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Upgrade CGSpace to DSpace 7.6.2
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<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>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2024-09/">September, 2024</a></h2>
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<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>
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<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>
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<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
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