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Peter gave feedback on the dc.rights proof of concept that I had sent him last week
We don&rsquo;t need to distinguish between internal and external works, so that makes it just a simple list
2018-02-01 18:04:07 +01:00
Yesterday I figured out how to monitor DSpace sessions using JMX
I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
2018-02-01 15:30:28 +01:00
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Peter gave feedback on the dc.rights proof of concept that I had sent him last week
We don&rsquo;t need to distinguish between internal and external works, so that makes it just a simple list
2018-02-01 18:04:07 +01:00
Yesterday I figured out how to monitor DSpace sessions using JMX
I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
2018-02-01 15:30:28 +01:00
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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>
<p class="blog-post-meta"><time datetime="2018-02-01T16:28:54&#43;02:00">Thu Feb 01, 2018</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>
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<h2 id="2018-02-01">2018-02-01</h2>
<ul>
<li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li>
<li>We don&rsquo;t need to distinguish between internal and external works, so that makes it just a simple list</li>
2018-02-01 18:04:07 +01:00
<li>Yesterday I figured out how to monitor DSpace sessions using JMX</li>
<li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu&rsquo;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>
2018-02-01 15:30:28 +01:00
</ul>
<p></p>
2018-02-01 18:04:07 +01:00
<p><img src="/cgspace-notes/2018/02/jmx_dspace_sessions-day.png" alt="DSpace Sessions" /></p>
<ul>
<li>Run all system updates and reboot DSpace Test</li>
<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>
</ul>
<pre><code># munin-run jmx_dspace_sessions
v_.value 223
v_jspui.value 1
v_oai.value 0
</code></pre>
2018-02-03 08:44:31 +01:00
<h2 id="2018-02-03">2018-02-03</h2>
<ul>
<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>
<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>
2018-02-03 23:00:51 +01:00
<li>I finally took a look at the second round of cleanups Peter had sent me for author affiliations in mid January</li>
<li>After trimming whitespace and quickly scanning for encoding errors I applied them on CGSpace:</li>
2018-02-03 08:44:31 +01:00
</ul>
2018-02-03 23:00:51 +01:00
<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'
$ ./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'
</code></pre>
<ul>
<li>Then I started a full Discovery reindex:</li>
</ul>
<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
2018-02-04 10:26:07 +01:00
real 96m39.823s
user 14m10.975s
sys 2m29.088s
2018-02-03 23:00:51 +01:00
</code></pre>
<ul>
<li>Generate a new list of affiliations for Peter to sort through:</li>
</ul>
<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;
COPY 3723
</code></pre>
<ul>
<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>
</ul>
<pre><code># time zcat --force /var/log/nginx/* | grep -cE &quot;[0-9]{1,2}/Jan/2018&quot;
3126109
real 0m23.839s
user 0m27.225s
sys 0m1.905s
</code></pre>
2018-02-05 18:08:05 +01:00
<h2 id="2018-02-05">2018-02-05</h2>
<ul>
<li>Toying with correcting authors with trailing spaces via PostgreSQL:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_value=REGEXP_REPLACE(text_value, '\s+$' , '') where resource_type_id=2 and metadata_field_id=3 and text_value ~ '^.*?\s+$';
UPDATE 20
</code></pre>
<ul>
<li>I tried the <code>TRIM(TRAILING from text_value)</code> function and it said it changed 20 items but the spaces didn&rsquo;t go away</li>
<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>
<li>Anyways, Peter wants a new list of authors to clean up, so I exported another CSV:</li>
</ul>
<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;
COPY 55630
</code></pre>
2018-02-06 13:03:07 +01:00
<h2 id="2018-02-06">2018-02-06</h2>
<ul>
<li>UptimeRobot says CGSpace is down this morning around 9:15</li>
<li>I see 308 PostgreSQL connections in <code>pg_stat_activity</code></li>
<li>The usage otherwise seemed low for REST/OAI as well as XMLUI in the last hour:</li>
</ul>
<pre><code># date
Tue Feb 6 09:30:32 UTC 2018
# 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 &quot;6/Feb/2018:(08|09)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2 223.185.41.40
2 66.249.64.14
2 77.246.52.40
4 157.55.39.82
4 193.205.105.8
5 207.46.13.63
5 207.46.13.64
6 154.68.16.34
7 207.46.13.66
1548 50.116.102.77
# 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 &quot;6/Feb/2018:(08|09)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
77 213.55.99.121
86 66.249.64.14
101 104.196.152.243
103 207.46.13.64
118 157.55.39.82
133 207.46.13.66
136 207.46.13.63
156 68.180.228.157
295 197.210.168.174
752 144.76.64.79
</code></pre>
<ul>
<li>I did notice in <code>/var/log/tomcat7/catalina.out</code> that Atmire&rsquo;s update thing was running though</li>
<li>So I restarted Tomcat and now everything is fine</li>
<li>Next time I see that many database connections I need to save the output so I can analyze it later</li>
<li>I&rsquo;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>
<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>
<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>
<li>I re-deployed CGSpace with the new task time of 3PM, ran all system updates, and restarted the server</li>
<li>Also, I changed the name of the DSpace fallback pool on DSpace Test and CGSpace to be called &lsquo;dspaceCli&rsquo; so that I can distinguish it in <code>pg_stat_activity</code></li>
<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>
<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>
<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>
<li>I&rsquo;m not actually sure if the Solr web application uses the database though, so I&rsquo;ll have to check later and remove it if necessary</li>
2018-02-06 13:03:46 +01:00
<li>I deployed the changes on DSpace Test only for now, so I will monitor and make them on CGSpace later this week</li>
2018-02-06 13:03:07 +01:00
</ul>
2018-02-07 11:34:36 +01:00
<h2 id="2018-02-07">2018-02-07</h2>
<ul>
<li>Abenet wrote to ask a question about the ORCiD lookup not working for one CIAT user on CGSpace</li>
<li>I tried on DSpace Test and indeed the lookup just doesn&rsquo;t work!</li>
<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>
<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>
<li>But the old URL is hard coded in DSpace and it doesn&rsquo;t work anyways, because it currently redirects you to <code>https://pub.orcid.org/v2.0/v1.2</code></li>
<li>So I guess we have to disable that shit once and for all and switch to a controlled vocabulary</li>
2018-02-07 17:33:26 +01:00
<li>CGSpace crashed again, this time around <code>Wed Feb 7 11:20:28 UTC 2018</code></li>
<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>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' &gt; /tmp/pg_stat_activity.txt
$ grep -c 'PostgreSQL JDBC' /tmp/pg_stat_activity*
/tmp/pg_stat_activity1.txt:300
/tmp/pg_stat_activity2.txt:272
/tmp/pg_stat_activity3.txt:168
/tmp/pg_stat_activity4.txt:5
/tmp/pg_stat_activity5.txt:6
</code></pre>
<ul>
<li>Interestingly, all of those 751 connections were idle!</li>
</ul>
<pre><code>$ grep &quot;PostgreSQL JDBC&quot; /tmp/pg_stat_activity* | grep -c idle
751
</code></pre>
<ul>
<li>Since I was restarting Tomcat anyways, I decided to deploy the changes to create two different pools for web and API apps</li>
<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>
</ul>
<p><img src="/cgspace-notes/2018/02/jmx_dspace-sessions-day.png" alt="DSpace Sessions" /></p>
<ul>
<li>Indeed it seems like there were over 1800 sessions today around the hours of 10 and 11 AM:</li>
</ul>
<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
1828
</code></pre>
<ul>
<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>
<li>What&rsquo;s interesting is that the DSpace log says the connections are all busy:</li>
</ul>
<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].
</code></pre>
<ul>
<li>&hellip; but in PostgreSQL I see them <code>idle</code> or <code>idle in transaction</code>:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -c dspaceWeb
250
$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c idle
250
$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c &quot;idle in transaction&quot;
187
</code></pre>
<ul>
<li>What the fuck, does DSpace think all connections are busy?</li>
<li>I suspect these are issues with abandoned connections or maybe a leak, so I&rsquo;m going to try adding the <code>removeAbandoned='true'</code> parameter which is apparently off by default</li>
<li>I will try <code>testOnReturn='true'</code> too, just to add more validation, because I&rsquo;m fucking grasping at straws</li>
2018-02-07 17:34:39 +01:00
<li>Also, WTF, there was a heap space error randomly in catalina.out:</li>
2018-02-07 11:34:36 +01:00
</ul>
2018-02-07 17:34:39 +01:00
<pre><code>Wed Feb 07 15:01:54 UTC 2018 | Query:containerItem:91917 AND type:2
Exception in thread &quot;http-bio-127.0.0.1-8081-exec-58&quot; java.lang.OutOfMemoryError: Java heap space
</code></pre>
2018-02-07 23:55:28 +01:00
<ul>
<li>I&rsquo;m trying to find a way to determine what was using all those Tomcat sessions, but parsing the DSpace log is hard because some IPs are IPv6, which contain colons!</li>
<li>Looking at the first crash this morning around 11, I see these IPv4 addresses making requests around 10 and 11AM:</li>
</ul>
<pre><code>$ grep -E '^2018-02-07 (10|11)' dspace.log.2018-02-07 | grep -o -E 'ip_addr=[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}' | sort -n | uniq -c | sort -n | tail -n 20
34 ip_addr=46.229.168.67
34 ip_addr=46.229.168.73
37 ip_addr=46.229.168.76
40 ip_addr=34.232.65.41
41 ip_addr=46.229.168.71
44 ip_addr=197.210.168.174
55 ip_addr=181.137.2.214
55 ip_addr=213.55.99.121
58 ip_addr=46.229.168.65
64 ip_addr=66.249.66.91
67 ip_addr=66.249.66.90
71 ip_addr=207.46.13.54
78 ip_addr=130.82.1.40
104 ip_addr=40.77.167.36
151 ip_addr=68.180.228.157
174 ip_addr=207.46.13.135
194 ip_addr=54.83.138.123
198 ip_addr=40.77.167.62
210 ip_addr=207.46.13.71
214 ip_addr=104.196.152.243
</code></pre>
<ul>
<li>These IPs made thousands of sessions today:</li>
</ul>
<pre><code>$ grep 104.196.152.243 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
530
$ grep 207.46.13.71 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
859
$ grep 40.77.167.62 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
610
$ grep 54.83.138.123 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
8
$ grep 207.46.13.135 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
826
$ grep 68.180.228.157 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
727
$ grep 40.77.167.36 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
181
$ grep 130.82.1.40 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
24
$ grep 207.46.13.54 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
166
$ grep 46.229.168 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
992
</code></pre>
<ul>
<li>Let&rsquo;s investigate who these IPs belong to:
<ul>
<li>104.196.152.243 is CIAT, which is already marked as a bot via nginx!</li>
<li>207.46.13.71 is Bing, which is already marked as a bot in Tomcat&rsquo;s Crawler Session Manager Valve!</li>
<li>40.77.167.62 is Bing, which is already marked as a bot in Tomcat&rsquo;s Crawler Session Manager Valve!</li>
<li>207.46.13.135 is Bing, which is already marked as a bot in Tomcat&rsquo;s Crawler Session Manager Valve!</li>
<li>68.180.228.157 is Yahoo, which is already marked as a bot in Tomcat&rsquo;s Crawler Session Manager Valve!</li>
<li>40.77.167.36 is Bing, which is already marked as a bot in Tomcat&rsquo;s Crawler Session Manager Valve!</li>
<li>207.46.13.54 is Bing, which is already marked as a bot in Tomcat&rsquo;s Crawler Session Manager Valve!</li>
<li>46.229.168.x is Semrush, which is already marked as a bot in Tomcat&rsquo;s Crawler Session Manager Valve!</li>
</ul></li>
<li>Nice, so these are all known bots that are already crammed into one session by Tomcat&rsquo;s Crawler Session Manager Valve.</li>
<li>What in the actual fuck, why is our load doing this? It&rsquo;s gotta be something fucked up with the database pool being &ldquo;busy&rdquo; but everything is fucking idle</li>
<li>One that I should probably add in nginx is 54.83.138.123, which is apparently the following user agent:</li>
</ul>
<pre><code>BUbiNG (+http://law.di.unimi.it/BUbiNG.html)
</code></pre>
<ul>
<li>This one makes two thousand requests per day or so recently:</li>
</ul>
<pre><code># grep -c BUbiNG /var/log/nginx/access.log /var/log/nginx/access.log.1
/var/log/nginx/access.log:1925
/var/log/nginx/access.log.1:2029
</code></pre>
<ul>
<li>And they have 30 IPs, so fuck that shit I&rsquo;m going to add them to the Tomcat Crawler Session Manager Valve nowwww</li>
<li>Lots of discussions on the dspace-tech mailing list over the last few years about leaky transactions being a known problem with DSpace</li>
<li>Helix84 recommends restarting PostgreSQL instead of Tomcat because it restarts quicker</li>
<li>This is how the connections looked when it crashed this afternoon:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
290 dspaceWeb
</code></pre>
<ul>
<li>This is how it is right now:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
5 dspaceWeb
</code></pre>
<ul>
<li>So is this just some fucked up XMLUI database leaking?</li>
<li>I notice there is an issue (that I&rsquo;ve probably noticed before) on the Jira tracker about this that was fixed in DSpace 5.7: <a href="https://jira.duraspace.org/browse/DS-3551">https://jira.duraspace.org/browse/DS-3551</a></li>
<li>I seriously doubt this leaking shit is fixed for sure, but I&rsquo;m gonna cherry-pick all those commits and try them on DSpace Test and probably even CGSpace because I&rsquo;m fed up with this shit</li>
<li>If I do, I need to remember to remove them when I rebase <code>5_x-prod</code> on top of the latest upstream 5.x branch later</li>
</ul>
2018-02-01 15:30:28 +01:00
</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/2018-02/">February, 2018</a></li>
<li><a href="/cgspace-notes/2018-01/">January, 2018</a></li>
<li><a href="/cgspace-notes/2017-12/">December, 2017</a></li>
<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
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<h4>Links</h4>
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<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>
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