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

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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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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>