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Update notes for 2018-02-07

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Alan Orth 2018-02-07 18:33:26 +02:00
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53
content/post/2018-02.md
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@ -139,3 +139,56 @@ Tue Feb 6 09:30:32 UTC 2018
- According to [the announcement](https://groups.google.com/forum/#!topic/orcid-api-users/qfg-HwAB1bk) the v1 API was moved from `http://pub.orcid.org/` to `https://pub.orcid.org/v1.2` until March 1st when it will be discontinued for good
- But the old URL is hard coded in DSpace and it doesn't work anyways, because it currently redirects you to `https://pub.orcid.org/v2.0/v1.2`
- So I guess we have to disable that shit once and for all and switch to a controlled vocabulary
- CGSpace crashed again, this time around `Wed Feb 7 11:20:28 UTC 2018`
- I took a few snapshots of the PostgreSQL activity at the time and as the minutes went on and the connections were very high at first but reduced on their own:
```
$ psql -c 'select * from pg_stat_activity' > /tmp/pg_stat_activity.txt
$ grep -c 'PostgreSQL JDBC' /tmp/pg_stat_activity*
/tmp/pg_stat_activity1.txt:300
/tmp/pg_stat_activity2.txt:272
/tmp/pg_stat_activity3.txt:168
/tmp/pg_stat_activity4.txt:5
/tmp/pg_stat_activity5.txt:6
```
- Interestingly, all of those 751 connections were idle!
```
$ grep "PostgreSQL JDBC" /tmp/pg_stat_activity* | grep -c idle
751
```
- Since I was restarting Tomcat anyways, I decided to deploy the changes to create two different pools for web and API apps
- Looking the Munin graphs, I can see that there were almost double the normal number of DSpace sessions at the time of the crash (and also yesterday!):
![DSpace Sessions](/cgspace-notes/2018/02/jmx_dspace-sessions-day.png)
- Indeed it seems like there were over 1800 sessions today around the hours of 10 and 11 AM:
```
$ grep -E '^2018-02-07 (10|11)' dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
1828
```
- CGSpace went down again a few hours later, and now the connections to the dspaceWeb pool are maxed at 250 (the new limit I imposed with the new separate pool scheme)
- What's interesting is that the DSpace log says the connections are all busy:
```
org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-328] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:250; busy:250; idle:0; lastwait:5000].
```
- ... but in PostgreSQL I see them `idle` or `idle in transaction`:
```
$ psql -c 'select * from pg_stat_activity' | grep -c dspaceWeb
250
$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c idle
250
$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c "idle in transaction"
187
```
- What the fuck, does DSpace think all connections are busy?
- I suspect these are issues with abandoned connections or maybe a leak, so I'm going to try adding the `removeAbandoned='true'` parameter which is apparently off by default
- I will try `testOnReturn='true'` too, just to add more validation, because I'm fucking grasping at straws

66
public/2018-02/index.html
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@ -23,7 +23,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-pl
<meta property="article:published_time" content="2018-02-01T16:28:54&#43;02:00"/>
<meta property="article:modified_time" content="2018-02-06T14:03:46&#43;02:00"/>
<meta property="article:modified_time" content="2018-02-07T12:34:36&#43;02:00"/>
@ -57,9 +57,9 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-pl
"@type": "BlogPosting",
"headline": "February, 2018",
"url": "https://alanorth.github.io/cgspace-notes/2018-02/",
"wordCount": "995",
"wordCount": "1334",
"datePublished": "2018-02-01T16:28:54&#43;02:00",
"dateModified": "2018-02-06T14:03:46&#43;02:00",
"dateModified": "2018-02-07T12:34:36&#43;02:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -274,6 +274,66 @@ Tue Feb 6 09:30:32 UTC 2018
<li>According to <a href="https://groups.google.com/forum/#!topic/orcid-api-users/qfg-HwAB1bk">the announcement</a> the v1 API was moved from <code>http://pub.orcid.org/</code> to <code>https://pub.orcid.org/v1.2</code> until March 1st when it will be discontinued for good</li>
<li>But the old URL is hard coded in DSpace and it doesn&rsquo;t work anyways, because it currently redirects you to <code>https://pub.orcid.org/v2.0/v1.2</code></li>
<li>So I guess we have to disable that shit once and for all and switch to a controlled vocabulary</li>
<li>CGSpace crashed again, this time around <code>Wed Feb 7 11:20:28 UTC 2018</code></li>
<li>I took a few snapshots of the PostgreSQL activity at the time and as the minutes went on and the connections were very high at first but reduced on their own:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' &gt; /tmp/pg_stat_activity.txt
$ grep -c 'PostgreSQL JDBC' /tmp/pg_stat_activity*
/tmp/pg_stat_activity1.txt:300
/tmp/pg_stat_activity2.txt:272
/tmp/pg_stat_activity3.txt:168
/tmp/pg_stat_activity4.txt:5
/tmp/pg_stat_activity5.txt:6
</code></pre>
<ul>
<li>Interestingly, all of those 751 connections were idle!</li>
</ul>
<pre><code>$ grep &quot;PostgreSQL JDBC&quot; /tmp/pg_stat_activity* | grep -c idle
751
</code></pre>
<ul>
<li>Since I was restarting Tomcat anyways, I decided to deploy the changes to create two different pools for web and API apps</li>
<li>Looking the Munin graphs, I can see that there were almost double the normal number of DSpace sessions at the time of the crash (and also yesterday!):</li>
</ul>
<p><img src="/cgspace-notes/2018/02/jmx_dspace-sessions-day.png" alt="DSpace Sessions" /></p>
<ul>
<li>Indeed it seems like there were over 1800 sessions today around the hours of 10 and 11 AM:</li>
</ul>
<pre><code>$ grep -E '^2018-02-07 (10|11)' dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
1828
</code></pre>
<ul>
<li>CGSpace went down again a few hours later, and now the connections to the dspaceWeb pool are maxed at 250 (the new limit I imposed with the new separate pool scheme)</li>
<li>What&rsquo;s interesting is that the DSpace log says the connections are all busy:</li>
</ul>
<pre><code>org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-328] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:250; busy:250; idle:0; lastwait:5000].
</code></pre>
<ul>
<li>&hellip; but in PostgreSQL I see them <code>idle</code> or <code>idle in transaction</code>:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -c dspaceWeb
250
$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c idle
250
$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c &quot;idle in transaction&quot;
187
</code></pre>
<ul>
<li>What the fuck, does DSpace think all connections are busy?</li>
<li>I suspect these are issues with abandoned connections or maybe a leak, so I&rsquo;m going to try adding the <code>removeAbandoned='true'</code> parameter which is apparently off by default</li>
<li>I will try <code>testOnReturn='true'</code> too, just to add more validation, because I&rsquo;m fucking grasping at straws</li>
</ul>

10
public/sitemap.xml
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@ -4,7 +4,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/2018-02/</loc>
<lastmod>2018-02-06T14:03:46+02:00</lastmod>
<lastmod>2018-02-07T12:34:36+02:00</lastmod>
</url>
<url>
@ -149,7 +149,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2018-02-06T14:03:46+02:00</lastmod>
<lastmod>2018-02-07T12:34:36+02:00</lastmod>
<priority>0</priority>
</url>
@ -160,7 +160,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2018-02-06T14:03:46+02:00</lastmod>
<lastmod>2018-02-07T12:34:36+02:00</lastmod>
<priority>0</priority>
</url>
@ -172,13 +172,13 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/post/</loc>
<lastmod>2018-02-06T14:03:46+02:00</lastmod>
<lastmod>2018-02-07T12:34:36+02:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
<lastmod>2018-02-06T14:03:46+02:00</lastmod>
<lastmod>2018-02-07T12:34:36+02:00</lastmod>
<priority>0</priority>
</url>