Gridtools::find_active_cell_around_point and parallel::shared::Triangulation<dim>

[Gennadiy Rishkin]

Hello,

It seems that Gridtools::find_active_cell_around_point does not work with parallel::shared::Triangulation. Is this the case?

#include <deal.II/grid/grid_tools.h> is included.

I get the error:

test.cc:(.text._ZN4testILi3EE9make_gridEv[_ZN4testILi3EE9make_gridEv]+0x1f75): undefined reference to `dealii::parallel::shared::Triangulation<3, 3>::active_cell_iterator dealii::GridTools::find_active_cell_around_point<3, dealii::parallel::shared::Triangulation, 3>(dealii::parallel::shared::Triangulation<3, 3> const&, dealii::Point<3, double> const&)'
collect2: error: ld returned 1 exit status

Gennadiy

[Gennadiy Rishkin]

Hello,

Was this a deliberate design? I'm using the development sources.

Could I please get some suggestions on how to implement this with parallel::shared::Triangulation.

Thank you.

Gennadiy

[Bruno Turcksin]

Gennadiy,

as far as I know it's not a deliberate design. It's just that the function is not explicitly instantiated. This is done in source/grid/grid_tools.inst.in. I think the first thing to try is to add parallel::shared::Triangulation to the list of TRIANGULATION_AND_DOFHANDLERS  in cmake/config/template-arguments.in If that doesn't work you can to try to instantiate only the functions that you need.

Best,

Bruno

On Monday, December 7, 2015 at 12:41:49 PM UTC-6, Gennadiy Rishkin wrote:

Hello,

Was this a deliberate design? I'm using the development sources.

Could I please get some suggestions on how to implement this with parallel::shared::Triangulation.

Thank you.

Gennadiy

[Wolfgang Bangerth]

Gennadiy,

It's a bug. I've opened this report here:
https://github.com/dealii/dealii/issues/1958

I'll have a bug in a couple of days.

Best
W.

--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@math.tamu.edu
www: http://www.math.tamu.edu/~bangerth/

[Wolfgang Bangerth]

Gennadiy,

Can you try this:
https://github.com/dealii/dealii/pull/1959
?

[Gennadiy Rishkin]

Hello,

I made all the changes. The error is now

CMakeFiles/test.dir/source/test.cc.o: In function `test<1>::make_grid()':
test.cc:(.text._ZN4testILi1EE9make_gridEv[_ZN4testILi1EE9make_gridEv]+0x4fd): undefined reference to `dealii::parallel::shared::Triangulation<1, 1>::active_cell_iterator dealii::GridTools::find_active_cell_around_point<1, dealii::parallel::shared::Triangulation, 1>(dealii::parallel::shared::Triangulation<1, 1> const&, dealii::Point<1, double> const&)'
CMakeFiles/test.dir/source/test.cc.o: In function `test<2>::make_grid()':
test.cc:(.text._ZN4testILi2EE9make_gridEv[_ZN4testILi2EE9make_gridEv]+0x528): undefined reference to `dealii::parallel::shared::Triangulation<2, 2>::active_cell_iterator dealii::GridTools::find_active_cell_around_point<2, dealii::parallel::shared::Triangulation, 2>(dealii::parallel::shared::Triangulation<2, 2> const&, dealii::Point<2, double> const&)'
CMakeFiles/test.dir/source/test.cc.o: In function `test<3>::make_grid()':
test.cc:(.text._ZN4testILi3EE9make_gridEv[_ZN4testILi3EE9make_gridEv]+0x5bb): undefined reference to `dealii::parallel::shared::Triangulation<3, 3>::active_cell_iterator dealii::GridTools::find_active_cell_around_point<3, dealii::parallel::shared::Triangulation, 3>(dealii::parallel::shared::Triangulation<3, 3> const&, dealii::Point<3, double> const&)'
/home/gennadiy/deal.II/lib/libdeal_II.so.8.4.0-pre: undefined reference to `std::vector<dealii::parallel::shared::Triangulation<1, 1>::active_cell_iterator, std::allocator<dealii::parallel::shared::Triangulation<1, 1>::active_cell_iterator> > dealii::GridTools::compute_active_cell_halo_layer<dealii::parallel::shared::Triangulation<1, 1> >(dealii::parallel::shared::Triangulation<1, 1> const&, std::function<bool (dealii::parallel::shared::Triangulation<1, 1>::active_cell_iterator const&)> const&)'
/home/gennadiy/deal.II/lib/libdeal_II.so.8.4.0-pre: undefined reference to `std::vector<dealii::parallel::shared::Triangulation<1, 3>::active_cell_iterator, std::allocator<dealii::parallel::shared::Triangulation<1, 3>::active_cell_iterator> > dealii::GridTools::compute_active_cell_halo_layer<dealii::parallel::shared::Triangulation<1, 3> >(dealii::parallel::shared::Triangulation<1, 3> const&, std::function<bool (dealii::parallel::shared::Triangulation<1, 3>::active_cell_iterator const&)> const&)'
/home/gennadiy/deal.II/lib/libdeal_II.so.8.4.0-pre: undefined reference to `std::vector<dealii::parallel::shared::Triangulation<1, 2>::active_cell_iterator, std::allocator<dealii::parallel::shared::Triangulation<1, 2>::active_cell_iterator> > dealii::GridTools::compute_active_cell_halo_layer<dealii::parallel::shared::Triangulation<1, 2> >(dealii::parallel::shared::Triangulation<1, 2> const&, std::function<bool (dealii::parallel::shared::Triangulation<1, 2>::active_cell_iterator const&)> const&)'
/home/gennadiy/deal.II/lib/libdeal_II.so.8.4.0-pre: undefined reference to `std::vector<dealii::parallel::shared::Triangulation<3, 3>::active_cell_iterator, std::allocator<dealii::parallel::shared::Triangulation<3, 3>::active_cell_iterator> > dealii::GridTools::compute_active_cell_halo_layer<dealii::parallel::shared::Triangulation<3, 3> >(dealii::parallel::shared::Triangulation<3, 3> const&, std::function<bool (dealii::parallel::shared::Triangulation<3, 3>::active_cell_iterator const&)> const&)'
/home/gennadiy/deal.II/lib/libdeal_II.so.8.4.0-pre: undefined reference to `std::vector<dealii::parallel::shared::Triangulation<2, 2>::active_cell_iterator, std::allocator<dealii::parallel::shared::Triangulation<2, 2>::active_cell_iterator> > dealii::GridTools::compute_active_cell_halo_layer<dealii::parallel::shared::Triangulation<2, 2> >(dealii::parallel::shared::Triangulation<2, 2> const&, std::function<bool (dealii::parallel::shared::Triangulation<2, 2>::active_cell_iterator const&)> const&)'
/home/gennadiy/deal.II/lib/libdeal_II.so.8.4.0-pre: undefined reference to `std::vector<dealii::parallel::shared::Triangulation<2, 3>::active_cell_iterator, std::allocator<dealii::parallel::shared::Triangulation<2, 3>::active_cell_iterator> > dealii::GridTools::compute_active_cell_halo_layer<dealii::parallel::shared::Triangulation<2, 3> >(dealii::parallel::shared::Triangulation<2, 3> const&, std::function<bool (dealii::parallel::shared::Triangulation<2, 3>::active_cell_iterator const&)> const&)'

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[Wolfgang Bangerth]

Gennadiy,
do you have a small test you could share that demonstrates the problem?
Best
W.

> <mailto:bang...@tamu.edu>> wrote:
>
>
> Gennadiy,
>
> It seems that Gridtools::find_active_cell_around_point does not
> work with
> parallel::shared::Triangulation. Is this the case?
>
> #include <deal.II/grid/grid_tools.h> is included.
>
> I get the error:
>
> test.cc:(.text._ZN4testILi3EE9make_gridEv[_ZN4testILi3EE9make_gridEv]+0x1f75):
> undefined reference to `dealii::parallel::shared::Triangulation<3,
> 3>::active_cell_iterator
> dealii::GridTools::find_active_cell_around_point<3,
> dealii::parallel::shared::Triangulation,
> 3>(dealii::parallel::shared::Triangulation<3, 3> const&,
> dealii::Point<3,
> double> const&)'
> collect2: error: ld returned 1 exit status
>
>
> Can you try this:
> https://github.com/dealii/dealii/pull/1959
> ?
>
>
> Best
> W.
>
> --
> ------------------------------------------------------------------------
> Wolfgang Bangerth email: bang...@math.tamu.edu

> <mailto:bang...@math.tamu.edu>

> www:
> http://www.math.tamu.edu/~bangerth/
>
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>

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[Gennadiy Rishkin]

Hi Wolfgang,

Here's a small test:

#include <deal.II/base/logstream.h>
#include <deal.II/base/multithread_info.h>
#include <deal.II/base/conditional_ostream.h>
#include <deal.II/base/utilities.h>
#include <deal.II/distributed/shared_tria.h>
#include <deal.II/grid/tria.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/tria_accessor.h>
#include <deal.II/grid/tria_iterator.h>
#include <deal.II/grid/grid_tools.h>
#include <deal.II/base/utilities.h>

#include <iostream>

using namespace dealii;

int main (int argc, char **argv)
{
    try
    {
        Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);

        parallel::shared::Triangulation<3> triangulation( MPI_COMM_WORLD );

        const unsigned int this_mpi_process = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD);
               
        std::vector< unsigned int > repetitions(3); repetitions[0] = 10/10; repetitions[1] = 60/10; repetitions[2] = 10/10;
        Point<3> p1(-1.0,0.0, 0.0);
        Point<3> p2(1.0, 3.0, 1.0);
        GridGenerator::subdivided_hyper_rectangle( triangulation, repetitions, p1, p2 );
   
        std::cout << "Number of active cells  : " << triangulation.n_active_cells() << std::endl;
        std::cout << "Total number of cells   : " << triangulation.n_cells() << std::endl;
        std::cout << "total number of vertices: " << triangulation.n_vertices() << std::endl;
       
        Point<3> p( 0.0, 0.75, 0.5 );
       
        typename Triangulation<3>::active_cell_iterator cell = triangulation.begin_active();
       

        // Offending Line

        cell = GridTools::find_active_cell_around_point( triangulation, p );
    }
    catch (std::exception &exc)
    {
        std::cerr << std::endl << std::endl
                << "----------------------------------------------------"
                << std::endl;
        std::cerr << "Exception on processing: " << std::endl
                << exc.what() << std::endl
                << "Aborting!" << std::endl
                << "----------------------------------------------------"
                << std::endl;

        return 1;
    }
    catch (...)
    {
        std::cerr << std::endl << std::endl
                << "----------------------------------------------------"
                << std::endl;
        std::cerr << "Unknown exception!" << std::endl
                << "Aborting!" << std::endl
                << "----------------------------------------------------"
                << std::endl;
        return 1;
    };

    return 0;
}

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[Wolfgang Bangerth]

Gennadyi,
your test compiles, links, and runs find on my system with the patch I
linked to previously:
https://github.com/dealii/dealii/pull/1959/files
Does it not for you?
Best
W.

> <mailto:bang...@math.tamu.edu <mailto:bang...@math.tamu.edu>>

> www:
> http://www.math.tamu.edu/~bangerth/
>
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[Gennadiy Rishkin]

The requested URL kept failing. I may have applied the patch incorreclty. How do I apply it?

Gennadiy

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[Wolfgang Bangerth]

On 12/08/2015 11:31 AM, Gennadiy Rishkin wrote:
> The requested URL kept failing. I may have applied the patch
> incorreclty. How do I apply it?

If you have a current checkout from the git repository, do this:

git checkout -b bangerth-fix-instantiations master
git pull https://github.com/bangerth/dealii.git fix-instantiations

Best
W.

--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@math.tamu.edu

www: http://www.math.tamu.edu/~bangerth/

[Gennadiy Rishkin]

Thanks Wolfgang. That worked. Code's running fine now.

Gennadiy

                                www: http://www.math.tamu.edu/~bangerth/