[Users] HDF5 and C++

Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] bernard.j.kelly at nasa.gov
Thu Dec 9 13:08:56 CST 2010

Done: it's at: https://trac.einsteintoolkit.org/ticket/143

Thanks, Erik.


On 12/9/10 12:26 PM, "Erik Schnetter" <schnetter at cct.lsu.edu> wrote:

>Can you open a full bug report on <http://trac.einsteintoolkit.org>,
>including the options you use for configuring Cactus, thorn list,
>On Thu, Dec 9, 2010 at 5:23 PM, Kelly, Bernard J.
><bernard.j.kelly at nasa.gov> wrote:
>> Hi Erik.
>> Both John and I are compiling with HDF5_DIR=BUILD. We're using the
>> available macports version of openmpi. This is exactly what gives the
>> "incompatible --enable-cxx" error message John mentioned in his report.
>> Bernard
>> On 12/9/10 12:16 PM, "Erik Schnetter" <schnetter at cct.lsu.edu> wrote:
>>>On Thu, Dec 9, 2010 at 5:04 PM, John Baker <john.g.baker at nasa.gov>
>>>> Hi,
>>>>     There was some discussion of HDF5 and c++ recently on
>>>> this list (See:
>>>> ). And also on the trac list in October.
>>>> In relation to these, our group has been having several problems
>>>> related to HDF5 and c++ recently.
>>>>      On many of the production environments where we run, there is no
>>>> hdf5 build available which includes cpp support.  In particular a
>>>> failed when searching for libhdf5_hl_cpp.   We worked around this by
>>>> removing these libraries from the list in
>>>> ExternalLibraries/HDF5/HDF5.sh.  This seemed to work, but required our
>>>> hacking the repository version of the code and presumably could cause
>>>> failure with any thorns needing HDF5 C++ support.
>>>>     At the same time (actually going back to the first ETK release) I
>>>> have had difficulty compiling on MacOS, (the macports hdf5-18 doesn't
>>>> support fortran or c++ with openmpi).  I don't generally need hdf5
>>>> I'm doing development on my laptop, but it would be good to have it
>>>> working.  I recently tried using the HDF5=BUILD option on Mac, but
>>>> seemed to lead to the same problem in different form.  The HDF5
>>>> configuration failed with a complaint that --enable-cxx was
>>>> with MPI compilers.
>>>>     Getting to the point now, I have some questions:
>>>> 1. Is there a good reason why HDF5 needs the C++ libraries in Cactus?
>>>> 2. Does hdf5 1.8.5 even support the c++ interface?
>>>> 3. What should we be doing differently to work around these issues?
>>>Yes, we have source code that calls HDF5 from C++, and also code that
>>>calls HDF5 from Fortran. We therefore use HDF5 with both C++ and
>>>Fortran interfaces enabled. At the same time we build only the serial
>>>version, because the parallel version does not support the C++
>>>interface (for whatever reason).
>>>If the system HDF5 library is not good enough, then this should be
>>>auto-detected, and Cactus should build HDF5 on its own. You can also
>>>specify this manually with HDF5=BUILD. This should work -- this is our
>>>catch-all fallback solution and is supposed to be very robust (except
>>>on systems where the HDF5 configure-make-make install steps don't
>>>Your problems read as if you tried to build a parallel version of
>>>HDF5. This should not happen on its own. Did you enable that yourself?
>>>Erik Schnetter <schnetter at cct.lsu.edu>
>>>Users mailing list
>>>Users at einsteintoolkit.org
>Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/

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