Doh. I got my email threads mixed up. Sorry for the noise.
___________________________________________________________
Mike Jackson
On Apr 17, 2012, at 3:38 PM, Allen D Byrne wrote:
> Mike,
> I am under the assumption that this is a different issue and Stephane is not
> using MinGW.
> Allen
>
> The original email was using these parameters:
>
> I have to use CMake now for the same results and here are the options used,
> with the same sources (hdf5-1.8.8):
> cmake -DCMAKE_INSTALL_PREFIX:STRING=${INSTALL} \
> -DCMAKE_C_COMPILER:FILEPATH=/usr/local/openmpi/1.5.3-intel/bin/mpicc \
> -DCMAKE_CXX_COMPILER:FILEPATH=/usr/local/openmpi/1.5.3-intel/bin/mpiCC \
> -DCMAKE_Fortran_COMPILER:FILEPATH=/usr/local/openmpi/1.5.3-intel/bin/mpif90 \
> -DBUILD_TESTING:BOOL=ON
> -DMPI_LIBRARY:FILEPATH=/usr/local/openmpi/1.5.3-intel/lib/libmpi.so \
> -DMPI_INCLUDE_PATH:STRING=/usr/local/openmpi/1.5.3-intel/include/ \
> -DHDF5_BUILD_FORTRAN:BOOL=ON \
> -DHDF5_BUILD_HL_LIB:BOOL=ON \
> -DHDF5_BUILD_TOOLS:BOOL=ON \
> -DHDF5_ENABLE_PARALLEL:BOOL=ON \
> -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON \
> -DMPIEXEC_NUMPROC_FLAG:STRING=-np \
> -DMPIEXEC_MAX_NUMPROCS:STRING=4096 \
> \"-DMPIEXEC_PREFLAGS:STRING=-N 1 -d 1\" \
> -DMPIEXEC:FILEPATH=/usr/local/openmpi/1.5.3-intel/bin/mpirun ..
>
>
> > After you compiled HDF5 with MinGW and CMake did you run the HDF5 tests? If
> > all the tests pass then this would indicate an error in your Makefiles. If
> > lots of the tests fail then this would indicate an error in the CMake side
> > of things.
> > --
> > Mike Jackson <www.bluequartz.net>
> >
> > On Apr 17, 2012, at 3:06 PM, Stéphane Backaert wrote:
> >
> > > Allen,
> > >
> > > I just checked: H5_HAVE_PARALLEL is set to 1 in the file H5pubconf.h. And
> > > I put libhdf5_f90cstub in my LDFLAGS...
> > > I must admit that I am a bit lost this time!
> > > Is there a way to test the libraries ? I mean, the compilation process
> > > does not complain, my CMake parameters, sent before, are right, so I
> > > guess that my link process is wrong...
> > > By the way, why libhdf5_f90cstub is present with CMake and not with
> > > autotools?
> > >
> > > All of this is due to the CMake...grrr
> > >
> > > Best,
> > >
> > > Stephane
> > >
> > > On Apr 17, 2012, at 8:41 PM, Allen D Byrne wrote:
> > >
> > >> Stéphane,
> > >> The undefined references seem to indicate it is looking for parallel
> > >> references? Maybe the fortran library failed to build properly, or
> > >> didn't include a parallel library? Is H5_HAVE_PARALLEL defined in the
> > >> H5pubconf.h file? h5pset_fapl_mpio_c is in the H5FDmpiof.c file which
> > >> should be in the libhdf5_f90cstub library.
> > >>
> > >> Allen
> > >>
> > >> > Allen,
> > >> >
> > >> > I will look into this HDF5-CMake issue a bit further: I think I can
> > >> > learn a lot from this investigation!
> > >> > But now I would like make some progress.
> > >> > Basically, my only problem is the linking of my code with the hdf5-vfd
> > >> > libraries. I can link my code with h5 libraries compiled with
> > >> > configure/make, with h5pfc (easy) but also without it. Actually, I
> > >> > already took care of those libraries explicitly/manually in my
> > >> > makefile. So I can link without h5pfc.
> > >> >
> > >> > With the CMake libraries (and thus without h5pfc), here is the kind of
> > >> > messages I get when I link my code with hdf5:
> > >> >
> > >> > /home/ucl/tfl/sbackaer/local/stow/hdf5-vfd-1.8.8_cmake/lib/libhdf5_fortran.a(H5_ff.f90.o):
> > >> > In function `h5lib_mp_h5open_f_':
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5_ff.f90:(.text+0x2e):
> > >> > undefined reference to `h5init_types_c_'
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5_ff.f90:(.text+0xba):
> > >> > undefined reference to `h5init_flags_c_'
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5_ff.f90:(.text+0xc8):
> > >> > undefined reference to `h5init1_flags_c_'
> > >> > ...
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5FDmpioff.f90:(.text+0x17):
> > >> > undefined reference to `h5pset_fapl_mpio_c_'
> > >> > /home/ucl/tfl/sbackaer/local/stow/hdf5-vfd-1.8.8_cmake/lib/libhdf5_fortran.a(H5FDmpioff.f90.o):
> > >> > In function `h5fdmpio_mp_h5pget_fapl_mpio_f_':
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5FDmpioff.f90:(.text+0x27):
> > >> > undefined reference to `h5pget_fapl_mpio_c_'
> > >> > /home/ucl/tfl/sbackaer/local/stow/hdf5-vfd-1.8.8_cmake/lib/libhdf5_fortran.a(H5FDmpioff.f90.o):
> > >> > In function `h5fdmpio_mp_h5pset_dxpl_mpio_f_':
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5FDmpioff.f90:(.text+0x37):
> > >> > undefined reference to `h5pset_dxpl_mpio_c_'
> > >> > /home/ucl/tfl/sbackaer/local/stow/hdf5-vfd-1.8.8_cmake/lib/libhdf5_fortran.a(H5FDmpioff.f90.o):
> > >> > In function `h5fdmpio_mp_h5pget_dxpl_mpio_f_':
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5FDmpioff.f90:(.text+0x47):
> > >> > undefined reference to `h5pget_dxpl_mpio_c_'
> > >> > /home/ucl/tfl/sbackaer/local/stow/hdf5-vfd-1.8.8_cmake/lib/libhdf5_fortran.a(H5FDmpioff.f90.o):
> > >> > In function `h5fdmpio_mp_h5pset_fapl_mpiposix_f_':
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5FDmpioff.f90:(.text+0x74):
> > >> > undefined reference to `h5pset_fapl_mpiposix_c_'
> > >> > /home/ucl/tfl/sbackaer/local/stow/hdf5-vfd-1.8.8_cmake/lib/libhdf5_fortran.a(H5FDmpioff.f90.o):
> > >> > In function `h5fdmpio_mp_h5pget_fapl_mpiposix_f_':
> > >> > /home/ucl/tfl/sbackaer/local/build/hdf5-vfd-1.8.8/fortran/src/H5FDmpioff.f90:(.text+0x90):
> > >> > undefined reference to `h5pget_fapl_mpiposix_c_'
> > >> >
> > >> > There are hundreds of lines like those!! All messages are only related
> > >> > to libhdf5_fortran.a.
> > >> >
> > >> > I had to adapt my makefile because there are two new libraries:
> > >> > libhdf5_f90cstub and libhdf5_hl_f90cstub but it is the same explicit
> > >> > way of linking as "configure/make"!
> > >> >
> > >> > Is this mean something for anyone?? I know what a undefined reference
> > >> > means, why there??
> > >> >
> > >> > Best,
> > >> >
> > >> > Stephane
> > >> >
> > >> > _______________________________________________
> > >> > Hdf-forum is for HDF software users discussion.
> > >> > [email protected]
> > >> > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
> > >> >
> > >
> > > _______________________________________________
> > > Hdf-forum is for HDF software users discussion.
> > > [email protected]
> > > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
> >
> >
> > _______________________________________________
> > Hdf-forum is for HDF software users discussion.
> > [email protected]
> > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
> >
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
