JabRef freezing completely

[j0hannes]

JabRef version 5.0 dev

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

Steps to reproduce the behavior:

1. Open JabRef
2. Click on File > Open

JabRef freezes and won't react to anything. Closing the application via Ctrl+C is not possible. After killing it, a zombie process remains in the process table.

When restarting the application afterwards, it will silently exit (see log).

end of strace log when starting again

stat("/opt/JabRef/lib/runtime/lib/server/libjvm.so", {st_mode=S_IFREG|0644, st_size=21224120, ...}) = 0
openat(AT_FDCWD, "/opt/JabRef/lib/runtime/lib/server/libjvm.so", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0@\317(\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0644, st_size=21224120, ...}) = 0
mmap(NULL, 23865440, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f01d5414000
mprotect(0x7f01d674e000, 2097152, PROT_NONE) = 0
mmap(0x7f01d694e000, 1064960, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x133a000) = 0x7f01d694e000
mmap(0x7f01d6a52000, 542816, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f01d6a52000
close(3)                                = 0
mprotect(0x7f01d694e000, 819200, PROT_READ) = 0
getpid()                                = 68382
getpid()                                = 68382
mmap(NULL, 1052672, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS|MAP_STACK, -1, 0) = 0x7f01d5313000
clone(child_stack=0x7f01d5412fb0, flags=CLONE_VM|CLONE_FS|CLONE_FILES|CLONE_SIGHAND|CLONE_THREAD|CLONE_SYSVSEM|CLONE_SETTLS|CLONE_PARENT_SETTID|CLONE_CHILD_CLEARTID, parent_tid=[68383], tls=0x7f01d5413700, child_tidptr=0x7f01d54139d0) = 68383
futex(0x7f01d54139d0, FUTEX_WAIT, 68383, NULLERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...

(JabRef:68382): Gdk-WARNING **: 13:42:59.381: XSetErrorHandler() called with a GDK error trap pushed. Don't do that.
) = 0
munmap(0x7f01d6cee000, 2163720)         = 0
munmap(0x7f01d6f21000, 1198144)         = 0
futex(0x7f0150047198, FUTEX_WAKE_PRIVATE, 2147483647) = 1
futex(0x7f0150047148, FUTEX_WAKE_PRIVATE, 1) = 1
futex(0x7f013bebe9d0, FUTEX_WAIT, 68423, NULL) = -1 EAGAIN (Resource temporarily unavailable)
futex(0x7f015000aed8, FUTEX_WAKE_PRIVATE, 2147483647) = 1
futex(0x7f015000ae88, FUTEX_WAKE_PRIVATE, 1) = 1
munmap(0x7f01c66d2000, 160619379)       = 0
close(3)                                = 0
getpid()                                = 68382
exit_group(0)                           = ?
+++ exited with 0 +++  ```
</details>

[j0hannes]

I could nail it down to a problem with the underlying file system. JabRef tried to list the directory that it had used last. That directory was on a virtual filesystem which was unresponsive at that time, so the application became a zombie process after being killing.