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  Ubuntu: HDF5 error: HDF5 header version does not match with the HDF5 library
     
  Add Date : 2018-11-21      
         
         
         
  Today in the implementation of a python script used hdf5 encountered the following error

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 1.8.11, 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 (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 -prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat = 2 -Wunreachable-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

Languages:
----------
                        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)

 

Good yesterday, today, how there is a problem. He recalled a moment like yesterday updated anaconda, could lead to a conflict, the view, indeed. hdf5 library Anaconda 1.8.9 is installed, but prior to the adoption pip intall h5py library should be the 1.8.11, the mountain can not be two tigers, then delete the old version

sudo pip uninstall h5py

Press Enter, and she has h5py previous version in the system comes with python


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
     
         
         
         
  More:      
 
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