libmesh-users

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

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

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*)

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

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

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*)
>
>

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

[Alexander L. <ale...@gm...>]

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*)
> >
> >
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

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

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

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*)
>> >
>> >
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Libmesh-users mailing list
>> Lib...@li...
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>
>
>

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

[Alexander L. <ale...@gm...>]

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*)
>>> >
>>> >
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Libmesh-users mailing list
>>> Lib...@li...
>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>> 

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

[Alexander L. <ale...@gm...>]

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*)
>>> >
>>> >
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Libmesh-users mailing list
>>> Lib...@li...
>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>
>>
>>

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*)
>>>> >
>>>> >
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Libmesh-users mailing list
>>>> Lib...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>
>>>
>>>
>

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

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

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*)
>>>>> >
>>>>> >
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> Libmesh-users mailing list
>>>>> Lib...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>
>>>>
>>>>
>>

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

[Alexander L. <ale...@gm...>]

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*)
>>>>>> >
>>>>>> >
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>> _______________________________________________
>>>>>> Libmesh-users mailing list
>>>>>> Lib...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>
>>>>>
>>>>>
>>>

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

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

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*)
>>>>>>> >
>>>>>>> >
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>> _______________________________________________
>>>>>>> Libmesh-users mailing list
>>>>>>> Lib...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>>
>>>>>>
>>>>>>
>>>>
>

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

[Alexander L. <ale...@gm...>]

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*)
>>>>>>>> >
>>>>>>>> >
>>>>>>>> ------------------------------------------------------------
>>>>>>>> ------------------
>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>> _______________________________________________
>>>>>>>> Libmesh-users mailing list
>>>>>>>> Lib...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>

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

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

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*)
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>> _______________________________________________
>>>>>>>>> Libmesh-users mailing list
>>>>>>>>> Lib...@li...
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>
>

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

[Alexander L. <ale...@gm...>]

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*)
>>>>>>>>>> >
>>>>>>>>>> >
>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>> ------------------
>>>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Libmesh-users mailing list
>>>>>>>>>> Lib...@li...
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>
>>

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

[Alexander L. <ale...@gm...>]

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/126feb95
>>>> 4ba89c5739794dd286ed8a47c2735be8)
>>>>
>>>> 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/lib
>>>>> Mesh/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_vecto
>>>>>>>>>>> r(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::__cx
>>>>>>>>>>> x11::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::__cx
>>>>>>>>>>> x11::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*)
>>>>>>>>>>> >
>>>>>>>>>>> >
>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>> ------------------
>>>>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Libmesh-users mailing list
>>>>>>>>>>> Lib...@li...
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>
>>>
>

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

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

# 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
>>>>>>>>>>>> Lib...@li...
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>
>>
>