Core dumped after loading h5py

[Peter Leitner]

Hello,

I wonder if anyone experienced the same problem as I did: out of the sudden my python programs loading the h5py module no longer worked. After debugging I found that it happens exactly when loading h5py
>>> import h5py
I get some cryptical error message in the terminal (printed below) and in the Spyder IDE it simply says:
"It seems the kernel died unexpectedly. Use 'Restart kernel' to continue using this console."

Now since my programs worked like a charm so far I suspected my regular system updates to be responsible. However downgrading again from python3-h5py-2.5.0... to 2.4 did not remedy the problem. The report saying a clash between hdf5 header files and hdf5 library is responsible (see below) does not help me much, since I don't install hdf5 header files or the library separately - since this was taken care of automatically by the opensuse setup tool yast, which as so often immediately after system upgrades does not load either. For that reason I would probably need some terminal-based install command for the latest hdf5 library and hdf5 header files, so that they match again. Unfortunately, I did not find such in the hdf5 web documentation.

Has anyone got the same error causing python3 to abort and/or does anyone know what could be done? (I'm afraid this is problem is opensuse-specific and not occurring in other distributions but I might be wrong due to lack of experience). Any help is appreciated! Thank you very much!

Kind regards, Peter



>>> import h5py
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.15, library is 1.8.16
            SUMMARY OF THE HDF5 CONFIGURATION
            =================================

General Information:
-------------------
                   HDF5 Version: 1.8.16
                 Configure mode: production
                    Host system: x86_64-suse-linux-gnu
                       Byte sex: little-endian
                      Libraries: static, shared
             Installation point: /usr/lib64/mpi/gcc/openmpi

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/lib64/mpi/gcc/openmpi/bin/mpicc
                         CFLAGS: -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g
                      H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wc99-c11-compat -O3 -fstdarg-opt
                      AM_CFLAGS:
                       CPPFLAGS:
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE
               Shared C Library: yes
               Static C Library: yes
  Statically Linked Executables: no
                        LDFLAGS:
                     H5_LDFLAGS:
                     AM_LDFLAGS:
                Extra libraries: -lpthread -lz -ldl -lm
                       Archiver: ar
                         Ranlib: ranlib
              Debugged Packages:
                    API Tracing: no

Languages:
----------
                        Fortran: yes
               Fortran Compiler: /usr/lib64/mpi/gcc/openmpi/bin/mpif90 ( Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,java,ada,go --enable-checking=release --with-gxx-include-dir=/usr/include/c++/5 --enable-ssp --disable-libssp --disable-libvtv --enable-libmpx --disable-plugin --with-bugurl=http://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --disable-libgcj --with-slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable-libstdcxx-allocator=new --disable-libstdcxx-pch --enable-version-specific-runtime-libs --enable-linker-build-id --enable-linux-futex --program-suffix=-5 --without-system-libunwind --enable-multilib --with-arch-32=x86-64 --with-tune=generic --build=x86_64-suse-linux --host=x86_64-suse-linux built with gcc version 5.3.1 20151207 [gcc-5-branch revision 231355] (SUSE Linux))
          Fortran 2003 Compiler: yes
                  Fortran Flags:
               H5 Fortran Flags: 
               AM Fortran Flags:
         Shared Fortran Library: yes
         Static Fortran Library: yes

                            C++: no

Features:
---------
                  Parallel HDF5: yes
             High Level library: yes
                   Threadsafety: yes
            Default API Mapping: v18
 With Deprecated Public Symbols: yes
         I/O filters (external): deflate(zlib)
                            MPE:
                     Direct VFD: no
                        dmalloc: no
Clear file buffers before write: yes
           Using memory checker: no
         Function Stack Tracing: no
      Strict File Format Checks: no
   Optimization Instrumentation: no
Bye...
Aborted (core dumped)

[Peter Leitner]

Thank you - problem solved, found a way to downgrade hdf5-libs without using the yast setup tool.

[Hayu Nur Mahron]

Thank you - problem solved, found a way to downgrade hdf5-libs without using the yast setup tool.

Hi Leitner, what did you do to make it solved? I've this problem too. Thanks!