Bug#855130: med-fichier: MED library is not compatible with HDF5 1.10

[Gilles Filippini]

Source: med-fichier
Version: 3.0.6-11
Severity: grave
Justification: renders package unusable

Hi,

From the Salome Platform support forum [1]:

> Problems with Salome and Code Saturne in Debian
> Posted by Elektrix at January 03. 2017
> 
> Hello all,
> 
> I'm trying to set up a CFD case with Salome, export the mesh in a MED file and then process it with Code Saturne. CS doesn't read the MED file and gives the error in the preprocessing stage:
> 
> _MEDdatasetRd.c [139] : Erreur à la lecture du dataset
> _MEDdatasetRd.c [139] : COO
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
>   #000: ../../../src/H5Dio.c line 170 in H5Dread(): can't read data
>     major: Dataset
>     minor: Read failed
>   #001: ../../../src/H5Dio.c line 418 in H5D__read(): unable to set up type info
>     major: Dataset
>     minor: Unable to initialize object
>   #002: ../../../src/H5Dio.c line 953 in H5D__typeinfo_init(): not a datatype
>     major: Invalid arguments to routine
>     minor: Inappropriate type
> _MEDdatasetRd.c [142] : _dataset = 2
> _MEDdatasetRd.c [143] : _i = 0
> _MEDdatasetRd.c [144] : (*filter).memspace[_i] = 2
> _MEDdatasetRd.c [145] : (*filter).diskspace[_i] = 3
> _MEDmeshAdvancedRd30.c [462] : Erreur à la lecture du dataset
> _MEDmeshAdvancedRd30.c [462] :
> _MEDmeshAdvancedRd30.c [463] : meshname = "Mesh_water"
> _MEDmeshAdvancedRd30.c [463] : numit = -1
> _MEDmeshAdvancedRd30.c [463] : numdt = -1
> _MEDmeshAdvancedRd30.c [463] : _datagroupname2 = "NOE"
> _MEDmeshAdvancedRd30.c [464] : _datagroupname3 = ""
> _MEDmeshAdvancedRd30.c [464] : _profilename = "MED_NO_PROFILE_INTERNAL"
> 
> The problem can be because I installed Salome from the SALOME-7.6.0-DB07.tgz archive whilst Code Saturne is a Debian package and is installed via the Debian package system which is much easier than installing the original package. So the med and hdf5 libraries of CS come from the Debian repositories. I can't use newer versions of Salome (7.7.1 or 7.8.0) as they produce MED3.1 files but my CS reads only MED3.0 files.
> 
> The details of my machine:
> 
> Debian stretch (testing) on AMD64
> 
> Salome 7.6.0 from SALOME-7.6.0-DB07.tgz
> 
> Code Saturne 4.3 Debian package
> 
> libmed 3.0.6-10.1 Debian package
> 
> hdf5 1.10.0 Debian package
> 
> Not knowing if this problem comes from how I create the mesh I tried to run one of the test cases from the Code Saturne tutorials but ran into other problems.
> 
> If you need any other information pleas let me know. Any hint on how to go further is very welcome.
> 
> Best regards
> 
> Elektrix

....

> Re: Problems with Salome and Code Saturne in Debian
> Posted by Yvan Fournier at Monday 16:21
> 
> Hello,
> 
> I was contacted by the Debian maintainer relative to this, so it seems the bug was reported.
> 
> The root problem is that the MED library is not compatible with HDF5 1.10 yet. So reverting to HDF5 1.8 as indicated is the solution for now, but the better solution would be for MED to handle compatibility with both HDF5 1.8 and HDF5 1.10 (or at least 1.10 for future versions).
> 
> Best regards,
> 
> Yvan

[1] http://www.salome-platform.org/forum/forum_9/122041955

Thanks,

_g.