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Re: Bug#657949: Cannot install libhdf5-mpi-dev and libnetcdf-dev

Hi Francesco,

Do you recommend that we build the next NetCDF from 4.1.1 or should we
use the 4.1.3 from experimental as the base?


On 2012-02-07 13:17, Francesco P. Lovergine wrote:
> 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.

Alastair McKinstry  , <alastair@sceal.ie> , <mckinstry@debian.org>    http://blog.sceal.ie

Anyone who believes exponential growth can go on forever in a finite world
is either a madman or an economist - Kenneth Boulter, Economist.

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