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

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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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>>>>>>>>>> _______________________________________________
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>
>>