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Add notes for 2020-11-17

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Alan Orth
2020-11-17 22:14:56 +02:00
parent a50ad3ac76
commit d7a6467475
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@ -39,7 +39,7 @@ So far we’ve spent at least fifty hours to process the statistics and stat
"@type": "BlogPosting",
"headline": "November, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-11/",
"wordCount": "1762",
"wordCount": "2131",
"datePublished": "2020-11-01T13:11:54+02:00",
"dateModified": "2020-11-16T10:53:45+02:00",
"author": {
@ -391,6 +391,101 @@ org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error whil
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</code></pre><h2 id="2020-11-16">2020-11-16</h2>
<ul>
<li>Users are having issues submitting items to CGSpace
<ul>
<li>Looking at the data I see that connections skyrocketed since DSpace 6 upgrade yesterday, and they are all in &ldquo;waiting for lock&rdquo; state:</li>
</ul>
</li>
</ul>
<p><img src="/cgspace-notes/2020/11/postgres_connections_ALL-week.png" alt="PostgreSQL connections week">
<img src="/cgspace-notes/2020/11/postgres_locks_ALL-week.png" alt="PostgreSQL locks week"></p>
<ul>
<li>There are almost 1,500 locks:</li>
</ul>
<pre><code>$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1494
</code></pre><ul>
<li>I sent a mail to the dspace-tech mailing list to ask for help&hellip;
<ul>
<li>For now I just restarted PostgreSQL and a few users were able to complete submissions&hellip;</li>
</ul>
</li>
<li>While processing the statistics-2018 Solr core I got the <em>same</em> memory error that I have gotten every time I processed this core in testing:</li>
</ul>
<pre><code>Exception: Java heap space
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3332)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:124)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:448)
at java.lang.StringBuffer.append(StringBuffer.java:270)
at java.io.StringWriter.write(StringWriter.java:101)
at org.apache.solr.common.util.XML.writeXML(XML.java:133)
at org.apache.solr.client.solrj.util.ClientUtils.writeVal(SourceFile:160)
at org.apache.solr.client.solrj.util.ClientUtils.writeXML(SourceFile:128)
at org.apache.solr.client.solrj.request.UpdateRequest.writeXML(UpdateRequest.java:365)
at org.apache.solr.client.solrj.request.UpdateRequest.getXML(UpdateRequest.java:281)
at org.apache.solr.client.solrj.request.RequestWriter.getContentStream(RequestWriter.java:67)
at org.apache.solr.client.solrj.request.RequestWriter$LazyContentStream.getDelegate(RequestWriter.java:95)
at org.apache.solr.client.solrj.request.RequestWriter$LazyContentStream.getName(RequestWriter.java:105)
at org.apache.solr.client.solrj.impl.HttpSolrServer.createMethod(HttpSolrServer.java:302)
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.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
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)
</code></pre><ul>
<li>I increased the Java heap memory to 4096MB and restarted the processing
<ul>
<li>After a few hours I got the following error, which I have gotten several times over the last few months:</li>
</ul>
</li>
</ul>
<pre><code>Exception: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error while creating field 'p_group_id{type=uuid,properties=indexed,stored,multiValued}' from value '10'
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
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.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:68)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:54)
at org.dspace.util.SolrUpgradePre6xStatistics.batchUpdateStats(SolrUpgradePre6xStatistics.java:161)
at org.dspace.util.SolrUpgradePre6xStatistics.run(SolrUpgradePre6xStatistics.java:456)
at org.dspace.util.SolrUpgradePre6xStatistics.main(SolrUpgradePre6xStatistics.java:365)
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)
</code></pre><h2 id="2020-11-17">2020-11-17</h2>
<ul>
<li>Chat with Peter about using some remaining CRP Livestock open access money to fund more work on OpenRXV / AReS
<ul>
<li>I will create GitHub issues for each of the things we talked about and then create ToRs to send to CodeObia for a quote</li>
</ul>
</li>
<li>Continue migrating Solr statistics to DSpace 6 UUID format after the upgrade on Sunday</li>
<li>Regarding the IWMI issue about flagships and strategic priorities we can use CRP Livestock as an example because all their <a href="https://cgspace.cgiar.org/handle/10568/80102">flagships are mapped to collections</a></li>
<li>Database issues are worse today&hellip;</li>
</ul>
<p><img src="/cgspace-notes/2020/11/postgres_connections_ALL-week2.png" alt="PostgreSQL connections week">
<img src="/cgspace-notes/2020/11/postgres_locks_ALL-week2.png" alt="PostgreSQL locks week"></p>
<ul>
<li>There are over 2,000 locks:</li>
</ul>
<pre><code>$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
2071
</code></pre><!-- raw HTML omitted -->
@ -412,6 +507,8 @@ org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error whil
<ol class="list-unstyled">
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
<li><a href="/cgspace-notes/2020-10/">October, 2020</a></li>
@ -420,8 +517,6 @@ org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error whil
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
<li><a href="/cgspace-notes/2020-07/">July, 2020</a></li>
</ol>
</section>