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Due to the current gap in continued funding from the U.S. National Science Foundation (NSF), the NSF Unidata Program Center has temporarily paused most operations. See NSF Unidata Pause in Most Operations for details.
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
<http://www.laas.umn.edu/CurrentStudents/MeettheStudents/ThiagodosSantos/index.htm>*
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