HDF5报错：HDF5 library version mismatched error
报错信息
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: 2019-03-04
Configured by: Visual Studio 14 2015 Win64
Host system: Windows-10.0.17763
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
14.0/VC/bin/x86_amd64/cl.exe 19.0.24218.1
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
14.0/VC/bin/x86_amd64/cl.exe 19.0.24218.1
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...
报错原因
HDF5库版本不匹配，python环境中HDF5版本为1.10.4；HDF5库版本为1.10.5。
解决方法
-
安装版本匹配的HDF5库（1.10.4），并修改LD_LIBRARY_PATH，使其指向匹配版本；
-
修改python环境中hdf5版本，conda update hdf5=1.10.5 -c conda-forge，注意使用第三方源，目前anaconda源中hdf5最高版本为1.10.4；
-
将HDF5_DISABLE_VERSION_CHECK设置为1，忽略警告。
个人倾向于方法2。