CGSpace Notes

December, 2015

Posted on
#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

CCAFS item

  • 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