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

[Timo Heister]

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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-- 
Timo Heister
http://www.math.clemson.edu/~heister/