When I hit tensorboard in the terminal, I get the following error:
(anaconda3-2.4.1) [~/dev/python/deeplearning]$tensorboard --logdir=./data
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 1.8.17
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.17
Configured on: Wed Jul 5 10:32:52 CDT 2017
Configured by: [email protected]
Configure mode: production
Host system: i386-apple-darwin13.4.0
Uname information: Darwin atx-osx109-1.corp.continuum.io 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64
Byte sex: little-endian
Libraries: shared
Installation point: /Users/h7kayama/.pyenv/versions/anaconda3-2.4.1
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/clang ( Apple LLVM version 6.0 )
CFLAGS: -arch x86_64
H5_CFLAGS: -O3
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/Users/h7kayama/.pyenv/versions/anaconda3-2.4.1/include
Shared C Library: yes
Static C Library: no
Statically Linked Executables: no
LDFLAGS: -arch x86_64
H5_LDFLAGS:
AM_LDFLAGS: -L/Users/h7kayama/.pyenv/versions/anaconda3-2.4.1/lib
Extra libraries: -lpthread -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 6.0 )
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: yes
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...
Abort trap: 6
The cause is that the HDF5 version does not match.
Headers are 1.8.15, library is 1.8.17
Once you uninstall h5py,
(anaconda3-2.4.1) [~/dev/python/deeplearning]$pip uninstall h5py
Uninstalling h5py-2.5.0:
/Users/h7kayama/.pyenv/versions/anaconda3-2.4.1/lib/python3.5/site-packages/h5py
/Users/h7kayama/.pyenv/versions/anaconda3-2.4.1/lib/python3.5/site-packages/h5py-2.5.0-py3.5-macosx-10.5-x86_64.egg-info
Proceed (y/n)? y
Successfully uninstalled h5py-2.5.0
I installed h5py again and it was fixed.
(anaconda3-2.4.1) [~/dev/python/deeplearning]$pip install h5py
Collecting h5py
Downloading h5py-2.7.0-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.5MB)
100% |████████████████████████████████| 4.5MB 94kB/s
Requirement already satisfied: six in /Users/h7kayama/.pyenv/versions/anaconda3-2.4.1/lib/python3.5/site-packages (from h5py)
Requirement already satisfied: numpy>=1.7 in /Users/h7kayama/.pyenv/versions/anaconda3-2.4.1/lib/python3.5/site-packages (from h5py)
Installing collected packages: h5py
Successfully installed h5py-2.7.0
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