Bug#1125167: vtk9: libucs crashes the JVM
jMaxR
jmax.red at zaclys.net
Sat Jan 10 00:25:25 GMT 2026
Package: vtk9
Version: 9.3.0+dfsg1-4+b1
Severity: normal
Dear Maintainer,
Running the VTK library via the Java JNI interface systematically causes the
JVM to crash.
The application I am developing uses the Debian packages libvtk9.3,
libvtk9-java, and openjdk-21-jdk.
It worked fine on the previous version of Debian, but I recently updated my
system to trixie and it no longer works. From what I understand, libvtk-java
requires openmpi40, which in turn requires libucx0. And it seems that the
problem lies in the latter package.
The error message is as follows:
[debian:622989:0:622995] Caught signal 11 (Erreur de segmentation: address not
mapped to object at address 0xc)
==== backtrace (tid: 622995) ====
0 /lib/x86_64-linux-gnu/libucs.so.0(ucs_handle_error+0x2bc) [0x7fb28555e64c]
1 /lib/x86_64-linux-gnu/libucs.so.0(+0x3182f) [0x7fb28555e82f]
2 /lib/x86_64-linux-gnu/libucs.so.0(+0x319fa) [0x7fb28555e9fa]
3 [0x7fb3444a7a05]
=================================
followed by the classic JVM crash message.
Sometimes the crash message is more verbose (see attached file).
I don't know if the problem is related to Debian packaging or upstream
sources.
But I recompiled the upstream sources without the OpenMPI option, and once I
linked again my application to this new VTK installation, the problem no
longer
occurs.
Best regards
JMaxR
-- System Information:
Debian Release: 13.2
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'stable-security'), (500,
'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.12.57+deb13-amd64 (SMP w/16 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages vtk9 depends on:
ii libc6 2.41-12
ii libgcc-s1 14.2.0-19
ii libstdc++6 14.2.0-19
ii libvtk9.3 9.3.0+dfsg1-4+b1
vtk9 recommends no packages.
Versions of packages vtk9 suggests:
pn vtk9-doc <none>
pn vtk9-examples <none>
-- no debconf information
-------------- next part --------------
[1767875411.147977] [debian:618682:0] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 8 was not set in ucs
[1767875411.148000] [debian:618682:1] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 8 was not set in ucs
[1767875411.148008] [debian:618682:1] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 1 was not set in ucs
[1767875411.148017] [debian:618682:2] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 11 was not set in ucs
[1767875411.148028] [debian:618682:0] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 1 was not set in ucs
[debian:618682:0:618727] Caught signal 11 (Erreur de segmentation: invalid permissions for mapped object at address 0x7f7ab3f9f000)
[debian:618682:2:618714] Caught signal 11 (Erreur de segmentation: invalid permissions for mapped object at address 0x7f7ab3f9f000)
[1767875411.148078] [debian:618682:0] spinlock.c:29 UCX WARN ucs_recursive_spinlock_destroy() failed: busy
[1767875411.148080] [debian:618682:2] spinlock.c:29 UCX WARN ucs_recursive_spinlock_destroy() failed: busy
[1767875411.148033] [debian:618682:3] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 8 was not set in ucs
[1767875411.148093] [debian:618682:3] spinlock.c:29 UCX WARN ucs_recursive_spinlock_destroy() failed: busy
[1767875411.148021] [debian:618682:1] spinlock.c:29 UCX WARN ucs_recursive_spinlock_destroy() failed: busy
[1767875411.148110] [debian:618682:3] spinlock.c:29 UCX WARN ucs_recursive_spinlock_destroy() failed: busy
[1767875411.148095] [debian:618682:4] debug.c:1300 UCX WARN ucs_debug_disable_signal: signal 8 was not set in ucs
[1767875411.148125] [debian:618682:1] spinlock.c:29 UCX WARN ucs_recursive_spinlock_destroy() failed: busy
[debian:618682:3:618723] Caught signal 11 (Erreur de segmentation: invalid permissions for mapped object at address 0x7f7ab3f9f000)
[debian:618682:1:618722] Caught signal 11 (Erreur de segmentation: invalid permissions for mapped object at address 0x7f7ab3f9f000)
[debian:618682:4:618726] Caught signal 11 (Erreur de segmentation: invalid permissions for mapped object at address 0x7f7ab3f9f000)
==== backtrace (tid: 618727) ====
0 /lib/x86_64-linux-gnu/libucs.so.0(ucs_handle_error+0x2bc) [0x7f79edbb464c]
1 /lib/x86_64-linux-gnu/libucs.so.0(+0x3182f) [0x7f79edbb482f]
2 /lib/x86_64-linux-gnu/libucs.so.0(+0x319fa) [0x7f79edbb49fa]
3 [0x7f7a948f31a0]
=================================
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f7a948f31a0 (sent by kill), pid=618682, tid=618727
#
# JRE version: OpenJDK Runtime Environment (21.0.9+10) (build 21.0.9+10-Debian-1deb13u1)
# Java VM: OpenJDK 64-Bit Server VM (21.0.9+10-Debian-1deb13u1, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64)
# Problematic frame:
# J 678 c1 java.util.concurrent.ForkJoinPool.scan(Ljava/util/concurrent/ForkJoinPool$WorkQueue;II)I java.base at 21.0.9 (263 bytes) @ 0x00007f7a948f31a0 [0x00007f7a948f2d20+0x0000000000000480]
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/lib/systemd/systemd-coredump %P %u %g %s %t %c %h %d %F" (or dumping to /home/redonnet/Recherche/Code/Tests/core.618682)
#
==== backtrace (tid: 618714) ====
0 /lib/x86_64-linux-gnu/libucs.so.0(ucs_handle_error+0x2bc) [0x7f79edbb464c]
1 /lib/x86_64-linux-gnu/libucs.so.0(+0x3182f) [0x7f79edbb482f]
2 /lib/x86_64-linux-gnu/libucs.so.0(+0x319fa) [0x7f79edbb49fa]
3 [0x7f7a948f31a0]
=================================
[thread 618714 also had an error]
# An error report file with more information is saved as:
# hs_err_pid618682.log
==== backtrace (tid: 618723) ====
0 /lib/x86_64-linux-gnu/libucs.so.0(ucs_handle_error+0x2bc) [0x7f79edbb464c]
1 /lib/x86_64-linux-gnu/libucs.so.0(+0x3182f) [0x7f79edbb482f]
2 /lib/x86_64-linux-gnu/libucs.so.0(+0x319fa) [0x7f79edbb49fa]
3 [0x7f7a948f31a0]
=================================
[thread 618723 also had an error]
==== backtrace (tid: 618722) ====
0 /lib/x86_64-linux-gnu/libucs.so.0(ucs_handle_error+0x2bc) [0x7f79edbb464c]
1 /lib/x86_64-linux-gnu/libucs.so.0(+0x3182f) [0x7f79edbb482f]
2 /lib/x86_64-linux-gnu/libucs.so.0(+0x319fa) [0x7f79edbb49fa]
3 [0x7f7a948f31a0]
=================================
[thread 618722 also had an error]
==== backtrace (tid: 618726) ====
0 /lib/x86_64-linux-gnu/libucs.so.0(ucs_handle_error+0x2bc) [0x7f79edbb464c]
1 /lib/x86_64-linux-gnu/libucs.so.0(+0x3182f) [0x7f79edbb482f]
2 /lib/x86_64-linux-gnu/libucs.so.0(+0x319fa) [0x7f79edbb49fa]
3 [0x7f7a948f31a0]
=================================
[thread 618726 also had an error]
[1,021s][warning][os] Loading hsdis library failed
#
# If you would like to submit a bug report, please visit:
# https://bugs.debian.org/openjdk-21
#
More information about the debian-science-maintainers
mailing list