HDF5 library version mismatched error

[GoogleCodeExporter]

Hello,

I am using DaVinci for analysis of CUB files on an Ubuntu 12.04 LTS. After an 
'install_check()' run, I get the following message:

dv> install_check()

Davinci Core Version:   2.11
Operating System:   linux
Home Location:      /usr/share/davinci
Library Location:   /usr/share/davinci/library
Script Files Location:  /usr/share/davinci/library/script_files
Examples Location:  http://davinci.asu.edu/examples
Checking for newer version at ASU-MSFF...       UNABLE TO CONNECT

Checking for URL remote file loading...         FAILED!
Testing simple math...                  PASSED
Testing array math...                   PASSED
Testing matrix multiplication/inversion...      PASSED
Testing davinci generic reader...           FAILED!
Testing PDS/ISIS header/cube reader...          FAILED!
Testing for ISIS writer (write_isis_cub)...         NOT INCLUDED
Checking for "geom_ghost()"...              NOT INCLUDED
Testing "where" statement...                SKIPPED!
Checking remote function list...            UNABLE TO CONNECT
Checking for modules... Found thm           PASSED
Testing a module function (thm.sstretch)...         SKIPPED!
Testing for the User Defined Function Library...    PASSED
Testing a User Defined Function (dcs)...        SKIPPED!
Testing ENVI reader...                  PASSED
Testing VICAR writer/reader...              PASSED
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 1.8.9, library is 1.8.10
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
           HDF5 Version: 1.8.10
          Configured on: Mon Feb 11 05:51:11 UTC 2013
          Configured by: root@localhost.localdomain
         Configure mode: production
            Host system: x86_64-redhat-linux-gnu
          Uname information: Linux localhost.localdomain 3.6.10-4.fc18.x86_64 #1 SMP Tue Dec 11 18:01:27 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
               Byte sex: little-endian
              Libraries: 
         Installation point: /usr

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /bin/gcc ( gcc (GCC) 4.7.2 20121001 )
                         CFLAGS: -O0 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4  -m64 -mtune=generic
                      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 -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -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: yes
  Statically Linked Executables: no
                        LDFLAGS: -Wl,-z,relro 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
        Extra libraries:  -lz -lrt -lm 
               Archiver: ar
             Ranlib: ranlib
          Debugged Packages: 
            API Tracing: no

Languages:
----------
                        Fortran: yes
               Fortran Compiler: /bin/gfortran ( GNU Fortran (GCC) 4.7.2 20121001 )
          Fortran 2003 Compiler: yes
                  Fortran Flags: 
               H5 Fortran Flags:  
               AM Fortran Flags:  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4  -m64 -mtune=generic -I/usr/lib64/gfortran/modules
         Shared Fortran Library: yes
         Static Fortran Library: yes

                            C++: yes
                   C++ Compiler: /bin/g++ ( g++ (GCC) 4.7.2 20121001 )
                      C++ Flags: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4  -m64 -mtune=generic
                   H5 C++ Flags:  
                   AM C++ Flags: 
             Shared C++ Library: yes
             Static C++ Library: yes

Features:
---------
                  Parallel HDF5: no
             High Level library: yes
                   Threadsafety: no
            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...
Testing HDF writer/reader... 

I will be extremely grateful if somebody helps me out. I suspect DaVinci is not 
functioning properly due to HDF5 library mismatch.

Please help

Subha

Original issue reported on code.google.com by battix87 on 20 May 2014 at 8:08

[GoogleCodeExporter]

What does this have to do with netcdf4-python?

Anyway, it means you picked a different versions of the HDF5 libraries and 
headers in the build process.  

Original comment by whitaker.jeffrey@gmail.com on 20 May 2014 at 8:20