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Bug#1114938: dune-grid: FTBFS in bookworm: Test #8: subsamplingvtktest ....................................***Failed

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  Bug#1114938: dune-grid: FTBFS in bookworm: Test #8: subsamplingvtktest ....................................***Failed Markus Blatt <markus@dr-blatt.de> - 2025-09-12 17:30 +0200
    Bug#1114938: dune-grid: FTBFS in bookworm: Test #8: subsamplingvtktest ....................................***Failed Markus Blatt <markus@dr-blatt.de> - 2025-09-15 08:30 +0200
    Bug#1114938: Alternative workaround in dune-grid for ftbfs Markus Blatt <markus@dr-blatt.de> - 2025-09-16 19:10 +0200
    Bug#1114938: patch available for vtk9 in bookworm (was Re: Bug#1114938: dune-grid: FTBFS in bookworm: Test #8: subsamplingvtktest ....................................***Failed) Santiago Vila <sanvila@debian.org> - 2025-09-16 20:20 +0200
      Bug#1114938: patch available for vtk9 in bookworm (was Re: Bug#1114938: dune-grid: FTBFS in bookworm: Test #8: subsamplingvtktest ....................................***Failed) Markus Blatt <markus@dr-blatt.de> - 2025-09-16 21:00 +0200

#397800 — Bug#1114938: dune-grid: FTBFS in bookworm: Test #8: subsamplingvtktest ....................................***Failed

HI

On 11.09.25 22:56, Santiago Vila wrote:
> Package: src:dune-grid
> Version: 2.9.0-2
> Severity: serious
> Control: fixed -1 2.10.0-1
> Tags: ftbfs bookworm
>
> Dear maintainer:
>
> During a rebuild of all packages in bookworm, your package failed to build.
>
> [ Note: The bug is marked as fixed with the version in trixie, but
>    packages in bookworm must still build in bookworm ].
>
> Below you will find how the build ends (probably the most relevant part,
> but not necessarily).
[... snip... ]
>
> 2025-09-07 09:09:32.467 (   0.232s) [        5DA9C040]       vtkXMLParser.cxx:375    ERR| vtkXMLDataParser (0x33894400): Error parsing XML in stream at line 28, column 0, byte index 1721: not well-formed (invalid token)
> 2025-09-07 09:09:32.467 (   0.232s) [        5DA9C040]       vtkXMLReader.cxx:521    ERR| vtkXMLUnstructuredGridReader (0x338a1620): Error parsing input file.  ReadXMLInformation aborting.
> 2025-09-07 09:09:32.467 (   0.232s) [        5DA9C040]       vtkExecutive.cxx:752    ERR| vtkCompositeDataPipeline (0x33869fe0): Algorithm vtkXMLUnstructuredGridReader(0x338a1620) returned failure for request: vtkInformation (0x3389eea0)
>    Debug: Off
>    Modified Time: 116247
>    Reference Count: 1
>    Registered Events: (none)
>    Request: REQUEST_INFORMATION
>    ALGORITHM_AFTER_FORWARD: 1
>    FORWARD_DIRECTION: 0
>
>
> ERROR in ./s0002-vtktest-3D-leafview-nonconforming-appendedraw.pvtu
> CHECK   FAILED:
> TEST    FAILED: 1/1 checks failed in this test.
> --------------------------------------------------------------------------
> Primary job  terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpiexec detected that one or more processes exited with non-zero status, thus causing
> the job to be terminated. The first process to do so was:


This is bug 1064762 that has now probably been added to bookworm by a 
patch to vtk9.

I can work around this here by simply deactivating test, but this kind 
of reading of the vtk files I cannot fix here. dune-grid just writes 
those files.

The underlying problem can only be fixed in VTK. though. It might affect 
other packes.

How should we proceed?

Best,

Markus

[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064762

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#398097

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On 12.09.25 17:58, Santiago Vila wrote:
> On Fri, Sep 12, 2025 at 04:58:33PM +0200, Markus Blatt wrote:
>
>> This is bug 1064762 that has now probably been added to bookworm by a patch
>> to vtk9.
>>
>> I can work around this here by simply deactivating test, but this kind of
>> reading of the vtk files I cannot fix here. dune-grid just writes those
>> files.
>>
>> The underlying problem can only be fixed in VTK. though. It might affect
>> other packes.
>>
>> How should we proceed?
> I think it all depends on much effort we[*] are willing to make.
>
> At this point in the life of bookworm (which is 2/3 of its supported
> period), there are already at least 60 different ftbfs bugs, so I
> would say that fixing the FTBFS problem alone (disabling the offending
> tests, if that's your plan and you know how to do it) would be more
> than acceptable and a lot better than nothing.

I'll start with that then.

This will leave the main problem, though:

Due to the security fix in expat [1], you will not be able to process 
any binary vtk files in bookworm
(e.g. visualize them in paraview) anymore.

To fix that we would need to backport [2] to vtk9

[1] 
https://tracker.debian.org/news/1647706/accepted-expat-250-1deb12u2-source-into-proposed-updates/

[2]<https://gitlab.kitware.com/vtk/vtk/-/issues/19258#note_1510307>https://gitlab.kitware.com/vtk/vtk/-/commit/db8f9efca220c9d16a30958e179abae3379d0011

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#398276 — Bug#1114938: Alternative workaround in dune-grid for ftbfs

Hi,

Am Mon, Sep 15, 2025 at 03:55:57PM +0200 schrieb Markus Blatt:
>
>As the problem appears also when trying to view vtk files in paraview, I opted to fix this
>in vtk. I did backport a fix that is already available in stable (to fix the same bug
>1064762, see [1]) to bookworm. This fixes running the tests in dune-grid
>and will prevent users of other packages experiencing problems when dealing with vtk files
>containing raw data.
>
>I am only a maintainer of dune-grid and cannot upload the fixed package myself. You will
>find the fix in branch bookworm on salsa [2] (based on the latest bookworm release). I simply
>cherry-picked the previous fix to bookworm.
>

In addition I have also provided a workaround in dune-grid on salsa in branch bookworm [3],
in case that is more convenient. I still think that fixing vtk9 is the better option, as it prevents
more problems.

Again I am only a maintainer of dune-grid and probably cannnot upload to bookworm (or at least
I do not know how). Would be cool if somebody would upload either of the approaches.

Best,

Markus

>
>[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064762
>[2] https://salsa.debian.org/science-team/vtk9/-/tree/bookworm?ref_type=heads

[3] <https://salsa.debian.org/science-team/dune-grid/-/tree/bookworm?ref_type=heads>

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#398281 — Bug#1114938: patch available for vtk9 in bookworm (was Re: Bug#1114938: dune-grid: FTBFS in bookworm: Test #8: subsamplingvtktest ....................................***Failed)

On Mon, Sep 15, 2025 at 03:55:57PM +0200, Markus Blatt wrote:

> As the problem appears also when trying to view vtk files in paraview, I opted to fix this
> in vtk. I did backport a fix that is already available in stable (to fix the same bug
> 1064762, see [1]) to bookworm. This fixes running the tests in dune-grid
> and will prevent users of other packages experiencing problems when dealing with vtk files
> containing raw data.
> 
> I am only a maintainer of dune-grid and cannot upload the fixed package myself. You will
> find the fix in branch bookworm on salsa [2] (based on the latest bookworm release). I simply
> cherry-picked the previous fix to bookworm.

Thanks a lot!

Since you already did the required work, fixing vtk9 properly looks
indeed the better option now.

I've converted your bookworm branch into a proper team upload (see the
most recent commit), which I plan to upload soon (with proper credit
of course).

Will probably ask you for help regarding the bug to release.debian.org
that we will have to send.

Cc: Anton Gladky, the usual maintainer, so that he is aware, and also
in case he has something to say about this.

Thanks.

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#398284 — Bug#1114938: patch available for vtk9 in bookworm (was Re: Bug#1114938: dune-grid: FTBFS in bookworm: Test #8: subsamplingvtktest ....................................***Failed)

Am Tue, Sep 16, 2025 at 08:10:46PM +0200 schrieb Santiago Vila:
>On Mon, Sep 15, 2025 at 03:55:57PM +0200, Markus Blatt wrote:
>
>> As the problem appears also when trying to view vtk files in paraview, I opted to fix this
>> in vtk. I did backport a fix that is already available in stable (to fix the same bug
>> 1064762, see [1]) to bookworm. This fixes running the tests in dune-grid
>> and will prevent users of other packages experiencing problems when dealing with vtk files
>> containing raw data.
>>
>> [...]
>
>Thanks a lot!
>
>Since you already did the required work, fixing vtk9 properly looks
>indeed the better option now.
>
>I've converted your bookworm branch into a proper team upload (see the
>most recent commit), which I plan to upload soon (with proper credit
>of course).
>

Cool. Looks good to me.

>Will probably ask you for help regarding the bug to release.debian.org
>that we will have to send.

Sure. I'll be glad to help if I can.

Markus

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