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
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