Re: big issue with latest hdf5 upgrade to 1.10 in stretch

[Christophe Trophime <christophe.trophime@lncmi.cnrs.fr>]

----- 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...

> libmed1v5 already depends on libhdf5-openmpi-100  1.10.0-patch1+docs-3
> 
> Drew
>