【问题标题】:HDF5 library version mismatched error with latest Tensorflow build for windows x64HDF5 库版本与 Windows x64 的最新 Tensorflow 版本不匹配错误
【发布时间】:2017-03-23 17:39:43
【问题描述】:

由于 Windows 的 Tensorflow 1.0.1 版本中仍然存在 bug,我安装了最新的夜间构建 tensorflow cpu

不幸的是,这个版本,现在内核由于不同的原因崩溃,我得到这个错误:

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

脚本在调用 tf.contrib.layers.convolution2d 时崩溃

我使用的是 Windows 10 x64,并且我已经安装了为其他库发布的所有可用更新

这里是我的安装包列表

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)

【问题讨论】:

    标签: python tensorflow conda


    【解决方案1】:

    您在 conda 环境中安装了 1.18.15 hdf5,Tensorflow 的某些依赖项具有更新的 hdf5 1.8.18header 文件。

    尝试将您的 conda hdf5 库 更新到更新的 1.8.18 或使用以下命令:

    set HDF5_DISABLE_VERSION_CHECK=2 
    

    这应该禁用警告,但不提供正确执行的任何保证,因此最好将 hdf5 库更新到相同的版本 1.8.18。

    【讨论】:

      【解决方案2】:

      我遇到了类似的错误消息:

      Headers are 1.10.3, library is 1.10.4
      

      尝试通过运行在 R 中安装“rhd5”时:

      BiocManager::install("rhdf5")
      

      我通过在 shell 中设置环境变量“HDF5_DISABLE_VERSION_CHECK”解决了这个问题:

      export HDF5_DISABLE_VERSION_CHECK=1
      

      然后再次进入R,继续安装rhdf5。

      【讨论】:

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