2019-01-02
- Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning
I don’t see anything interesting in the web server logs around that time though:
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
92 40.77.167.4
99 210.7.29.100
120 38.126.157.45
177 35.237.175.180
177 40.77.167.32
216 66.249.75.219
225 18.203.76.93
261 46.101.86.248
357 207.46.13.1
903 54.70.40.11
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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
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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:
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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
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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:
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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
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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.
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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
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2018-05-01
- I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
- 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
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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:
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