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[netCDF #OPQ-607149]: Error: "'H5F_LIBVER_18' undeclared"

Hi Michela,

> I tried to install on a Ubuntu 11.10 system netcdf with hdf5 and zlib.
> Unfortunately the installing process of netcdf fails.
> Downloaded zlib-1.2.6
> Downloaded hdf5-1.8.8
> Downloaded netcdf-4.2
> Extracted directories in "/home/fisicatecnica/workwrf/".
> --------------------------------------------------
> In /home/fisicatecnica/workwrf/zlib-1.2.6
> --------------------------------------------------
> ./configure
> --prefix=/home/fisicatecnica/workwrf/zlib-1.2.6
> make
> make install

The --prefix= option you used installs the software in the zlib source
directory.  This is not recommended, because source directories may
have their own lib/ and include/ directories that you could overwrite
when you later run "make install".  Also, installation directories for
libraries are meant to be permanent repositories where applications
can make use of the libraries, but source directories can typically be
moved or deleted after the software is successfully installed

This probably did not cause the problem you are seeing later, but is
just advice that better choices would be something like
--prefix=/usr/local or --prefix=/home/fisicatecnica that don't try to
install the library on top of the source files.

> --------------------------------------------------
> In /home/fisicatecnica/workwrf/hdf5-1.8.8
> --------------------------------------------------
> ./configure
> --with-zlib=/home/fisicatecnica/workwrf/zlib-1.2.6
> --prefix=/home/fisicatecnica/workwrf/hdf5-1.8.8
> make
> make install

Similar comments apply here, where you are installing HDF5 in its
source directory ...

> export 
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/fisicatecnica/workwrf/zlib-1.2.6/lib
> export 
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/fisicatecnica/workwrf/hdf5-1.8.8/lib
> --------------------------------------------------
> In /home/fisicatecnica/workwrf/netcdf-4.2
> --------------------------------------------------
> ./configure
> --prefix=/home/fisicatecnica/workwrf/netcdf-4.2
> --enable-netcdf4
> --with-zlib=/home/fisicatecnica/workwrf/zlib-1.2.6
> --enable-large-file-tests

The actual problem is that setting LD_LIBRARY_PATH is not enough to
compile code that makes use of a library.  Libraries have header files
such as zlib.h, hdf5.h, and netcdf.h that the compiler must know how
to find when it is compiling code that makes use of functions in the

That's why we recomend for netCDF-4.2 that you instead use the
environment variables "LDFLAGS" and "CPPFLAGS" to say where the
libraries are installed.

For example, if you had installed zlib and hdf5 using
--prefix=/home/fisicatecnica, that would have created lib/ and
include/ directories ubder that prefix directory, and then you could
compile and build netCDF-4.2 with:

  ./configure --prefix=/home/fisicatecnica 
  make check
  make install

The "--enable-netcdf4" option is not needed with netCDF-4.2, because
it is the default, if the HDF5 library is found by the configure
script, which it will be if you have set LDFLAGS and CPPFLAGS

I recommend not to use "--enable-large-file-tests", because they make
the testing take much longer and can easily cause the test to run out
of disk space while running "make check".  That option is really for
developers who are making changes to netCDF source code, not for
people installing it.

You can also set LD_LIBRARY_PATH if you want to, but it's not
necessary to compile, check, and install netCDF.  It may be needed for
later programs that make use of the netCDF library, depending on how
they are compiled and linked.

> While running the Makefile this error message appears:
> nc4file.c: In function 'nc4_create_file':
> nc4file.c:279:38: error: 'H5F_LIBVER_18' undeclared (first use in this 
> function)
> nc4file.c:279:38: note: each undeclared identifier is reported only once for 
> each function it appears in
> make[2]: *** [libnetcdf4_la-nc4file.lo] Errore 1
> make[2]: uscita dalla directory 
> "/home/fisicatecnica/workwrf/netcdf-4.2/libsrc4"
> make[1]: *** [all-recursive] Errore 1
> make[1]: uscita dalla directory "/home/fisicatecnica/workwrf/netcdf-4.2"
> make: *** [all] Errore 2


Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu

Ticket Details
Ticket ID: OPQ-607149
Department: Support netCDF
Priority: Normal
Status: Closed