Re: Bug#657949: Cannot install libhdf5-mpi-dev and libnetcdf-dev
On Tue, Feb 07, 2012 at 09:28:00AM +0000, Alastair McKinstry wrote:
> On 2012-02-02 01:43, Steve M. Robbins wrote:
> > Hi,
> >
> > I'd like to contribute towards a solution for this. I'm forwarding to
> > debian-devel to get some others' ideas.
> > Naively, I don't understand why netcdf can't offer multiple variants,
> > just as hdf5 does. Or, at least, one package libnetcdf-mpi-dev that
> > links with the "default" MPI implementation.
> >> I am not involved in the netcdf. You should report a bug on this
> >> package.
> > I'm prepared to do so, but I'd first like to get agreement that
> > netcdf is where the problem lies. Netcdf maintainers, please
> > chime in!
> >
> >
> > I think we can no longer live in the status quo (see all the blockers
> > of #631019), so something has to give. Even if it is painful, perhaps
> > Debian could pioneer something and pass patches back to upstream?
> >
> > Thoughts?
> >
> > -Steve
> >
> As of now, I have several packages (eg ADIOS, CDO) that used to build
> against netcdf and libhdf5-mpi-dev
> that don't. Without fixes to netCDF (I appreciate what Francesco says
> about netcdf upstream
> not giving the libraries proper names), there needs to be a regression:
> either the packages
> build with netcdf but no MPI, or MPI but no netcdf.
>
The problem is the following: with latest update to hdf5, the chain of
dependencies changed, so that now libnetcdf6 depends on the pure serial
version of hdf5, while the previous one depended on serial or parallel:
Version: 1:4.1.1-6+b1
Depends: libc6 (>= 2.7), libcurl3-gnutls (>= 7.16.2), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3), libhdf5-7 (>= 1.8.7), libquadmath0 (>= 4.6), libstdc++6 (>= 4.4.0)
Version: 1:4.1.1-6
Depends: libc6 (>= 2.7), libcurl3-gnutls (>= 7.16.2-1), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3), libhdf5-serial-1.8.4 | libhdf5-1.8.4, libquadmath0 (>= 4.6), libstdc++6 (>= 4.4.0)
So at least at packaging level, that should be fixed to follow the previous criteria.
That said, indeed NetCDF provides nc_create_par and nc_open_par in both serial
and parallel versions, but needs to be built with --enable-parallel to take
advantage of parallel I/O in HDF5, else it works in pure serial mode.
--
Francesco P. Lovergine
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