netcdf4/hdf5/mpi (-dev) on Debian sid
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? Thanks in advance, Best regards, Sylwester ___ Pkg-grass-devel mailing list Pkg-grass-devel@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-grass-devel
Re: netcdf4/hdf5/mpi (-dev) on Debian sid
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, 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. -- Francesco P. Lovergine ___ Pkg-grass-devel mailing list Pkg-grass-devel@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-grass-devel
Re: netcdf4/hdf5/mpi (-dev) on Debian sid
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/ Please consider your environmental responsibility before printing this e-mail. ___ Pkg-grass-devel mailing list Pkg-grass-devel@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-grass-devel
Re: netcdf4/hdf5/mpi (-dev) on Debian sid
Hi again, On Jan 30, 2012, at 7:29 PM, Sylwester Arabas wrote: >> ... >> 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. Quoting the netcdf INSTALL file: > 3.4.1 Building HDF5 for Parallel I/O > > For parallel I/O to work, HDF5 must be installed with -enable-parallel, > and an MPI library (and related libraries) must be made available to > the HDF5 configure... and > 3.4.3 Building NetCDF > - > To build netCDF with parallel I/O, build as usual, but point the > configure at a version of HDF5 that has been built for parallel I/O. HTH, Sylwester -- http://www.igf.fuw.edu.pl/~slayoo/ Please consider your environmental responsibility before printing this e-mail. ___ Pkg-grass-devel mailing list Pkg-grass-devel@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-grass-devel
Re: netcdf4/hdf5/mpi (-dev) on Debian sid
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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