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[netCDF #RZV-501204]: NetCDF 4.0 gfortran/Linux & WRF3.2



Hi Hugh,

Sorry it's taken so long to respond to your question ...

> I'm trying to build WRF3.2 on Linux.  This apparently requires
> that a recent version of NetCDF be available, first.  I downloaded
> NetCDF 4.0 binaries for Linux and installed the various bits in
> /user/local/bin, /user/local/lib, etc.

I think WRF3.2 does not require netCDF-4 features such as compression
and chunking, so you could have built netCDF with the --disable-netcdf-4
flag to configure, to make sure it didn't try to include the netCDF-4
features supported by an HDF5 library.  If you did not specify
--disable-netcdf-4 and an HDF5 library was installed where the configure
script could find it, then your netCDF installation would have been
built to depend on the HDF5 library, requiring linking with something
like

   ... -L/usr/local/netcdf/lib -L/usr/local/hdf5/lib -lnetcdf -lhdf5_hl -lhdf5 
-lz

if the HDF5 library was installed in /usr/local/hdf5/lib, for example.

> At compile time for WRF, the build fails.  It looks like there's
> a hard-coded path in the netcdf library:
> 
> mpif90 -f90=ifort -o wrf.exe  -g -O3 -w -ftz -align all -fno-alias -fp-model 
> precise -FR -convert big_endian  -ip  wrf.o ../main/module_wrf_top.o 
> libwrflib.a 
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/external/fftpack/fftpack5/libfftpack.a 
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/external/io_grib1/libio_grib1.a 
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/external/io_grib_share/libio_grib_share.a 
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/external/io_int/libwrfio_int.a 
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/external/esmf_time_f90/libesmf_time.a 
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/external/RSL_LITE/librsl_lite.a 
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/frame/module_internal_header_util.o 
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/frame/pack_utils.o  
> /home/hmcaffey/WL/WRF3/3.2/WRFV3/external/io_netcdf/libwrfio_nf.a 
> -L/usr/local/lib  -lnetcdf
> 
> /usr/local/lib/libnetcdf.a(nc4attr.o): In function `nc_del_att':
> /dan/netcdf/n4_dan/netcdf-4.0/libsrc4/nc4attr.c:817: undefined reference to 
> `H5Dclose'
> /dan/netcdf/n4_dan/netcdf-4.0/libsrc4/nc4attr.c:806: undefined reference to 
> `H5Adelete'
> ... many more of these undefined references
> 
> Result is that 'wrf.exe' is not generated.
> 
> Where is "/dan/netcdf/n4_dan" coming from?  Is this why my build is failing?

It looks like /dan/netcdf/n4_dan/netcdf-4.0/ was where you built netCDF from 
source.
Did you run "make check" and "make install" after building it?  Running "make 
install"
is recommended rather than trying to copy libraries and include files manually 
into
the install directories.  A program named "nc-config" is also installed which 
should
help in determining how to link to netCDF, by running "nc-config --fflags" to 
see
what include files are needed and "nc-config --flibs" to see how libraries need 
to
be linked.

I recommend you try downloading the more recent netcdf-4.1.1 distribution, 
because it
has fixes for some nc-config problems in the 4.0 distribution.  When building, 
specify
--disable-netcdf-4 if necessary and follow the installation instructions by 
invoking
"make  check" and "make install".

--Russ
 

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



Ticket Details
===================
Ticket ID: RZV-501204
Department: Support netCDF
Priority: Critical
Status: Closed


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