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

Tue Oct 11 21:51:18 PDT 2016

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-ta5yRYsqeUsEDgxhc
> qsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1I
> YuzKV_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_access
> or.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-ta5yRYsqeUsEDgxhc
> qsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1I
> YuzKV_Zk&m=Iq5T1c5Ha5z1DNUXITqTR6TqZrHmG0TGyTBNKgmBzD8&s=6MI
> BgqN12tDhwVHiA6hEsfXoTH76VQwsXmsP_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>_______________________________________________
> > Aspect-devel mailing list
> > Aspect-devel at geodynamics.org
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> TR6TqZrHmG0TGyTBNKgmBzD8&s=ogNzlC_wGb2zMkzTsld5m3T70_VQl7kUXOk946_cHSM&e=
> >
> >
> >
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>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/
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