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thread is never joined, JabRef is kept open after closing #5862

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reox opened this issue Jan 23, 2020 · 3 comments
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thread is never joined, JabRef is kept open after closing #5862

reox opened this issue Jan 23, 2020 · 3 comments
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bug Confirmed bugs or reports that are very likely to be bugs os: linux

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@reox
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reox commented Jan 23, 2020

Similar to #4458, the JabRef executable is kept open after closing.
I started gdb and printed the current bt:

#0  0x00007f613f6e4fd7 in pthread_join () at /lib64/libpthread.so.0
#1  0x00007f613f4d4f4d in CallJavaMainInNewThread () at /home/reox/apps/JabRef/lib/runtime/lib/libjli.so
#2  0x00007f613f4d155d in ContinueInNewThread () at /home/reox/apps/JabRef/lib/runtime/lib/libjli.so
#3  0x00007f613f4d2b78 in JLI_Launch () at /home/reox/apps/JabRef/lib/runtime/lib/libjli.so
#4  0x00007f61467e737a in JavaLibrary::JavaVMCreate(unsigned long, char**) () at /home/reox/apps/JabRef/bin/../lib/libapplauncher.so
#5  0x00007f61467e53e2 in JavaVirtualMachine::launchVM(JavaOptions&, std::__cxx11::list<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&) () at /home/reox/apps/JabRef/bin/../lib/libapplauncher.so
#6  0x00007f61467e6804 in JavaVirtualMachine::StartJVM() () at /home/reox/apps/JabRef/bin/../lib/libapplauncher.so
#7  0x00007f61467e6f44 in RunVM() () at /home/reox/apps/JabRef/bin/../lib/libapplauncher.so
#8  0x00007f61467f9275 in start_launcher () at /home/reox/apps/JabRef/bin/../lib/libapplauncher.so
#9  0x0000000000401a3e in main ()

So it looks like that some thread is never exiting.
a killall JabRef seems to solve the issue.
I suspected that the autosave might have to do with it, but now that I disabled it, JabRef still does not close correctly.
Even after a few hours it is not closed (I noticed it as I had several instances open at the same time, where one was from the last day already)

JabRef 5.0-beta.360--2020-01-21--7ddfd9f
Linux 3.10.0-1062.1.1.el7.centos.plus.x86_64 amd64 
Java 13.0.2
@reox reox changed the title JabRef is kept open after closing thread is never joined, JabRef is kept open after closing Jan 23, 2020
@Siedlerchr Siedlerchr added bug Confirmed bugs or reports that are very likely to be bugs os: linux labels Jan 23, 2020
@Siedlerchr
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On Windows JabRef closes fine. So it might be only linux related somehow

@calixtus
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I sometimes see a similar behaviour in Windows, when launching JabRef with 'gradlew run', especially if I close JabRef quickly after running. Maybe related...

@tobiasdiez
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Reason is probably that

private final DelayTaskThrottler throttler;
is never shut down

Siedlerchr added a commit that referenced this issue Jan 26, 2020
# By Carl Christian Snethlage (9) and others
# Via Carl Christian Snethlage (5) and GitHub (1)
* upstream/master:
  Fixed Test
  Refactored constructors, PreferencesService and some minor improvements.
  Remove ampersand escape when writing to bib file (#5869)
  Fix #5862. It was indeed the throttler (at least it is working now for me) (#5868)
  duplicate query parameter removed (#5865)
  Minor refactoring, and changed comment
  forgotten l10n resources
  Minor visual adjustments
  Removed description, fixed ok button and added some minor improvements
  Moved GroupDescription-stuff to proper class
  Added hintTextFlow, some rewording and changed the hierarchicalContext RadioButtons to a ComboBox
  Converted GroupDialog to mvvm pattern

# Conflicts:
#	src/main/resources/l10n/JabRef_en.properties
Siedlerchr added a commit that referenced this issue Jan 30, 2020
* master: (297 commits)
  Replace link to Workspace set-up with new one (#5896)
  Fixes making paths of linked files relative (web urls will not be touched anymore) (#5879)
  Switch to our IntelliJ config (#5881)
  Bump unirest-java from 3.4.00 to 3.4.01 (#5874)
  Bump junit-vintage-engine from 5.5.2 to 5.6.0 (#5875)
  Bump checkstyle from 8.28 to 8.29 (#5876)
  Bump junit-jupiter from 5.5.2 to 5.6.0 (#5877)
  Bump junit-platform-launcher from 1.5.2 to 1.6.0 (#5878)
  Change \ to /
  Bump byte-buddy-parent from 1.10.6 to 1.10.7 (#5873)
  Fix opening pdf with okular in linux (#5253) (#5855)
  Fixed Test
  Refactored constructors, PreferencesService and some minor improvements.
  Remove ampersand escape when writing to bib file (#5869)
  Fix #5862. It was indeed the throttler (at least it is working now for me) (#5868)
  duplicate query parameter removed (#5865)
  New Crowdin translations (#5864)
  Minor refactoring, and changed comment
  Bump antlr4 from 4.7.2 to 4.8-1 (#5852)
  Reintroducing master table index column (#5844)
  ...
koppor pushed a commit that referenced this issue Feb 1, 2022
76f23a2 Fix the order for conference papers in APA styles (#5875)
5125c43 Fix bibliography date sorting (#5876)
873df06 Change order of publisher and publisher-place (#5874)
8066c66 Fix independent for BioScientific Review
9cc567e Add AMA brackets w 2 dependents (#5871)
c33dd24 Create medicine-publishing.csl (#5866)
9cb9cdb Fishery&wildlife journals: Remove publishers for articles (#5868)
fbd9165 Update universitatsmedizin-gottingen.csl (#5864)
c563f03 Update mla8 and mla9 (#5859)
98d6a03 [ASM] Add DOI for preprints. (#5862)
05e7071 Create current-neurology-aktualnosci-neurologiczne.csl (#5858)
78d771d Update journal-of-clinical-neurophysiology.csl (#5857)

git-subtree-dir: buildres/csl/csl-styles
git-subtree-split: 76f23a2
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