[aspect-devel] Boundary composition

Timo Heister heister at clemson.edu
Sun Oct 2 10:43:00 PDT 2016 

This looks like a bug in deal.II and might be a combination of a 3d
mesh with periodic boundary conditions.

On Fri, Sep 30, 2016 at 2:41 PM, John Naliboff <jbnaliboff at ucdavis.edu> wrote:
> Hi Lev,
>
> I just ran the file and looked at the error message with Ying He (one of DG
> authors).  Neither of us has seen this error message before.  Ying is going
> to take a closer look later, but in the meantime I would try simplifying
> your model down further (one compositional field, basic inflow/outflow) to
> see if you can point to the issue.
>
> Cheers,
> John
>
> *************************************************
> John Naliboff
> Assistant Project Scientist, CIG
> Earth & Planetary Sciences Dept., UC Davis
>
> On 09/30/2016 10:36 AM, Lev Karatun wrote:
>
> 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
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>>
>>
>
>
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-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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