GDAL: HDF5 library version mismatched error

[kalefranz]

From @brendancol on June 23, 2016 21:7

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
          Configured on: Mon Apr  4 16:17:55 CDT 2016
          Configured by: ilan@atx-xserve-02.corp.continuum.io
         Configure mode: production
            Host system: i386-apple-darwin11.4.2
          Uname information: Darwin atx-xserve-02.corp.continuum.io 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
               Byte sex: little-endian
              Libraries: shared
         Installation point: /opt/anaconda1anaconda2anaconda3

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/clang ( Apple LLVM version 4.2 )
                         CFLAGS: -arch x86_64
                      H5_CFLAGS:  -O3
                      AM_CFLAGS:
                       CPPFLAGS:
                    H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:
               Shared C Library: yes
               Static C Library: no
  Statically Linked Executables: no
                        LDFLAGS: -arch x86_64
                     H5_LDFLAGS:
                     AM_LDFLAGS:
        Extra libraries: -lz -ldl -lm
               Archiver: ar
             Ranlib: ranlib
          Debugged Packages:
            API Tracing: no

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

                            C++: yes
                   C++ Compiler: /usr/bin/clang++ ( Apple LLVM version 4.2 )
                      C++ Flags: -arch x86_64
                   H5 C++ Flags:  -O3
                   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...

Copied from original issue: conda/conda#2844

[marscher]

confirmed on Linux x86-64, Py27, same hdf5 lib.

[yeganer]

Any progress on this issue? I just got the same error message with the same versions.

For me the error is confusing as both pandas and h5py allow me to interact with files without a problem but pyne=0.5 produced this crash.

[szq0214]

@yeganer You need to update your h5py. conda install h5py solves my problem.