display:flex;"><span>│ 3 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1042 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
|
||
</span></span><span style="display:flex;"><span>└────┴──────────────┴─────────────┴─────────┴─────────┴──────────┴────────┴──────┴───────────┴──────────┴──────────┴──────────┴──────────┘
|
||
</span></span></code></pre></div><ul>
|
||
<li>I bet if I look in the logs I’d find some kind of heavy traffic on the frontend, causing high caching for Angular SSR</li>
|
||
</ul>
|
||
<h2 id="2024-09-08">2024-09-08</h2>
|
||
<ul>
|
||
<li>Analyzing memory use in our DSpace hosts, which have 32GB of memory
|
||
<ul>
|
||
<li>Effective cache of PostgreSQL is estimated at 11GB, which seems way high since the database is only 2GB</li>
|
||
<li>Realistically this should be how we adjust, with PostgreSQL using ~8GB (or less) and each dspace-angular process pinned at 2GB…</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<blockquote>
|
||
<p>Total - Solr - Tomcat Postgres - Nginx - Angular
|
||
31366 − (1024×4.4) − 7168 − (8×1024) − 512 - (4x2048) = 2796.4 left…</p>
|
||
</blockquote>
|
||
<ul>
|
||
<li>I put some of these changes in on DSpace Test and will monitor this week</li>
|
||
</ul>
|
||
<h2 id="2024-09-10">2024-09-10</h2>
|
||
<ul>
|
||
<li>Some bot in South Africa made a ton of requests on the API and made the load hit the roof:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code># grep -E '10/Sep/2024:[10-11]' /var/log/nginx/api-access.log | awk '{print $1}' | sort | uniq -c | sort -h
|
||
...
|
||
149720 102.182.38.90
|
||
</code></pre><ul>
|
||
<li>They are using several user agents so are obviously a bot:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:130.0) Gecko/20100101 Firefox/130.0
|
||
Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:109.0) Gecko/20100101 Firefox/111.0
|
||
Mozilla/5.0 (Windows; U; Windows NT 6.1; rv:11.0) Gecko/20100101 Firefox/11.0
|
||
</code></pre><ul>
|
||
<li>I added them to the list of bot networks in nginx and the load went down</li>
|
||
</ul>
|
||
<h2 id="2024-09-11">2024-09-11</h2>
|
||
<ul>
|
||
<li>Upgrade DSpace 7 Test to Ubuntu 24.04</li>
|
||
<li>I did some minor maintenance to test dspace-statistics-api with Python 3.12
|
||
<ul>
|
||
<li>I tagged version 1.4.4 and released it on GitHub</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2024-09-14">2024-09-14</h2>
|
||
<ul>
|
||
<li>Noticed a persistent higher than usual load on CGSpace and checked the server logs
|
||
<ul>
|
||
<li>Found some new data center subnets to block because they were making thousands of requests with normal user agents</li>
|
||
</ul>
|
||
</li>
|
||
<li>I enabled HTTP/3 in nginx</li>
|
||
<li>I enabled the SSR patch in Angular: <a href="https://github.com/DSpace/dspace-angular/issues/3110">https://github.com/DSpace/dspace-angular/issues/3110</a></li>
|
||
</ul>
|
||
<h2 id="2024-09-16">2024-09-16</h2>
|
||
<ul>
|
||
<li>Experiment with the <!-- raw HTML omitted -->dspace-statistics-api-js<!-- raw HTML omitted --> on DSpace 7 Test
|
||
<ul>
|
||
<li>In the past it always caused Solr to run out of memory, but I increased Solr’s heap from 2g to 3g and it runs without crashing</li>
|
||
<li>I attached VisualVM to Solr with a 3g and 4g heap and iterated over 1260 pages of results in the dspace-statistics-api-js:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<p><img src="/cgspace-notes/2024/09/2024-09-16-Solr-3g-heap.png" alt="Solr with 3g heap"></p>
|
||
<p><img src="/cgspace-notes/2024/09/2024-09-16-Solr-4g-heap.png" alt="Solr with 4g heap"></p>
|
||
<h2 id="2024-09-23">2024-09-23</h2>
|
||
<ul>
|
||
<li>Upgrade PostgreSQL from version 14 to 15 on DSpace Test the same way I did last year:</li>
|
||
</ul>
|
||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># apt update
|
||
</span></span><span style="display:flex;"><span># apt install postgresql-15
|
||
</span></span><span style="display:flex;"><span># Update configs with Ansible
|
||
</span></span><span style="display:flex;"><span># systemctl stop tomcat9
|
||
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">14</span> main stop
|
||
</span></span><span style="display:flex;"><span># tar -cvzpf var-lib-postgresql-14.tar.gz /var/lib/postgresql/14
|
||
</span></span><span style="display:flex;"><span># tar -cvzpf etc-postgresql-14.tar.gz /etc/postgresql/14
|
||
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">15</span> main stop
|
||
</span></span><span style="display:flex;"><span># pg_dropcluster <span style="color:#ae81ff">15</span> main
|
||
</span></span><span style="display:flex;"><span># pg_upgradecluster <span style="color:#ae81ff">14</span> main
|
||
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">15</span> main start
|
||
</span></span><span style="display:flex;"><span>...
|
||
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
|
||
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>ERROR: could not find function "xml_is_well_formed" in file "/usr/lib/postgresql/15/lib/pgxml.so"
|
||
</span></span><span style="display:flex;"><span>ERROR: function public.xml_is_well_formed(text) does not exist
|
||
</span></span><span style="display:flex;"><span>ERROR: could not find function "xml_is_well_formed" in file "/usr/lib/postgresql/15/lib/pgxml.so"
|
||
</span></span><span style="display:flex;"><span>ERROR: function public.xml_valid(text) does not exist
|
||
</span></span></code></pre></div><ul>
|
||
<li>After that I <a href="https://adamj.eu/tech/2021/04/13/reindexing-all-tables-after-upgrading-to-postgresql-13/">re-indexed the database indexes</a> using a query:</li>
|
||
</ul>
|
||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ su - postgres
|
||
</span></span><span style="display:flex;"><span>$ cat /tmp/generate-reindex.sql
|
||
</span></span><span style="display:flex;"><span>SELECT 'REINDEX TABLE CONCURRENTLY ' || quote_ident(relname) || ' /*' || pg_size_pretty(pg_total_relation_size(C.oid)) || '*/;'
|
||
</span></span><span style="display:flex;"><span>FROM pg_class C
|
||
</span></span><span style="display:flex;"><span>LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
|
||
</span></span><span style="display:flex;"><span>WHERE nspname = 'public'
|
||
</span></span><span style="display:flex;"><span> AND C.relkind = 'r'
|
||
</span></span><span style="display:flex;"><span> AND nspname !~ '^pg_toast'
|
||
</span></span><span style="display:flex;"><span>ORDER BY pg_total_relation_size(C.oid) ASC;
|
||
</span></span><span style="display:flex;"><span>$ psql dspace < /tmp/generate-reindex.sql > /tmp/reindex.sql
|
||
</span></span><span style="display:flex;"><span>$ <trim the extra stuff from /tmp/reindex.sql>
|
||
</span></span><span style="display:flex;"><span>$ psql dspace < /tmp/reindex.sql
|
||
</span></span></code></pre></div><ul>
|
||
<li>The database shrunk by 186MB!</li>
|
||
</ul>
|
||
<h2 id="2024-09-29">2024-09-29</h2>
|
||
<ul>
|
||
<li>I upgraded the database on CGSpace to PostgreSQL 15</li>
|
||
</ul>
|
||
<!-- raw HTML omitted -->
|
||
|
||
|
||
|
||
|
||
|
||
</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">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2024-12/">December, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-11/">November, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-10/">October, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-08/">August, 2024</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 dir="auto">
|
||
|
||
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>
|