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<meta property="og:title" content="February, 2018" />
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<meta property="og:description" content="2018-02-01
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Peter gave feedback on the dc.rights proof of concept that I had sent him last week
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We don’t need to distinguish between internal and external works, so that makes it just a simple list
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Yesterday I figured out how to monitor DSpace sessions using JMX
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I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
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<meta name="twitter:description" content="2018-02-01
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Peter gave feedback on the dc.rights proof of concept that I had sent him last week
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We don’t need to distinguish between internal and external works, so that makes it just a simple list
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Yesterday I figured out how to monitor DSpace sessions using JMX
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I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">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"><a href="https://alanorth.github.io/cgspace-notes/2018-02/">February, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-02-01T16:28:54+02:00">Thu Feb 01, 2018</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-02-01">2018-02-01</h2>
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<ul>
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<li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li>
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<li>We don’t need to distinguish between internal and external works, so that makes it just a simple list</li>
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<li>Yesterday I figured out how to monitor DSpace sessions using JMX</li>
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<li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu’s <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="/cgspace-notes/2018-01/">in 2018-01</a></li>
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</ul>
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<p></p>
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<p><img src="/cgspace-notes/2018/02/jmx_dspace_sessions-day.png" alt="DSpace Sessions" /></p>
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<ul>
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<li>Run all system updates and reboot DSpace Test</li>
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<li>Wow, I packaged up the <code>jmx_dspace_sessions</code> stuff in the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> and deployed it on CGSpace and it totally works:</li>
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</ul>
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<pre><code># munin-run jmx_dspace_sessions
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v_.value 223
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v_jspui.value 1
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v_oai.value 0
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</code></pre>
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<h2 id="2018-02-03">2018-02-03</h2>
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<ul>
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<li>Bram from Atmire responded about the high load caused by the Solr updater script and said it will be fixed with the updates to DSpace 5.8 compatibility: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=566">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=566</a></li>
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<li>We will close that ticket for now and wait for the 5.8 stuff: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560</a></li>
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<li>I finally took a look at the second round of cleanups Peter had sent me for author affiliations in mid January</li>
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<li>After trimming whitespace and quickly scanning for encoding errors I applied them on CGSpace:</li>
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</ul>
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<pre><code>$ ./delete-metadata-values.py -i /tmp/2018-02-03-Affiliations-12-deletions.csv -f cg.contributor.affiliation -m 211 -d dspace -u dspace -p 'fuuu'
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$ ./fix-metadata-values.py -i /tmp/2018-02-03-Affiliations-1116-corrections.csv -f cg.contributor.affiliation -t correct -m 211 -d dspace -u dspace -p 'fuuu'
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</code></pre>
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<ul>
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<li>Then I started a full Discovery reindex:</li>
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</ul>
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<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
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real 96m39.823s
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user 14m10.975s
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sys 2m29.088s
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</code></pre>
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<ul>
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<li>Generate a new list of affiliations for Peter to sort through:</li>
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</ul>
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<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv;
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COPY 3723
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</code></pre>
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<ul>
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<li>Oh, and it looks like we processed over 3.1 million requests in January, up from 2.9 million in <a href="/cgspace-notes/2017-12/">December</a>:</li>
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</ul>
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<pre><code># time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Jan/2018"
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3126109
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real 0m23.839s
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user 0m27.225s
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sys 0m1.905s
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</code></pre>
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<h2 id="2018-02-05">2018-02-05</h2>
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<ul>
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<li>Toying with correcting authors with trailing spaces via PostgreSQL:</li>
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</ul>
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<pre><code>dspace=# update metadatavalue set text_value=REGEXP_REPLACE(text_value, '\s+$' , '') where resource_type_id=2 and metadata_field_id=3 and text_value ~ '^.*?\s+$';
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UPDATE 20
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</code></pre>
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<ul>
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<li>I tried the <code>TRIM(TRAILING from text_value)</code> function and it said it changed 20 items but the spaces didn’t go away</li>
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<li>This is on a fresh import of the CGSpace database, but when I tried to apply it on CGSpace there were no changes detected. Weird.</li>
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<li>Anyways, Peter wants a new list of authors to clean up, so I exported another CSV:</li>
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</ul>
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<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors-2018-02-05.csv with csv;
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COPY 55630
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</code></pre>
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<h2 id="2018-02-06">2018-02-06</h2>
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<ul>
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<li>UptimeRobot says CGSpace is down this morning around 9:15</li>
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<li>I see 308 PostgreSQL connections in <code>pg_stat_activity</code></li>
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<li>The usage otherwise seemed low for REST/OAI as well as XMLUI in the last hour:</li>
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</ul>
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<pre><code># date
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Tue Feb 6 09:30:32 UTC 2018
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# cat /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E "6/Feb/2018:(08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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2 223.185.41.40
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2 66.249.64.14
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2 77.246.52.40
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4 157.55.39.82
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4 193.205.105.8
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5 207.46.13.63
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5 207.46.13.64
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6 154.68.16.34
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7 207.46.13.66
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1548 50.116.102.77
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# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 /var/log/nginx/error.log /var/log/nginx/error.log.1 | grep -E "6/Feb/2018:(08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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77 213.55.99.121
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86 66.249.64.14
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101 104.196.152.243
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103 207.46.13.64
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118 157.55.39.82
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133 207.46.13.66
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136 207.46.13.63
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156 68.180.228.157
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295 197.210.168.174
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752 144.76.64.79
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</code></pre>
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<ul>
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<li>I did notice in <code>/var/log/tomcat7/catalina.out</code> that Atmire’s update thing was running though</li>
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<li>So I restarted Tomcat and now everything is fine</li>
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<li>Next time I see that many database connections I need to save the output so I can analyze it later</li>
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<li>I’m going to re-schedule the taskUpdateSolrStatsMetadata task as <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=566">Bram detailed in ticket 566</a> to see if it makes CGSpace stop crashing every morning</li>
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<li>If I move the task from 3AM to 3PM, deally CGSpace will stop crashing in the morning, or start crashing ~12 hours later</li>
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<li>Eventually Atmire has said that there will be a fix for this high load caused by their script, but it will come with the 5.8 compatability they are already working on</li>
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<li>I re-deployed CGSpace with the new task time of 3PM, ran all system updates, and restarted the server</li>
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<li>Also, I changed the name of the DSpace fallback pool on DSpace Test and CGSpace to be called ‘dspaceCli’ so that I can distinguish it in <code>pg_stat_activity</code></li>
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<li>I implemented some changes to the pooling in the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> so that each DSpace web application can use its own pool (web, api, and solr)</li>
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<li>Each pool uses its own name and hopefully this should help me figure out which one is using too many connections next time CGSpace goes down</li>
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<li>Also, this will mean that when a search bot comes along and hammers the XMLUI, the REST and OAI applications will be fine</li>
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<li>I’m not actually sure if the Solr web application uses the database though, so I’ll have to check later and remove it if necessary</li>
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<li>I deployed the changes on DSpace Test only for now, so I will monitor and make them on CGSpace later this week</li>
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</ul>
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<h2 id="2018-02-07">2018-02-07</h2>
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<ul>
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<li>Abenet wrote to ask a question about the ORCiD lookup not working for one CIAT user on CGSpace</li>
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<li>I tried on DSpace Test and indeed the lookup just doesn’t work!</li>
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<li>The ORCiD code in DSpace appears to be using <code>http://pub.orcid.org/</code>, but when I go there in the browser it redirects me to <code>https://pub.orcid.org/v2.0/</code></li>
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<li>According to <a href="https://groups.google.com/forum/#!topic/orcid-api-users/qfg-HwAB1bk">the announcement</a> the v1 API was moved from <code>http://pub.orcid.org/</code> to <code>https://pub.orcid.org/v1.2</code> until March 1st when it will be discontinued for good</li>
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<li>But the old URL is hard coded in DSpace and it doesn’t work anyways, because it currently redirects you to <code>https://pub.orcid.org/v2.0/v1.2</code></li>
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<li>So I guess we have to disable that shit once and for all and switch to a controlled vocabulary</li>
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<li>CGSpace crashed again, this time around <code>Wed Feb 7 11:20:28 UTC 2018</code></li>
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<li>I took a few snapshots of the PostgreSQL activity at the time and as the minutes went on and the connections were very high at first but reduced on their own:</li>
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</ul>
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<pre><code>$ psql -c 'select * from pg_stat_activity' > /tmp/pg_stat_activity.txt
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$ grep -c 'PostgreSQL JDBC' /tmp/pg_stat_activity*
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/tmp/pg_stat_activity1.txt:300
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/tmp/pg_stat_activity2.txt:272
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/tmp/pg_stat_activity3.txt:168
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/tmp/pg_stat_activity4.txt:5
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/tmp/pg_stat_activity5.txt:6
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</code></pre>
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<ul>
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<li>Interestingly, all of those 751 connections were idle!</li>
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</ul>
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<pre><code>$ grep "PostgreSQL JDBC" /tmp/pg_stat_activity* | grep -c idle
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751
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</code></pre>
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<ul>
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<li>Since I was restarting Tomcat anyways, I decided to deploy the changes to create two different pools for web and API apps</li>
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<li>Looking the Munin graphs, I can see that there were almost double the normal number of DSpace sessions at the time of the crash (and also yesterday!):</li>
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</ul>
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<p><img src="/cgspace-notes/2018/02/jmx_dspace-sessions-day.png" alt="DSpace Sessions" /></p>
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<ul>
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<li>Indeed it seems like there were over 1800 sessions today around the hours of 10 and 11 AM:</li>
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</ul>
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<pre><code>$ grep -E '^2018-02-07 (10|11)' dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
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1828
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</code></pre>
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<ul>
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<li>CGSpace went down again a few hours later, and now the connections to the dspaceWeb pool are maxed at 250 (the new limit I imposed with the new separate pool scheme)</li>
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<li>What’s interesting is that the DSpace log says the connections are all busy:</li>
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</ul>
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<pre><code>org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-328] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:250; busy:250; idle:0; lastwait:5000].
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</code></pre>
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<ul>
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<li>… but in PostgreSQL I see them <code>idle</code> or <code>idle in transaction</code>:</li>
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</ul>
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<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -c dspaceWeb
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250
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$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c idle
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250
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$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c "idle in transaction"
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187
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</code></pre>
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<ul>
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<li>What the fuck, does DSpace think all connections are busy?</li>
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<li>I suspect these are issues with abandoned connections or maybe a leak, so I’m going to try adding the <code>removeAbandoned='true'</code> parameter which is apparently off by default</li>
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<li>I will try <code>testOnReturn='true'</code> too, just to add more validation, because I’m fucking grasping at straws</li>
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<li>Also, WTF, there was a heap space error randomly in catalina.out:</li>
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</ul>
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<pre><code>Wed Feb 07 15:01:54 UTC 2018 | Query:containerItem:91917 AND type:2
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Exception in thread "http-bio-127.0.0.1-8081-exec-58" java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2018-02/">February, 2018</a></li>
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<li><a href="/cgspace-notes/2018-01/">January, 2018</a></li>
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<li><a href="/cgspace-notes/2017-12/">December, 2017</a></li>
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<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
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<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</body>
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</html>
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