CGSpace Notes

2018-12-01

• Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK
• I manually installed OpenJDK, then removed Oracle JDK, then re-ran the Ansible playbook to update all configuration files, etc
• Then I ran all system updates and restarted the server

2018-12-02

• I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week

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:

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