[aspect-devel] Boundary composition

Fri Sep 30 10:36:54 PDT 2016

Sorry about multiple emails, forgot to attach the prm file that I used.

Best regards,
Lev Karatun.

2016-09-30 13:32 GMT-04:00 Lev Karatun <lev.karatun at gmail.com>:

> Hi Timo,
>
> this is what I got from running debug mode through gdb:
>
> --------------------------------------------------------
> An error occurred in line <917> of file </home/lev/aspect/dealii_
> debug/include/deal.II/grid/tria_iterator.h> in function
>     const Accessor& dealii::TriaRawIterator<Accessor>::operator*() const
> [with Accessor = dealii::CellAccessor<3, 3>]
> The violated condition was:
>     Accessor::structure_dimension!=Accessor::dimension || state() ==
> IteratorState::valid
> The name and call sequence of the exception was:
>     ExcDereferenceInvalidCell(accessor)
> Additional Information:
> You tried to dereference a cell iterator for which this is not possible.
> More information on this iterator: level=-1, index=-1, state=past_the_end
>
> Stacktrace:
> -----------
> #0  /home/lev/aspect/aspect_debug/aspect: dealii::TriaRawIterator<dealii::CellAccessor<3,
> 3> >::operator*() const
> #1  /home/lev/aspect/aspect_debug/aspect: dealii::TriaRawIterator<dealii::CellAccessor<3,
> 3> >::operator->() const
> #2  /home/lev/aspect/dealii_debug/lib/libdeal_II.g.so.8.5.0-pre:
> dealii::CellAccessor<3, 3>::neighbor_of_neighbor_internal(unsigned int)
> const
> #3  /home/lev/aspect/aspect_debug/aspect: dealii::CellAccessor<3,
> 3>::neighbor_face_no(unsigned int) const
> #4  /home/lev/aspect/dealii_debug/lib/libdeal_II.g.so.8.5.0-pre:
> #5  /home/lev/aspect/dealii_debug/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)
> #6  /home/lev/aspect/aspect_debug/aspect: aspect::Simulator<3>::setup_
> system_matrix(std::vector<dealii::IndexSet, std::allocator<dealii::IndexSet>
> > const&)
> #7  /home/lev/aspect/aspect_debug/aspect: aspect::Simulator<3>::setup_
> dofs()
> #8  /home/lev/aspect/aspect_debug/aspect: aspect::Simulator<3>::run()
> #9  /home/lev/aspect/aspect_debug/aspect: main
> --------------------------------------------------------
>
>
> Program received signal SIGABRT, Aborted.
> 0x0000003edf232625 in raise () from /lib64/libc.so.6
> Missing separate debuginfos, use: debuginfo-install
> librdmacm-1.0.19.1-1.1.el6_7.x86_64
> (gdb) bt
> #0  0x0000003edf232625 in raise () from /lib64/libc.so.6
> #1  0x0000003edf233e05 in abort () from /lib64/libc.so.6
> #2  0x00007ffff4959156 in dealii::deal_II_exceptions::internals::abort
> (exc=..., nothrow=false)
>     at /home/lev/aspect/dealii_debug/source/base/exceptions.cc:322
> #3  0x0000000001467e2b in dealii::deal_II_exceptions::
> internals::issue_error<dealii::TriaRawIterator<dealii::CellAccessor<3, 3>
> >::ExcDereferenceInvalidCell> (handling=dealii::deal_II_
> exceptions::internals::abort_on_exception, file=0x1dc0cc8
> "/home/lev/aspect/dealii_debug/include/deal.II/grid/tria_iterator.h",
>     line=917, function=0x1dc5240 "const Accessor& dealii::TriaRawIterator<Accessor>::operator*()
> const [with Accessor = dealii::CellAccessor<3, 3>]",
>     cond=0x1dc1648 "Accessor::structure_dimension!=Accessor::dimension ||
> state() == IteratorState::valid",
>     exc_name=0x1dc1620 "ExcDereferenceInvalidCell(accessor)", e=...) at
> /home/lev/aspect/dealii_debug/include/deal.II/base/exceptions.h:266
> #4  0x00000000019fb095 in dealii::TriaRawIterator<dealii::CellAccessor<3,
> 3> >::operator* (this=0x7fffffff7a90)
>     at /home/lev/aspect/dealii_debug/include/deal.II/grid/tria_
> iterator.h:915
> #5  0x00000000019f4f8e in dealii::TriaRawIterator<dealii::CellAccessor<3,
> 3> >::operator-> (this=0x7fffffff7a90)
>     at /home/lev/aspect/dealii_debug/include/deal.II/grid/tria_
> iterator.h:959
> #6  0x00007ffff5052ccc in dealii::CellAccessor<3, 3>::neighbor_of_neighbor_internal
> (this=0x7fffffff7e90, neighbor=3)
>     at /home/lev/aspect/dealii_debug/source/grid/tria_accessor.cc:1675
> #7  0x000000000132bcf8 in dealii::CellAccessor<3, 3>::neighbor_face_no
> (this=0x7fffffff7e90, neighbor=3)
>     at /home/lev/aspect/dealii_debug/include/deal.II/grid/tria_
> accessor.templates.h:3469
> #8  0x00007ffff41a44a5 in dealii::DoFTools::internal::(anonymous
> namespace)::make_flux_sparsity_pattern<dealii::DoFHandler<3, 3>,
> dealii::TrilinosWrappers::BlockSparsityPattern> (dof=..., sparsity=...,
> constraints=..., keep_constrained_dofs=false, int_mask=..., flux_mask=...,
> subdomain_id=0)
>     at /home/lev/aspect/dealii_debug/source/dofs/dof_tools_sparsity.cc:806
> #9  0x00007ffff42aaca3 in dealii::DoFTools::make_flux_
> sparsity_pattern<dealii::DoFHandler<3, 3>, dealii::TrilinosWrappers::BlockSparsityPattern>
> (dof=...,
>     sparsity=..., constraints=..., keep_constrained_dofs=false,
> int_mask=..., flux_mask=..., subdomain_id=0)
>     at /home/lev/aspect/dealii_debug/source/dofs/dof_tools_
> sparsity.cc:1255
> #10 0x000000000144d1c6 in aspect::Simulator<3>::setup_system_matrix
> (this=0x7fffffff9380, system_partitioning=std::vector of length 8,
> capacity 8 = {...})
>     at /home/lev/aspect/aspect_debug/source/simulator/core.cc:1106
> #11 0x00000000014463ce in aspect::Simulator<3>::setup_dofs
> (this=0x7fffffff9380) at /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:1444
> #12 0x0000000001445363 in aspect::Simulator<3>::run (this=0x7fffffff9380)
> at /home/lev/aspect/aspect_debug/source/simulator/core.cc:2360
> #13 0x0000000001727506 in main (argc=2, argv=0x7fffffffe0f8) at
> /home/lev/aspect/aspect_debug/source/main.cc:487
>
> Best regards,
> Lev Karatun.
>
> 2016-09-30 10:12 GMT-04:00 Timo Heister <heister at clemson.edu>:
>
>> Lev,
>>
>> are you running in debug mode? If not, please do so. It would also be
>> great to run this in gdb and get a full backtrace for us (let me know
>> if you need help on how to do this).
>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
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