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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-12-02T10:43:00&#43;03:00">Fri Dec 02, 2016</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="2016-12-02">2016-12-02</h2>
<ul>
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
</ul>
<pre><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
</code></pre>
<ul>
<li>I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade</li>
<li>I&rsquo;ve raised a ticket with Atmire to ask</li>
<li>Another worrying error from dspace.log is:</li>
</ul>
<pre><code>org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:972)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:789)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:111)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter.doFilter(DSpaceCocoonServletFilter.java:274)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.servlet.multipart.DSpaceMultipartFilter.doFilter(DSpaceMultipartFilter.java:119)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
at com.googlecode.psiprobe.Tomcat70AgentValve.invoke(Tomcat70AgentValve.java:44)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at com.atmire.statistics.generator.TopNDSODatasetGenerator.toDatasetQuery(SourceFile:39)
at com.atmire.statistics.display.StatisticsDataVisitsMultidata.createDataset(SourceFile:108)
at org.dspace.statistics.content.StatisticsDisplay.createDataset(SourceFile:384)
at org.dspace.statistics.content.StatisticsDisplay.getDataset(SourceFile:404)
at com.atmire.statistics.mostpopular.JSONStatsMostPopularGenerator.generateJsonData(SourceFile:170)
at com.atmire.statistics.mostpopular.JSONStatsMostPopularGenerator.generate(SourceFile:246)
at com.atmire.app.xmlui.aspect.statistics.JSONStatsMostPopular.generate(JSONStatsMostPopular.java:145)
at sun.reflect.GeneratedMethodAccessor296.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy96.process(Unknown Source)
at org.apache.cocoon.components.treeprocessor.sitemap.ReadNode.invoke(ReadNode.java:94)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
at org.apache.cocoon.components.treeprocessor.sitemap.PipelineNode.invoke(PipelineNode.java:143)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
at org.apache.cocoon.components.treeprocessor.sitemap.PipelinesNode.invoke(PipelinesNode.java:81)
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:239)
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:171)
at org.apache.cocoon.components.treeprocessor.TreeProcessor.process(TreeProcessor.java:247)
at org.apache.cocoon.components.treeprocessor.sitemap.MountNode.invoke(MountNode.java:117)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
at org.apache.cocoon.components.treeprocessor.sitemap.PipelineNode.invoke(PipelineNode.java:143)
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
at org.apache.cocoon.components.treeprocessor.sitemap.PipelinesNode.invoke(PipelinesNode.java:81)
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:239)
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:171)
at org.apache.cocoon.components.treeprocessor.TreeProcessor.process(TreeProcessor.java:247)
at org.apache.cocoon.servlet.RequestProcessor.process(RequestProcessor.java:351)
at org.apache.cocoon.servlet.RequestProcessor.service(RequestProcessor.java:169)
at org.apache.cocoon.sitemap.SitemapServlet.service(SitemapServlet.java:84)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:468)
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:443)
at org.apache.cocoon.servletservice.spring.ServletFactoryBean$ServiceInterceptor.invoke(ServletFactoryBean.java:264)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy89.service(Unknown Source)
at org.dspace.springmvc.CocoonView.render(CocoonView.java:113)
at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1180)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:950)
... 35 more
</code></pre>
<ul>
<li>The first error I see in dspace.log this morning is:</li>
</ul>
<pre><code>2016-12-02 03:00:46,656 ERROR org.dspace.authority.AuthorityValueFinder @ anonymous::Error while retrieving AuthorityValue from solr:query\colon; id\colon;&quot;b0b541c1-ec15-48bf-9209-6dbe8e338cdc&quot;
org.apache.solr.client.solrj.SolrServerException: Server refused connection at: http://localhost:8081/solr/authority
</code></pre>
<ul>
<li>Looking through DSpace&rsquo;s solr log I see that about 20 seconds before this, there were a few 30+ KiB solr queries</li>
<li>The last logs here right before Solr became unresponsive (and right after I restarted it five hours later) were:</li>
</ul>
<pre><code>2016-12-02 03:00:42,606 INFO org.apache.solr.core.SolrCore @ [statistics] webapp=/solr path=/select params={q=containerItem:72828+AND+type:0&amp;shards=localhost:8081/solr/statistics-2010,localhost:8081/solr/statistics&amp;fq=-isInternal:true&amp;fq=-(author_mtdt:&quot;CGIAR\+Institutional\+Learning\+and\+Change\+Initiative&quot;++AND+subject_mtdt:&quot;PARTNERSHIPS&quot;+AND+subject_mtdt:&quot;RESEARCH&quot;+AND+subject_mtdt:&quot;AGRICULTURE&quot;+AND+subject_mtdt:&quot;DEVELOPMENT&quot;++AND+iso_mtdt:&quot;en&quot;+)&amp;rows=0&amp;wt=javabin&amp;version=2} hits=0 status=0 QTime=19
2016-12-02 08:28:23,908 INFO org.apache.solr.servlet.SolrDispatchFilter @ SolrDispatchFilter.init()
</code></pre>
<ul>
<li>DSpace&rsquo;s own Solr logs don&rsquo;t give IP addresses, so I will have to enable Nginx&rsquo;s logging of <code>/solr</code> so I can see where this request came from</li>
<li>I enabled logging of <code>/rest/</code> and I think I&rsquo;ll leave it on for good</li>
<li>Also, the disk is nearly full because of log file issues, so I&rsquo;m running some compression on DSpace logs</li>
<li>Normally these stay uncompressed for a month just in case we need to look at them, so now I&rsquo;ve just compressed anything older than 2 weeks so we can get some disk space back</li>
</ul>
<h2 id="2016-12-04">2016-12-04</h2>
<ul>
<li>I got a weird report from the CGSpace checksum checker this morning</li>
<li>It says 732 bitstreams have potential issues, for example:</li>
</ul>
<pre><code>------------------------------------------------
Bitstream Id = 6
Process Start Date = Dec 4, 2016
Process End Date = Dec 4, 2016
Checksum Expected = a1d9eef5e2d85f50f67ce04d0329e96a
Checksum Calculated = a1d9eef5e2d85f50f67ce04d0329e96a
Result = Bitstream marked deleted in bitstream table
-----------------------------------------------
...
------------------------------------------------
Bitstream Id = 77581
Process Start Date = Dec 4, 2016
Process End Date = Dec 4, 2016
Checksum Expected = 9959301aa4ca808d00957dff88214e38
Checksum Calculated =
Result = The bitstream could not be found
-----------------------------------------------
</code></pre>
<ul>
<li>The first one seems ok, but I don&rsquo;t know what to make of the second one&hellip;</li>
<li>I had a look and there is indeed no file with the second checksum in the assetstore (ie, looking in <code>[dspace-dir]/assetstore/99/59/30/...</code>)</li>
<li>For what it&rsquo;s worth, there is no item on DSpace Test or S3 backups with that checksum either&hellip;</li>
<li>In other news, I&rsquo;m looking at JVM settings from the Solr 4.10.2 release, from <code>bin/solr.in.sh</code>:</li>
</ul>
<pre><code># These GC settings have shown to work well for a number of common Solr workloads
GC_TUNE=&quot;-XX:-UseSuperWord \
-XX:NewRatio=3 \
-XX:SurvivorRatio=4 \
-XX:TargetSurvivorRatio=90 \
-XX:MaxTenuringThreshold=8 \
-XX:+UseConcMarkSweepGC \
-XX:+UseParNewGC \
-XX:ConcGCThreads=4 -XX:ParallelGCThreads=4 \
-XX:+CMSScavengeBeforeRemark \
-XX:PretenureSizeThreshold=64m \
-XX:CMSFullGCsBeforeCompaction=1 \
-XX:+UseCMSInitiatingOccupancyOnly \
-XX:CMSInitiatingOccupancyFraction=50 \
-XX:CMSTriggerPermRatio=80 \
-XX:CMSMaxAbortablePrecleanTime=6000 \
-XX:+CMSParallelRemarkEnabled \
-XX:+ParallelRefProcEnabled \
-XX:+AggressiveOpts&quot;
</code></pre>
<ul>
<li>I need to try these because they are recommended by the Solr project itself</li>
<li>Also, as always, I need to read <a href="https://wiki.apache.org/solr/ShawnHeisey">Shawn Heisey&rsquo;s wiki page on Solr</a></li>
</ul>
<h2 id="2016-12-05">2016-12-05</h2>
<ul>
<li>I did some basic benchmarking on a local DSpace before and after the JVM settings above, but there wasn&rsquo;t anything amazingly obvious</li>
<li>I want to make the changes on DSpace Test and monitor the JVM heap graphs for a few days to see if they change the JVM GC patterns or anything (munin graphs)</li>
<li>Spin up new CGSpace server on Linode</li>
<li>I did a few traceroutes from Jordan and Kenya and it seems that Linode&rsquo;s Frankfurt datacenter is a few less hops and perhaps less packet loss than the London one, so I put the new server in Frankfurt</li>
<li>Do initial provisioning</li>
</ul>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2016-12/">December, 2016</a></li>
<li><a href="/cgspace-notes/2016-11/">November, 2016</a></li>
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
</ol>
</section>
<section class="sidebar-module">
<h4>Links</h4>
<ol class="list-unstyled">
<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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