SegFault when using jnius with numpy

This ticket is similar to https://github.com/numpy/numpy/issues/15691 As I am not sure where the issue exactly is - jnius or numpy? Using jnius+numpy causes issues in CentOS7 when python is installed with anaconda.

Reproducing code example:

I can reproduce this exactly with:

$ docker run --rm -it centos:7 /bin/bash
# yum install -y wget bzip2 which java-1.8.0-openjdk-devel
# wget https://repo.anaconda.com/miniconda/Miniconda3-4.7.12-Linux-x86_64.sh
# bash ./Miniconda3-4.7.12-Linux-x86_64.sh -b
# /root/miniconda3/bin/pip install pyjnius==1.2.1 numpy==1.17.4
# /root/miniconda3/bin/python
>>> import jnius
>>> import numpy as np
>>> tmp = np.linalg.inv(np.random.rand(24, 24))
Segmentation fault

Error message:

GDB Traceback for the SegFault:

(gdb) r
Starting program: /root/miniconda3/bin/python run.py
warning: Error disabling address space randomization: Operation not permitted
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Detaching after fork from child process 533.
Detaching after fork from child process 535.
Detaching after fork from child process 536.

Program received signal SIGSEGV, Segmentation fault.
0x00007f3026ee82b4 in ?? ()
Missing separate debuginfos, use: debuginfo-install glibc-2.17-260.el7_6.3.x86_64 java-1.8.0-openjdk-headless-1.8.0.242.b08-0.el7_7.x86_64
(gdb) bt
#0  0x00007f3026ee82b4 in ?? ()
#1  0x0000000000000246 in ?? ()
#2  0x00007f3026ee8160 in ?? ()
#3  0x00007f303829a6f8 in Abstract_VM_Version::_reserve_for_allocation_prefetch ()
   from /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-0.el7_7.x86_64/jre/lib/amd64/server/libjvm.so
#4  0x00007fff1187df20 in ?? ()
#5  0x00007f3037d804dd in VM_Version::get_processor_features() ()
   from /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-0.el7_7.x86_64/jre/lib/amd64/server/libjvm.so
Backtrace stopped: previous frame inner to this frame (corrupt stack?)
(gdb)

Numpy/Python version information:

• Numpy - 1.17.4
• Jnius - 1.2.1
• Python - 3.7.4 / Anaconda 4.7.12
• GCC - 7.3.0
• Linux x86-64 - CentOS 7

Note: It is reproducible on

• Anaconda 4.5.4 / Python 3.6.5 / GCC 7.2.0
• CentOS7’s yum python3 package (3.6.8) / GCC 4.8.5

It is not reproducible on MacOS.

[seberg]

Just to note that in https://github.com/numpy/numpy/issues/15691 we tracked it down to be probably related to threading. I.e. setting OMP_NUM_THREADS=1 which disables the threading in openblas (or MKL if that is used here) makes things pass. It would be nice to know whether this is more likely an issue with jnius, an issue with OpenBLAS, or a general clash without an easy solution.

[tshirtman]

built from source

>>> numpy.show_config()
blas_mkl_info:
  NOT AVAILABLE
blis_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
atlas_3_10_blas_threads_info:
  NOT AVAILABLE
atlas_3_10_blas_info:
  NOT AVAILABLE
atlas_blas_threads_info:
  NOT AVAILABLE
atlas_blas_info:
  NOT AVAILABLE
accelerate_info:
  NOT AVAILABLE
blas_info:
    libraries = ['blas', 'blas']
    library_dirs = ['/usr/lib/x86_64-linux-gnu']
    include_dirs = ['/usr/local/include', '/usr/include', '/home/gabriel/.virtualenvs/jnius37/include']
    language = c
    define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
    define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
    libraries = ['blas', 'blas']
    library_dirs = ['/usr/lib/x86_64-linux-gnu']
    include_dirs = ['/usr/local/include', '/usr/include', '/home/gabriel/.virtualenvs/jnius37/include']
    language = c
lapack_mkl_info:
  NOT AVAILABLE
openblas_lapack_info:
  NOT AVAILABLE
openblas_clapack_info:
  NOT AVAILABLE
flame_info:
  NOT AVAILABLE
atlas_3_10_threads_info:
  NOT AVAILABLE
atlas_3_10_info:
  NOT AVAILABLE
atlas_threads_info:
  NOT AVAILABLE
atlas_info:
  NOT AVAILABLE
lapack_info:
    libraries = ['lapack', 'lapack']
    library_dirs = ['/usr/lib/x86_64-linux-gnu']
    language = f77
lapack_opt_info:
    libraries = ['lapack', 'lapack', 'blas', 'blas']
    library_dirs = ['/usr/lib/x86_64-linux-gnu']
    language = c
    define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
    include_dirs = ['/usr/local/include', '/usr/include', '/home/gabriel/.virtualenvs/jnius37/include']

from wheel:

>>> numpy.show_config()
blas_mkl_info:
  NOT AVAILABLE
blis_info:
  NOT AVAILABLE
openblas_info:
    libraries = ['openblas', 'openblas']
    library_dirs = ['/usr/local/lib']
    language = c
    define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
    libraries = ['openblas', 'openblas']
    library_dirs = ['/usr/local/lib']
    language = c
    define_macros = [('HAVE_CBLAS', None)]
lapack_mkl_info:
  NOT AVAILABLE
openblas_lapack_info:
    libraries = ['openblas', 'openblas']
    library_dirs = ['/usr/local/lib']
    language = c
    define_macros = [('HAVE_CBLAS', None)]
lapack_opt_info:
    libraries = ['openblas', 'openblas']
    library_dirs = ['/usr/local/lib']
    language = c
    define_macros = [('HAVE_CBLAS', None)]