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@ -331,5 +331,154 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
|
||||
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- I deleted the ilri/AReS repository on GitHub since we haven't updated it in two years
|
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- All development is happening in https://github.com/ilri/openRXV now
|
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- 10PM and the server is down again, with locks through the roof:
|
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|
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```console
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$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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12198
|
||||
```
|
||||
|
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- I see that there are tons of PostgreSQL connections getting abandoned today, compared to very few in the past few weeks:
|
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|
||||
```console
|
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$ journalctl -u tomcat7 --since=today | grep -c 'ConnectionPool abandon'
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1838
|
||||
$ journalctl -u tomcat7 --since=2021-03-20 --until=2021-04-05 | grep -c 'ConnectionPool abandon'
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3
|
||||
```
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|
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- I even restarted the server and connections were low for a few minutes until they shot back up:
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|
||||
```console
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$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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13
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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8651
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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8940
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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10504
|
||||
```
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- I had to go to bed and I bet it will crash and be down for hours until I wake up...
|
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- What the hell is this user agent?
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|
||||
```
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||||
54.197.119.143 - - [06/Apr/2021:19:18:11 +0200] "GET /handle/10568/16499 HTTP/1.1" 499 0 "-" "GetUrl/1.0 wdestiny@umich.edu (Linux)"
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```
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## 2021-04-07
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- CGSpace was still down from last night of course, with tons of database locks:
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|
||||
```console
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$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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12168
|
||||
```
|
||||
|
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- I restarted the server again and the locks came back
|
||||
- Atmire responded to the message from yesterday
|
||||
- The noticed something in the logs about emails failing to be sent
|
||||
- There appears to be an issue sending mails on workflow tasks when a user in that group has an invalid email address:
|
||||
|
||||
```console
|
||||
2021-04-01 12:45:11,414 WARN org.dspace.workflowbasic.BasicWorkflowServiceImpl @ a.akwarandu@cgiar.org:session_id=2F20F20D4A8C36DB53D42DE45DFA3CCE:notifyGroupofTask:cannot email user group_id=aecf811b-b7e9-4b6f-8776-3d372e6a048b workflow_item_id=33085\colon; Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException\colon; 501 5.1.3 Invalid address
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```
|
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- The issue is not the named user above, but a member of the group...
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- And the group does have users with invalid email addresses (probably accounts created automatically after authenticating with LDAP):
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![DSpace group](/cgspace-notes/2021/04/group-invalid-email.png)
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- I extracted all the group IDs from recent logs that had users with invalid email addresses:
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```console
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$ grep -a -E 'email user group_id=\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' /home/cgspace.cgiar.org/log/dspace.log.* | grep -o -E '\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' | sort | uniq
|
||||
0a30d6ae-74a6-4eee-a8f5-ee5d15192ee6
|
||||
1769137c-36d4-42b2-8fec-60585e110db7
|
||||
203c8614-8a97-4ac8-9686-d9d62cb52acc
|
||||
294603de-3d09-464e-a5b0-09e452c6b5ab
|
||||
35878555-9623-4679-beb8-bb3395fdf26e
|
||||
3d8a5efa-5509-4bf9-9374-2bc714aceb99
|
||||
4238208a-f848-47cb-9dd2-43f9f954a4af
|
||||
44939b84-1894-41e7-b3e6-8c8d1781057b
|
||||
49ba087e-75a3-45ce-805c-69eeda0f786b
|
||||
4a6606ce-0284-421d-bf80-4dafddba2d42
|
||||
527de6aa-9cd0-4988-bf5f-c9c92ba2ac10
|
||||
54cd1b16-65bf-4041-9d84-fb2ea3301d6d
|
||||
58982847-5f7c-4b8b-a7b0-4d4de702136e
|
||||
5f0b85be-bd23-47de-927d-bca368fa1fbc
|
||||
646ada17-e4ef-49f6-9378-af7e58596ce1
|
||||
7e2f4bf8-fbc9-4b2f-97a4-75e5427bef90
|
||||
8029fd53-f9f5-4107-bfc3-8815507265cf
|
||||
81faa934-c602-4608-bf45-de91845dfea7
|
||||
8611a462-210c-4be1-a5bb-f87a065e6113
|
||||
8855c903-ef86-433c-b0be-c12300eb0f84
|
||||
8c7ece98-3598-4de7-a885-d61fd033bea8
|
||||
8c9a0d01-2d12-4a99-84f9-cdc25ac072f9
|
||||
8f9f888a-b501-41f3-a462-4da16150eebf
|
||||
94168f0e-9f45-4112-ac8d-3ba9be917842
|
||||
96998038-f381-47dc-8488-ff7252703627
|
||||
9768f4a8-3018-44e9-bf58-beba4296327c
|
||||
9a99e8d2-558e-4fc1-8011-e4411f658414
|
||||
a34e6400-78ed-45c0-a751-abc039eed2e6
|
||||
a9da5af3-4ec7-4a9b-becb-6e3d028d594d
|
||||
abf5201c-8be5-4dee-b461-132203dd51cb
|
||||
adb5658c-cef3-402f-87b6-b498f580351c
|
||||
aecf811b-b7e9-4b6f-8776-3d372e6a048b
|
||||
ba5aae61-ea34-4ac1-9490-4645acf2382f
|
||||
bf7f3638-c7c6-4a8f-893d-891a6d3dafff
|
||||
c617ada0-09d1-40ed-b479-1c4860a4f724
|
||||
cff91d44-a855-458c-89e5-bd48c17d1a54
|
||||
e65171ae-a2bf-4043-8f54-f8457bc9174b
|
||||
e7098b40-4701-4ca2-b9a9-3a1282f67044
|
||||
e904f122-71dc-439b-b877-313ef62486d7
|
||||
ede59734-adac-4c01-8691-b45f19088d37
|
||||
f88bd6bb-f93f-41cb-872f-ff26f6237068
|
||||
f985f5fb-be5c-430b-a8f1-cf86ae4fc49a
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fe800006-aaec-4f9e-9ab4-f9475b4cbdc3
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```
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## 2021-04-08
|
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- I can't believe it but the server has been down for twelve hours or so
|
||||
- The locks have not changed since I went to bed last night:
|
||||
|
||||
```console
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
12070
|
||||
```
|
||||
|
||||
- I restarted PostgreSQL and Tomcat and the locks go straight back up!
|
||||
|
||||
```console
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
13
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
986
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
1194
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
1212
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
1489
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
2124
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
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5934
|
||||
```
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## 2021-04-09
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- Atmire managed to get CGSpace back up by killing all the PostgreSQL connections yesterday
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- I don't know how they did it...
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- They also think it's weird that restarting PostgreSQL didn't kill the connections
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- They asked some more questions, like for example if there were also issues on DSpace Test
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- Strangely enough, I checked DSpace Test and notice a clear spike in PostgreSQL locks on the morning of April 6th as well!
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![PostgreSQL locks week CGSpace](/cgspace-notes/2021/04/postgres_locks_ALL-week-PROD.png)
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![PostgreSQL locks week DSpace Test](/cgspace-notes/2021/04/postgres_locks_ALL-week-TEST.png)
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- I definitely need to look into that!
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<!-- vim: set sw=2 ts=2: -->
|
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|
@ -24,7 +24,7 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
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<meta property="og:type" content="article" />
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||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-04/" />
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<meta property="article:published_time" content="2021-04-01T09:50:54+03:00" />
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<meta property="article:modified_time" content="2021-04-06T22:33:43+03:00" />
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<meta property="article:modified_time" content="2021-04-06T22:48:44+03:00" />
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@ -54,9 +54,9 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
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"@type": "BlogPosting",
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"headline": "April, 2021",
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||||
"url": "https://alanorth.github.io/cgspace-notes/2021-04/",
|
||||
"wordCount": "1824",
|
||||
"wordCount": "2530",
|
||||
"datePublished": "2021-04-01T09:50:54+03:00",
|
||||
"dateModified": "2021-04-06T22:33:43+03:00",
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||||
"dateModified": "2021-04-06T22:48:44+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -462,6 +462,143 @@ $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid =
|
||||
<li>All development is happening in <a href="https://github.com/ilri/openRXV">https://github.com/ilri/openRXV</a> now</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>10PM and the server is down again, with locks through the roof:</li>
|
||||
</ul>
|
||||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
12198
|
||||
</code></pre><ul>
|
||||
<li>I see that there are tons of PostgreSQL connections getting abandoned today, compared to very few in the past few weeks:</li>
|
||||
</ul>
|
||||
<pre><code class="language-console" data-lang="console">$ journalctl -u tomcat7 --since=today | grep -c 'ConnectionPool abandon'
|
||||
1838
|
||||
$ journalctl -u tomcat7 --since=2021-03-20 --until=2021-04-05 | grep -c 'ConnectionPool abandon'
|
||||
3
|
||||
</code></pre><ul>
|
||||
<li>I even restarted the server and connections were low for a few minutes until they shot back up:</li>
|
||||
</ul>
|
||||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
13
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
8651
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
8940
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
10504
|
||||
</code></pre><ul>
|
||||
<li>I had to go to bed and I bet it will crash and be down for hours until I wake up…</li>
|
||||
<li>What the hell is this user agent?</li>
|
||||
</ul>
|
||||
<pre><code>54.197.119.143 - - [06/Apr/2021:19:18:11 +0200] "GET /handle/10568/16499 HTTP/1.1" 499 0 "-" "GetUrl/1.0 wdestiny@umich.edu (Linux)"
|
||||
</code></pre><h2 id="2021-04-07">2021-04-07</h2>
|
||||
<ul>
|
||||
<li>CGSpace was still down from last night of course, with tons of database locks:</li>
|
||||
</ul>
|
||||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
12168
|
||||
</code></pre><ul>
|
||||
<li>I restarted the server again and the locks came back</li>
|
||||
<li>Atmire responded to the message from yesterday
|
||||
<ul>
|
||||
<li>The noticed something in the logs about emails failing to be sent</li>
|
||||
<li>There appears to be an issue sending mails on workflow tasks when a user in that group has an invalid email address:</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
<pre><code class="language-console" data-lang="console">2021-04-01 12:45:11,414 WARN org.dspace.workflowbasic.BasicWorkflowServiceImpl @ a.akwarandu@cgiar.org:session_id=2F20F20D4A8C36DB53D42DE45DFA3CCE:notifyGroupofTask:cannot email user group_id=aecf811b-b7e9-4b6f-8776-3d372e6a048b workflow_item_id=33085\colon; Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException\colon; 501 5.1.3 Invalid address
|
||||
</code></pre><ul>
|
||||
<li>The issue is not the named user above, but a member of the group…</li>
|
||||
<li>And the group does have users with invalid email addresses (probably accounts created automatically after authenticating with LDAP):</li>
|
||||
</ul>
|
||||
<p><img src="/cgspace-notes/2021/04/group-invalid-email.png" alt="DSpace group"></p>
|
||||
<ul>
|
||||
<li>I extracted all the group IDs from recent logs that had users with invalid email addresses:</li>
|
||||
</ul>
|
||||
<pre><code class="language-console" data-lang="console">$ grep -a -E 'email user group_id=\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' /home/cgspace.cgiar.org/log/dspace.log.* | grep -o -E '\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' | sort | uniq
|
||||
0a30d6ae-74a6-4eee-a8f5-ee5d15192ee6
|
||||
1769137c-36d4-42b2-8fec-60585e110db7
|
||||
203c8614-8a97-4ac8-9686-d9d62cb52acc
|
||||
294603de-3d09-464e-a5b0-09e452c6b5ab
|
||||
35878555-9623-4679-beb8-bb3395fdf26e
|
||||
3d8a5efa-5509-4bf9-9374-2bc714aceb99
|
||||
4238208a-f848-47cb-9dd2-43f9f954a4af
|
||||
44939b84-1894-41e7-b3e6-8c8d1781057b
|
||||
49ba087e-75a3-45ce-805c-69eeda0f786b
|
||||
4a6606ce-0284-421d-bf80-4dafddba2d42
|
||||
527de6aa-9cd0-4988-bf5f-c9c92ba2ac10
|
||||
54cd1b16-65bf-4041-9d84-fb2ea3301d6d
|
||||
58982847-5f7c-4b8b-a7b0-4d4de702136e
|
||||
5f0b85be-bd23-47de-927d-bca368fa1fbc
|
||||
646ada17-e4ef-49f6-9378-af7e58596ce1
|
||||
7e2f4bf8-fbc9-4b2f-97a4-75e5427bef90
|
||||
8029fd53-f9f5-4107-bfc3-8815507265cf
|
||||
81faa934-c602-4608-bf45-de91845dfea7
|
||||
8611a462-210c-4be1-a5bb-f87a065e6113
|
||||
8855c903-ef86-433c-b0be-c12300eb0f84
|
||||
8c7ece98-3598-4de7-a885-d61fd033bea8
|
||||
8c9a0d01-2d12-4a99-84f9-cdc25ac072f9
|
||||
8f9f888a-b501-41f3-a462-4da16150eebf
|
||||
94168f0e-9f45-4112-ac8d-3ba9be917842
|
||||
96998038-f381-47dc-8488-ff7252703627
|
||||
9768f4a8-3018-44e9-bf58-beba4296327c
|
||||
9a99e8d2-558e-4fc1-8011-e4411f658414
|
||||
a34e6400-78ed-45c0-a751-abc039eed2e6
|
||||
a9da5af3-4ec7-4a9b-becb-6e3d028d594d
|
||||
abf5201c-8be5-4dee-b461-132203dd51cb
|
||||
adb5658c-cef3-402f-87b6-b498f580351c
|
||||
aecf811b-b7e9-4b6f-8776-3d372e6a048b
|
||||
ba5aae61-ea34-4ac1-9490-4645acf2382f
|
||||
bf7f3638-c7c6-4a8f-893d-891a6d3dafff
|
||||
c617ada0-09d1-40ed-b479-1c4860a4f724
|
||||
cff91d44-a855-458c-89e5-bd48c17d1a54
|
||||
e65171ae-a2bf-4043-8f54-f8457bc9174b
|
||||
e7098b40-4701-4ca2-b9a9-3a1282f67044
|
||||
e904f122-71dc-439b-b877-313ef62486d7
|
||||
ede59734-adac-4c01-8691-b45f19088d37
|
||||
f88bd6bb-f93f-41cb-872f-ff26f6237068
|
||||
f985f5fb-be5c-430b-a8f1-cf86ae4fc49a
|
||||
fe800006-aaec-4f9e-9ab4-f9475b4cbdc3
|
||||
</code></pre><h2 id="2021-04-08">2021-04-08</h2>
|
||||
<ul>
|
||||
<li>I can’t believe it but the server has been down for twelve hours or so
|
||||
<ul>
|
||||
<li>The locks have not changed since I went to bed last night:</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
12070
|
||||
</code></pre><ul>
|
||||
<li>I restarted PostgreSQL and Tomcat and the locks go straight back up!</li>
|
||||
</ul>
|
||||
<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
13
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
986
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
1194
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
1212
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
1489
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
2124
|
||||
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
|
||||
5934
|
||||
</code></pre><h2 id="2021-04-09">2021-04-09</h2>
|
||||
<ul>
|
||||
<li>Atmire managed to get CGSpace back up by killing all the PostgreSQL connections yesterday
|
||||
<ul>
|
||||
<li>I don’t know how they did it…</li>
|
||||
<li>They also think it’s weird that restarting PostgreSQL didn’t kill the connections</li>
|
||||
<li>They asked some more questions, like for example if there were also issues on DSpace Test</li>
|
||||
<li>Strangely enough, I checked DSpace Test and notice a clear spike in PostgreSQL locks on the morning of April 6th as well!</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
<p><img src="/cgspace-notes/2021/04/postgres_locks_ALL-week-PROD.png" alt="PostgreSQL locks week CGSpace">
|
||||
<img src="/cgspace-notes/2021/04/postgres_locks_ALL-week-TEST.png" alt="PostgreSQL locks week DSpace Test"></p>
|
||||
<ul>
|
||||
<li>I definitely need to look into that!</li>
|
||||
</ul>
|
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|
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|
||||
|
||||
|
||||
|
@ -3,19 +3,19 @@
|
||||
xmlns:xhtml="http://www.w3.org/1999/xhtml">
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2021-04/</loc>
|
||||
<lastmod>2021-04-06T22:33:43+03:00</lastmod>
|
||||
<lastmod>2021-04-06T22:48:44+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
|
||||
<lastmod>2021-04-06T22:33:43+03:00</lastmod>
|
||||
<lastmod>2021-04-06T22:48:44+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2021-04-06T22:33:43+03:00</lastmod>
|
||||
<lastmod>2021-04-06T22:48:44+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||
<lastmod>2021-04-06T22:33:43+03:00</lastmod>
|
||||
<lastmod>2021-04-06T22:48:44+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||
<lastmod>2021-04-06T22:33:43+03:00</lastmod>
|
||||
<lastmod>2021-04-06T22:48:44+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2021-03/</loc>
|
||||
<lastmod>2021-04-05T19:36:44+03:00</lastmod>
|
||||
|
BIN
static/2021/04/group-invalid-email.png
Normal file
BIN
static/2021/04/group-invalid-email.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 90 KiB |
BIN
static/2021/04/postgres_locks_ALL-week-PROD.png
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BIN
static/2021/04/postgres_locks_ALL-week-PROD.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 11 KiB |
BIN
static/2021/04/postgres_locks_ALL-week-TEST.png
Normal file
BIN
static/2021/04/postgres_locks_ALL-week-TEST.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 9.7 KiB |
Loading…
Reference in New Issue
Block a user