Problems with ncl 6.0.0 binary and HDF5: version mismatch

From: Christian Pagé <page.christian_at_nyahnyahspammersnyahnyah>
Date: Wed Jul 27 2011 - 09:45:34 MDT


When trying to read a NetCDF4 encoded file with the NCL 6.0.0 binary, here
is what I get... a problem of mismatch between HDF5 headers at compile time
and library at link time.
The NCL 6.0.0 binary is the following:
I verified with ldd that no .so HDF5 library is loaded, it has been linked
% ldd /usr/local/bin/ncl => /lib64/ (0x00000034f7000000) => /usr/lib64/ (0x00000034f8400000) => /usr/lib64/ (0x00000034f9400000) => /lib64/ (0x00000034f6800000) => /lib64/ (0x00000034f6c00000) => /usr/lib64/ (0x0000003e2fe00000) => /lib64/ (0x0000003e2fa00000) => /lib64/ (0x00000034f6400000)
        /lib64/ (0x00000034f5400000) => /usr/lib64/ (0x00000034f8000000) => /usr/lib64/ (0x00000034f8c00000)

Copyright (C) 1995-2011 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.0.0
The use of this software is governed by a License Agreement.
See for more details.
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
-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

                       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
Christian Pagé
Ingénieur de recherche en climat, CERFACS, Toulouse

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Received on Wed Jul 27 09:46:06 2011

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