Ubuntu: HDF5 error: HDF5headerversion does not match HDF5library

When executing a python script that uses hdf5 today, the following error is reported! * ** HDF5libraryversionmismatchederror *** TheHDF5headerfilesusedtocompilethisapplicationdonotmatchtheversionusedbytheHDF5librarytowhichth

When executing a python script that uses hdf5 today, the following error occurs:

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 upload uption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5
Linked with a different version of static or shared HDF5 library.
You shoshould 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 1.8.11, library is 1.8.9
Summary of the HDF5 CONFIGURATION
======================================

General Information:
-------------------
HDF5 Version: 1.8.9
Configured on: Fri Dec 20 12:54:14 CST 2013
Configured by: ilan @ CentOS5x64
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux centos5x64 2.6.18-348. el5 #1 SMP Tue Jan 8 17:53:53 EST 2013 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point:/opt/anaconda1anaconda2anaconda3

Compiling Options:
------------------
Compilation Mode: production
C Compiler:/usr/bin/gcc (GCC) 4.1.2 20080704)
CFLAGS:
H5_CFLAGS: -std = c99-pedantic-Wall-Wextra-Wundef-Wshadow-Wpointer-arith-Wbad-function-cast-Wcast-qual-Wcast-align-Wwrite-strings-Wconversion-Waggregate -return-Wstrict-prototypes-Wmissing-declarations-Wredundant-decls-Wnested-externs-Winline-Wno-long-Wfloat-equal-Wmissing-format-attribute -Wmissing-noreturn-Wpacked-Wdisabled-optimization-Wformat = 2-response-code-Wendif-labels-Wdeclaration-after-statement-Wold-style-definition-Winvalid-pch-Wvariadic -macros-Wnonnull-Winit-self-Wmissing-include-dirs-Wswitch-default-Wswitch-enum-Wunused-macros-Wunsafe-loop-optimizations-Wc ++-compat-Wvolatile -register-var-O3-fomit-frame-pointer-finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS:-D_POSIX_C_SOURCE = 199506L-DNDEBUG-UH5_DEBUG_API
AM_CPPFLAGS:-D_LARGEFILE_SOURCE-D_LARGEFILE64_SOURCE-D_BSD_SOURCE
Shared C Library: yes
Static C Library: no
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries:-lpthread-lz-lrt-lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no

Ages:
----------
Fortran: no

C ++: 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)
I/O filters (internal): shuffle, fletcher32, nbit, scaleoffset
MPE: no
Direct VFD: no
Dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
Bye...
Aborted (core dumped)

 

Yesterday was still good. Why is there a problem today. I recalled that I updated anaconda yesterday, which may lead to a conflict. We can see that this is true. The hdf5 library installed in Anaconda is 1.8.9. Previously, the pip intall h5py library was 1.8.11, so the old version was deleted.

Sudo pip uninstall h5py

Press enter. The previous h5py version is available in the python system.

Uninstalling h5py:
/Usr/local/lib/python2.7/dist-packages/h5py-2.3.1.egg-info
/Usr/local/lib/python2.7/dist-packages/h5py/_ init _. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ init _. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ conv. so
/Usr/local/lib/python2.7/dist-packages/h5py/_ errors. so
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/_ init _. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/_ init _. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/attrs. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/attrs. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/base. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/base. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/dataset. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/dataset. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/datatype. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/datatype. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/dims. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/dims. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/files. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/files. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/filters. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/filters. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/group. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/group. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/selections. py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/selections. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/selections2.py
/Usr/local/lib/python2.7/dist-packages/h5py/_ hl/selections2.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/_ objects. so
/Usr/local/lib/python2.7/dist-packages/h5py/_ proxy. so
/Usr/local/lib/python2.7/dist-packages/h5py/defs. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5.so
/Usr/local/lib/python2.7/dist-packages/h5py/h5a. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5ac. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5d. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5ds. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5f. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5fd. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5g. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5i. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5l. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5o. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5p. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5r. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5s. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5t. so
/Usr/local/lib/python2.7/dist-packages/h5py/h5z. so
/Usr/local/lib/python2.7/dist-packages/h5py/highlevel. py
/Usr/local/lib/python2.7/dist-packages/h5py/highlevel. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/ipy_completer.py
/Usr/local/lib/python2.7/dist-packages/h5py/ipy_completer.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/_ init _. py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/_ init _. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/common. py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/common. pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_attrs.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_attrs.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_attrs_data.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_attrs_data.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_base.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_base.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_dataset.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_dataset.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_datatype.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_datatype.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_dimension_scales.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_dimension_scales.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_file.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_file.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_group.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_group.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_h5.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_h5.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_h5f.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_h5f.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_h5p.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_h5p.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_h5t.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_h5t.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_objects.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_objects.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_selections.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_selections.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_slicing.py
/Usr/local/lib/python2.7/dist-packages/h5py/tests/test_slicing.pyc
/Usr/local/lib/python2.7/dist-packages/h5py/utils. so
/Usr/local/lib/python2.7/dist-packages/h5py/version. py
/Usr/local/lib/python2.7/dist-packages/h5py/version. pyc
Proceed (y/n )? Y
Successfully uninstalled h5py

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