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Russ Rew: H5Fflush not found in libhdf5.a resulting in configure error

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  • Subject: Russ Rew: H5Fflush not found in libhdf5.a resulting in configure error
  • Date: Wed, 31 Mar 2010 13:48:24 -0600
I'm forwarding this, Cc:ing support-netcdf, to get the answer into the
archives.

The symptom was when building netCDF-4.1.1-rc1 on a MacOS-X 10.6 system,
the following  error message occurred in running configure:

  $ CC=/usr/bin/gcc FC='' CXX='' ./configure --with-hdf5=$HDFDIR 
--with-zlib=/usr/lib
   ...
   checking for H5Fflush in -lhdf5... no
  configure: error: Can't find the hdf5 header and/or library, or can't link a 
program to it. HDF5 must be built with zlib; the location of zlib must be 
specified for netCDF-4 with the --with-zlib option. If HDF5 was also built with 
szlib, then the location of szlib must also be specified with the --with-slib 
option.

There were two causes identified for this in different instances:

 1.  A leftover shared 32-bit libhdf5.so from a previous build, which
     hid the search in the 64-bit libhdf5.a.  Removing the old shared
     library made things work.  This was revealed by looking at
     config.log instead of the error message from configure.

 2.  Omitting "-m64" from CFLAGS when configuring and specifying a
     64-bit HDF5 library in $HDFDIR.  In this case explicit "-m64" flags
     were also needed for FFLAGS and FCFLAGS for the corresponding
     gfortran compiles.

--Russ