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Update notes for 2018-04-10
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@ -210,7 +210,7 @@ X-XSS-Protection: 1; mode=block
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- Looks like the number of total requests processed by nginx in March went down from the previous months:
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- In other news, it looks like the number of total requests processed by nginx in March went down from the previous months:
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```
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# time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Mar/2018"
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@ -220,3 +220,58 @@ real 0m13.658s
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user 0m16.533s
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sys 0m1.087s
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```
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- In other other news, the database cleanup script has an issue again:
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```
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$ dspace cleanup -v
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...
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Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
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Detail: Key (bitstream_id)=(151626) is still referenced from table "bundle".
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```
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- The solution is, as always:
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```
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$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (151626);'
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UPDATE 1
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```
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- Looking at abandoned connections in Tomcat:
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```
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# zcat /var/log/tomcat7/catalina.out.[1-9].gz | grep -c 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon'
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2115
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```
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- Apparently from these stacktraces we should be able to see which code is not closing connections properly
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- Here's a pretty good overview of days where we had database issues recently:
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```
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# zcat /var/log/tomcat7/catalina.out.[1-9].gz | grep 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon' | awk '{print $1,$2, $3}' | sort | uniq -c | sort -n
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1 Feb 18, 2018
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1 Feb 19, 2018
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1 Feb 20, 2018
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1 Feb 24, 2018
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2 Feb 13, 2018
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3 Feb 17, 2018
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5 Feb 16, 2018
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5 Feb 23, 2018
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5 Feb 27, 2018
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6 Feb 25, 2018
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40 Feb 14, 2018
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63 Feb 28, 2018
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154 Mar 19, 2018
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202 Feb 21, 2018
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264 Feb 26, 2018
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268 Mar 21, 2018
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524 Feb 22, 2018
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570 Feb 15, 2018
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```
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- In Tomcat 8.5 the `removeAbandoned` property has been split into two: `removeAbandonedOnBorrow` and `removeAbandonedOnMaintenance`
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- See: https://tomcat.apache.org/tomcat-8.5-doc/jndi-datasource-examples-howto.html#Database_Connection_Pool_(DBCP_2)_Configurations
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- I assume we want `removeAbandonedOnBorrow` and make updates to the Tomcat 8 templates in Ansible
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- After reading more documentation I see that Tomcat 8.5's default DBCP seems to now be Commons DBCP2 instead of Tomcat DBCP
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- It can be overridden in Tomcat's _server.xml_ by setting `factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"` in the `<Resource>`
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- I think we should use this default, so we'll need to remove some other settings that are specific to Tomcat's DBCP like `jdbcInterceptors` and `abandonWhenPercentageFull`
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@ -38,7 +38,7 @@ COPY 54701
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<meta property="article:published_time" content="2017-11-02T09:37:54+02:00"/>
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<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00"/>
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<meta property="article:modified_time" content="2018-04-10T08:27:55+03:00"/>
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@ -89,7 +89,7 @@ COPY 54701
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"url": "https://alanorth.github.io/cgspace-notes/2017-11/",
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"wordCount": "5428",
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"datePublished": "2017-11-02T09:37:54+02:00",
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"dateModified": "2018-03-09T22:10:33+02:00",
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"dateModified": "2018-04-10T08:27:55+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -21,7 +21,7 @@ Catalina logs at least show some memory errors yesterday:
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<meta property="article:published_time" content="2018-04-01T16:13:54+02:00"/>
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<meta property="article:modified_time" content="2018-04-04T17:01:08+03:00"/>
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<meta property="article:modified_time" content="2018-04-10T08:27:55+03:00"/>
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@ -53,9 +53,9 @@ Catalina logs at least show some memory errors yesterday:
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"@type": "BlogPosting",
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"headline": "April, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-04/",
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"wordCount": "1005",
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"wordCount": "1297",
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"datePublished": "2018-04-01T16:13:54+02:00",
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"dateModified": "2018-04-04T17:01:08+03:00",
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"dateModified": "2018-04-10T08:27:55+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -351,7 +351,7 @@ X-XSS-Protection: 1; mode=block
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<p><img src="/cgspace-notes/2018/04/jmx_dspace_sessions-week.png" alt="Tomcat sessions week" /></p>
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<ul>
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<li>Looks like the number of total requests processed by nginx in March went down from the previous months:</li>
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<li>In other news, it looks like the number of total requests processed by nginx in March went down from the previous months:</li>
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</ul>
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<pre><code># time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Mar/2018"
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@ -362,6 +362,67 @@ user 0m16.533s
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sys 0m1.087s
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</code></pre>
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<ul>
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<li>In other other news, the database cleanup script has an issue again:</li>
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</ul>
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<pre><code>$ dspace cleanup -v
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...
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Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
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Detail: Key (bitstream_id)=(151626) is still referenced from table "bundle".
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</code></pre>
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<ul>
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<li>The solution is, as always:</li>
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</ul>
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<pre><code>$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (151626);'
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UPDATE 1
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</code></pre>
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<ul>
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<li>Looking at abandoned connections in Tomcat:</li>
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</ul>
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<pre><code># zcat /var/log/tomcat7/catalina.out.[1-9].gz | grep -c 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon'
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2115
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</code></pre>
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<ul>
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<li>Apparently from these stacktraces we should be able to see which code is not closing connections properly</li>
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<li>Here’s a pretty good overview of days where we had database issues recently:</li>
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</ul>
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<pre><code># zcat /var/log/tomcat7/catalina.out.[1-9].gz | grep 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon' | awk '{print $1,$2, $3}' | sort | uniq -c | sort -n
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1 Feb 18, 2018
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1 Feb 19, 2018
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1 Feb 20, 2018
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1 Feb 24, 2018
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2 Feb 13, 2018
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3 Feb 17, 2018
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5 Feb 16, 2018
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5 Feb 23, 2018
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5 Feb 27, 2018
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6 Feb 25, 2018
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40 Feb 14, 2018
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63 Feb 28, 2018
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154 Mar 19, 2018
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202 Feb 21, 2018
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264 Feb 26, 2018
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268 Mar 21, 2018
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524 Feb 22, 2018
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570 Feb 15, 2018
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</code></pre>
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<ul>
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<li>In Tomcat 8.5 the <code>removeAbandoned</code> property has been split into two: <code>removeAbandonedOnBorrow</code> and <code>removeAbandonedOnMaintenance</code></li>
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<li>See: <a href="https://tomcat.apache.org/tomcat-8.5-doc/jndi-datasource-examples-howto.html#Database_Connection_Pool_(DBCP_2)_Configurations">https://tomcat.apache.org/tomcat-8.5-doc/jndi-datasource-examples-howto.html#Database_Connection_Pool_(DBCP_2)_Configurations</a></li>
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<li>I assume we want <code>removeAbandonedOnBorrow</code> and make updates to the Tomcat 8 templates in Ansible</li>
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<li>After reading more documentation I see that Tomcat 8.5’s default DBCP seems to now be Commons DBCP2 instead of Tomcat DBCP</li>
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<li>It can be overridden in Tomcat’s <em>server.xml</em> by setting <code>factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"</code> in the <code><Resource></code></li>
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<li>I think we should use this default, so we’ll need to remove some other settings that are specific to Tomcat’s DBCP like <code>jdbcInterceptors</code> and <code>abandonWhenPercentageFull</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/2018-04/</loc>
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<lastmod>2018-04-04T17:01:08+03:00</lastmod>
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<lastmod>2018-04-10T08:27:55+03:00</lastmod>
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</url>
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<url>
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@ -29,7 +29,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2017-11/</loc>
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<lastmod>2018-03-09T22:10:33+02:00</lastmod>
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<lastmod>2018-04-10T08:27:55+03:00</lastmod>
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</url>
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<url>
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@ -159,7 +159,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2018-04-04T17:01:08+03:00</lastmod>
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<lastmod>2018-04-10T08:27:55+03:00</lastmod>
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<priority>0</priority>
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</url>
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@ -170,7 +170,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2018-04-04T17:01:08+03:00</lastmod>
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<lastmod>2018-04-10T08:27:55+03:00</lastmod>
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<priority>0</priority>
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</url>
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@ -182,13 +182,13 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
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<lastmod>2018-04-04T17:01:08+03:00</lastmod>
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<lastmod>2018-04-10T08:27:55+03:00</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>2018-04-04T17:01:08+03:00</lastmod>
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<lastmod>2018-04-10T08:27:55+03:00</lastmod>
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<priority>0</priority>
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</url>
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