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 #
