mirror of
https://github.com/alanorth/cgspace-notes.git
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Add notes for 2018-01-17
This commit is contained in:
parent
a9d72279de
commit
75b65f1f66
GPG Key ID:
0FB860CC9C45B1B9
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@ -717,3 +717,105 @@ sys 0m2.210s
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- I removed Tsega's access to Linode dashboard as well
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- I ended up creating a Jira issue for my `db.jndi` documentation fix: [DS-3803](https://jira.duraspace.org/browse/DS-3803)
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- The DSpace developers said they wanted each pull request to be associated with a Jira issue
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## 2018-01-17
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- Abenet asked me to proof and upload 54 records for LIVES
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- A few records were missing countries (even though they're all from Ethiopia)
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- Also, there are whitespace issues in many columns, and the items are mapped to the LIVES and ILRI articles collections, not Theses
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- In any case, importing them like this:
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```
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$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
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$ dspace import -a -e aorth@mjanja.ch -s /tmp/2018-01-16\ LIVES/SimpleArchiveFormat -m lives.map &> lives.log
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```
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- And fantastic, before I started the import there were 10 PostgreSQL connections, and then CGSpace crashed during the upload
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- When I looked there were 210 PostgreSQL connections!
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- I don't see any high load in XMLUI or REST/OAI:
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```
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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 | grep -E "17/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
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381 40.77.167.124
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403 213.55.99.121
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431 207.46.13.60
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445 157.55.39.113
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445 157.55.39.231
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449 95.108.181.88
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453 68.180.229.254
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593 54.91.48.104
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757 104.196.152.243
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776 66.249.66.90
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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 "17/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
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11 205.201.132.14
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11 40.77.167.124
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15 35.226.23.240
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16 157.55.39.231
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16 66.249.64.155
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18 66.249.66.90
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22 95.108.181.88
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58 104.196.152.243
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4106 70.32.83.92
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9229 45.5.184.196
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```
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- But I do see this strange message in the dspace log:
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```
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2018-01-17 07:59:25,856 INFO org.apache.http.impl.client.SystemDefaultHttpClient @ I/O exception (org.apache.http.NoHttpResponseException) caught when processing request to {}->http://localhost:8081: The target server failed to respond
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2018-01-17 07:59:25,856 INFO org.apache.http.impl.client.SystemDefaultHttpClient @ Retrying request to {}->http://localhost:8081
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```
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- I have NEVER seen this error before, and there is no error before or after that in DSpace's solr.log
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- Tomcat's catalina.out does show something interesting, though, right at that time:
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```
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[====================> ]40% time remaining: 7 hour(s) 14 minute(s) 45 seconds. timestamp: 2018-01-17 07:57:02
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[====================> ]40% time remaining: 7 hour(s) 14 minute(s) 45 seconds. timestamp: 2018-01-17 07:57:11
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[====================> ]40% time remaining: 7 hour(s) 14 minute(s) 44 seconds. timestamp: 2018-01-17 07:57:37
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[====================> ]40% time remaining: 7 hour(s) 16 minute(s) 5 seconds. timestamp: 2018-01-17 07:57:49
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Exception in thread "http-bio-127.0.0.1-8081-exec-627" java.lang.OutOfMemoryError: Java heap space
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at org.apache.lucene.util.FixedBitSet.clone(FixedBitSet.java:576)
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at org.apache.solr.search.BitDocSet.andNot(BitDocSet.java:222)
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at org.apache.solr.search.SolrIndexSearcher.getProcessedFilter(SolrIndexSearcher.java:1067)
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at org.apache.solr.search.SolrIndexSearcher.getDocListNC(SolrIndexSearcher.java:1557)
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at org.apache.solr.search.SolrIndexSearcher.getDocListC(SolrIndexSearcher.java:1433)
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at org.apache.solr.search.SolrIndexSearcher.search(SolrIndexSearcher.java:514)
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at org.apache.solr.handler.component.QueryComponent.process(QueryComponent.java:485)
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at org.apache.solr.handler.component.SearchHandler.handleRequestBody(SearchHandler.java:218)
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at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:135)
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at org.apache.solr.core.SolrCore.execute(SolrCore.java:1967)
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at org.apache.solr.servlet.SolrDispatchFilter.execute(SolrDispatchFilter.java:777)
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at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:418)
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at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:207)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.dspace.solr.filters.LocalHostRestrictionFilter.doFilter(LocalHostRestrictionFilter.java:50)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:221)
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at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
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at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
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at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
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at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
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at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
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at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
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at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
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at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:436)
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at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
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at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
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at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
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at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
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at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
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```
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- You can see the timestamp above, which is some Atmire nightly task I think, but I can't figure out which one
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- So I restarted Tomcat and tried the import again, which finished very quickly and without errors!
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```
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$ dspace import -a -e aorth@mjanja.ch -s /tmp/2018-01-16\ LIVES/SimpleArchiveFormat -m lives2.map &> lives2.log
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```
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- Looking at the JVM graphs from Munin it does look like the heap ran out of memory (see the blue dip just before the green spike when I restarted Tomcat):
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@ -92,7 +92,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
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<meta property="article:published_time" content="2018-01-02T08:35:54-08:00"/>
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<meta property="article:modified_time" content="2018-01-16T15:40:31+02:00"/>
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<meta property="article:modified_time" content="2018-01-16T19:38:10+02:00"/>
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@ -194,9 +194,9 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
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"@type": "BlogPosting",
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"headline": "January, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-01/",
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"wordCount": "3900",
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"wordCount": "4373",
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"datePublished": "2018-01-02T08:35:54-08:00",
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"dateModified": "2018-01-16T15:40:31+02:00",
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"dateModified": "2018-01-16T19:38:10+02:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -1053,6 +1053,115 @@ sys 0m2.210s
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<li>The DSpace developers said they wanted each pull request to be associated with a Jira issue</li>
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</ul>
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<h2 id="2018-01-17">2018-01-17</h2>
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<ul>
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<li>Abenet asked me to proof and upload 54 records for LIVES</li>
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<li>A few records were missing countries (even though they’re all from Ethiopia)</li>
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<li>Also, there are whitespace issues in many columns, and the items are mapped to the LIVES and ILRI articles collections, not Theses</li>
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<li>In any case, importing them like this:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
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$ dspace import -a -e aorth@mjanja.ch -s /tmp/2018-01-16\ LIVES/SimpleArchiveFormat -m lives.map &> lives.log
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</code></pre>
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<ul>
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<li>And fantastic, before I started the import there were 10 PostgreSQL connections, and then CGSpace crashed during the upload</li>
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<li>When I looked there were 210 PostgreSQL connections!</li>
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<li>I don’t see any high load in XMLUI or REST/OAI:</li>
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</ul>
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<pre><code># 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 | grep -E "17/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
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381 40.77.167.124
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403 213.55.99.121
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431 207.46.13.60
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445 157.55.39.113
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445 157.55.39.231
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449 95.108.181.88
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453 68.180.229.254
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593 54.91.48.104
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757 104.196.152.243
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776 66.249.66.90
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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 "17/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
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11 205.201.132.14
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11 40.77.167.124
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15 35.226.23.240
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16 157.55.39.231
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16 66.249.64.155
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18 66.249.66.90
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22 95.108.181.88
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58 104.196.152.243
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4106 70.32.83.92
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9229 45.5.184.196
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</code></pre>
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<ul>
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<li>But I do see this strange message in the dspace log:</li>
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</ul>
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<pre><code>2018-01-17 07:59:25,856 INFO org.apache.http.impl.client.SystemDefaultHttpClient @ I/O exception (org.apache.http.NoHttpResponseException) caught when processing request to {}->http://localhost:8081: The target server failed to respond
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2018-01-17 07:59:25,856 INFO org.apache.http.impl.client.SystemDefaultHttpClient @ Retrying request to {}->http://localhost:8081
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</code></pre>
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<ul>
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<li>I have NEVER seen this error before, and there is no error before or after that in DSpace’s solr.log</li>
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<li>Tomcat’s catalina.out does show something interesting, though, right at that time:</li>
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</ul>
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<pre><code>[====================> ]40% time remaining: 7 hour(s) 14 minute(s) 45 seconds. timestamp: 2018-01-17 07:57:02
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[====================> ]40% time remaining: 7 hour(s) 14 minute(s) 45 seconds. timestamp: 2018-01-17 07:57:11
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[====================> ]40% time remaining: 7 hour(s) 14 minute(s) 44 seconds. timestamp: 2018-01-17 07:57:37
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[====================> ]40% time remaining: 7 hour(s) 16 minute(s) 5 seconds. timestamp: 2018-01-17 07:57:49
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Exception in thread "http-bio-127.0.0.1-8081-exec-627" java.lang.OutOfMemoryError: Java heap space
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at org.apache.lucene.util.FixedBitSet.clone(FixedBitSet.java:576)
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at org.apache.solr.search.BitDocSet.andNot(BitDocSet.java:222)
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at org.apache.solr.search.SolrIndexSearcher.getProcessedFilter(SolrIndexSearcher.java:1067)
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at org.apache.solr.search.SolrIndexSearcher.getDocListNC(SolrIndexSearcher.java:1557)
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at org.apache.solr.search.SolrIndexSearcher.getDocListC(SolrIndexSearcher.java:1433)
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at org.apache.solr.search.SolrIndexSearcher.search(SolrIndexSearcher.java:514)
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at org.apache.solr.handler.component.QueryComponent.process(QueryComponent.java:485)
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at org.apache.solr.handler.component.SearchHandler.handleRequestBody(SearchHandler.java:218)
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at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:135)
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at org.apache.solr.core.SolrCore.execute(SolrCore.java:1967)
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at org.apache.solr.servlet.SolrDispatchFilter.execute(SolrDispatchFilter.java:777)
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at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:418)
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at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:207)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.dspace.solr.filters.LocalHostRestrictionFilter.doFilter(LocalHostRestrictionFilter.java:50)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:221)
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at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
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at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
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at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
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at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
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at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
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at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
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at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
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at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:436)
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at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
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at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
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at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
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at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
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at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
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</code></pre>
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<ul>
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<li>You can see the timestamp above, which is some Atmire nightly task I think, but I can’t figure out which one</li>
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<li>So I restarted Tomcat and tried the import again, which finished very quickly and without errors!</li>
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</ul>
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<pre><code>$ dspace import -a -e aorth@mjanja.ch -s /tmp/2018-01-16\ LIVES/SimpleArchiveFormat -m lives2.map &> lives2.log
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</code></pre>
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<ul>
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<li>Looking at the JVM graphs from Munin it does look like the heap ran out of memory (see the blue dip just before the green spike when I restarted Tomcat):</li>
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</ul>
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<p><img src="/cgspace-notes/2018/01/tomcat-jvm-day.png" alt="Tomcat JVM Heap" /></p>
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@ -4,7 +4,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2018-01/</loc>
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<lastmod>2018-01-16T15:40:31+02:00</lastmod>
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<lastmod>2018-01-16T19:38:10+02:00</lastmod>
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</url>
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<url>
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@ -144,7 +144,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2018-01-16T15:40:31+02:00</lastmod>
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<lastmod>2018-01-16T19:38:10+02:00</lastmod>
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<priority>0</priority>
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</url>
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@ -155,7 +155,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2018-01-16T15:40:31+02:00</lastmod>
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<lastmod>2018-01-16T19:38:10+02:00</lastmod>
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<priority>0</priority>
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</url>
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@ -167,13 +167,13 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/post/</loc>
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<lastmod>2018-01-16T15:40:31+02:00</lastmod>
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<lastmod>2018-01-16T19:38:10+02:00</lastmod>
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<priority>0</priority>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
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<lastmod>2018-01-16T15:40:31+02:00</lastmod>
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<lastmod>2018-01-16T19:38:10+02:00</lastmod>
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<priority>0</priority>
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</url>
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Reference in New Issue
Block a user