HDF5 library version mismatched error with latest Tensorflow build for windows x64

Question

Due to a bug still present in Tensorflow 1.0.1 release for windows I have installed the latest nightly build tensorflow cpu

Unfortunately with this version, now kernel crashes for a different reason and I get this 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'.
Headers are 1.8.15, library is 1.8.18
      SUMMARY OF THE HDF5 CONFIGURATION
      =================================

General Information:
-------------------
                   HDF5 Version: 1.8.18
                  Configured on: 2017-03-06
                  Configured by: Visual Studio 14 2015 Win64
                 Configure mode: CMAKE 3.7.2
                    Host system: Windows-10.0.14393
              Uname information: Windows
                       Byte sex: little-endian
                      Libraries:
             Installation point: C:/Program Files/HDF5

Compiling Options:
------------------
               Compilation Mode:
                     C Compiler: C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/bin/x86_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: X:inclib-vc14-x64/zlib.lib;X:/inclib-vc14-x64/libsz.lib;X:/inclib-vc14-x64/libaec.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/x86_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: OFF
            Default API Mapping: v18
 With Deprecated Public Symbols: ON
         I/O filters (external):  DEFLATE DECODE ENCODE
                            MPE:
                     Direct VFD:
                        dmalloc:
Clear file buffers before write: ON
           Using memory checker: OFF
         Function Stack Tracing: OFF
      Strict File Format Checks: OFF

The script crashes whentf.contrib.layers.convolution2d is invoked

I'm using windows 10 x64 and I have installed all available update released for the others libraries

Here the list of packages of my setup

alabaster (0.7.10)
anaconda-clean (1.0)
anaconda-client (1.6.2)
anaconda-navigator (1.5)
anaconda-project (0.4.1)
appdirs (1.4.3)
argcomplete (1.8.2)
asn1crypto (0.22.0)
astroid (1.4.9)
astropy (1.3.1)
Babel (2.3.4)
backports.shutil-get-terminal-size (1.0.0)
beautifulsoup4 (4.5.3)
bitarray (0.8.1)
blaze (0.10.1)
bleach (2.0.0)
bokeh (0.12.4)
boto (2.46.1)
Bottleneck (1.2.0)
cffi (1.10.0)
chardet (2.3.0)
chest (0.2.3)
click (6.7)
cloudpickle (0.2.2)
clyent (1.2.2)
colorama (0.3.7)
comtypes (1.1.3)
conda (4.3.14)
conda-build (2.1.7)
conda-verify (2.0.0)
configobj (5.0.6)
contextlib2 (0.5.4)
cryptography (1.8.1)
cycler (0.10.0)
Cython (0.25.2)
cytoolz (0.8.2)
dask (0.14.1)
datashape (0.5.4)
decorator (4.0.11)
dill (0.2.6)
docutils (0.13.1)
dynd (c328ab7)
entrypoints (0.2.2)
et-xmlfile (1.0.1)
fastcache (1.0.2)
filelock (2.0.7)
Flask (0.12)
Flask-Cors (3.0.2)
gevent (1.2.1)
glue-core (0.10.1)
glue-vispy-viewers (0.7.2)
glueviz (0.10.1)
greenlet (0.4.12)
h5py (2.7.0)
HeapDict (1.0.0)
html5lib (0.999999999)
idna (2.5)
imagesize (0.7.1)
ipykernel (4.5.2)
ipython (5.3.0)
ipython-genutils (0.2.0)
ipywidgets (6.0.0)
isort (4.2.5)
itsdangerous (0.24)
jdcal (1.3)
jedi (0.10.0)
Jinja2 (2.9.5)
jsonschema (2.6.0)
jupyter (1.0.0)
jupyter-client (5.0.0)
jupyter-console (5.1.0)
jupyter-core (4.3.0)
lazy-object-proxy (1.2.2)
llvmlite (0.16.0)
locket (0.2.0)
lxml (3.7.3)
MarkupSafe (1.0)
matplotlib (2.0.0)
mccabe (0.6.1)
menuinst (1.4.4)
mistune (0.7.4)
mpmath (0.19)
multipledispatch (0.4.9)
nb-anacondacloud (1.2.0)
nb-conda (2.0.0)
nb-conda-kernels (2.0.0)
nbconvert (5.1.1)
nbformat (4.3.0)
nbpresent (3.0.2)
networkx (1.11)
nltk (3.2.2)
nose (1.3.7)
notebook (4.4.1)
numba (0.31.0)
numexpr (2.6.2)
numpy (1.12.1)
numpydoc (0.6.0)
odo (0.5.0)
olefile (0.44)
opencv-python (3.2.0.6)
openpyxl (2.4.5)
packaging (16.8)
pandas (0.19.2)
pandocfilters (1.4.1)
partd (0.3.7)
path.py (10.1)
pathlib2 (2.2.1)
patsy (0.4.1)
pep8 (1.7.0)
pickleshare (0.7.4)
Pillow (4.0.0)
pip (9.0.1)
pkginfo (1.4.1)
ply (3.10)
prompt-toolkit (1.0.13)
protobuf (3.2.0)
psutil (5.2.0)
py (1.4.33)
pyasn1 (0.2.3)
pycosat (0.6.2)
pycparser (2.17)
pycrypto (2.6.1)
pycurl (7.43.0)
pyflakes (1.5.0)
Pygments (2.2.0)
pylint (1.6.5)
PyOpenGL (3.1.0)
pyOpenSSL (16.2.0)
pyparsing (2.2.0)
pyreadline (2.1)
pytest (3.0.7)
python-dateutil (2.6.0)
pytz (2016.10)
pywin32 (220)
PyYAML (3.12)
pyzmq (16.0.2)
QtAwesome (0.4.4)
qtconsole (4.2.1)
QtPy (1.2.1)
requests (2.13.0)
rope-py3k (0.9.4.post1)
scikit-image (0.12.3)
scikit-learn (0.18.1)
scipy (0.19.0)
seaborn (0.7.1)
setuptools (34.3.2)
simplegeneric (0.8.1)
singledispatch (3.4.0.3)
six (1.10.0)
snowballstemmer (1.2.1)
sockjs-tornado (1.0.3)
Sphinx (1.5.3)
spyder (3.1.3)
SQLAlchemy (1.1.6)
statsmodels (0.8.0)
sympy (1.0)
tables (3.3.0)
tensorflow (1.0.1)
testpath (0.3)
toolz (0.8.2)
tornado (4.4.2)
traitlets (4.3.2)
unicodecsv (0.14.1)
wcwidth (0.1.7)
webencodings (0.5)
Werkzeug (0.12.1)
wheel (0.29.0)
widgetsnbextension (2.0.0)
win-unicode-console (0.5)
wrapt (1.10.10)
xlrd (1.0.0)
XlsxWriter (0.9.6)
xlwings (0.10.4)
xlwt (1.2.0)

Answer 1

You have 1.18.15 hdf5 library installed in conda environment , some dependency of Tensorflow has newer hdf5 1.8.18 header files.

Try to update your conda hdf5 library to newer 1.8.18 or alternatively use the command:

set HDF5_DISABLE_VERSION_CHECK=2 

This should disable the warning but doesn't offer any warranty of correct execution, so It's better to update hdf5 library to the same version 1.8.18.

Answer 2

I ran into a similar error message like:

Headers are 1.10.3, library is 1.10.4

while trying to install 'rhd5' in R by running:

BiocManager::install("rhdf5")

And I solved it by setting the environment variable "HDF5_DISABLE_VERSION_CHECK" within the shell:

export HDF5_DISABLE_VERSION_CHECK=1

And then enter into R again and went on with the rhdf5 installation.