[dune-fem] Petsc test fails in parallel case

Thu Jul 31 13:45:25 CEST 2014

Hi all,

I ran the l2projection_petsc in the trunk of dune-fem, and it fails with both YaspGrid and ALUGrid.
I ran my little example with the trunk as well, and it fails likewise.
The error seems to be in the creation of the Petsc vector for the discrete function:

Exception [ErrorHandler:../../../dune/fem/misc/petsc/petsccommon.hh:80]: PETSc Error in the PETSc function 'VecScatterCreate_PtoS' at /usr/local_machine/petsc-3.5.0-source/src/vec/vec/utils/vpscat.c:2339: 'Petsc has generated inconsistent data'. Error message: 'ith 10 block entry 177 not owned by any process, upper bound 125'

Should you need any further info, just let me know.
Best,
Andrea
__________________________________________________________

Andrea Sacconi
PhD student, Applied Mathematics
AMMP Section, Department of Mathematics, Imperial College London,
London SW7 2AZ, UK
a.sacconi11 at imperial.ac.uk

________________________________________
From: Tobias Malkmus [tomalk at mathematik.uni-freiburg.de]
Sent: 31 July 2014 11:43
To: Sacconi, Andrea; Dedner, Andreas; dune-fem at dune-project.org
Subject: Re: [dune-fem] Petsc test fails in parallel case

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Hi Andrea

So now i agree that there is a petsc error.
For the release and your small test example i was abled to reproduce
the error you showed me in one of the mails.
I will have a look into it.

Best Tobias

On 07/31/2014 11:54 AM, Sacconi, Andrea wrote:
> Hi all,
>
> thanks for your answers!
>
> I think instead that there is a problem with Petsc, somewhere. I
> attach a very simple, silly example, which actually initialises
> Petsc and creates a grid and two discrete functions over it. This
> test fails _IN_PARALLEL_, where the first discrete function is
> created. If I replace the Petsc discrete function with either an
> ISTL block vector function or an Adaptive Discrete Function,
> everything works fine.
>
> I cut part of the test, where I actually assemble a mass matrix and
> test the CG solver from Petsc and compare its performance to the CG
> Inverse Operator from dune-fem and the CG from ISTL. Again, Petsc
> doesn't proceed (same error above), while both dune-fem and ISTL
> classes work perfectly fine.
>
> I forgot to mention, I'm using the stable release 1.4.0 and not the
> trunk.
>
> Cheers, Andrea
> __________________________________________________________
>
> Andrea Sacconi PhD student, Applied Mathematics AMMP Section,
> Department of Mathematics, Imperial College London, London SW7 2AZ,
> UK a.sacconi11 at imperial.ac.uk
>
> ________________________________________ From:
> dune-fem-bounces+a.sacconi11=imperial.ac.uk at dune-project.org
> [dune-fem-bounces+a.sacconi11=imperial.ac.uk at dune-project.org] on
> behalf of Tobias Malkmus [tomalk at mathematik.uni-freiburg.de] Sent:
> 31 July 2014 10:02 To: Dedner, Andreas; dune-fem at dune-project.org
> Subject: Re: [dune-fem] Petsc test fails in parallel case
>
> Hi Andreas
>
> I tested it with YaspGrid<2> and the test fails, due to some
> communication errors within Yasp. Since the problem also exists for
> the l2projection_istl test i assume that this is a bug which is not
> related to Petsc.
>
> Best Tobias
>
> On 07/31/2014 10:35 AM, Dedner, Andreas wrote:
>> Hi Tobias. Thanks for taking a look.. Could you repeat the test
>> with yasp<2> because that was the default in the test within the
>> release version. Thanks Andreas
>
>
>> Sent from Samsung Mobile
>
>
>> -------- Original message -------- From: Tobias Malkmus
>> Date:31/07/2014 09:14 (GMT+00:00) To: dune-fem at dune-project.org
>> Subject: Re: [dune-fem] Petsc test fails in parallel case
>
>> Hi Andrea and Andreas
>
>> I tested the l2projection test for petsc (now in
>> dune/fem/test/l2projection_petsc) and the solver example within
>> the howto with the newest petsc version ( 3.5 ).
>
>> I can not see any problems in parallel/ serial using
>> ALURGRID_SIMPLEX as the grid type and openmpi 1.8.1 in the master
>> branch.
>
>> For the release branch the 'old' test fails at another place. I
>> will look into it. The solver example still works fine.
>
>> As Andreas allready said, petsc tries to catch all errors and
>> reports them to dune. Dune (fem) reports them as a Petsc error,
>> although it might be a SegFault or an other system error.
>
>> In you case Andrea, Petsc reports a segmentation fault: PETSC
>> ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>
>> First try to compile this test with CXXFLAGS="-Wall -g" to enable
>> all the asserts. Please report the error messages from this
>> test.
>
>> Could you please further check wether the solver example in the
>> howto shows the same behavior.
>
>
>> Best Tobias
>
>> On 07/30/2014 10:18 PM, Andreas Dedner wrote:
>>> Hi Andrea.
>
>>> That test has apparently been removed from dune-fem  - at least
>>> it is not there in the master. So it might be old....
>
>>> I had a short look. I seems to me that if you only compile
>>> l2projection then it does not use petsc. You need
>>> PETSCLINEAROPERATOR == 1 and that is defined if you compile
>>> l2projection_petscmatrix And have usepetsc: true in the
>>> parameter file.
>
>>> So I don't really see why you are getting a petsc error with
>>> l2projextion since it should not be using petsc.... But perhaps
>>> I missed something. Have you tried the example in the
>>> dune-fem-howto - I am sure that that worked with the older
>>> version of petsc.
>
>>> I tested it myself and I also get an error. In my case an
>>> assert is triggered. Are you defining NDEBUG? If so then that
>>> might explain the problem and I have noticed that sometimes
>>> there when is a segmentation fault somewhere a petsc error is
>>> produced although it has nothing to do with petsc So perhaps
>>> that is what is happing here.
>
>>> The assert btw. is incodimindexset.hh with some invalide index
>>> being used. That is going to need a bit more investigation I'm
>>> afraid. Could you please also test the example_solver from the
>>> dune-fem-howto - I just don't want to fix some test in
>>> dune-fem which is not used anymore anyway....
>
>>> Best Andreas
>
>
>>> On 30/07/14 18:50, Sacconi, Andrea wrote:
>>>> Hi all,
>>>>
>>>> I would like to ask you another question about Petsc and its
>>>> usage in dune-fem. Recently, I installed the latest release
>>>> of this library (3.5.0), and thanks to a patch from Tobias
>>>> Malkmus, it now compiles correctly with dune-fem-1.4.0.
>>>>
>>>> I ran the demo test contained in
>>>> dune/fem/petsc/tests/l2projection, and I am sorry to say that
>>>> it failed in the parallel case. You can find attached the
>>>> output of the parallel run with 4 processors.
>>>>
>>>> Some additional info:
>>>>
>>>> gcc version 4.8.2 OpenMPI 1.6.5 Parmetis: 4.0.3 Petsc 3.5.0)
>>>> >> I don't know what I'm doing wrong, since I ran the demo
>>>> tests in Petsc and they all passed without errors. If you
>>>> need any further information, just let me know.
>>>>
>>>> Cheers, Andrea
>>>> __________________________________________________________
>>>>
>>>> Andrea Sacconi PhD student, Applied Mathematics AMMP
>>>> Section, Department of Mathematics, Imperial College London,
>>>> London SW7 2AZ, UK a.sacconi11 at imperial.ac.uk
>>>>
>>>>
>>>> _______________________________________________ dune-fem
>>>> mailing list dune-fem at dune-project.org
>>>> http://lists.dune-project.org/mailman/listinfo/dune-fem
>
>
>
>
>>> _______________________________________________ dune-fem
>>> mailing list dune-fem at dune-project.org
>>> http://lists.dune-project.org/mailman/listinfo/dune-fem
>
>
>
>
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>
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- --
Tobias Malkmus                 <tomalk at mathematik.uni-freiburg.de>

Mathematisches Institut               Tel: +49 761 203 5627
Abt. für Angewandte Mathematik        Universität Freiburg
Hermann-Herder-Str. 10
79104 Freiburg

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