HDF5 library and header mismatch error

Question

I am using Anaconda on Ubuntu x64. When I run a simple python program, I get this error message and a [python] kernel dump. I have seen other questions with similar problems, but all the answers I see don't resolve my issue. I have tried removing and reinstalling h5py with both pip and conda, but I get the same error:

idf@DellInsp:~/Documents/Projects/python3$ python3 testtables.py 

With this code inside testtables.py

import tables
tables.test()


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:    3.2.2
HDF5 version:        1.8.11
NumPy version:       1.10.1
Numexpr version:     2.4.4 (not using Intel's VML/MKL)
Zlib version:        1.2.8 (in Python interpreter)
Blosc version:       1.4.4 (2015-05-05)
Blosc compressors:   blosclz (1.0.2.1), lz4 (1.2.0), lz4hc (1.2.0), snappy (1.1.1), zlib (1.2.8)
Cython version:      0.23.4
Python version:      3.5.0 |Anaconda 2.4.0 (64-bit)| (default, Oct 19 2015, 21:57:25) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
Platform:            Linux-3.19.0-39-lowlatency-x86_64-with-debian-jessie-sid
Byte-ordering:       little
Detected cores:      4
Default encoding:    utf-8
Default FS encoding: utf-8
Default locale:      (en_US, UTF-8)
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the --heavy flag to this script
(or set the 'heavy' parameter in case you are using tables.test() call).
The whole suite will take more than 4 hours to complete on a relatively
modern CPU and around 512 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
/home/idf/anaconda3/lib/python3.5/site-packages/tables/filters.py:292: FiltersWarning: compression library ``bzip2`` is not available; using ``zlib`` instead
  % (complib, default_complib), FiltersWarning)
/home/idf/anaconda3/lib/python3.5/site-packages/tables/filters.py:292: FiltersWarning: compression library ``lzo`` is not available; using ``zlib`` instead
  % (complib, default_complib), FiltersWarning)
/home/idf/anaconda3/lib/python3.5/site-packages/tables/atom.py:570: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
  for arg in inspect.getargspec(self.__init__)[0]
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 1.8.11, library is 1.8.15
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
           HDF5 Version: 1.8.15-patch1
          Configured on: Wed Oct 14 16:46:37 CDT 2015
          Configured by: ilan@centos5x64.corp.continuum.io
         Configure mode: production
            Host system: x86_64-unknown-linux-gnu
          Uname information: Linux centos5x64.corp.continuum.io 2.6.18-400.1.1.el5 #1 SMP Thu Dec 18 00:59:53 EST 2014 x86_64 x86_64 x86_64 GNU/Linux
               Byte sex: little-endian
              Libraries: shared
         Installation point: /home/ilan/minonda/envs/_build

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )
                         CFLAGS: 
                      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 -Wno-long-long -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 -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -O3 -fomit-frame-pointer -finline-functions
                      AM_CFLAGS: 
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_DEFAULT_SOURCE -D_BSD_SOURCE -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: no
  Statically Linked Executables: no
                        LDFLAGS: 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
        Extra libraries: -lrt -lz -ldl -lm 
               Archiver: ar
             Ranlib: ranlib
          Debugged Packages: 
            API Tracing: no

Languages:
----------
                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/bin/g++ ( g++ (GCC) 4.1.2 20080704 )
                      C++ Flags: 
                   H5 C++ Flags:  
                   AM C++ Flags: 
             Shared C++ Library: yes
             Static C++ Library: no

Features:
---------
                  Parallel HDF5: no
             High Level library: yes
                   Threadsafety: no
            Default API Mapping: v18
 With Deprecated Public Symbols: yes
         I/O filters (external): deflate(zlib)
                            MPE: no
                     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)
idf@DellInsp:~/Documents/Projects/python3$ 

Answer 1

After trying several options, an uninstall followed by re-install solved the problem:

pip uninstall h5py
pip install h5py

Answer 2

I had this same error as well. I was trying to use the default debian package libhdf5-dev. I would encourage debi / pip to update. You have to find the proper version here: https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.15-patch1/src/ and build it from source. once you have it

tar -xvf hdf5-1.8.15-patch1
cd hdf5-1.8.15-patch1
./configure --prefix=/usr/local/hdf5 
make
make check
make install
make check-install
pip install h5py

Please note, this can be done with other versions of hdf5 as well. This is just the one that corresponds to the version from the pip repositories.

Answer 3

I removed then installed version the latest version of Anaconda. This resolved this issues.