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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
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< meta name = "twitter:title" content = "December, 2015" / >
< meta name = "twitter:description" content = "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
2019-05-05 15:45:12 +02:00
2018-02-11 17:28:23 +01:00
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< h1 class = "blog-title" > < a href = "https://alanorth.github.io/cgspace-notes/" rel = "home" > CGSpace Notes< / a > < / h1 >
< p class = "lead blog-description" > Documenting day-to-day work on the < a href = "https://cgspace.cgiar.org" > CGSpace< / a > repository.< / p >
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< h2 class = "blog-post-title" > < a href = "https://alanorth.github.io/cgspace-notes/2015-12/" > December, 2015< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2015-12-02T13:18:00+03:00" > Wed Dec 02, 2015< / time > by Alan Orth in
< i class = "fa fa-tag" aria-hidden = "true" > < / i > < a href = "/cgspace-notes/tags/notes" rel = "tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2015-12-02" > 2015-12-02< / h2 >
< ul >
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< li > < p > Replace < code > lzop< / code > with < code > xz< / code > in log compression cron jobs on DSpace Test—it uses less space:< / p >
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< pre > < code > # 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
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< / code > < / pre > < / li >
< / ul >
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< ul >
< li > I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper< / li >
< li > Need to remember to go check if everything is ok in a few days and then change CGSpace< / li >
< li > CGSpace went down again (due to PostgreSQL idle connections of course)< / li >
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< li > < p > Current database settings for DSpace are < code > db.maxconnections = 30< / code > and < code > db.maxidle = 8< / code > , yet idle connections are exceeding this:< / p >
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< pre > < code > $ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
39
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< / code > < / pre > < / li >
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< li > < p > I restarted PostgreSQL and Tomcat and it’ s back< / p > < / li >
< li > < p > On a related note of why CGSpace is so slow, I decided to finally try the < code > pgtune< / code > script to tune the postgres settings:< / p >
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< pre > < code > # 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
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< / code > < / pre > < / li >
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< li > < p > It introduced the following new settings:< / p >
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< pre > < code > 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
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< / code > < / pre > < / li >
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< li > < p > Now I need to go read PostgreSQL docs about these options, and watch memory settings in munin etc< / p > < / li >
< li > < p > For what it’ s worth, now the REST API should be faster (because of these PostgreSQL tweaks):< / p >
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< pre > < code > $ 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
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< / code > < / pre > < / li >
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< li > < p > Last week it was an average of 8 seconds… now this is < sup > 1< / sup > ⁄ < sub > 4< / sub > of that< / p > < / li >
< li > < p > CCAFS noticed that one of their items displays only the Atmire statlets: < a href = "https://cgspace.cgiar.org/handle/10568/42445" > https://cgspace.cgiar.org/handle/10568/42445< / a > < / p > < / li >
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< / ul >
< p > < img src = "/cgspace-notes/2015/12/ccafs-item-no-metadata.png" alt = "CCAFS item" / > < / p >
< ul >
< li > The authorizations for the item are all public READ, and I don’ t see any errors in dspace.log when browsing that item< / li >
< li > I filed a ticket on Atmire’ s issue tracker< / li >
< li > I also filed a ticket on Atmire’ s issue tracker for the PostgreSQL stuff< / li >
< / ul >
< h2 id = "2015-12-03" > 2015-12-03< / h2 >
< ul >
< li > CGSpace very slow, and monitoring emailing me to say its down, even though I can load the page (very slowly)< / li >
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< li > < p > Idle postgres connections look like this (with no change in DSpace db settings lately):< / p >
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< pre > < code > $ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
29
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< / code > < / pre > < / li >
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< li > < p > I restarted Tomcat and postgres… < / p > < / li >
< li > < p > Atmire commented that we should raise the JVM heap size by ~500M, so it is now < code > -Xms3584m -Xmx3584m< / code > < / p > < / li >
< li > < p > 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< / p > < / li >
< li > < p > A possible side effect is that I see that the REST API is twice as fast for the request above now:< / p >
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< pre > < code > $ 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
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< / code > < / pre > < / li >
< / ul >
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< h2 id = "2015-12-05" > 2015-12-05< / h2 >
< ul >
< li > CGSpace has been up and down all day and REST API is completely unresponsive< / li >
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< li > < p > PostgreSQL idle connections are currently:< / p >
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< pre > < code > postgres@linode01:~$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
28
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< / code > < / pre > < / li >
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< li > < p > 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< / p > < / li >
< li > < p > The PostgreSQL stats from Munin all point to something database-related with the DSpace 5 upgrade around mid– < / p > < / li >
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< / ul >
< p > < img src = "/cgspace-notes/2015/12/postgres_bgwriter-year.png" alt = "PostgreSQL bgwriter (year)" / >
< img src = "/cgspace-notes/2015/12/postgres_cache_cgspace-year.png" alt = "PostgreSQL cache (year)" / >
< img src = "/cgspace-notes/2015/12/postgres_locks_cgspace-year.png" alt = "PostgreSQL locks (year)" / >
< img src = "/cgspace-notes/2015/12/postgres_scans_cgspace-year.png" alt = "PostgreSQL scans (year)" / > < / p >
< h2 id = "2015-12-07" > 2015-12-07< / h2 >
< ul >
< li > Atmire sent < a href = "https://github.com/ilri/DSpace/pull/161" > some fixes< / a > to DSpace’ s REST API code that was leaving contexts open (causing the slow performance and database issues)< / li >
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< li > < p > After deploying the fix to CGSpace the REST API is consistently faster:< / p >
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< pre > < code > $ 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
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< / code > < / pre > < / li >
< / ul >
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< h2 id = "2015-12-08" > 2015-12-08< / h2 >
< ul >
< li > 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< / li >
< li > 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< / li >
< / ul >
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< h4 > Recent Posts< / h4 >
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< li > < a href = "/cgspace-notes/2019-05/" > May, 2019< / a > < / li >
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< li > < a href = "/cgspace-notes/posts/" > Posts< / a > < / li >
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< li > < a href = "/cgspace-notes/2019-05/" > May, 2019< / a > < / li >
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< li > < a href = "/cgspace-notes/2019-04/" > April, 2019< / a > < / li >
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< li > < a href = "/cgspace-notes/2019-03/" > March, 2019< / a > < / li >
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< h4 > Links< / h4 >
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< li > < a href = "https://cgspace.cgiar.org" > CGSpace< / a > < / li >
< li > < a href = "https://dspacetest.cgiar.org" > DSpace Test< / a > < / li >
< li > < a href = "https://github.com/ilri/DSpace" > CGSpace @ GitHub< / a > < / li >
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