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.
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.
On Wed, Sep 02, 2009 at 04:50:29PM -0400, Carlos Moffat wrote: > Hello, > > I'm trying to compile NetCDF v4.0.1 to run the ROMS model > (http://www.myroms.org) in a parallel configuration. > > What I've done so far is to install MPICH2 with the configuration > > ./configure --enable-f90 --with-mpe --with-romio --prefix=/usr/local looks good > and HDF5 (v1.8.3) with the options: > > CC=mpicc LIBS="-lm -lz" CPPFLAGS="-DpgiFortran" ./configure > --enable-parallel --enable-fortran --prefix=/usr/local > > (I believe the "LIBS" options are not necessary here but they don't > hurt). A 'make check' works nicely here. yup, this looks good too. > I have the intel fortran compiler installed (v11.0). When I compile > netcdf v4.0.1 with: > > CC=mpicc CPPFLAGS="-DpgiFortran" LIBS="-lm -lz -lhdf5" ./configure > --enable-netcdf-4 --prefix=/usr/local > > using 'make check', the the build fails with the output I've pasted > below. It looks like the HDF5 libraries were compiled without the > necessary MPI support, but my understanding is that the > '--enable-parallel' flag should do this. Am I missing something? Actually the errors you get *confirm* that HDF5 was compiled with MPI support: it's the HDF5 library that is requesting MPI symbols, but there is no mpi library in your link command. > libtool: link: ifort -I../fortran -I../libsrc4 -I../f90 -g -o nf_test > test_get.o test_put.o nf_error.o nf_test.o test_read.o test_write.o > util.o fortlib.o ../libsrc4/.libs/libnetcdf.a -lhdf5_hl -lm -lz -lhdf5 > ../libsrc4/.libs/libnetcdf.a(nc4file.o): In function `nc_check_for_hdf5': > /home/cmoffat/Sandbox/netcdf-4.0.1/libsrc4/nc4file.c:141: undefined > reference to `MPI_File_open' I don't know why libtool wants to link with ifort here. I think instead you need to link with mpif90. If you would prefer to link "by hand", then you will have to add the '-L/path/to/mpi -lmpich2' commands to your link step. you could also compile/link with the 'h5pcc' script, but that's essentially the mpi wrapper scripts with one or two more HDF5 libraries in there. You've accomplished the same thing with your 'LIBS=' line when compiling netcdf4. Maybe if you try setting the fortran compiler to mpif90 when you configure netcdf 4 that will make things work better? ==rob -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA
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