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

Thu Oct 13 11:29:34 PDT 2016

Firstly, make sure you’re doing a completely clean install, removing all the previous. If this persists, I think it’s best to open an issue on the dealii github page https://github.com/dealii/deali/issues/new , as this is brand new code (feel free to do this, just adding the info you provided below). As a fix in the meantime, it may be enough to remove the word ‘typename’ from /home/lev/aspect/dealii/source/grid/grid_reordering.cc line 558. When reporting the bug (if it persists), it will probably be helpful to provide the compiler version.

Sam

On 13 Oct 2016, at 18:57, Lev Karatun <lev.karatun at gmail.com<mailto:lev.karatun at gmail.com>> wrote:

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