Re: [Libmesh-users] ExodusII_IO::write_discontinuous_timestep trouble with subdomains

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# git pull origin pull/1836/head

On Mon, Aug 27, 2018 at 7:01 PM Alexander Lindsay <ale...@gm...>
wrote:

> How did you apply my patch?
>
> On Mon, Aug 27, 2018 at 4:00 PM, Alexander Lindsay <
> ale...@gm...> wrote:
>
>> Yes it is
>>
>> On Mon, Aug 27, 2018 at 3:59 PM, Renato Poli <re...@gm...> wrote:
>>
>>> Is that "p"?
>>>
>>> On Mon, Aug 27, 2018 at 5:51 PM Alexander Lindsay <
>>> ale...@gm...> wrote:
>>>
>>>> Like this? This is how it looks for me.
>>>>
>>>> On Mon, Aug 27, 2018 at 12:21 PM, Renato Poli <re...@gm...>
>>>> wrote:
>>>>
>>>>> Hi Alexander,
>>>>>
>>>>> It did run, but the values were not assigned at the right elements.
>>>>> Please find a paraview figure attached.
>>>>> It was produced by the example I sent (open mesh.e in paraview).
>>>>> The pressure subdomain should be a circle in the center.
>>>>>
>>>>> I would guess the problem lies in lines 1141-2 below (just a guess):
>>>>>                           soln[nv*(nn++) + (var + var_num)] +=
>>>>>                             nodal_soln[n];
>>>>> (
>>>>> https://github.com/libMesh/libmesh/pull/1836/files/126feb954ba89c5739794dd286ed8a47c2735be8
>>>>> )
>>>>>
>>>>> rgds,
>>>>> Renato
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Aug 27, 2018 at 12:35 PM Alexander Lindsay <
>>>>> ale...@gm...> wrote:
>>>>>
>>>>>> Renato, please check to see whether
>>>>>> https://github.com/libMesh/libmesh/pull/1836 fixes your issue. It
>>>>>> appears to work to me on the example you sent
>>>>>>
>>>>>> On Sat, Aug 25, 2018 at 3:16 PM, Renato Poli <re...@gm...>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Alexander,
>>>>>>>
>>>>>>> Please find attached the example you asked.
>>>>>>> I used introduction_ex3 as a basis... it got a little messy, I hope
>>>>>>> it is enough.
>>>>>>> Please let me know otherwise.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Renato
>>>>>>>
>>>>>>> On Sat, Aug 25, 2018 at 12:42 PM Renato Poli <re...@gm...>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Sure.... please give me a couple of hours.
>>>>>>>>
>>>>>>>> On Sat, Aug 25, 2018 at 12:04 PM Alexander Lindsay <
>>>>>>>> ale...@gm...> wrote:
>>>>>>>>
>>>>>>>>> Renato, could you create a minimum example that generates the
>>>>>>>>> discontinuous error, and either share it here or create a ticket on github?
>>>>>>>>> That would be useful for fixing the issue and adding a test in libmesh to
>>>>>>>>> ensure we support the capability.
>>>>>>>>>
>>>>>>>>> On Sat, Aug 25, 2018 at 8:33 AM, Alexander Lindsay <
>>>>>>>>> ale...@gm...> wrote:
>>>>>>>>>
>>>>>>>>>> Ah yes...key difference between "empty" and "zero"...
>>>>>>>>>>
>>>>>>>>>> On Aug 25, 2018, at 7:03 AM, Renato Poli <re...@gm...>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> No success. Stack trace below.
>>>>>>>>>>
>>>>>>>>>> Note that, if I define my variable _only_ on its domain (where there is fluid) it works.
>>>>>>>>>>
>>>>>>>>>> In this case, the problem is in ExodusII_IO::write_discontinuous_timestep.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>>>>>>>>> [0]PETSC ERROR: Object is in wrong state
>>>>>>>>>> [0]PETSC ERROR: Matrix is missing diagonal entry 0
>>>>>>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>>>>>>>>>> [0]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
>>>>>>>>>> [0]PETSC ERROR: obj/bin/abada_sc11 on a linux-gnu-opt named dev-vb by dev Sat Aug 25 09:55:36 2018
>>>>>>>>>> [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/lib/mpich --with-shared-libraries=1 --with-debugging=yes --download-mumps --download-hypre --download-scalapack --download-spai --download-parms
>>>>>>>>>> [0]PETSC ERROR: #1 MatLUFactorSymbolic_SeqAIJ() line 301 in /opt/petsc-3.7.6/src/mat/impls/aij/seq/aijfact.c
>>>>>>>>>> [0]PETSC ERROR: #2 MatLUFactorSymbolic() line 2944 in /opt/petsc-3.7.6/src/mat/interface/matrix.c
>>>>>>>>>> [0]PETSC ERROR: #3 PCSetUp_LU() line 136 in /opt/petsc-3.7.6/src/ksp/pc/impls/factor/lu/lu.c
>>>>>>>>>> [0]PETSC ERROR: #4 PCSetUp() line 968 in /opt/petsc-3.7.6/src/ksp/pc/interface/precon.c
>>>>>>>>>> [0]PETSC ERROR: #5 KSPSetUp() line 390 in /opt/petsc-3.7.6/src/ksp/ksp/interface/itfunc.c
>>>>>>>>>> [0]PETSC ERROR: #6 KSPSolve() line 599 in /opt/petsc-3.7.6/src/ksp/ksp/interface/itfunc.c
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Renato
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Fri, Aug 24, 2018 at 11:49 PM Alexander Lindsay <
>>>>>>>>>> ale...@gm...> wrote:
>>>>>>>>>>
>>>>>>>>>>> If you're using PETSc as your underlying solver, try the options
>>>>>>>>>>> `-pc_factor_shift_type NONZERO -pc_factor_shift_amount 1e-15`
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Aug 23, 2018 at 2:58 PM, Renato Poli <re...@gm...>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi
>>>>>>>>>>>>
>>>>>>>>>>>> I am getting trouble here again ... really need some help.
>>>>>>>>>>>>
>>>>>>>>>>>> I have part of the domain without flow (and thus without the
>>>>>>>>>>>> pressure
>>>>>>>>>>>> variable defined).
>>>>>>>>>>>> As I could not export that (could not get
>>>>>>>>>>>> write_discontinuous_exodusII to
>>>>>>>>>>>> work) I just left the matrix empty, without major impact so far.
>>>>>>>>>>>> However, now I am using LU preconditioning, which does not
>>>>>>>>>>>> accept empty
>>>>>>>>>>>> entries in the diagonal.
>>>>>>>>>>>>
>>>>>>>>>>>> How can I get through?
>>>>>>>>>>>> Any suggestion?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks upfront.
>>>>>>>>>>>> Renato
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Aug 16, 2018 at 6:47 PM Renato Poli <re...@gm...>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> > Hi
>>>>>>>>>>>> >
>>>>>>>>>>>> > I see the stack trace below when writing a discontinuous
>>>>>>>>>>>> timestep
>>>>>>>>>>>> > (exo.write_discontinuous_timestep).
>>>>>>>>>>>> > It happens when my variable is set only in part of the domain.
>>>>>>>>>>>> > No problem arises if I use, instead:
>>>>>>>>>>>> exo.write_equation_systems(fname, es)
>>>>>>>>>>>> >
>>>>>>>>>>>> > Any hint/workaround/idea?
>>>>>>>>>>>> >
>>>>>>>>>>>> > Thanks,
>>>>>>>>>>>> > Renato
>>>>>>>>>>>> >
>>>>>>>>>>>> > This is how the variable is set.
>>>>>>>>>>>> > |  std::set<subdomain_id_type> active_subdomains;
>>>>>>>>>>>> > |  active_subdomains.clear();
>>>>>>>>>>>> > |  active_subdomains.insert(SUBDOMAIN_A);
>>>>>>>>>>>> > |  press_sys.add_variable ("p", SECOND, LAGRANGE, &
>>>>>>>>>>>> active_subdomains);
>>>>>>>>>>>> >
>>>>>>>>>>>> > 0: libMesh::print_trace(std::ostream&)
>>>>>>>>>>>> > 1: libMesh::MacroFunctions::report_error(char const*, int,
>>>>>>>>>>>> char const*,
>>>>>>>>>>>> > char const*)
>>>>>>>>>>>> > 2:
>>>>>>>>>>>> >
>>>>>>>>>>>> libMesh::EquationSystems::build_discontinuous_solution_vector(std::__debug::vector<double,
>>>>>>>>>>>> > std::allocator<double> >&,
>>>>>>>>>>>> > std::__debug::set<std::__cxx11::basic_string<char,
>>>>>>>>>>>> std::char_traits<char>,
>>>>>>>>>>>> > std::allocator<char> >,
>>>>>>>>>>>> std::less<std::__cxx11::basic_string<char,
>>>>>>>>>>>> > std::char_traits<char>, std::allocator<char> > >,
>>>>>>>>>>>> > std::allocator<std::__cxx11::basic_string<char,
>>>>>>>>>>>> std::char_traits<char>,
>>>>>>>>>>>> > std::allocator<char> > > > const*) const
>>>>>>>>>>>> > 3:
>>>>>>>>>>>> >
>>>>>>>>>>>> libMesh::ExodusII_IO::write_discontinuous_exodusII(std::__cxx11::basic_string<char,
>>>>>>>>>>>> > std::char_traits<char>, std::allocator<char> > const&,
>>>>>>>>>>>> > libMesh::EquationSystems const&,
>>>>>>>>>>>> > std::__debug::set<std::__cxx11::basic_string<char,
>>>>>>>>>>>> std::char_traits<char>,
>>>>>>>>>>>> > std::allocator<char> >,
>>>>>>>>>>>> std::less<std::__cxx11::basic_string<char,
>>>>>>>>>>>> > std::char_traits<char>, std::allocator<char> > >,
>>>>>>>>>>>> > std::allocator<std::__cxx11::basic_string<char,
>>>>>>>>>>>> std::char_traits<char>,
>>>>>>>>>>>> > std::allocator<char> > > > const*)
>>>>>>>>>>>> > 4:
>>>>>>>>>>>> >
>>>>>>>>>>>> libMesh::ExodusII_IO::write_timestep_discontinuous(std::__cxx11::basic_string<char,
>>>>>>>>>>>> > std::char_traits<char>, std::allocator<char> > const&,
>>>>>>>>>>>> > libMesh::EquationSystems const&, int, double,
>>>>>>>>>>>> > std::__debug::set<std::__cxx11::basic_string<char,
>>>>>>>>>>>> std::char_traits<char>,
>>>>>>>>>>>> > std::allocator<char> >,
>>>>>>>>>>>> std::less<std::__cxx11::basic_string<char,
>>>>>>>>>>>> > std::char_traits<char>, std::allocator<char> > >,
>>>>>>>>>>>> > std::allocator<std::__cxx11::basic_string<char,
>>>>>>>>>>>> std::char_traits<char>,
>>>>>>>>>>>> > std::allocator<char> > > > const*)
>>>>>>>>>>>> >
>>>>>>>>>>>> >
>>>>>>>>>>>>
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>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Libmesh-users mailing list
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>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>
>>
>