Hi,
I'm trying to compile my application with HDF5 on a BG/Q system. If I use
mpixlf2008_r -I<hdf5_path>/include -L<hdf5_path>/lib -lhdf5_fortran, I get
linking errors saying undefined references to a bunch of hdf5 routines. If
I use the h5pfc wrapper though, I am able to compile my program, but I want
to avoid doing that. What is the right way of compiling a parallel HDF5
fortran program without using the compiler wrapper?
-- Akshay
The -show switch of the wrapper script will show you exactly what flags and libraries it's using to compile a program. For example, on my system:
$ ./h5cc -show
gcc -I/usr/pppl/gcc/6.1-pkgs/szip-2.1/include -L/usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib /usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib/libhdf5_hl.a /usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib/libhdf5.a -L/usr/pppl/gcc/6.1-pkgs/szip-2.1/lib -lrt -lsz -lz -ldl -lm -Wl,-rpath -Wl,/usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib
$ ./h5fc -show
gfortran -I/usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/include -L/usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib /usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib/libhdf5hl_fortran.a /usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib/libhdf5_hl.a /usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib/libhdf5_fortran.a /usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib/libhdf5.a -L/usr/pppl/gcc/6.1-pkgs/szip-2.1/lib -lrt -lsz -lz -ldl -lm -Wl,-rpath -Wl,/usr/pppl/gcc/6.1-pkgs/hdf5-serial-1.8.17/lib
From the above, you can see that it for Fortran, it is using libhdf5hl_fortran libhdf5_hl libhdf5_fortran, and libhdf5
Since there's a good chance you and I used different configure options when building HDF5, you should use the -show switch with your own wrappers, and not just copy what you see here.
Prentice
On 08/12/2016 10:59 AM, Akshay Subramaniam wrote:
Hi,
I'm trying to compile my application with HDF5 on a BG/Q system. If I use mpixlf2008_r -I<hdf5_path>/include -L<hdf5_path>/lib -lhdf5_fortran, I get linking errors saying undefined references to a bunch of hdf5 routines. If I use the h5pfc wrapper though, I am able to compile my program, but I want to avoid doing that. What is the right way of compiling a parallel HDF5 fortran program without using the compiler wrapper?
-- Akshay
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Twitter: https://twitter.com/hdf5
You may have to include the path/lib to szip or zlib, and you need to link in the C HDF5 library (-lhdf5), and you may need to link in the high level HDF5 library, -lhdf5hl_fortran -lhdf5_hl
Scot
On Aug 12, 2016, at 9:59 AM, Akshay Subramaniam <akshaysubr@gmail.com> wrote:
Hi,
I'm trying to compile my application with HDF5 on a BG/Q system. If I use mpixlf2008_r -I<hdf5_path>/include -L<hdf5_path>/lib -lhdf5_fortran, I get linking errors saying undefined references to a bunch of hdf5 routines. If I use the h5pfc wrapper though, I am able to compile my program, but I want to avoid doing that. What is the right way of compiling a parallel HDF5 fortran program without using the compiler wrapper?
-- Akshay
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
