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Update notes for 2018-03-21
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@ -370,3 +370,48 @@ COPY 56156
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```
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- Afterwards we'll want to do some batch tagging of ORCID identifiers to these names
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## 2018-03-20
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- CGSpace crashed again this afternoon, I'm not sure of the cause but there are a lot of SQL errors in the DSpace log:
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```
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2018-03-21 15:11:08,166 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error -
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java.sql.SQLException: Connection has already been closed.
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```
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- I have no idea why so many connections were abandoned this afternoon:
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```
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# grep 'Mar 21, 2018' /var/log/tomcat7/catalina.out | grep -c 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon'
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268
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```
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- DSpace Test crashed again due to Java heap space, this is from the DSpace log:
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```
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2018-03-21 15:18:48,149 ERROR org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter @ Serious Error Occurred Processing Request!
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org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.OutOfMemoryError: Java heap space
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```
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- And this is from the Tomcat Catalina log:
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```
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Mar 21, 2018 11:20:00 AM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
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SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]]
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java.lang.OutOfMemoryError: Java heap space
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```
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- But there are tons of heap space errors on DSpace Test actually:
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```
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# grep -c 'java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
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319
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```
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- I guess we need to give it more RAM because it now has CGSpace's large Solr core
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- I will increase the memory from 3072m to 4096m
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- Update [Ansible playbooks](https://github.com/ilri/rmg-ansible-public) to use [PostgreSQL JBDC driver](https://jdbc.postgresql.org/) 42.2.2
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- Deploy the new JDBC driver on DSpace Test
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- I'm also curious to see how long the `dspace index-discovery -b` takes on DSpace Test where the DSpace installation directory is on one of Linode's new block storage volumes
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- I should also check the raw read speed with `hdparm -tT /dev/sdc`
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@ -20,7 +20,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
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<meta property="article:published_time" content="2018-03-02T16:07:54+02:00"/>
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<meta property="article:modified_time" content="2018-03-20T21:04:10+02:00"/>
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<meta property="article:modified_time" content="2018-03-21T11:44:06+02:00"/>
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@ -51,9 +51,9 @@ Export a CSV of the IITA community metadata for Martin Mueller
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"@type": "BlogPosting",
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"headline": "March, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-03/",
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"wordCount": "2113",
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"wordCount": "2343",
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"datePublished": "2018-03-02T16:07:54+02:00",
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"dateModified": "2018-03-20T21:04:10+02:00",
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"dateModified": "2018-03-21T11:44:06+02:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -538,6 +538,58 @@ COPY 56156
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<li>Afterwards we’ll want to do some batch tagging of ORCID identifiers to these names</li>
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</ul>
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<h2 id="2018-03-20-1">2018-03-20</h2>
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<ul>
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<li>CGSpace crashed again this afternoon, I’m not sure of the cause but there are a lot of SQL errors in the DSpace log:</li>
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</ul>
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<pre><code>2018-03-21 15:11:08,166 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error -
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java.sql.SQLException: Connection has already been closed.
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</code></pre>
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<ul>
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<li>I have no idea why so many connections were abandoned this afternoon:</li>
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</ul>
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<pre><code># grep 'Mar 21, 2018' /var/log/tomcat7/catalina.out | grep -c 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon'
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268
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</code></pre>
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<ul>
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<li>DSpace Test crashed again due to Java heap space, this is from the DSpace log:</li>
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</ul>
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<pre><code>2018-03-21 15:18:48,149 ERROR org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter @ Serious Error Occurred Processing Request!
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org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>And this is from the Tomcat Catalina log:</li>
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</ul>
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<pre><code>Mar 21, 2018 11:20:00 AM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
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SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]]
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java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>But there are tons of heap space errors on DSpace Test actually:</li>
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</ul>
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<pre><code># grep -c 'java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
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319
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</code></pre>
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<ul>
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<li>I guess we need to give it more RAM because it now has CGSpace’s large Solr core</li>
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<li>I will increase the memory from 3072m to 4096m</li>
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<li>Update <a href="https://github.com/ilri/rmg-ansible-public">Ansible playbooks</a> to use <a href="https://jdbc.postgresql.org/">PostgreSQL JBDC driver</a> 42.2.2</li>
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<li>Deploy the new JDBC driver on DSpace Test</li>
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<li>I’m also curious to see how long the <code>dspace index-discovery -b</code> takes on DSpace Test where the DSpace installation directory is on one of Linode’s new block storage volumes</li>
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<li>I should also check the raw read speed with <code>hdparm -tT /dev/sdc</code></li>
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</ul>
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@ -4,7 +4,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2018-03/</loc>
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<lastmod>2018-03-20T21:04:10+02:00</lastmod>
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<lastmod>2018-03-21T11:44:06+02:00</lastmod>
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</url>
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<url>
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@ -154,7 +154,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2018-03-20T21:04:10+02:00</lastmod>
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<lastmod>2018-03-21T11:44:06+02:00</lastmod>
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<priority>0</priority>
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</url>
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@ -165,7 +165,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2018-03-20T21:04:10+02:00</lastmod>
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<lastmod>2018-03-21T11:44:06+02:00</lastmod>
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<priority>0</priority>
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</url>
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@ -177,13 +177,13 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
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<lastmod>2018-03-20T21:04:10+02:00</lastmod>
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<lastmod>2018-03-21T11:44:06+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>2018-03-20T21:04:10+02:00</lastmod>
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<lastmod>2018-03-21T11:44:06+02:00</lastmod>
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<priority>0</priority>
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</url>
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