CGSpace Notes

2018-11-01

• Finalize AReS Phase I and Phase II ToRs
• Send a note about my dspace-statistics-api to the dspace-tech mailing list

2018-11-03

• Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage
• Today these are the top 10 IPs:

# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Nov/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
   1300 66.249.64.63
   1384 35.237.175.180
   1430 138.201.52.218
   1455 207.46.13.156
   1500 40.77.167.175
   1979 50.116.102.77
   2790 66.249.64.61
   3367 84.38.130.177
   4537 70.32.83.92
  22508 66.249.64.59

• The 66.249.64.x are definitely Google
• 70.32.83.92 is well known, probably CCAFS or something, as it’s only a few thousand requests and always to REST API
• 84.38.130.177 is some new IP in Latvia that is only hitting the XMLUI, using the following user agent:

Mozilla/5.0 (Windows NT 5.1) AppleWebKit/535.1 (KHTML, like Gecko) Chrome/14.0.792.0 Safari/535.1

• They at least seem to be re-using their Tomcat sessions:

$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=84.38.130.177' dspace.log.2018-11-03 | sort | uniq
342

• 50.116.102.77 is also a regular REST API user
• 40.77.167.175 and 207.46.13.156 seem to be Bing
• 138.201.52.218 seems to be on Hetzner in Germany, but is using this user agent:

Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:62.0) Gecko/20100101 Firefox/62.0

• And it doesn’t seem they are re-using their Tomcat sessions:

$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=138.201.52.218' dspace.log.2018-11-03 | sort | uniq
1243

• Ah, we’ve apparently seen this server exactly a year ago in 2017-11, making 40,000 requests in one day…
• I wonder if it’s worth adding them to the list of bots in the nginx config?

2018-10-01

• Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items
• I created a GitHub issue to track this #389, because I’m super busy in Nairobi right now

2018-09-02

• New PostgreSQL JDBC driver version 42.2.5
• I’ll update the DSpace role in our Ansible infrastructure playbooks and run the updated playbooks on CGSpace and DSpace Test
• Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month
• I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:

2018-08-01

• DSpace Test had crashed at some point yesterday morning and I see the following in dmesg:

[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB

• Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight
• From the DSpace log I see that eventually Solr stopped responding, so I guess the java process that was OOM killed above was Tomcat’s
• I’m not sure why Tomcat didn’t crash with an OutOfMemoryError…
• Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core
• The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes
• I ran all system updates on DSpace Test and rebooted it

2018-07-01

• I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:

$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace

• During the mvn package stage on the 5.8 branch I kept getting issues with java running out of memory:

There is insufficient memory for the Java Runtime Environment to continue.

2018-06-04

• Test the DSpace 5.8 module upgrades from Atmire (#378)
  • There seems to be a problem with the CUA and L&R versions in pom.xml because they are using SNAPSHOT and it doesn’t build
• I added the new CCAFS Phase II Project Tag PII-FP1_PACCA2 and merged it into the 5_x-prod branch (#379)
• I proofed and tested the ILRI author corrections that Peter sent back to me this week:

$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n

• I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in March, 2018
• Time to index ~70,000 items on CGSpace:

$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b                                  

real    74m42.646s
user    8m5.056s
sys     2m7.289s

2018-05-01

• I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
  • http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E
  • http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
• Then I reduced the JVM heap size from 6144 back to 5120m
• Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use

2018-04-01

• I tried to test something on DSpace Test but noticed that it’s down since god knows when
• Catalina logs at least show some memory errors yesterday:

2018-03-02

• Export a CSV of the IITA community metadata for Martin Mueller

2018-02-01

• Peter gave feedback on the dc.rights proof of concept that I had sent him last week
• We don’t need to distinguish between internal and external works, so that makes it just a simple list
• Yesterday I figured out how to monitor DSpace sessions using JMX
• I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01