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

January 30th, 2012 - 01:10 am ET by Steve M. Robbins | Report spam
Package: libhdf5-mpi-dev
Version: 1.8.8-5
Severity: important

I can install libhdf5-mpi-dev
I can install libnetcdf-dev
but I cannot install both together:

root@riemann:/tmp/minc-2.1.00# apt-get install libhdf5-mpi-dev libnetcdf-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libnetcdf-dev is already the newest version.
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:
libhdf5-mpi-dev : Depends: libhdf5-openmpi-dev but it is not going to be installed
E: Broken packages

If I add dependencies libhdf5-openmpi-dev, etc), I eventually come to:

root@riemann:/tmp/minc-2.1.00# apt-get install libhdf5-mpi-dev libnetcdf-dev libhdf5-openmpi-dev libhdf5-openmpi-7 libnetcdf6
Reading package lists... Done
Building dependency tree
Reading state information... Done
libnetcdf-dev is already the newest version.
libnetcdf6 is already the newest version.
libnetcdf6 set to manually installed.
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:
libhdf5-7 : Conflicts: libhdf5-1.8
Conflicts: libhdf5-7
libhdf5-openmpi-7 : Conflicts: libhdf5-1.8
Conflicts: libhdf5-7
E: Broken packages

Now I'm really confused: libhdf5-7 conflicts with itself?

-Steve


Debian Release: wheezy/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 3.1.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages libhdf5-mpi-dev depends on:
ii libhdf5-openmpi-dev <none>
ii mpi-default-dev 1.0.1

libhdf5-mpi-dev recommends no packages.

libhdf5-mpi-dev suggests no packages.



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#1 Sylvestre Ledru
January 31st, 2012 - 10:50 am ET | Report spam
reassign 657949 hdf5
forcemerge 591346 657949
thanks

Le lundi 30 janvier 2012 à 00:02 -0600, Steve M. Robbins a écrit :
Package: libhdf5-mpi-dev
Version: 1.8.8-5
Severity: important

I can install libhdf5-mpi-dev
I can install libnetcdf-dev
but I cannot install both together:


Even if I am not happy about this change, it is expected.
libnetcdf-dev depends on libnetcdf7 which depends on libhdf5-7.
libhdf5-openmpi-7 conflicts with libhdf5-7.

Before I had the silly idea to become a hdf5 maintainer, I reported this
bug myself #591346.
For now, I haven't find the right solution to tackle this issue ...
Suggestions are welcome.

Now I'm really confused: libhdf5-7 conflicts with itself?


No, it doesn't.
There is a confusion between the name of the "Provides:" libhdf5-7
and the package name "also" libhdf5-7.

Sylvestre





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#2 Steve M. Robbins
January 31st, 2012 - 11:10 pm ET | Report spam

On Tue, Jan 31, 2012 at 04:41:06PM +0100, Sylvestre Ledru wrote:
reassign 657949 hdf5
forcemerge 591346 657949
thanks

Le lundi 30 janvier 2012 à 00:02 -0600, Steve M. Robbins a écrit :
> Package: libhdf5-mpi-dev
> Version: 1.8.8-5
> Severity: important
>
> I can install libhdf5-mpi-dev
> I can install libnetcdf-dev
> but I cannot install both together:
Even if I am not happy about this change, it is expected.



Unfortunately, minc build-depends on both these packages, so this
breaks the minc build. (Similarly, it breaks cdo; see #657669).

Now what?

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.

Thanks,
-Steve







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#3 Sylvestre Ledru
February 01st, 2012 - 09:30 am ET | Report spam
Le mardi 31 janvier 2012 à 21:56 -0600, Steve M. Robbins a écrit :
On Tue, Jan 31, 2012 at 04:41:06PM +0100, Sylvestre Ledru wrote:
> reassign 657949 hdf5
> forcemerge 591346 657949
> thanks
>
> Le lundi 30 janvier 2012 à 00:02 -0600, Steve M. Robbins a écrit :
> > Package: libhdf5-mpi-dev
> > Version: 1.8.8-5
> > Severity: important
> >
> > I can install libhdf5-mpi-dev
> > I can install libnetcdf-dev
> > but I cannot install both together:
> Even if I am not happy about this change, it is expected.

Unfortunately, minc build-depends on both these packages, so this
breaks the minc build. (Similarly, it breaks cdo; see #657669).

Now what?


For now, unfortunately, I don't have any solution to offer.
Sorry :/

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.

Sylvestre




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#4 Francesco P. Lovergine
February 01st, 2012 - 11:50 am ET | Report spam
On Tue, Jan 31, 2012 at 04:41:06PM +0100, Sylvestre Ledru wrote:
Even if I am not happy about this change, it is expected.
libnetcdf-dev depends on libnetcdf7 which depends on libhdf5-7.
libhdf5-openmpi-7 conflicts with libhdf5-7.

Before I had the silly idea to become a hdf5 maintainer, I reported this
bug myself #591346.
For now, I haven't find the right solution to tackle this issue ...
Suggestions are welcome.




The solution is having upstream adopting a sane naming scheme for mpi-enabled
flavor libraries instead of using always the same names for all. Unfortunately
they were still not available for that at the time of my last poking.
Diverging from upstream is not a good idea, so we still have to live in a non
perfect world...

Francesco P. Lovergine



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#5 Francesco P. Lovergine
February 10th, 2012 - 06:20 pm ET | Report spam
On Wed, Feb 01, 2012 at 09:57:39AM +0100, Sylvestre Ledru wrote:
Le mardi 31 janvier 2012 à 21:56 -0600, Steve M. Robbins a écrit :
> On Tue, Jan 31, 2012 at 04:41:06PM +0100, Sylvestre Ledru wrote:
> > reassign 657949 hdf5
> > forcemerge 591346 657949
> > thanks
> >
> > Le lundi 30 janvier 2012 à 00:02 -0600, Steve M. Robbins a écrit :
> > > Package: libhdf5-mpi-dev
> > > Version: 1.8.8-5
> > > Severity: important
> > >
> > > I can install libhdf5-mpi-dev
> > > I can install libnetcdf-dev
> > > but I cannot install both together:
> > Even if I am not happy about this change, it is expected.
>
> Unfortunately, minc build-depends on both these packages, so this
> breaks the minc build. (Similarly, it breaks cdo; see #657669).
>
> Now what?
For now, unfortunately, I don't have any solution to offer.
Sorry :/

> 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.

Sylvestre





Sylvestre,

the right solution for me is fixing debian/shlibs.in in hdf5 to suggest
the right combinatin of serial AND parallel flavors:

libhdf5_cpp 7 @
libhdf5_fortran 7 @
libhdf5 7 @ | @ | @
libh5test 7 @ | @ | @
libhdf5_hl 7 @ | @ | @
libhdf5_hl_cpp 7 @ | @ | @
libhdf5hl_fortran 7 @ | @ | @

Does it make sense?

Francesco P. Lovergine



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