Jabref: hangs if opening one of several files

[JoKalliauer]

JabRef version JabRef 5.0-beta.382--2020-01-28--0b53d4b on Ubuntu 18.04

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

Steps to reproduce the behavior:

1. Open watson.bib.txt in JabRef on Linux (can't reproduce on Windows)
2. click on the file-button of the entry
3. choose the second one
4. File opens (The file must exist, otherwise the problem does not occur)
5. Mouse moves, but clicking does not do anything and keyboard also does not interact, but computer sill runs e.g. Systemmonitor does still update graphics, but does not interact with input (all programms cummulated: 30% RAM-usage, ~5%CPU usage)
6. ssh to my PC, and kill JabRef
7. everything works again, JabRef gone. (25% RAM-usage, ~5%CPU usage)

[PorcelainMouse]

Symptoms sound like #5919 , except I don't understand the connection with this specific file.

[JoKalliauer]

JabRef 5.0-beta.407--2020-02-06--9407bef
Linux 4.15.0-87-generic amd64
Java 13.0.2

I just checked and "alt" "F4" works (pressing twize once for the LibreOffice/PDF-viewer and second for Jabref) and Print also works, but "Windows-Key"/"apple-Key"/"super-key" (don't know the name) did not work.

The error exists also with sudo swapoff -a (at least with the older version JabRef 5.0-beta.382--2020-01-28--0b53d4b )

[AEgit]

JabRef 5.0-beta.407--2020-02-06--9407bef
Linux 5.3.0-28-generic amd64
Java 13.0.2

I can confirm this issue for Linux. As far as I can tell, the problem arises when someone tries to open a file. It does not matter, what type of file - I have tried to use a different PDF and even a .txt file instead and it would still crash the application (though with the .txt file it might be necessary to use the context menu for the file (Right click -> Open) to trigger the crash).

In three cases, an error log file was generated. I am not sure, whether these error log files relate to the actual issue or whether they just show, that I had to shut down the whole system to get it back working, but in case they are useful, here they are:

Error log file 1:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fedce027ff6, pid=6375, tid=6428
#
# JRE version: OpenJDK Runtime Environment 
(Zulu13.29+9-CA) (13.0.2+6) (build 13.0.2+6-MTS)
# Java VM: OpenJDK 64-Bit Server VM (13.0.2+6-MTS, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# C  [libc.so.6+0x42ff6]
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   http://www.azulsystems.com/support/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  S U M M A R Y ------------

Command Line: -Djava.library.path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/lib/app:/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/bin -Djava.launcher.path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/bin --module-path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/lib/app/mods -Djdk.module.main=org.jabref org.jabref/org.jabref.JabRefLauncher

Host: Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz, 2 cores, 3G, Ubuntu 18.04.4 LTS
Time: Fri Feb  7 14:29:01 2020 EST elapsed time: 297 seconds (0d 0h 4m 57s)

---------------  T H R E A D  ---------------

Current thread (0x00007fed742c4000):  JavaThread "JavaFX Application Thread" [_thread_in_native, id=6428, stack(0x00007fed6c026000,0x00007fed6c127000)]

Stack: [0x00007fed6c026000,0x00007fed6c127000]

Error log file 2:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f014e0feff6, pid=2067, tid=2091
#
# JRE version: OpenJDK Runtime Environment 
(Zulu13.29+9-CA) (13.0.2+6) (build 13.0.2+6-MTS)
# Java VM: OpenJDK 64-Bit Server VM (13.0.2+6-MTS, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# C  [libc.so.6+0x42ff6]
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   http://www.azulsystems.com/support/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  S U M M A R Y ------------

Command Line: -Djava.library.path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/lib/app:/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/bin -Djava.launcher.path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/bin --module-path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/lib/app/mods -Djdk.module.main=org.jabref org.jabref/org.jabref.JabRefLauncher

Host: Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz, 2 cores, 3G, Ubuntu 18.04.4 LTS
Time: Fri Feb  7 14:34:11 2020 EST elapsed time: 105 seconds (0d 0h 1m 45s)

---------------  T H R E A D  ---------------

Current thread (0x00007f00ec2b8800):  JavaThread "JavaFX Application Thread" [_thread_in_native, id=2091, stack(0x00007f00d9330000,0x00007f00d9431000)]

Stack: [0x00007f00d9330000,0x00007f00d9431000],  sp=0x00007f00d942ef70,  free space=1019k
Native frames: (J=compiled Java code, A=aot compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libc.so.6+0x42ff6]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  com.sun.glass.ui.gtk.GtkApplication._runLoop(Ljava/lang/Runnable;Z)V+0 org.jabref.merged.module
j  com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Ljava/lang/Runnable;Z)V+7 org.jabref.merged.module
j  com.sun.glass.ui.gtk.GtkApplication$$Lambda$99.run()V+12 org.jabref.merged.module
j  java.lang.Thread.run()V+11 [email protected]
v  ~StubRoutines::call_stub

siginfo: si_signo: 11 (SIGSEGV), si_code: 128 (SI_KERNEL), si_addr: 0x0000000000000000

Register to memory mapping:

RAX=0x000fe029c99dc860 is an unknown value
RBX=0x0000000000000001 is an unknown value
RCX=0x0 is NULL
RDX=0x00007f014e4a7c9f: <offset 0x00000000003ebc9f> in /lib/x86_64-linux-gnu/libc.so.6 at 0x00007f014e0bc000
RSP=0x00007f00d942ef70 is pointing into the stack for thread: 0x00007f00ec2b8800
RBP=0x0000000000000001 is an unknown value
RSI=0x0000000000000001 is an unknown value
RDI=0x0000000000000007 is an unknown value
R8 =0x00007f014e4a98b0: <offset 0x00000000003ed8b0> in /lib/x86_64-linux-gnu/libc.so.6 at 0x00007f014e0bc000
R9 =0x00007f00d9430700 is pointing into the stack for thread: 0x00007f00ec2b8800
R10=0x000000000000005f is an unknown value
R11=0x0 is NULL
R12=0x00007f014e4a7718: <offset 0x00000000003eb718> in /lib/x86_64-linux-gnu/libc.so.6 at 0x00007f014e0bc000
R13=0x000000000000072f is an unknown value
R14=0x00007f014e4ac628: <offset 0x00000000003f0628> in /lib/x86_64-linux-gnu/libc.so.6 at 0x00007f014e0bc000
R15=0x00000000004e3480 points into unknown readable memory: 40 8c 4e 00 00 00 00 00


Registers:
RAX=0x000fe029c99dc860, RBX=0x0000000000000001, RCX=0x0000000000000000, RDX=0x00007f014e4a7c9f
RSP=0x00007f00d942ef70, RBP=0x0000000000000001, RSI=0x0000000000000001, RDI=0x0000000000000007
R8 =0x00007f014e4a98b0, R9 =0x00007f00d9430700, R10=0x000000000000005f, R11=0x0000000000000000
R12=0x00007f014e4a7718, R13=0x000000000000072f, R14=0x00007f014e4ac628, R15=0x00000000004e3480
RIP=0x00007f014e0feff6, EFLAGS=0x0000000000010206, CSGSFS=0x002b000000000033, ERR=0x0000000000000000
  TRAPNO=0x000000000000000d

Top of Stack: (sp=0x00007f00d942ef70)
0x00007f00d942ef70:   0000000000000000

Error log file 3:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fa792e52ff6, pid=2101, tid=2223
#
# JRE version: OpenJDK Runtime Environment 
(Zulu13.29+9-CA) (13.0.2+6) (build 13.0.2+6-MTS)
# Java VM: OpenJDK 64-Bit Server VM (13.0.2+6-MTS, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# C  [libc.so.6+0x42ff6]
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport %p %s %c %d %P" (or dumping to /home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/bin/core.2101)
#
# If you would like to submit a bug report, please visit:
#   http://www.azulsystems.com/support/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  S U M M A R Y ------------

Command Line: -Djava.library.path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/lib/app:/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/bin -Djava.launcher.path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/bin --module-path=/home/osboxes/Documents/Software/JabRef-5.0-portable_linux/JabRef/lib/app/mods -Djdk.module.main=org.jabref org.jabref/org.jabref.JabRefLauncher

Host: Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz, 2 cores, 3G, Ubuntu 18.04.4 LTS
Time: Fri Feb  7 15:01:18 2020 EST elapsed time: 388 seconds (0d 0h 6m 28s)

---------------  T H R E A D  ---------------

Current thread (0x00007fa75c0ba000):  JavaThread "XToolkt-Shutdown-Thread" [_thread_in_native, id=2223, stack(0x00007fa6c2efd000,0x00007fa6c2ffe000)]

Stack: [0x00007fa6c2efd000,0x00007fa6c2ffe000],  sp=0x00007fa6c2ffbd70,  free space=1019k
Native frames: (J=compiled Java code, A=aot compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libc.so.6+0x42ff6]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  sun.awt.X11.XlibWrapper.InternAtom(JLjava/lang/String;I)J+0 [email protected]
j  sun.awt.X11.XAtom.<init>(JLjava/lang/String;Z)V+31 [email protected]
j  sun.awt.X11.XAtom.<init>(JLjava/lang/String;)V+4 [email protected]
j  sun.awt.X11.XAtom.get(Ljava/lang/String;)Lsun/awt/X11/XAtom;+17 [email protected]
j  sun.awt.X11.XSystemTrayPeer.<clinit>()V+12 [email protected]
v  ~StubRoutines::call_stub
j  sun.awt.X11.XToolkit.lambda$init$1()V+0 [email protected]
j  sun.awt.X11.XToolkit$$Lambda$169.run()V+4 [email protected]
j  java.lang.Thread.run()V+11 [email protected]
v  ~StubRoutines::call_stub

siginfo: si_signo: 11 (SIGSEGV), si_code: 128 (SI_KERNEL), si_addr: 0x0000000000000000

Register to memory mapping:

RAX=0x000ff4f264556760 is an unknown value
RBX=0x0000000000000001 is an unknown value
RCX=0x0 is NULL
RDX=0x00007fa7931fbc9f: 

[Siedlerchr]

I just merged a fix regarding opening files. Should be fixed now in master.
Please wait some time until the new master is uploaded.-

[AEgit]

JabRef 5.0-beta.432--2020-02-19--c768697
Linux 5.3.0-40-generic amd64
Java 13.0.2

Cannot confirm for the current master version. If I right-click on a file, the context menu will open. If I then press "Open" to open the file, the application that opens the file will hang and has to be forcefully shut down.
Note, that this issue does not appear any more if the file is opened with a simple left-click. As far as I can tell, this problem only arises now, if right-click and the associated context menu are used to open a file.

[Siedlerchr]

Okay, thanks for the update. Will look into it. Might be that the context Menu calls another method which I oversaw.

[JoKalliauer]

JabRef 5.0-beta.436--2020-02-20--505fc74
Linux 4.15.0-89-generic amd64
Java 13.0.2

On my PC the example above seems to be solved/fixed. @Siedlerchr : Thanks

I consider the issues as solved (on my Ubuntu) and could be closed.

[ilippert]

JabRef 5.1--2020-07-20--9cd9390
Linux 5.7.8-200.fc32.x86_64 amd64
Java 14.0.2

open file (F4) works for me on Fedora Linux.

In my reading, this issue can be closed.

[AEgit]

JabRef 5.1--2020-07-20--9cd9390
Linux 5.4.0-42-generic amd64
Java 14.0.2

Hmmm, it does not crash for me anymore, but there are other issues:

1) Every time I try to open a PDF, a new window "Open with" opens, which asks me which application should be used to open the PDF. Given that the default PDF reader should be set in Ubuntu (if I doubleclick a PDF in the file manager, it will automatically open, without asking me which application to use), this appears to be an undesired behaviour. Could it be linked to some sort of interaction between Snap and then Gnome Filemanager?

2) F4 does not work for me, i. e. no file is being opened if I press F4. A leftclick, however, allows me to open a PDF (well, if first shows the windows mentioned in 1) and after I select the application it opens the PDF).