jabref does not shut down (on Linux); process keeps running

[ilippert]

• Mandatory: I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists

JabRef 5.1--2020-05-29--ed275b6
Linux 5.6.14-300.fc32.x86_64 amd64
Java 14.0.1

Not on every run, but often, shutting down jabref does not cleanly proceed. A process continues to run for many minutes. Maybe related to #5071 ?

If you give me pointers for how to investigate this further, I am happy to do.

[ilippert]

This continues to be a problem with the recent builds.

CPU use is 50-60%. Far too high, slows down the system.

Processes continue to run even for hours

[ilippert]

JabRef 5.1--2020-06-08--b810356
Linux 5.6.16-300.fc32.x86_64 amd64
Java 14.0.1

Issue is still present - Jabref hangs my system... no error messages.

[ilippert]

Sorry, it is really quite terrible - jabref simply does not shut down - a process continues to run and slow down my computer. no error messages.

[Siedlerchr]

Seems to be some linux issue, I cannot reproduce it on Windows. Maybe some file watching is still in the background active?

[ilippert]

thanks for reacting. It is running for hours, literally... it must have been introduced, I assume, at some point before 2020-05-29--ed275b6. I am not aware of a change of my file system.

now
JabRef 5.1--2020-06-17--ef0a6bb
Linux 5.6.18-300.fc32.x86_64 amd64
Java 14.0.1

ok, I am testing systematically for some minutes:

• 3 minutes running with 1 file. no problem to shut down, CPU at around 2-10%
• 10 minutes running with 2 files. no problem to shut down, CPU at around 2-10%
• 3 minutes running with 3 files. problem to shut down, CPU at 50%. files in different folders
• 3 minutes running with 3 files. no problem to shut down, CPU at around 2-10% files in different folders
• 3 minutes running with 3 files. problem to shut down, CPU at 95%. I had to kill it. files in different folders
• 3 minutes running with 3 files. problem to shut down, CPU at 34%. I had to kill it. files in different folders
• 10 minutes running with 2 files. no problem to shut down, CPU at around 2-10%
• 5 minutes running with 3 files. no problem to shut down, CPU at around 2-10%. files in same folder.
• 30 minutes running with 2 files. no problem to shut down, CPU between 2-60% files in different folders

Hmm, I do not see any pattern.

[sanjayankur31]

I also see this on Fedora 32:

jabref-5.0.50001-1.x86_64

Often when I've closed Jabref, processes are still running:

3969481 /opt/jabref/bin/JabRef

I haven't tried the dev builds yet. I can collect more info if someone can tell me what info is needed.

[Siedlerchr]

Try a kill -QUIT <pid> to get thread dump from the jvm

Alternatively
You could try to use jconsole: https://docs.oracle.com/en/java/javase/14/management/using-jconsole.html#GUID-EFDD2B40-6E4B-45E9-84B2-5E6D609065AE
Or you could try jstack to get a thread dump.
https://programmer.ink/think/jdk14-performance-management-tool-introduction-to-jstack.html

[ilippert]

kill -QUIT <pid> does not generate any visible result; process is not killed.

Just to check: for jstack and jconsole - do I need to download jdk14 from oracle?

[Siedlerchr]

You need jdk 14, you can use the openjdk variant.
https://bell-sw.com/pages/downloads/

[ilippert]

Hi, please find the jstack -l -e output in the txt file

jstack-jabref.txt

[Siedlerchr]

Thanks, that looks indeed helpful. It is somehow related to the search and to the recent implementation of the authors parser #6552
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