First: HDF5 is supported by two build systems, autotools and CMake. They do
not produce the exact same build framework support.
Only the autotools process creates the h5cc, h5fc, etc.
CMake creates cmake config files and properties.
Second: You have a serial install created by autotools and a parallel install
created by CMake.
You will need to choose one build system to make it easier to do what you
want. Note that the libraries are the same it is just the support framework
for the files.
Allen
On Thursday, August 06, 2015 06:42:42 PM houssen wrote:
> I had no time to test more on this, but, I just wanted to notice
> that :
>
> 1. I have 2 HDF5 installs : one serial in the system (apt-get
> install => /usr/lib), and, one parallel (built from source =>
> /home/houssen/Programs/...)
> => I need 2 installs : I need to switch
> between 2 softwares who needs one serial, or, parallel HDF5 version.
> =>
> the first software is Fortran, the second is C : I need support for both
> C and Fortran.
>
> 2. When I module load "my" parallel version built from
> source, cmake find the correct install :
> ~> cmake -LA | grep
> HDF5
> HDF5_CXX_COMPILER_EXECUTABLE:FILEPATH=/USR/BIN/h5c++
> HDF5_C_COMPILER_EXECUTABLE:FILEPATH=/USR/BIN/h5cc
> HDF5_C_LIBRARY:PATH=/HOME/HOUSSEN/PROGRAMS/PHDF5/hdf5-1.8.15-patch1/local/li
> b/libhdf5.a
> HDF5_DIFF_EXECUTABLE:FILEPATH=/HOME/HOUSSEN/PROGRAMS/PHDF5/hdf5-1.8.15-patc
> h1/local/bin/h5diff
> HDF5_DIR:PATH=/HOME/HOUSSEN/PROGRAMS/PHDF5/hdf5-1.8.15-patch1/local/share/c
> make HDF5_Fortran_COMPILER_EXECUTABLE:FILEPATH=/USR/BIN/h5fc
>
> ...
> But now, I've just wrote these lines, I realize that some variable
> point to /usr/lib (HDF5_Fortran_COMPILER_EXECUTABLE) and some other
> don't (HDF5_C_LIBRARY) ?!
> I don't understand what's going on : it looks
> like the install of the parallel HDF5 (build from source) is incomplete
> ?!... However, I built and installed HDF5 this way
>
> ~/hdf5-1.8.15-patch1/BUILD> cmake -DHDF5_BUILD_FORTRAN=ON
> -DHDF5_ENABLE_F2003=ON -DHDF5_ENABLE_PARALLEL=ON
> -DCMAKE_INSTALL_PREFIX=/home/houssen/Programs/XXX ..; make; make
> install;
>
> Note : I didn't add C++ support (which could have been
> convenient to me) because it seems there is an incompatibility with the
> parallel flag.
>
> Franck
>
> ~> sudo apt-get install h5utils hdf5-tools
> libhdf5-dev libhdf5-serial-dev
> ~> dpkg -L
> libhdf5-7
> /.
> /usr
> /usr/lib
> /usr/lib/x86_64-linux-gnu
> /usr/lib/x86_64-linux-gnu/libhdf5_hl.so.7.0.0
> /usr/lib/x86_64-linux-gnu/libhdf5.so.7.0.0
> /usr/lib/x86_64-linux-gnu/libhdf5_fortran.so.7.0.0
> /usr/lib/x86_64-linux-gnu/libhdf5hl_fortran.so.7.0.0
> /usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so.7.0.0
> /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.7.0.0
> ...
>
> Le 2015-08-06 13:43, Peter Steinbach a écrit :
> > Hi Franck,
> >
> > I
>
> suspect it has something to do with your system or your
>
> > installation.
>
> I was finally able to build the cmake dummy package and
>
> > the CMakeCache
>
> contains the HDF5_IS_PARALLEL correctly!
>
> > Here are my module files
>
> again:
> > # cmake/3.3.0
> > set soft_path
>
> /sw/apps/$soft_ware/$soft_version
>
> > set soft_arch x86_64
> > module-whatis
>
> "${soft_ware} ${soft_version}"
>
> > prepend-path PATH
>
> $soft_path/bin
>
> > prepend-path LD_LIBRARY_PATH $soft_path/lib
>
> prepend-path CMAKE_PREFIX_PATH $soft_path/share/cmake-3.3
>
> > #
>
> hdf5/1.8.15-p1-openmpi
>
> > set path
>
> /sw/users/steinbac/software/$soft_ware/${soft_version}
>
> > set soft_arch
>
> x86_64
>
> > module-whatis "${soft_ware} ${soft_version}"
> >
> > append
>
> soft_dependencies "openmpi/1.8.5"
>
> > prepend-path PATH $path/bin
>
> prepend-path LD_LIBRARY_PATH $path/lib
>
> > I however have to say, that
>
> the FindHDF5 cmake module seems not to
>
> > like the situation if your
>
> environment exposes multiple cmake
>
> > installations, e.g.
>
> LD_LIBRARY_PATH=/path/to/custom/hdf5:/usr/lib
>
> > ^^^^^^^^ might also
>
> contain hdf5
>
> > libraries. The same holds for the PATH.
> >
> > Best,
>
> Peter
>
> > On 08/03/2015 02:19 PM, houssen wrote:
> >> Hello,
> >>
> >> I
>
> built HDF5 from source with CMake. I need parallel HDF5 so I set
>
> HDF5_ENABLE_PARALLEL=ON in ccmake : libhdf5.settings shows "Parallel
>
> HDF5: ON". So this is OK.
>
> >> Now with this CMakeLists.txt:
> >> ~> more
>
> CMakeLists.txt
>
> >> CMAKE_MINIMUM_REQUIRED ( VERSION 2.8 )
> >> FIND_PACKAGE
>
> ( HDF5 1.8 REQUIRED C )
>
> >> I do not get HDF5_IS_PARALLEL :
> >> ~>
>
> cmake .
>
> >> -- Configuring done
> >> -- Generating done
> >> -- Build files
>
> have been written to: /home/houssen/Downloads
>
> >> ~> cmake -LA | grep
>
> HDF
>
> >> HDF5_CXX_COMPILER_EXECUTABLE:FILEPATH=/usr/bin/h5c++
>
> HDF5_C_COMPILER_EXECUTABLE:FILEPATH=/usr/bin/h5cc
>
> HDF5_C_LIBRARY:PATH=/home/houssen/Programs/PHDF5/hdf5-1.8.15-patch1/local/li
> b/libhdf5.a
>
>
> HDF5_DIFF_EXECUTABLE:FILEPATH=/home/houssen/Programs/PHDF5/hdf5-1.8.15-patch
> 1/local/bin/h5diff
>
>
> HDF5_DIR:PATH=/home/houssen/Programs/PHDF5/hdf5-1.8.15-patch1/local/share/cm
> ake
>
>
> HDF5_Fortran_COMPILER_EXECUTABLE:FILEPATH=/usr/bin/h5fc
>
> >> Why
>
> HDF5_IS_PARALLEL is not available?
>
> >> Franck
>
> _______________________________________________
>
> >> Hdf-forum is for HDF
>
> software users discussion.
>
> >> [email protected]
>
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>
> Twitter: https://twitter.com/hdf5
>
>
> _______________________________________________
>
> > Hdf-forum is for HDF
>
> software users discussion.
>
> > [email protected]
>
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>
> Twitter: https://twitter.com/hdf5
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