addfile and HDF5 library version mismatch

From: Madeline Miller <madeline_at_nyahnyahspammersnyahnyah>
Date: Wed Jun 08 2011 - 16:55:52 MDT


I just installed NCL on a Linux Red Hat workstation. I used the pre-compiled
binary ncl_ncarg-6.0.0.Linux_RedHat_x86_64_nodap_gcc412.tar, which matches
my architecture and version of gcc.

I ran all the tests under the download instructions and they all worked
fine. Then, I tried opening a .nc file in NCL using the command

I created the .nc file using MATLAB on my Linux workstation, and am able to
read it on my Mac laptop using another version of NCL installed there.

However, on my Linux workstation it returns:

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
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 1.8.5, library is 1.8.6

General Information:
                   HDF5 Version: 1.8.6
                  Configured on: Mon May 23 09:21:22 MDT 2011
                  Configured by: haley@mirage1
                 Configure mode: production
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux mirage1 2.6.18-194.17.4.el5 #1 SMP
Wed Oct 20 13:03:08 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /fs/blizzard/contrib/ncl-6.0.0/external

Compiling Options:
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )
                         CFLAGS: -fPIC
                      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
                       CPPFLAGS: -D_FILE_OFFSET_BITS=64
-I/fs/blizzard/contrib/ncl-6.0.0/external/include -D_LARGEFILE_SOURCE
               Shared Libraries: no
               Static Libraries: yes
  Statically Linked Executables: no
                Extra libraries: -lsz -lz -lm
                       Archiver: ar
                         Ranlib: ranlib
              Debugged Packages:
                    API Tracing: no

                        Fortran: no
                            C++: no

                  Parallel HDF5: no
             High Level library: yes
                   Threadsafety: no
            Default API Mapping: v18
 With Deprecated Public Symbols: yes
         I/O filters (external): deflate(zlib),szip(encoder)
         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
             H5dump Packed Bits: yes

Does anyone know what the problem is and/or what I can do to fix this?



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Received on Wed Jun 8 18:03:43 2011

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