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

[Debian Bug Tracking System]

Processing control commands:

> tag -1 + patch
Bug #855130 [src:med-fichier] med-fichier: MED library is not compatible with 
HDF5 1.10
Added tag(s) patch.

-- 
855130: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=855130
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

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

[Gilles Filippini]

On Wed, 15 Feb 2017 20:05:59 +0100 Anton Gladky wrote:

thanks for your effort on this bug, very appreciate. Unfortunately
the provided patch does not solve the problem. med-fichier still
fails on autopkgtests and unit tests. I have to remove the patch
tag.


I've received a patch from upstream fixing almost everything. Just 2
testcases still failing. It'll need a bit more work.

Thx,

_g.

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

[Debian Bug Tracking System]

Processing control commands:

> tags -1 - patch
Bug #855130 [src:med-fichier] med-fichier: MED library is not compatible with 
HDF5 1.10
Removed tag(s) patch.

-- 
855130: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=855130
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

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

[Anton Gladky]

Control: tags -1 - patch

Hi Gilles,

thanks for your effort on this bug, very appreciate. Unfortunately
the provided patch does not solve the problem. med-fichier still
fails on autopkgtests and unit tests. I have to remove the patch
tag.

Best regards

Anton


2017-02-15 9:41 GMT+01:00 Gilles Filippini :
> Control: tags -1 + patch

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,

_gdiff -Nru med-fichier-3.0.6/debian/changelog med-fichier-3.0.6/debian/changelog
--- med-fichier-3.0.6/debian/changelog	2016-10-30 18:06:27.0 +0100
+++ med-fichier-3.0.6/debian/changelog	2017-02-13 18:02:35.0 +0100
@@ -1,3 +1,11 @@
+med-fichier (3.0.6-10.2) unstable; urgency=medium
+
+  * Non-maintainer upload
+  * New patch type_hdf_should_be_hid_t.patch fixing HDF5 1.10 support
+for the C API (closes: #855130)
+
+ -- Gilles Filippini   Mon, 13 Feb 2017 18:02:35 +0100
+
 med-fichier (3.0.6-10.1) unstable; urgency=medium
 
   * Non-maintainer upload
diff -Nru med-fichier-3.0.6/debian/patches/series med-fichier-3.0.6/debian/patches/series
--- med-fichier-3.0.6/debian/patches/series	2016-10-20 21:58:54.0 +0200
+++ med-fichier-3.0.6/debian/patches/series	2017-02-13 18:02:35.0 +0100
@@ -2,3 +2,4 @@
 hdf5_link.patch
 clang-ftbfs.diff
 fix-fid-type-in-medequivinfo.patch
+type_hdf_should_be_hid_t.patch
diff -Nru med-fichier-3.0.6/debian/patches/type_hdf_should_be_hid_t.patch med-fichier-3.0.6/debian/patches/type_hdf_should_be_hid_t.patch
--- med-fichier-3.0.6/debian/patches/type_hdf_should_be_hid_t.patch	1970-01-01 01:00:00.0 +0100
+++ med-fichier-3.0.6/debian/patches/type_hdf_should_be_hid_t.patch	2017-02-13 18:02:35.0 +0100
@@ -0,0 +1,152 @@
+Index: med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumLire232.c
+===
+--- med-fichier-3.0.6.orig/src/2.3.6/hdfi/MEDdatasetNumLire232.c
 med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumLire232.c
+@@ -71,8 +70,8 @@ void  _MEDdatasetNumLire232(int dummy,..
+   med_size   start_mem[1],start_data[1],*pflmem=0,*pfldsk=0;
+   med_size   stride[1],count[1],pcount[1],size[1],pflsize[1];
+   med_errret;
+-  inti,j,index,type_hdf;

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.