Note from 'configure --help'
`configure' configures netCDF 4.1.3 to adapt to many kinds of systems.
Usage: ./configure [OPTION]... [VAR=VALUE]...
To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE. See below for descriptions of some of the useful variables.
....
So please try putting the environment flags in the configure command. For
example:
./configure FC=mpif90 CC=mpicc CXX=mpicxx
--prefix=/Users/dossa013/software/cesm-software/netcdf-4.1.3 --enable-netcdf4
--enable-parallel --disable-shared --with-udunits=/Users/dossa013/software
--with-zlib=/Users/dossa013/software --with-szlib=/Users/dossa013/software
LDFLAGS=-L/Users/dossa013/software/cesm-software/hdf5-1.8.14/lib
CPPFLAGS=-I/Users/dossa013/software/cesm-software/hdf5-1.8.14/include
You can probably use the ${H5DIR} as a shortcut since it is set:
./configure FC=mpif90 CC=mpicc CXX=mpicxx
--prefix=/Users/dossa013/software/cesm-software/netcdf-4.1.3 --enable-netcdf4
--enable-parallel --disable-shared --with-udunits=/Users/dossa013/software
--with-zlib=/Users/dossa013/software --with-szlib=/Users/dossa013/software
LDFLAGS=-L/${H5DIR}/lib CPPFLAGS=-I/${H5DIR}/include
Cheers,
-- Ted
__________________________________________________________
| Edward Mansell <ted.mansell@xxxxxxxx>
| National Severe Storms Laboratory
|--------------------------------------------------------------
| "The contents of this message are mine personally and
| do not reflect any position of the U.S. Government or NOAA."
|--------------------------------------------------------------
On Dec 22, 2014, at 4:51 PM, Thiago V. dos Santos <dossa013@xxxxxxx> wrote:
> Hi all,
>
> I am trying to get netcdf 4.1.3 with parallel IO compiled to be able to run
> CESM on my Mac desktop (quadcore and 12GB).
>
> As a preparation for building netcdf, I have:
>
> 1) installed Xcode on my system;
>
>
> 2) installed f77, f90, c and cxx compilers using macports;
>
>
> 3) compiled udunits on my system;
>
>
> 4) compiled MPI from source explicitally pointing the above compilers when
> running configure, by using this command:
>
> ./configure CC=/opt/local/bin/gcc-mp-4.9 CXX=/opt/local/bin/c++-mp-4.9
> F77=/opt/local/bin/gfortran-mp-4.9 FC=/opt/local/bin/gfortran-mp-4.9
> --prefix=/Users/dossa013/software/cesm-software/mpich-3.1.3
>
>
> 5) compiled latest HDF5 (1.8.14) enabling zlib and parallel IO by using this
> command (did a make check and all tests PASSED):
>
> FC=mpif90 CC=mpicc ./configure
> --prefix=/Users/dossa013/software/cesm-software/hdf5-1.8.14 --enable-parallel
> --with-zlib=/Users/dossa013/software --with-szlib=/Users/dossa013/software
>
>
> However, I am having a really hard time trying to compile NetCDF 4.1.3. This
> is what I am trying:
>
> H5DIR=/Users/dossa013/software/cesm-software/hdf5-1.8.14
> CPPFLAGS="–I${H5DIR}/include"
> CXXFLAGS="-I${H5DIR}include"
> FFFLAGS="-I${H5DIR}/include"
> FCFLAGS="-I${H5DIR}/include"
> LDFLAGS="-L${H5DIR}/lib"
>
> ./configure FC=mpif90 CC=mpicc CXX=mpicxx
> --prefix=/Users/dossa013/software/cesm-software/netcdf-4.1.3 --enable-netcdf4
> --enable-parallel --disable-shared --with-udunits=/Users/dossa013/software
> --with-zlib=/Users/dossa013/software --with-szlib=/Users/dossa013/software
>
> Then everything seems to work ok but at a certain point it throws out this
> error message:
>
> checking for library containing H5Fflush... no
>
> configure: error: Can't find or link to the hdf5 library. Use
> --disable-netcdf-4, or see config.log for errors.
>
>
>
> I took a look at the config.log file, but I failed to find the reason why the
> script stopped. Has anyone ever seen this? Is there any better way to show
> netcdf where my HDF5 libraries ae located?
>
>
>
> Thank you all in advance and happy hollidays!
>
>
> --
> Thiago Veloso dos Santos
> PhD student
> Land and Atmospheric Science
> University of Minnesota
> http://www.laas.umn.edu/CurrentStudents/MeettheStudents/ThiagodosSantos/index.htm
> _______________________________________________
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit:
> http://www.unidata.ucar.edu/mailing_lists/
