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

[Renato P. <re...@gm...>]

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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>>>
>