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
