[aspect-devel] Boundary composition
John Naliboff
jbnaliboff at ucdavis.edu
Fri Sep 30 11:41:46 PDT 2016
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
> <mailto: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
> <mailto: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/
> <http://www.math.clemson.edu/%7Eheister/>
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