Your message dated Thu, 7 May 2026 00:41:52 +0200
with message-id <E1wKkwC-00000007f73-2kGl@sandy>
and subject line Re: Bug#1125167: vtk9: libucs crashes the JVM
has caused the Debian Bug report #1125167,
regarding vtk9: libucs crashes the JVM
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1125167: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1125167
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
[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
[email protected] (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
#
--- End Message ---
--- Begin Message ---
This libucs error has been resolved.
Testing it revealed an issue linking the java wrapper to the python (the
matplotlib plugin)
but this is logged in Bug#1128859, so we can close this java/libucs bug now.
--- End Message ---
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