Bug#667599: hdf5 upgrade Squeeze-> Wheezy (#667599, #667526)

Ana Guerrero ana at debian.org
Mon Jan 28 10:17:32 UTC 2013


There are *two* problems with the upgrade of hdf5 from Squeeze to Wheezy
that are a consequence of the problem of the fix for #566541.
One of then, reported in (#667599, #667526), can be solved easily
as explained by marga at
and others have hinted before. The second problem is related with this one
and more complicated to solve. I haved filed the bug report #699155 for this.

About this problem, in short, if you have installed the openmpi version,
the upgrade will install you the serial implementation,  and remove
the openmpi implementation.

E.g. minimal installation of squeeze where libhdf5-openmpi-1.8.4 and 
hdf5-tools are installed:

ii  hdf5-tools                          1.8.4-patch1-2               Hierarchical Data Format 5 (HDF5) - Runtime tools                    
ii  libhdf5-openmpi-1.8.4               1.8.4-patch1-2               Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version  

ii  libhdf5-serial-1.8.4                1.8.4-patch1-2               Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii  r-cran-hdf5                         1.6.9-2+b1                   GNU R package interfacing the NCSA HDF5 library    

If we update this system to Wheezy, you'll get:

# apt-get -u dist-upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
The following packages will be REMOVED:
  console-terminus defoma libept1 libhdf5-openmpi-1.8.4 libpango1.0-common libperl5.10 portmap x-ttcidfont-conf
The following NEW packages will be installed:
   368 upgraded, 174 newly installed, 8 to remove and 0 not upgraded.
Need to get 252 MB of archives.
After this operation, 302 MB of additional disk space will be used.
Do you want to continue [Y/n]? 

The openmpi version is upgraded with the serial version instead of being
replaced with libhdf5-openmpi-7.

In the case of dolfin-dev (#667599) in Squeeze, the package has the following 
dependency chain to hdf5 (as somebody else has analyzed already in the bug report):

dolfin-dev -> libdolfin1.0-dev -> libslepc3.0.0-dev -> libslepc3.0.0 -> libhdf5-openmpi-1.8.4 

and when upgraded, we have the reported problem.
In wheezy, libslepc3.2 depends explicitiy on the openmpi version only. 
This means if we install libslepc3.0.0 in wheezy we must switch all our system
to use the openmpi library.

For simgear-dev (#667526), the chain dependency  in Squeeze is:
simgear-dev -> simgear1.9.1 ->  libopenscenegraph65 -> libgdal1-1.6.0 -> libhdf5-serial-1.8.4 | libhdf5-1.8.4

Where libhdf5-1.8.4 could be provided by libhdf5-openmpi-1.8.4 and we have
the same problem that with dolfin-dev. Although in this case the dependency
can be satisfied both by the serial and the openmpi packages in Wheezy.
This is wrong because both libraries provided different ABIs as reported
in bug #699155

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