Bug#703439: H5Cpp.h missing in libhdf5-openmpi-dev and libhdf5-mpich2-dev?

2015-08-14 Thread Sylwester Arabas 

Package: libhdf5-mpi-dev
Version: 1.8.13

Hello,

Let me ping about the issue.

In my understanding, the unsupportedness, as in the case of 
C++/threading, is not meaning unusability, but rather incompleteness. 
Yet, in the case of C/C++ one can workaround the incompleteness with 
C-API calls while still using existing features of the C++ API.


Is there any really good reason not to enable it (having in mind that 
the unsupported threading/C++ combination is enabled)?


Thanks,
Sylwester

--
http://www.igf.fuw.edu.pl/~slayoo/

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Bug#703439: H5Cpp.h missing in libhdf5-openmpi-dev and libhdf5-mpich2-dev?

2013-03-19 Thread Sylwester Arabas 

Package: libhdf5-mpi-dev
Version: 1.8.10-patch1-1~exp2

Hello,

The libhdf5-dev package contains the /usr/include/H5Cpp.h file (the C++ 
API header for HDF5). It is not provided by any of the 
libhdf5-openmpi-dev and libhdf5-mpich2-dev packages. Is it intentional?


Thanks for help,
Sylwester

--
http://www.igf.fuw.edu.pl/~slayoo/

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Re: netcdf4/hdf5/mpi (-dev) on Debian sid

2012-01-31 Thread Sylwester Arabas 
Hi again,

On Jan 30, 2012, at 6:58 PM, Francesco P. Lovergine wrote:
 On Mon, Jan 30, 2012 at 04:16:40PM +0100, slayoo wrote:
 I'm trying to get a development set-up of the netcdf4 package
 on Debian sid with MPI-hdf5 support. Unfortunatelly, without sucess :(
 
 $ sudo apt-get -V install libhdf5-mpi-dev libnetcdf-dev
 ...
 Currently hdf5 does not provide an MPI version installable with the serial
 one, due to upstream bad habit of using the same name and sonames for all
 versions (serial,parallel and so on). So you have to use the serial version.
 One possibility would be providing parallel versions for all buildable
 chains of tools, as an alternative, but it would be very complicated.

Apparently, it seems that it's the only option - i.e. to provide
netcdf-openmpi, netcdf-mpich, ... etc packages. Here's an extract from
the netCDF source (libsrc4/nc4file.c):

  164 /* Get the 4-byte blob from the beginning of the file. Don't use posix
  165  * for parallel, use the MPI functions instead. */
  166 #ifdef USE_PARALLEL
  167if (use_parallel)
  168{
  169   MPI_File fh;
  170   MPI_Status status;
  171   int retval;
  172   if ((retval = MPI_File_open(comm, (char *)path, MPI_MODE_RDONLY,
  173   info, fh)) != MPI_SUCCESS)
  174  return NC_EPARINIT;
  175   if ((retval = MPI_File_read(fh, blob, MAGIC_NUMBER_LEN, MPI_CHAR,
  176   status)) != MPI_SUCCESS)
  177  return NC_EPARINIT;
  178   if ((retval = MPI_File_close(fh)) != MPI_SUCCESS)
  179  return NC_EPARINIT;
  180}
  181else
  182 #endif /* USE_PARALLEL */


So, if I get it right: if netCDF uses MPI calls within such ifdefs,
it has to be compiled with mpicc-like compiler calls, and hence the
binary packages for serial, openmpi, and mpich versions of netCDF
have to be different?

HTH,
Sylwester

--
http://www.igf.fuw.edu.pl/~slayoo/ 
Please consider your environmental responsibility before printing this e-mail.




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Re: netcdf4/hdf5/mpi (-dev) on Debian sid

2012-01-30 Thread Sylwester Arabas 
Hi Francesco,

Thanks for your answer.

On Jan 30, 2012, at 6:58 PM, Francesco P. Lovergine wrote:
 On Mon, Jan 30, 2012 at 04:16:40PM +0100, slayoo wrote:
 Dear Debian netcdf package maintainers,
 
 I'm trying to get a development set-up of the netcdf4 package
 on Debian sid with MPI-hdf5 support. Unfortunatelly, without sucess :(
 
 $ cat /etc/apt/sources.list | grep -v ^#
 deb http://ftp.icm.edu.pl/pub/Linux/debian/ sid main
 deb-src http://ftp.icm.edu.pl/pub/Linux/debian/ sid main
 $ sudo apt-get -V install libhdf5-mpi-dev libnetcdf-dev
 Reading package lists... Done
 Building dependency tree
 Reading state information... Done
 Some packages could not be installed. This may mean that you have
 requested an impossible situation or if you are using the unstable
 distribution that some required packages have not yet been created
 or been moved out of Incoming.
 The following information may help to resolve the situation:
 The following packages have unmet dependencies:
 libnetcdf-dev : Depends: libnetcdf6 (= 1:4.1.1-6+b1) but it is not
 going to be installed
 E: Broken packages
 
 Could you let me know if that's at all possible with Debian binary
 packages?
 Am I doing it the right way?
 
 
 Currently hdf5 does not provide an MPI version installable with the serial one

But I don't need the serial version at all. The only reason I wan't to install
HDF4 on this machine is to have the MPI IO available in netCDF4, and since it 
is implemented via HDF4 I need an MPI-enabled HDF4 install.

 ... due to upstream bad habit of using the same name and sonames for all
 versions (serial,parallel and so on). So you have to use the serial version.
 One possibility would be providing parallel versions for all buildable
 chains of tools, as an alternative, but it would be very complicated.
 See #591346 for information about this issue and try to convince upstream
 to support at least properly parallel flavors.

If I understand correctly, this bug refers to a hdf-mpi/hdf-serial conflict,
so again: my issue if kind of different.

Thanks,
Sylwester

--
http://www.igf.fuw.edu.pl/~slayoo/ 
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