[aspect-devel] Boundary composition (Ying He)
Ying He
yinghe at math.ucdavis.edu
Fri Sep 30 16:26:04 PDT 2016
Hi Lev,
Currently I only have my Macbook available to use, on which I don't have
the newest deal_II.g.so.8.5.0-pre installed. However, your prm files is
running OK on my mac machine with deal.ii 4.1. Also based on your debug
error messages, it seems something wrong related to
dealii::DoFTools::make_flux_sparsity_pattern function call. This deal.ii
function has some major changes just implemented recently in deal.ii
8.5pre when running with multiple processors for DG method. This change
only affect the memory consumption but not the accuracy. So before we
can fix the problem, you could still run your test problems in Aspect
with the release deal.ii version. Hope this help.
On 2016-09-30 12:00, aspect-devel-request at geodynamics.org wrote:
> Send Aspect-devel mailing list submissions to
> aspect-devel at geodynamics.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
> or, via email, send a message with subject or body 'help' to
> aspect-devel-request at geodynamics.org
>
> You can reach the person managing the list at
> aspect-devel-owner at geodynamics.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Aspect-devel digest..."
>
>
> Today's Topics:
>
> 1. Re: Boundary composition (John Naliboff)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 30 Sep 2016 11:41:46 -0700
> From: John Naliboff <jbnaliboff at ucdavis.edu>
> To: aspect-devel at geodynamics.org
> Subject: Re: [aspect-devel] Boundary composition
> Message-ID: <767c0289-21c3-8717-f0c1-0d2314960f73 at ucdavis.edu>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> 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/>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> <mailto:Aspect-devel at geodynamics.org>
>>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> <http://lists.geodynamics.org/pipermail/aspect-devel/attachments/20160930/041b00ea/attachment-0001.html>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
> ------------------------------
>
> End of Aspect-devel Digest, Vol 58, Issue 21
> ********************************************
--
Best,
Ying He
More information about the Aspect-devel
mailing list