Ubuntu
octave package

octave-cli crashed with SIGSEGV in __GI___sigtimedwait()

Bug #1958716 reported by Norbert
10
This bug affects 1 person
Affects Status Importance Assigned to Milestone
intel-mkl (Ubuntu)
New
Medium
Unassigned
octave (Ubuntu)
New
Undecided
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Bug Description

$ octave-cli --eval __run_test_suite__

Integrated test scripts:

  liboctave/array/Array.cc-tst ................................... pass 21/21
  liboctave/array/CMatrix.cc-tst ................................. pass 9/11
                                                                   FAIL 2
  liboctave/array/CSparse.cc-tst ................................. pass 10/10
  liboctave/array/Sparse.cc-tst .................................. pass 107/107
  liboctave/array/dMatrix.cc-tst ................................. pass 10/10
  liboctave/array/dSparse.cc-tst ................................. pass 12/12
  liboctave/array/fCMatrix.cc-tst ................................fatal: caught signal Segmentation fault -- stopping myself...
Segmentation fault (core dumped)

---

Octave does not work with Intel MKL;

$ dpkg -l | grep mkl
ii intel-mkl:amd64 2020.4.304-2 amd64 Intel® Math Kernel Library (Intel® MKL)
ii intel-mkl-cluster:amd64 2020.4.304-2 amd64 Intel® Math Kernel Library (Intel® MKL) (Cluster)
ii intel-mkl-doc 2020.4.304-2 all Intel® Math Kernel Library (Intel® MKL) (Doc)
ii intel-mkl-full:amd64 2020.4.304-2 amd64 Intel® Math Kernel Library (Intel® MKL) (Full)
ii libmkl-avx:amd64 2020.4.304-2 amd64 Intel® MKL: Kernel library for Intel® AVX enabled processors
ii libmkl-avx2:amd64 2020.4.304-2 amd64 Intel® MKL: Kernel library for Intel® AVX2 enabled processors
ii libmkl-avx512:amd64 2020.4.304-2 amd64 Intel® MKL: Kernel library for Intel® AVX-512 enabled processors
ii libmkl-avx512-mic:amd64 2020.4.304-2 amd64 Intel® MKL : Kernel library for Intel® AVX-512 Xeon Phi processors
ii libmkl-blacs-intelmpi-ilp64:amd64 2020.4.304-2 amd64 Intel® MKL : ILP64 BLACS routines for Intel® MPI and MPICH2+
ii libmkl-blacs-intelmpi-lp64:amd64 2020.4.304-2 amd64 Intel® MKL : LP64 BLACS routines for Intel® MPI and MPICH2+
ii libmkl-blacs-openmpi-ilp64:amd64 2020.4.304-2 amd64 Intel® MKL : ILP64 version of BLACS routines for Open MPI
ii libmkl-blacs-openmpi-lp64:amd64 2020.4.304-2 amd64 Intel® MKL : LP64 version of BLACS routines for Open MPI
ii libmkl-blacs-sgimpt-ilp64:amd64 2020.4.304-2 amd64 Intel® MKL : ILP64 version of BLACS routines for SGI MPT
ii libmkl-blacs-sgimpt-lp64:amd64 2020.4.304-2 amd64 Intel® MKL : LP64 version of BLACS routines for SGI MPI Toolkit
ii libmkl-cdft-core:amd64 2020.4.304-2 amd64 Intel® MKL : Cluster version of FFT functions
ii libmkl-computational-dev:amd64 2020.4.304-2 amd64 Static libs of intel-MKL: Computational Layer
ii libmkl-core:amd64 2020.4.304-2 amd64 Intel® MKL: Library dispatcher of Computational Layer
ii libmkl-def:amd64 2020.4.304-2 amd64 Intel® MKL: Default kernel library
ii libmkl-dev:amd64 2020.4.304-2 amd64 Intel® Math Kernel Library (Intel® MKL) (Dev)
ii libmkl-full-dev 2020.4.304-2 amd64 Intel® Math Kernel Library (Intel® MKL) (Full Version Dev)
ii libmkl-gf-ilp64:amd64 2020.4.304-2 amd64 Intel® MKL: ILP64 interface library for the GNU Fortran compilers
ii libmkl-gf-lp64:amd64 2020.4.304-2 amd64 Intel® MKL: LP64 interface library for the GNU Fortran compilers
ii libmkl-gnu-thread:amd64 2020.4.304-2 amd64 Intel® MKL: OpenMP threading library for GNU Fortran/C compilers
ii libmkl-intel-ilp64:amd64 2020.4.304-2 amd64 Intel® MKL: ILP64 interface library for the Intel compilers
ii libmkl-intel-lp64:amd64 2020.4.304-2 amd64 Intel® MKL: LP64 interface library for the Intel compilers
ii libmkl-intel-thread:amd64 2020.4.304-2 amd64 Intel® MKL: OpenMP threading library for the Intel compilers
ii libmkl-interface-dev:amd64 2020.4.304-2 amd64 Static libs of intel-MKL: Interface Layer
ii libmkl-locale 2020.4.304-2 amd64 Intel MKL: Locale Files Used by All Shared Objects
ii libmkl-mc:amd64 2020.4.304-2 amd64 Intel® MKL: Kernel library for Intel® SSSE3 enabled processors
ii libmkl-mc3:amd64 2020.4.304-2 amd64 Intel® MKL: Kernel library for Intel® SSE4.2 enabled processors
ii libmkl-meta-cluster:amd64 2020.4.304-2 amd64 Metapackage for Intel-MKL: Shared Object for Cluster
ii libmkl-meta-computational:amd64 2020.4.304-2 amd64 Metapackage of intel-MKL: Shared Objects for Computaional Layer
ii libmkl-meta-interface:amd64 2020.4.304-2 amd64 Metapackage of intel-MKL: Shared Objects of Interface Layer
ii libmkl-meta-threading:amd64 2020.4.304-2 amd64 Metapackage of intel-MKL: Shared Objects of Threading Layer
ii libmkl-pgi-thread:amd64 2020.4.304-2 amd64 Intel® MKL: OpenMP threading library for the PGI compiler
ii libmkl-rt:amd64 2020.4.304-2 amd64 Intel® MKL: Single Dynamic Library (SDL)
ii libmkl-scalapack-ilp64:amd64 2020.4.304-2 amd64 Intel® MKL : ScaLAPACK routine library supporting ILP64 interface
ii libmkl-scalapack-lp64:amd64 2020.4.304-2 amd64 Intel® MKL : ScaLAPACK routine library supporting LP64 interface
ii libmkl-sequential:amd64 2020.4.304-2 amd64 Intel® MKL: Sequential library
ii libmkl-tbb-thread:amd64 2020.4.304-2 amd64 Intel® MKL: Intel TBB threading library for the Intel compilers
ii libmkl-threading-dev:amd64 2020.4.304-2 amd64 Static libs of intel-MKL: Threading Layer
ii libmkl-vml-avx:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF optimized for Intel® AVX enabled processors
ii libmkl-vml-avx2:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF optimized for Intel® AVX2 enabled processors
ii libmkl-vml-avx512:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF optimized for AVX-512 on Xeon® processors
ii libmkl-vml-avx512-mic:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF optimized for AVX-512 on Xeon Phi™ processors
ii libmkl-vml-cmpt:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF for conditional numerical reproducibility
ii libmkl-vml-def:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF part of default kernels
ii libmkl-vml-mc:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF for Intel® SSSE3 enabled processors
ii libmkl-vml-mc2:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF for 45nm Hi-k Core2 and Xeon processor
ii libmkl-vml-mc3:amd64 2020.4.304-2 amd64 Intel® MKL : VM/VS/DF for Intel® SSE4.2 enabled processors

ProblemType: Crash
DistroRelease: Ubuntu 22.04
Package: octave 6.2.0-1
ProcVersionSignature: Ubuntu 5.13.0-19.19-generic 5.13.14
Uname: Linux 5.13.0-19-generic x86_64
ApportVersion: 2.20.11-0ubuntu75
Architecture: amd64
CasperMD5CheckResult: pass
CurrentDesktop: MATE
Date: Sat Jan 22 17:13:20 2022
ExecutablePath: /usr/bin/octave-cli
InstallationDate: Installed on 2022-01-15 (6 days ago)
InstallationMedia: Ubuntu-MATE 22.04 LTS "Jammy Jellyfish" - Alpha amd64 (20220115)
ProcCmdline: octave-cli
RebootRequiredPkgs: Error: path contained symlinks.
Signal: 11
SourcePackage: octave
StacktraceTop:
 __GI___sigtimedwait (set=set@entry=0x7f7ec983be00, info=info@entry=0x7f7eb9d02940, timeout=timeout@entry=0x0) at ../sysdeps/unix/sysv/linux/sigtimedwait.c:61
 __GI___sigwait (set=0x7f7ec983be00, sig=0x7f7eb9d029f4) at ../sysdeps/unix/sysv/linux/sigwait.c:28
 ?? () from /lib/x86_64-linux-gnu/liboctave.so.8
 start_thread (arg=<optimized out>) at pthread_create.c:435
 clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:100
Title: octave-cli crashed with SIGSEGV in __GI___sigtimedwait()
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm cdrom dip lpadmin lxd plugdev sambashare sudo
separator:

Revision history for this message
Norbert (nrbrtx) wrote :
information type: Private → Public
Revision history for this message
Norbert (nrbrtx) wrote :

$ export MKL_THREADING_LAYER=gnu
$ octave-cli --eval __run_test_suite__

Integrated test scripts:

  liboctave/array/Array.cc-tst ................................... pass 21/21
  liboctave/array/CMatrix.cc-tst .................................fatal: caught signal Segmentation fault -- stopping myself...
Segmentation fault (core dumped)

Does not help.

Revision history for this message
Apport retracing service (apport) wrote :

StacktraceTop:
 __GI___sigtimedwait (set=set@entry=0x7f7ec983be00 <sigmask>, info=info@entry=0x7f7eb9d02940, timeout=timeout@entry=0x0) at ../sysdeps/unix/sysv/linux/sigtimedwait.c:61
 __GI___sigwait (set=set@entry=0x7f7ec983be00 <sigmask>, sig=sig@entry=0x7f7eb9d029f4) at ../sysdeps/unix/sysv/linux/sigwait.c:28
 signal_watcher (arg=0x7f7eca5eca30 <octave::generic_sig_handler(int)>) at liboctave/wrappers/signal-wrappers.c:697
 start_thread (arg=<optimized out>) at pthread_create.c:435
 clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:100

tags: removed: need-amd64-retrace
Revision history for this message
Apport retracing service (apport) wrote : Stacktrace.txt
Revision history for this message
Apport retracing service (apport) wrote : StacktraceSource.txt
Revision history for this message
Apport retracing service (apport) wrote : ThreadStacktrace.txt
Changed in intel-mkl (Ubuntu):
importance: Undecided → Medium
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