cgspace-notes/content/posts/2015-12.md

+++
date = "2015-12-02T13:18:00+03:00"
author = "Alan Orth"
title = "December, 2015"
tags = ["Notes"]

+++
## 2015-12-02

- Replace `lzop` with `xz` in log compression cron jobs on DSpace Test—it uses less space:

```
# cd /home/dspacetest.cgiar.org/log
# ls -lh dspace.log.2015-11-18*
-rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
```

<!--more-->

- I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper
- Need to remember to go check if everything is ok in a few days and then change CGSpace
- CGSpace went down again (due to PostgreSQL idle connections of course)
- Current database settings for DSpace are `db.maxconnections = 30` and `db.maxidle = 8`, yet idle connections are exceeding this:

```
$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
39
```

- I restarted PostgreSQL and Tomcat and it's back
- On a related note of why CGSpace is so slow, I decided to finally try the `pgtune` script to tune the postgres settings:

```
# apt-get install pgtune
# pgtune -i /etc/postgresql/9.3/main/postgresql.conf -o postgresql.conf-pgtune
# mv /etc/postgresql/9.3/main/postgresql.conf /etc/postgresql/9.3/main/postgresql.conf.orig 
# mv postgresql.conf-pgtune /etc/postgresql/9.3/main/postgresql.conf
```

- It introduced the following new settings:

```
default_statistics_target = 50
maintenance_work_mem = 480MB
constraint_exclusion = on
checkpoint_completion_target = 0.9
effective_cache_size = 5632MB
work_mem = 48MB
wal_buffers = 8MB
checkpoint_segments = 16
shared_buffers = 1920MB
max_connections = 80
```

- Now I need to go read PostgreSQL docs about these options, and watch memory settings in munin etc
- For what it's worth, now the REST API should be faster (because of these PostgreSQL tweaks):

```
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.474
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
2.141
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.685
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.995
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.786
```

- Last week it was an average of 8 seconds... now this is 1/4 of that
- CCAFS noticed that one of their items displays only the Atmire statlets: https://cgspace.cgiar.org/handle/10568/42445

![CCAFS item](/cgspace-notes/2015/12/ccafs-item-no-metadata.png)

- The authorizations for the item are all public READ, and I don't see any errors in dspace.log when browsing that item
- I filed a ticket on Atmire's issue tracker
- I also filed a ticket on Atmire's issue tracker for the PostgreSQL stuff

## 2015-12-03

- CGSpace very slow, and monitoring emailing me to say its down, even though I can load the page (very slowly)
- Idle postgres connections look like this (with no change in DSpace db settings lately):

```
$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
29
```

- I restarted Tomcat and postgres...
- Atmire commented that we should raise the JVM heap size by ~500M, so it is now `-Xms3584m -Xmx3584m`
- We weren't out of heap yet, but it's probably fair enough that the DSpace 5 upgrade (and new Atmire modules) requires more memory so it's ok
- A possible side effect is that I see that the REST API is twice as fast for the request above now:

```
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.368
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.968
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.006
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.849
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.806
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.854
```

## 2015-12-05

- CGSpace has been up and down all day and REST API is completely unresponsive
- PostgreSQL idle connections are currently:

```
postgres@linode01:~$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
28
```

- I have reverted all the pgtune tweaks from the other day, as they didn't fix the stability issues, so I'd rather not have them introducing more variables into the equation
- The PostgreSQL stats from Munin all point to something database-related with the DSpace 5 upgrade around mid–late November

![PostgreSQL bgwriter (year)](/cgspace-notes/2015/12/postgres_bgwriter-year.png)
![PostgreSQL cache (year)](/cgspace-notes/2015/12/postgres_cache_cgspace-year.png)
![PostgreSQL locks (year)](/cgspace-notes/2015/12/postgres_locks_cgspace-year.png)
![PostgreSQL scans (year)](/cgspace-notes/2015/12/postgres_scans_cgspace-year.png)

## 2015-12-07

- Atmire sent [some fixes](https://github.com/ilri/DSpace/pull/161) to DSpace's REST API code that was leaving contexts open (causing the slow performance and database issues)
- After deploying the fix to CGSpace the REST API is consistently faster:

```
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.675
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.599
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.588
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.566
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.497
```

## 2015-12-08

- Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn't as good, but it's much faster and causes less IO/CPU load
- Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot's crawl rate to the "Let Google optimize" setting