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

[Gilles Filippini]

Control: tags -1 + patch

On 2017-02-14 14:37, Gilles Filippini wrote:
> 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

Patch proposal attached.
Thanks,

_g
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