Re: big issue with latest hdf5 upgrade to 1.10 in stretch
Christoph is right. Med-ficher fails on autopkgtests since the last
NMU. Unit tests are also failing, but they are not causing FTBFSs
due to explicit ignoring of its failures.
@Christoph, is there any chance to fix it in med-ficher?
Regards
Anton
2017-02-13 15:12 GMT+01:00 Christophe Trophime
<christophe.trophime@lncmi.cnrs.fr>:
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> Christophe TROPHIME
> Research Engineer
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> ----- Original Message -----
>> From: "Gilles Filippini" <pini@debian.org>
>> To: "Christophe Trophime" <christophe.trophime@lncmi.cnrs.fr>
>> Cc: dparsons@debian.org, debian-science@lists.debian.org
>> Sent: Monday, February 13, 2017 10:56:40 AM
>> Subject: Re: big issue with latest hdf5 upgrade to 1.10 in stretch
>>
>> Hi,
>>
>> On 2017-02-13 10:49, Christophe Trophime wrote:
>> > ----- Original Message -----
>> >> From: "Drew Parsons" <dparsons@debian.org>
>> >> To: "Christophe Trophime" <christophe.trophime@lncmi.cnrs.fr>,
>> >> debian-science@lists.debian.org
>> >> Sent: Monday, February 13, 2017 10:34:23 AM
>> >> Subject: Re: big issue with latest hdf5 upgrade to 1.10 in stretch
>> >>
>> >> On Mon, 2017-02-13 at 08:46 +0100, Christophe Trophime wrote:
>> >> > Hi,
>> >> > I would like to draw your attention to a problem that makes several
>> >> > packages unusable.
>> >> >
>> >> > Since the upgrade of hdf5 to version 1.10 there is an issue with the
>> >> > med-fichier library
>> >> > which is used for several packages including gmsh, code_saturne,
>> >> > code_aster.
>> >> >
>> >> > Actually med-fichier 3.xx do not support hdf5 format for version
>> >> > greater than 1.8.xx.
>> >> > So the upgrade of hdf5 breaks all the packages that rely on med-
>> >> > fichier library.
>> >> > This is a big issue especially as hdf5 1.10 will be in the next
>> >> > stable debian version.
>> >>
>> >>
>> >> What is the failure mode? med-fichier 3.0.6-10.1 has already been
>> >> patched to build against hdf5 1.10.
>> >>
>> >
>> > Typical failure is the following from Salome Forum:
>> > 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
>> > """
>> >
>> > Basically you can generate file but can no longer read it...
>>
>> Something like a test case as simple as possible would help.
>> Thanks in advance,
>
> Take any med file from saturne, aster and salome and you will run into the problem...
> It's maybe more a break of compatibility from med-fichier with hdf5 1.8.xx
>
>
>>
>> _g.
>>
>>
>
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