[aspect-devel] Boundary composition

Fri Sep 30 10:32:27 PDT 2016

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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