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Atmire responded about the issue with duplicate data in our Solr statistics
They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet
That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the cua_version field
I started processing those (about 411,000 records):
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Atmire responded about the issue with duplicate data in our Solr statistics
They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet
That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the cua_version field
I started processing those (about 411,000 records):
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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/2020-12/">December, 2020</a></h2>
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<time datetime="2020-12-01T11:32:54+02:00">Tue Dec 01, 2020</time>
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<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2020-12-01">2020-12-01</h2>
<ul>
<li>Atmire responded about the issue with duplicate data in our Solr statistics
<ul>
<li>They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet</li>
<li>That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
<li>I started processing those (about 411,000 records):</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
</code></pre><ul>
<li>AReS went down when the <code>renew-letsencrypt</code> service stopped the <code>angular_nginx</code> container in the pre-update hook and failed to bring it back up
<ul>
<li>I ran all system updates on the host and rebooted it and AReS came back up OK</li>
</ul>
</li>
</ul>
<h2 id="2020-12-02">2020-12-02</h2>
<ul>
<li>Udana emailed me yesterday to ask why the CGSpace usage statistics were showing &ldquo;No Data&rdquo;
<ul>
<li>I noticed a message in the Solr Admin UI that one of the statistics cores failed to load, but it is up and I can query it&hellip;</li>
<li>Nevertheless, I restarted Tomcat a few times to see if all cores would come up without an error message, but had no success (despite that all cores ARE up and I can query them, <em>sigh</em>)</li>
<li>I think I will move all the Solr yearly statistics back into the main statistics core</li>
</ul>
</li>
<li>Start testing export/import of yearly Solr statistics data into the main statistics core on DSpace Test, for example:</li>
</ul>
<pre><code>$ ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o statistics-2010.json -k uid
$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
$ curl -s &quot;http://localhost:8081/solr/statistics-2010/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary &quot;&lt;delete&gt;&lt;query&gt;*:*&lt;/query&gt;&lt;/delete&gt;&quot;
</code></pre><ul>
<li>I deployed Tomcat 7.0.107 on DSpace Test (CGSpace is still Tomcat 7.0.104)</li>
<li>I finished migrating all the statistics from the yearly shards back to the main core</li>
</ul>
<h2 id="2020-12-05">2020-12-05</h2>
<ul>
<li>I deleted all the yearly statistics shards and restarted Tomcat on DSpace Test (linode26)</li>
</ul>
<h2 id="2020-12-06">2020-12-06</h2>
<ul>
<li>Looking into the statistics on DSpace Test after I migrated them back to the main core
<ul>
<li>All stats are working as expected&hellip; indexing time for the DSpace Statistics API is the same&hellip; and I don&rsquo;t even see a difference in the JVM or memory stats in Munin other than a minor jump last week when I was processing them</li>
</ul>
</li>
<li>I will migrate them on CGSpace too I think
<ul>
<li>First I will start with the statistics-2010 and statistics-2015 cores because they were the ones that were failing to load recently (despite actually being available in Solr WTF)</li>
</ul>
</li>
</ul>
<p><img src="/cgspace-notes/2020/12/solr-statistics-2010-failed.png" alt="Error message in Solr admin UI about the statistics-2010 core failing to load"></p>
<ul>
<li>First the 2010 core:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o statistics-2010.json -k uid
$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
$ curl -s &quot;http://localhost:8081/solr/statistics-2010/update?softCommit=true&quot; -H &quot;Content-Type: text/xml&quot; --data-binary &quot;&lt;delete&gt;&lt;query&gt;*:*&lt;/query&gt;&lt;/delete&gt;&quot;
</code></pre><ul>
<li>Judging by the DSpace logs all these cores had a problem starting up in the last month:</li>
</ul>
<pre><code class="language-console" data-lang="console"># grep -rsI &quot;Unable to create core&quot; [dspace]/log/dspace.log.2020-* | grep -o -E &quot;statistics-[0-9]+&quot; | sort | uniq -c
24 statistics-2010
24 statistics-2015
18 statistics-2016
6 statistics-2018
</code></pre><ul>
<li>The message is always this:</li>
</ul>
<pre><code>org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error CREATEing SolrCore 'statistics-2016': Unable to create core [statistics-2016] Caused by: Lock obtain timed out: NativeFSLock@/[dspace]/solr/statistics-2016/data/index/write.lock
</code></pre><ul>
<li>I will migrate all these cores and see if it makes a difference, then probably end up migrating all of them
<ul>
<li>I removed the statistics-2010, statistics-2015, statistics-2016, and statistics-2018 cores and restarted Tomcat and <em>all the statistics cores came up OK and the CUA statistics are OK</em>!</li>
</ul>
</li>
</ul>
<h2 id="2020-12-07">2020-12-07</h2>
<ul>
<li>Run <code>dspace cleanup -v</code> on CGSpace to clean up deleted bitstreams</li>
<li>Atmire sent a <a href="https://github.com/ilri/DSpace/pull/457">pull request</a> to address the duplicate owningComm and owningColl
<ul>
<li>Built and deployed it on DSpace Test but I am not sure how to run it yet</li>
<li>I sent feedback to Atmire on their tracker: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839</a></li>
</ul>
</li>
<li>Abenet and Tezira are having issues with committing to the archive in their workflow
<ul>
<li>I looked at the server and indeed the locks and transactions are back up:</li>
</ul>
</li>
</ul>
<p><img src="/cgspace-notes/2020/12/postgres_transactions_ALL-day.png" alt="PostgreSQL Transactions day">
<img src="/cgspace-notes/2020/12/postgres_locks_ALL-day.png" alt="PostgreSQL Locks day">
<img src="/cgspace-notes/2020/12/postgres_querylength_ALL-day.png" alt="PostgreSQL Locks day">
<img src="/cgspace-notes/2020/12/postgres_connections_ALL-day.png" alt="PostgreSQL Connections day"></p>
<ul>
<li>There are apparently 1,700 locks right now:</li>
</ul>
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1739
</code></pre><h2 id="2020-12-08">2020-12-08</h2>
<ul>
<li>Atmire sent some instructions for using the DeduplicateValuesProcessor
<ul>
<li>I modified <code>atmire-cua-update.xml</code> as they instructed, but I get a million errors like this when I run AtomicStatisticsUpdateCLI with that configuration:</li>
</ul>
</li>
</ul>
<pre><code>Record uid: 64387815-d9a7-4605-8024-1c0a5c7520e0 couldn't be processed
com.atmire.statistics.util.update.atomic.ProcessingException: something went wrong while processing record uid: 64387815-d9a7-4605-8024-1c0a5c7520e0, an error occured in the com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.applyProcessors(SourceFile:304)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.processRecords(SourceFile:176)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.performRun(SourceFile:161)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.update(SourceFile:128)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI.main(SourceFile:78)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
Caused by: java.lang.UnsupportedOperationException
at org.apache.solr.common.SolrDocument$1.entrySet(SolrDocument.java:256)
at java.util.HashMap.putMapEntries(HashMap.java:512)
at java.util.HashMap.&lt;init&gt;(HashMap.java:490)
at com.atmire.statistics.util.update.atomic.record.Record.getFieldValuesMap(SourceFile:86)
at com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor.process(SourceFile:38)
at com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor.visit(SourceFile:34)
at com.atmire.statistics.util.update.atomic.record.UsageRecord.accept(SourceFile:23)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.applyProcessors(SourceFile:301)
... 10 more
</code></pre><ul>
<li>I sent some feedback to Atmire
<ul>
<li>They responded with an updated CUA (6.x-4.1.10-ilri-RC7) that has a fix for the duplicates processor <em>and</em> a possible fix for the database locking issues (a bug in CUASolrLoggerServiceImpl that causes an infinite loop and a Tomcat timeout)</li>
<li>I deployed the changes on DSpace Test and CGSpace, hopefully it will fix both issues!</li>
</ul>
</li>
<li>In other news, after I restarted Tomcat on CGSpace the statistics-2013 core didn&rsquo;t come back up properly, so I exported it and imported it into the main statistics core like I did for the others a few days ago</li>
<li>Sync DSpace Test with CGSpace&rsquo;s Solr, PostgreSQL database, and assetstore&hellip;</li>
</ul>
<h2 id="2020-12-09">2020-12-09</h2>
<ul>
<li>I was running the AtomicStatisticsUpdateCLI to remove duplicates on DSpace Test but it failed near the end of the statistics core (after 20 hours or so) with a memory error:</li>
</ul>
<pre><code>Successfully finished updating Solr Storage Reports | Wed Dec 09 15:25:11 CET 2020
Run 1 —  67% — 10,000/14,935 docs — 6m 6s — 6m 6s
Exception: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
at org.noggit.CharArr.toString(CharArr.java:164)
</code></pre><ul>
<li>I increased the JVM heap to 2048m and tried again, but it failed with a memory error again&hellip;</li>
<li>I increased the JVM heap to 4096m and tried again, but it failed with another error:</li>
</ul>
<pre><code>Successfully finished updating Solr Storage Reports | Wed Dec 09 15:53:40 CET 2020
Exception: parsing error
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: parsing error
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:530)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.QueryRequest.process(QueryRequest.java:91)
at org.apache.solr.client.solrj.SolrServer.query(SolrServer.java:301)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.getNextSetOfSolrDocuments(SourceFile:392)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.performRun(SourceFile:157)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.update(SourceFile:128)
at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI.main(SourceFile:78)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
Caused by: org.apache.solr.common.SolrException: parsing error
at org.apache.solr.client.solrj.impl.BinaryResponseParser.processResponse(BinaryResponseParser.java:45)
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:528)
... 14 more
Caused by: org.apache.http.TruncatedChunkException: Truncated chunk ( expected size: 8192; actual size: 2843)
at org.apache.http.impl.io.ChunkedInputStream.read(ChunkedInputStream.java:200)
at org.apache.http.conn.EofSensorInputStream.read(EofSensorInputStream.java:137)
at org.apache.solr.common.util.FastInputStream.readWrappedStream(FastInputStream.java:80)
at org.apache.solr.common.util.FastInputStream.refill(FastInputStream.java:89)
at org.apache.solr.common.util.FastInputStream.read(FastInputStream.java:125)
at org.apache.solr.common.util.FastInputStream.readFully(FastInputStream.java:152)
...
</code></pre><h2 id="2020-12-10">2020-12-10</h2>
<ul>
<li>The statistics-2019 core finished processing the duplicate removal so I started the statistics-2017 core</li>
<li>Peter asked me to add ONE HEALTH to ILRI subjects on CGSpace</li>
<li>A few items that got &ldquo;lost&rdquo; after approval during the database issues earlier this week seem to have gone back into their workflows
<ul>
<li>Abenet approved them again and they got new handles, phew</li>
</ul>
</li>
<li>Abenet was having an issue with the date filter on AReS and it turns out that it&rsquo;s the same <code>.keyword</code> issue I had noticed before that causes the filter to stop working
<ul>
<li>I fixed the filter to use the correct field name and filed a bug on OpenRXV: <a href="https://github.com/ilri/OpenRXV/issues/63">https://github.com/ilri/OpenRXV/issues/63</a></li>
</ul>
</li>
<li>I checked the Solr statistics on DSpace Test to see if the Atmire duplicates remover was working, but now I see a comical amount of duplicates&hellip;</li>
</ul>
<p><img src="/cgspace-notes/2020/12/solr-stats-duplicates.png" alt="Solr stats with dozens of duplicates"></p>
<ul>
<li>I sent feedback about this to Atmire</li>
<li>I will re-sync the Solr stats from CGSpace so we can try again&hellip;</li>
<li>In other news, it has been a few days since we deployed the fix for the database locking issue and things seem much better now:</li>
</ul>
<p><img src="/cgspace-notes/2020/12/postgres_connections_ALL-week.png" alt="PostgreSQL connections all week">
<img src="/cgspace-notes/2020/12/postgres_locks_ALL-week.png" alt="PostgreSQL locks all week"></p>
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<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
<li><a href="/cgspace-notes/2020-10/">October, 2020</a></li>
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
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