netcdf hdf5 mismatch

[basmac]

When a user runs ncdump on a netCDF4 compressed file, he gets the following HDF5 library error information. We did a selfupdate and outdated upgrade last Friday

bash-3.2# port installed|grep net
  netcdf @4.1.1_2+dap+netcdf4
  netcdf @4.1.1_3+dap+netcdf4
  netcdf @4.1.1_4+dap+netcdf4 (active)
  netcdf-devel @4.1.1_1 (active)
  netpbm @10.26.64_0 (active)
bash-3.2# port installed|grep -i hdf
  hdf4 @4.2.5_1 (active)
  hdf5-18 @1.8.5_0 (active)
  hdfeos @2.16v1.00_0
  hdfeos @2.17v1.00_0 (active)
  hdfeos5 @1.12_1
  hdfeos5 @1.13_0 (active)
bash-3.2#

[dmurray@mac16 grids]$ which ncdump
/opt/local/bin/ncdump

[dmurray@mac16 grids]$ ncdump filework.nc > ncdump.out
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 1.8.5, library is 1.8.4
            SUMMARY OF THE HDF5 CONFIGURATION
            =================================

General Information:
-------------------
                   HDF5 Version: 1.8.4-patch1
                  Configured on: Fri May 28 13:21:14 MDT 2010
                  Configured by: root@mac78.psd.esrl.noaa.gov
                 Configure mode: production
                    Host system: i386-apple-darwin10.3.0
              Uname information: Darwin mac78.psd.esrl.noaa.gov 10.3.0 Darwin Kernel Version 10.3.0: Fri Feb 26 11:58:09 PST 2010; root:xnu-1504.3.12~1/RELEASE_I386 i386
                       Byte sex: little-endian
                      Libraries:
             Installation point: /usr/local/ifort

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/local/bin/gcc (gcc-4.4.4)
                         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 -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O0 -fomit-frame-pointer -finline-functions
                      AM_CFLAGS:
                       CPPFLAGS:
                    H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: -I/usr/local/include
               Shared Libraries: yes
               Static Libraries: yes
  Statically Linked Executables: no
                        LDFLAGS:
                     AM_LDFLAGS:  -L/usr/local/lib
                Extra libraries:  -lz -lm
                       Archiver: ar
                         Ranlib: ranlib
              Debugged Packages:
                    API Tracing: no

Languages:
----------
                        Fortran: no
                            C++: no

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
 Linux Large File Support (LFS): no
Bye...
Abort  

[ryandesign (Ryan Carsten Schmidt)]

You need to use WikiFormatting so your posts are legible. Also please Cc applicable port maintainers.

I see a statement in your output that this was compiled with /usr/local/bin/gcc. It's not supported to have anything installed in /usr/local while using MacPorts as it interferes. Please move or remove /usr/local and rebuild the ports you're having trouble with to see if the problem remains.

[mamoll (Mark Moll)]

Perhaps uninstalling and reinstalling netcdf* is enough to fix the problem?

[basmac]

Uninstall and install was enough to fix it. The pain was there were 20 related installs I had to uninstall/install which relied on netcdf. thanks