[aspect-devel] get_dof_indices() only works on active cells

Thu Oct 13 11:58:47 PDT 2016

Lev,

please open an issue on deal.II github. In the mean time, just try to
delete the typename in dealii/source/grid/grid_reordering.cc line 558

Best

Bruno

2016-10-13 13:57 GMT-04:00 Lev Karatun <lev.karatun at gmail.com>:
> Thank you Sam!!
>
> I'm having trouble compiling the latest version of dealII unfortunately:
> [ 86%] Building CXX object
> source/grid/CMakeFiles/obj_grid.release.dir/grid_reordering.cc.o
> /home/lev/aspect/dealii/source/grid/grid_reordering.cc: In function ‘void
> dealii::internal::GridReordering2d::orient_one_set_of_parallel_edges(const
> std::vector<dealii::internal::GridReordering2d::Cell<2>,
> std::allocator<dealii::internal::GridReordering2d::Cell<2> > >&,
> std::vector<dealii::internal::GridReordering2d::Edge<2>,
> std::allocator<dealii::internal::GridReordering2d::Edge<2> > >&, unsigned
> int, unsigned int)’:
> /home/lev/aspect/dealii/source/grid/grid_reordering.cc:558: error: using
> ‘typename’ outside of template
>
> I understand it's not due to the change that you made though. Is it best to
> post this error message to dealII google group or is this mailing list fine?
>
> Best regards,
> Lev Karatun.
>
> 2016-10-13 9:58 GMT-04:00 Cox, Samuel P. <spc29 at leicester.ac.uk>:
>>
>> Hi Lev,
>>
>> I’ve posted a pull request at https://github.com/dealii/dealii/pull/3232
>> to fix this subtle bug. It’s a single line change. Thanks for your tips on
>> making the example smaller - it certainly helped!
>>
>> Bests,
>> Sam
>>
>>
>> On 12 Oct 2016, at 05:51, Lev Karatun <lev.karatun at gmail.com> wrote:
>>
>> Hi John, Sam, Timo,
>>
>> Thank you for the replies. The bug does occur on the updated version of
>> dealII. If I turn off periodic boundaries the solver fails to converge
>> exactly the step after the 1st refinement cycle (not counting the initial
>> one). When I disabled the adaptive refinement the error occurs at timestep
>> 30 instead of 10. When I disable both refiement and periodic b.c., the code
>> runs without any problems.
>>
>>> Do you mean that identical runs give an error at different time steps, or
>>> that varying some parameters changes the time of the error’s appearance?
>>
>> the latter. For example, if I change the frequency of mesh refinement from
>> 10 to 5 or 7 times steps, the code just hangs at timestep following the
>> refinemet instead. When I changed it to 3, the error occured after time step
>> 6 (2nd refinement cycle).
>>
>>> A smaller test case (since we're really interested in the mesh, not the
>>> multiple iterative solves and matrix assemblies) would definitely help.
>>
>>
>> I understand that, but unfortunately I wasn't able to reproduce the
>> problem on a small setup. The only things that I was able to simplify is
>> replacing the solver with IMPES and changing refinement frequency to 3 time
>> steps (in this case error occurs after the 6th time step)
>>
>> Best regards,
>> Lev Karatun.
>>
>> 2016-10-11 13:05 GMT-04:00 Cox, Samuel P. <spc29 at leicester.ac.uk>:
>>>
>>> I managed to get this running, but am not sure yet what is going on, as I
>>> can't devote any time to it.
>>>
>>> I'm using the latest dealii as of yesterday, so it includes the fix Timo
>>> mentioned.
>>>
>>> On 6 cores it crashed as Lev said, after timestep 10 after it adapts the
>>> mesh.
>>>
>>> On one core, it ran until timestep 11, failing to converge one of the
>>> solves. So it didn't hit the bug. If these are reproducible (I'm not going
>>> to try as the 1-core took me over 2h to run) it looks like some combination
>>> of periodicity and non-local ownership breaks the logic of the sparsity
>>> pattern function. That's as far as I've got. A smaller test case (since
>>> we're really interested in the mesh, not the multiple iterative solves and
>>> matrix assemblies) would definitely help.
>>>
>>> Sam
>>>
>>>
>>> On 11 Oct 2016 5:50 pm, Timo Heister <heister at clemson.edu> wrote:
>>>
>>> Lev,
>>>
>>> you are running into a bug that was fixed 5 days ago in the
>>> development version of deal.II:
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_pull_3210&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=Iq5T1c5Ha5z1DNUXITqTR6TqZrHmG0TGyTBNKgmBzD8&s=h1swr-LDAIQYp0muY6f7qBSHRxHD_KRiASfFbKV_zkk&e=
>>>
>>> It only happens if you use the development version of deal.II with DG
>>> and periodic boundaries. So you can update deal.II or change your
>>> setup.
>>>
>>> On Tue, Oct 11, 2016 at 2:19 AM, John Naliboff <jbnaliboff at ucdavis.edu>
>>> wrote:
>>> > Hi Lev,
>>> >
>>> > Does the error only occur with the periodic boundary conditions and/or
>>> > mesh
>>> > refinement?
>>> >
>>> > I’m honestly not sure what the specific issue is here as it relates to
>>> > the
>>> > DG method and the error message below.  Ying, Sam, et al. will
>>> > hopefully an
>>> > idea.
>>> >
>>> > Cheers,
>>> > John
>>> >
>>> > *************************************************
>>> > John Naliboff
>>> > Assistant Project Scientist, CIG
>>> > Earth & Planetary Sciences Dept., UC Davis
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > On Oct 10, 2016, at 10:47 PM, Lev Karatun <lev.karatun at gmail.com>
>>> > wrote:
>>> >
>>> > Hi everyone,
>>> >
>>> > I was trying to run a model with the discontinuous boundaries feature,
>>> > and
>>> > got the following error:
>>> >
>>> > [titan:62377] *** An error occurred in MPI_Allreduce
>>> > [titan:62377] *** reported by process [140014581841921,0]
>>> > [titan:62377] *** on communicator MPI COMMUNICATOR 3 DUP FROM 0
>>> > [titan:62377] *** MPI_ERR_IN_STATUS: error code in status
>>> > [titan:62377] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
>>> > will
>>> > now abort,
>>> > [titan:62377] ***    and potentially your MPI job)
>>> >
>>> > After making the problem smaller and running in debug version, I got
>>> > the
>>> > following error:
>>> >
>>> > --------------------------------------------------------
>>> > An error occurred in line <3334> of file
>>> >
>>> > </home/lev/aspect/dealiitest/include/deal.II/dofs/dof_accessor.templates.h>
>>> > in function
>>> >     void dealii::DoFCellAccessor<DoFHandlerType,
>>> > lda>::get_dof_indices(std::vector<unsigned int, std::allocator<unsigned
>>> > int>
>>> >>&) const [with DoFHandlerType = dealii::DoFHandler<3, 3>, bool
>>> > level_dof_access = true]
>>> > The violated condition was:
>>> >     this->active()
>>> > Additional information:
>>> >     get_dof_indices() only works on active cells.
>>> >
>>> > Stacktrace:
>>> > -----------
>>> > #0  /home/lev/aspect/dealiitest/lib/libdeal_II.g.so.8.5.0-pre:
>>> > dealii::DoFCellAccessor<dealii::DoFHandler<3, 3>,
>>> > true>::get_dof_indices(std::vector<unsigned int,
>>> > std::allocator<unsigned
>>> > int> >&) const
>>> > #1  /home/lev/aspect/dealiitest/lib/libdeal_II.g.so.8.5.0-pre:
>>> > #2  /home/lev/aspect/dealiitest/lib/libdeal_II.g.so.8.5.0-pre: void
>>> > dealii::DoFTools::make_flux_sparsity_pattern<dealii::DoFHandler<3, 3>,
>>> > dealii::TrilinosWrappers::BlockSparsityPattern>(dealii::DoFHandler<3,
>>> > 3>
>>> > const&, dealii::TrilinosWrappers::BlockSparsityPattern&,
>>> > dealii::ConstraintMatrix const&, bool, dealii::Table<2,
>>> > dealii::DoFTools::Coupling> const&, dealii::Table<2,
>>> > dealii::DoFTools::Coupling> const&, unsigned int)
>>> > #3  ../aspect:
>>> > aspect::Simulator<3>::setup_system_matrix(std::vector<dealii::IndexSet,
>>> > std::allocator<dealii::IndexSet> > const&)
>>> > #4  ../aspect: aspect::Simulator<3>::setup_dofs()
>>> > #5  ../aspect: aspect::Simulator<3>::refine_mesh(unsigned int)
>>> > #6  ../aspect: aspect::Simulator<3>::maybe_refine_mesh(double, unsigned
>>> > int&)
>>> > #7  ../aspect: aspect::Simulator<3>::run()
>>> > #8  ../aspect: main
>>> > --------------------------------------------------------
>>> >
>>> >
>>> > --------------------------------------------------------------------------
>>> > mpirun noticed that process rank 1 with PID 60556 on node titan exited
>>> > on
>>> > signal 11 (Segmentation fault).
>>> >
>>> > --------------------------------------------------------------------------
>>> >
>>> >
>>> > Both Aspect and dealII are updated to the latest version. The problems
>>> > seems
>>> > to appear at different stages of the simulation, but always after a
>>> > mesh
>>> > refinement cycle. I attached the prm file used to reproduce the
>>> > problem. The
>>> > fork containing the plugins is here
>>> >
>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lkaratun_aspect_tree_nz&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=Iq5T1c5Ha5z1DNUXITqTR6TqZrHmG0TGyTBNKgmBzD8&s=6MIBgqN12tDhwVHiA6hEsfXoTH76VQwsXmsP_HsuO0M&e=
>>> > If someone could give me an idea of what can cause the problem, I would
>>> > appreciate it.
>>> >
>>> > Thanks in advance!
>>> >
>>> > Best regards,
>>> > Lev Karatun.
>>> > <268s_fail.prm>_______________________________________________
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>>> >
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>>> >
>>> >
>>> >
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>>> >
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>>>
>>> --
>>> Timo Heister
>>> http://www.math.clemson.edu/~heister/
>>> _______________________________________________
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>>>
>>>
>>>
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>>
>>
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