Warning! ***HDF5 library version mismatched error*** python pandas windows

Question

I'm using pandas/python to save a DataFrame in a HDFStore format. When I apply the my_data_frame.to_hdf(arguments...) command I have an error message:Warning! ***HDF5 library version mismatched error *** and my program is stopped.

I'm working on Windows 7 (64bits), using Python 3.5.2 :: Anaconda 4.1.1 (64-bit).

I've been reading about this error message and as it says it's a problem between the version of HDF5 installed on my computer and the one used by Anacondas. According this post, a simple "conda install -c anaconda hdf5=1.8.18" could resolve my problem but I'm still having the same message error.

Thanks for your help guys.

Here I put a complete log of the error:

    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 1.8.18
          SUMMARY OF THE HDF5 CONFIGURATION
          =================================

    General Information:
    -------------------
                       HDF5 Version: 1.8.18
                      Configured on: 2017-05-31
                      Configured by: NMake Makefiles
                     Configure mode: CMAKE 3.8.0
                        Host system: Windows-6.3.9600
                  Uname information: Windows
                           Byte sex: little-endian
                          Libraries:
                 Installation point: C:/bld/hdf5_1496269860661/_b_env/Library

    Compiling Options:
    ------------------
                   Compilation Mode: RELEASE
                         C Compiler: C:/Program Files (x86)/Microsoft Visual Studio
    14.0/VC/bin/amd64/cl.exe
                             CFLAGS: /DWIN32 /D_WINDOWS /W3
                          H5_CFLAGS:
                          AM_CFLAGS:
                           CPPFLAGS:
                        H5_CPPFLAGS:
                        AM_CPPFLAGS:
                   Shared C Library: YES
                   Static C Library: YES
      Statically Linked Executables: OFF
                            LDFLAGS: /machine:x64
                         AM_LDFLAGS:
                    Extra libraries: C:/bld/hdf5_1496269860661/_b_env/Library/lib/z.
    lib
                           Archiver:
                             Ranlib:
                  Debugged Packages:
                        API Tracing: OFF

    Languages:
    ----------
                            Fortran: OFF
                   Fortran Compiler:
              Fortran 2003 Compiler:
                      Fortran Flags:
                   H5 Fortran Flags:
                   AM Fortran Flags:
             Shared Fortran Library: YES
             Static Fortran Library: YES

                                C++: ON
                       C++ Compiler: C:/Program Files (x86)/Microsoft Visual Studio
    14.0/VC/bin/amd64/cl.exe
                          C++ Flags: /DWIN32 /D_WINDOWS /W3 /GR /EHsc
                       H5 C++ Flags:
                       AM C++ Flags:
                 Shared C++ Library: YES
                 Static C++ Library: YES

    Features:
    ---------
                      Parallel HDF5: OFF
                 High Level library: ON
                       Threadsafety: ON
                Default API Mapping: v18
     With Deprecated Public Symbols: ON
             I/O filters (external):  DEFLATE
                                MPE:
                         Direct VFD:
                            dmalloc:
    Clear file buffers before write: ON
               Using memory checker: OFF
             Function Stack Tracing: OFF
          Strict File Format Checks: OFF
       Optimization Instrumentation:

Solution 1

 Headers are 1.8.15, library is 1.8.18

Your error information shows, then, that you need install the 1.8.15 version.

conda install -c anaconda hdf5=1.8.15

Solution 2

Try to uninstall h5py module and install it again. This fixed it for me

1. pip uninstall h5py
2. pip install h5py

Solution 3

For some reason uninstalling with conda and then installing hdf5 again with conda is not working. However, if you use pip to uninstall and then conda to install hdf5, it's working.

So try:

pip uninstall hdf5
conda install hdf5

Solution 4

The only procedure that worked for me on macOS was to create a virtualenv:

virtualenv -p python3 myenv
. myenv/bin/activate
pip3 install h5py==1.10.4 # or whichever version you want

Absolutely nothing else worked!

You may need a brew install hdf5

github issue that did not help:

https://github.com/h5py/h5py/issues/1068

View more solutions

Comments

[Oscar Mike]

Thanks this worked! Is there a way to upgrade the Headers instead of downgrading the library?

[Sovm]

This worked, and NOT the accepted answer. I'm curious - why?

[VideoPac]

After searching for hours to a solution, this quick one worked for me. Thanks !!!

[a.t.]

The accepted answer also did not work for me, correctly downgrading/changing the version of the library to version of the the headers did not solve the problem. For me, pip uninstall h5py followed by conda install h5py worked.

[Cassova]

This didn't work for me. But the below answer about reinstalling h5py worked!

[khaverim]

ERROR: No matching distribution found for h5py==1.10.4 did you need a different version?..

[jtlz2]

@khaverim Maybe that version is no longer available via pip?