CGSpace 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
  

• 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

• 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

2015-12-07

• Atmire sent some fixes 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