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

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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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>>>>>>>>> _______________________________________________
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>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>
>