HDF5 library version error - HDF5 ver 1.10.4
Solution 1
Maybe I am late, but I resolved this problem by upgrading hdf5 to 1.10.5.
On Windows 10, with anaconda you can do this:
conda install -c conda-forge hdf5=1.10.5
Solution 2
I'll leave this here, since it's a top stack thread for me without clear answer.
pip uninstall h5py
pip install h5py
If you are using conda to install tensorflow it installs h5py with 1.10.5 version and on top installs hdf5 1.10.4. Creating conflict that resolves after pip "juggling" since 1.10.4 satisfies the latest h5py.
Solution 3
I have the same problem with Windows 10. Here is what I did
Install some requirements for TensorFlow > 2.0 https://www.tensorflow.org/install/pip?lang
Create conda virtual environment:
conda create -n ai python==3.7.6
conda activate ai
conda install pandas matplotlib scikit-learn scrapy seaborn
conda install -c anaconda tensorflow
Solution 4
I had following same issue.
Warning! HDF5 library version mismatched error Headers are 1.10.4, library is 1.10.6
My solution is making another conda environment and do every conda w/ 'conda-forge'. Since hdf5 1.10.4 was installed with following command on my win10 PC w/ no GPU. Python is 3.7.10.
conda install tensorflow
By above command, 1.10.4 came with. So, I should have done following.
conda install conda-forge tensorflow
Then, 1.10.6 was installed. 'conda-forge' w/ conda install is highly recommended.
Mirko Piccolo
Building Engineer, coding with R and PHYTON is my passion and hobby. In the free-time I love do sport analytics and forecast. Proud 9gagger and motorbiker
Updated on June 05, 2022Comments
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Mirko Piccolo almost 2 years
I'm trying to import some packages with spyder (OS x64), Anaconda and pyton 3.x The error is pretty famous in the internet. The solution proposed is to match the version of the library 1.10.5 with the HDF5 (mine is 1.10.4)
The question is that I can't find HDF5 version 1.10.5 and, the other hand, cannot understand what I could downgrade.
At this link: https://anaconda.org/conda-forge/hdf5 seems exist version 1.10.5 but when I type in the prompt of anaconda
conda install -c conda-forge hdf5the version remain 1.10.4.Here the warning:
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 1.10.4, library is 1.10.5 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ HDF5 Version: 1.10.5 Configured on: 2019 Configured by: Visual Studio 15 2017 Win64 Host system: Windows.0.17763 Uname information: Windows Byte sex: little‑endian Installation point: C:/Program Files/HDF5 Compiling Options: ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ Build Mode: Debugging Symbols: Asserts: Profiling: Optimization Level: Linking Options: ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ Libraries: Statically Linked Executables: OFF LDFLAGS: /machine:x64 H5_LDFLAGS: AM_LDFLAGS: Extra libraries: Archiver: Ranlib: Languages: ‑‑‑‑‑‑‑‑‑‑ C: yes C Compiler: C:/Program Files (x86)/Microsoft Visual Studio/2017/Community/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x64/cl.exe 19.16.27027.1 CPPFLAGS: H5_CPPFLAGS: AM_CPPFLAGS: CFLAGS: /DWIN32 /D_WINDOWS /W3 H5_CFLAGS: AM_CFLAGS: Shared C Library: YES Static C Library: YES Fortran: OFF Fortran 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/2017/Community/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x64/cl.exe 19.16.27027.1 C++ Flags: /DWIN32 /D_WINDOWS /W3 /GR /EHsc H5 C++ Flags: AM C++ Flags: Shared C++ Library: YES Static C++ Library: YES JAVA: OFF JAVA Compiler: Features: ‑‑‑‑‑‑‑‑‑ Parallel HDF5: OFF Parallel Filtered Dataset Writes: Large Parallel I/O: High‑level library: ON Threadsafety: OFF Default API mapping: v110 With deprecated public symbols: ON I/O filters (external): DEFLATE DECODE ENCODE MPE: Direct VFD: dmalloc: Packages w/ extra debug output: API Tracing: OFF Using memory checker: OFF Memory allocation sanity checks: OFF Function Stack Tracing: OFF Strict File Format Checks: OFF Optimization Instrumentation: Bye...Here all the packages installed:
# packages in environment at C:\Users\Megaport\Anaconda3\envs\venv: # # Name Version Build Channel _py-xgboost-mutex 2.0 cpu_0 _tflow_select 2.3.0 mkl absl-py 0.8.0 pypi_0 pypi alabaster 0.7.12 py37_0 asn1crypto 0.24.0 py37_0 astor 0.8.0 pypi_0 pypi astroid 2.2.5 py37_0 atomicwrites 1.3.0 py37_1 attrs 19.1.0 py37_1 babel 2.7.0 py_0 backcall 0.1.0 py37_0 blas 1.0 mkl bleach 3.1.0 py37_0 ca-certificates 2019.5.15 1 certifi 2019.6.16 py37_1 cffi 1.12.3 py37h7a1dbc1_0 chardet 3.0.4 py37_1003 cloudpickle 1.2.1 py_0 colorama 0.4.1 py37_0 cryptography 2.7 py37h7a1dbc1_0 cycler 0.10.0 py37_0 decorator 4.4.0 py37_1 defusedxml 0.6.0 py_0 docutils 0.15.2 py37_0 entrypoints 0.3 py37_0 fastcache 1.1.0 py37he774522_0 freetype 2.9.1 ha9979f8_1 gast 0.2.2 pypi_0 pypi google-pasta 0.1.7 pypi_0 pypi grpcio 1.23.0 pypi_0 pypi h5py 2.10.0 pypi_0 pypi hdf5 1.10.4 h7ebc959_0 icc_rt 2019.0.0 h0cc432a_1 icu 58.2 ha66f8fd_1 idna 2.8 py37_0 imagesize 1.1.0 py37_0 importlib_metadata 0.19 py37_0 intel-openmp 2019.4 245 ipykernel 5.1.2 py37h39e3cac_0 ipython 7.8.0 py37h39e3cac_0 ipython_genutils 0.2.0 py37_0 isort 4.3.21 py37_0 jedi 0.15.1 py37_0 jinja2 2.10.1 py37_0 joblib 0.13.2 py37_0 jpeg 9b hb83a4c4_2 jsonschema 3.0.2 py37_0 jupyter_client 5.3.1 py_0 jupyter_core 4.5.0 py_0 keras 2.2.4 0 keras-applications 1.0.8 py_0 keras-base 2.2.4 py37_0 keras-preprocessing 1.1.0 py_1 keyring 18.0.0 py37_0 kiwisolver 1.1.0 py37ha925a31_0 lazy-object-proxy 1.4.2 py37he774522_0 libmklml 2019.0.5 0 libpng 1.6.37 h2a8f88b_0 libprotobuf 3.8.0 h7bd577a_0 libsodium 1.0.16 h9d3ae62_0 libxgboost 0.90 0 m2w64-gcc-libgfortran 5.3.0 6 m2w64-gcc-libs 5.3.0 7 m2w64-gcc-libs-core 5.3.0 7 m2w64-gmp 6.1.0 2 m2w64-libwinpthread-git 5.0.0.4634.697f757 2 markdown 3.1.1 py37_0 markupsafe 1.1.1 py37he774522_0 matplotlib 3.1.1 py37hc8f65d3_0 mccabe 0.6.1 py37_1 mistune 0.8.4 py37he774522_0 mkl 2019.4 245 mkl-service 2.0.2 py37he774522_0 mkl_fft 1.0.14 py37h14836fe_0 mkl_random 1.0.2 py37h343c172_0 more-itertools 7.2.0 py37_0 mpmath 1.1.0 py37_0 msys2-conda-epoch 20160418 1 nbconvert 5.5.0 py_0 nbformat 4.4.0 py37_0 numpy 1.17.2 pypi_0 pypi numpy-base 1.16.4 py37hc3f5095_0 numpydoc 0.9.1 py_0 openssl 1.1.1c he774522_1 opt-einsum 3.0.1 pypi_0 pypi packaging 19.1 py37_0 pandas 0.25.1 py37ha925a31_0 pandoc 2.2.3.2 0 pandocfilters 1.4.2 py37_1 parso 0.5.1 py_0 pickleshare 0.7.5 py37_0 pip 19.2.2 py37_0 pluggy 0.12.0 py_0 prompt_toolkit 2.0.9 py37_0 protobuf 3.9.1 pypi_0 pypi psutil 5.6.3 py37he774522_0 py 1.8.0 py37_0 py-xgboost 0.90 py37_0 py-xgboost-cpu 0.90 py37_0 pycodestyle 2.5.0 py37_0 pycparser 2.19 py37_0 pyflakes 2.1.1 py37_0 pygments 2.4.2 py_0 pylint 2.3.1 py37_0 pyopenssl 19.0.0 py37_0 pyparsing 2.4.2 py_0 pyqt 5.9.2 py37h6538335_2 pyreadline 2.1 py37_1 pyrsistent 0.14.11 py37he774522_0 pysocks 1.7.0 py37_0 pytest 5.0.1 py37_0 python 3.7.4 h5263a28_0 python-dateutil 2.8.0 py37_0 pytz 2019.2 py_0 pywin32 223 py37hfa6e2cd_1 pyyaml 5.1.2 py37he774522_0 pyzmq 18.1.0 py37ha925a31_0 qt 5.9.7 vc14h73c81de_0 qtawesome 0.5.7 py37_1 qtconsole 4.5.4 py_0 qtpy 1.9.0 py_0 requests 2.22.0 py37_0 rope 0.14.0 py_0 scikit-learn 0.21.2 py37h6288b17_0 scipy 1.3.1 py37h29ff71c_0 setuptools 41.2.0 pypi_0 pypi sip 4.19.8 py37h6538335_0 six 1.12.0 pypi_0 pypi snowballstemmer 1.9.0 py_0 sphinx 2.1.2 py_0 sphinxcontrib-applehelp 1.0.1 py_0 sphinxcontrib-devhelp 1.0.1 py_0 sphinxcontrib-htmlhelp 1.0.2 py_0 sphinxcontrib-jsmath 1.0.1 py_0 sphinxcontrib-qthelp 1.0.2 py_0 sphinxcontrib-serializinghtml 1.1.3 py_0 spyder 3.3.6 py37_0 spyder-kernels 0.5.1 py37_0 sqlite 3.29.0 he774522_0 sympy 1.4 py37_0 tb-nightly 1.15.0a20190806 pypi_0 pypi tensorboard 1.14.0 py37he3c9ec2_0 tensorflow 1.14.0 mkl_py37h7908ca0_0 tensorflow-base 1.14.0 mkl_py37ha978198_0 tensorflow-estimator 1.14.0 py_0 termcolor 1.1.0 pypi_0 pypi testpath 0.4.2 py37_0 tornado 6.0.3 py37he774522_0 traitlets 4.3.2 py37_0 urllib3 1.24.2 py37_0 vc 14.1 h0510ff6_4 vs2015_runtime 14.16.27012 hf0eaf9b_0 wcwidth 0.1.7 py37_0 webencodings 0.5.1 py37_1 werkzeug 0.15.6 pypi_0 pypi wheel 0.33.6 pypi_0 pypi win_inet_pton 1.1.0 py37_0 wincertstore 0.2 py37_0 wrapt 1.11.2 py37he774522_0 yaml 0.1.7 hc54c509_2 zeromq 4.3.1 h33f27b4_3 zipp 0.5.2 py_0 zlib 1.2.11 h62dcd97_3Anyway, I don't understand why in the prompt HDF5 is version 1.10.4 and in the warning, version of HDF5 is 1.10.5
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Jorvan almost 4 yearsMy friend, I've been all day trying to solve it. Tried almost everything, and then I found your answer and decided to give a shot. You don't imagine my relief when it worked. Thank you <3