Re: mpi.h vs. hdf5.h

[Juan Pablo Carbajal]

On Fri, Apr 24, 2015 at 4:46 PM, Juan Pablo Carbajal
<address@hidden> wrote:
> On Fri, Apr 24, 2015 at 3:38 PM, Mike Miller <address@hidden> wrote:
>> On Fri, Apr 24, 2015 at 12:58:44 +0200, Juan Pablo Carbajal wrote:
>>> The problem came back in Ubuntu 15.04 none of the previous solutions
>>> work this time.
>>>
>>> I have both libraries installed (apparently it is allowed in 15.04)
>>
>> Right, the latest packages allow co-installation, but also require you
>> to choose your flavor and specify the include and library paths when
>> compiling.
>>
>>> CFLAGS="-I/usr/lib/openmpi/include -I/usr/include/hdf5/openmpi"
>>> CPPFLAGS="-I/usr/lib/openmpi/include -I/usr/include/hdf5/openmpi"
>>> LDFLAGS="-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi/" ./configure
>>>
>>> However compilation fails
>> [...]
>>> Suggestions?
>>
>> The new packaging for HDF5 means you don't have to compile against an
>> MPI HDF5 library if you don't want to, so I don't.
>
> That's ok, I wouldn't either I need to check if dolphin and fem-fenics
> will be happy with that.
>
>>
>> If you really want to link against one of the MPI flavors of HDF5, it
>> looks like you will have to add -lmpi++ to your LIBS variable. Or
>> compile Octave with one of the MPI compiler wrappers.
>>
>> FWIW I compile Octave with
>>
>>     ../configure --with-hdf5-includedir=/usr/include/hdf5/serial \
>>                  --with-hdf5-libdir=/usr/lib/x86_64-linux-gnu/hdf5/serial
>>
>
> Yay! Thanks a lot! This worked indeed... you are a hdf5 guru :)
>
>> More details: your error looks vaguely familiar to me. I think it's
>> because HDF5 is a C library, so it doesn't link against the C++ MPI
>> library when it is built. But when you build a C++ program against it,
>> the includes pull in all of the MPI C++ definitions, so you do need the
>> C++ MPI library.
>>
>> HTH,
>>
>> --
>> mike

:( This worked for configure, but at make time I still get

                 from ../../stable/libinterp/octave-value/ov-cell.cc:40:
../../stable/libinterp/corefcn/oct-hdf5.h:27:18: fatal error: hdf5.h:
No such file or directory
 #include <hdf5.h>
                  ^
compilation terminated.
Makefile:8556: recipe for target 'octave-value/ov-cell.df' failed
make[2]: *** [octave-value/ov-cell.df] Error 1
mv operators/ops.cc-t operators/ops.cc
updating parse-tree/oct-parse.output
updating parse-tree/oct-parse.h
make[2]: Leaving directory '/home/juanpi/Devel/octave/stable-build/libinterp'
Makefile:2123: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/juanpi/Devel/octave/stable-build'
Makefile:1988: recipe for target 'all' failed
make: *** [all] Error 2