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Marching cubes reset #82

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354089b
Reset cell IDs and offsets for each MC rebuild
streeve Feb 10, 2023
849a4e6
Allocate with zero init - remove separate deepcopy
streeve Feb 10, 2023
8ed9ac9
Add MC member functions for facet size/capacity
streeve Feb 20, 2023
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64 changes: 46 additions & 18 deletions src/Picasso_MarchingCubes.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ struct Data
Kokkos::View<int*** [2], MemorySpace> cell_case_ids_and_offsets;

// Number of facets.
int num_facet;
std::size_t num_facet;

// Facets. Facets are only created for owned cells.
Kokkos::View<double* [3][3], MemorySpace> facets;
Expand All @@ -60,13 +60,11 @@ struct Data
auto cell_space = mesh.localGrid()->indexSpace(
Cajita::Ghost{}, Cajita::Cell{}, Cajita::Local{} );

// Purposely initializing to zero here.
cell_case_ids_and_offsets =
Kokkos::View<int*** [2], typename Mesh::memory_space>(
Kokkos::ViewAllocateWithoutInitializing(
"cell_case_ids_and_offset" ),
cell_space.extent( 0 ), cell_space.extent( 1 ),
cell_space.extent( 2 ) );
Kokkos::deep_copy( cell_case_ids_and_offsets, 0 );
"cell_case_ids_and_offset", cell_space.extent( 0 ),
cell_space.extent( 1 ), cell_space.extent( 2 ) );
num_facet = 0;
facets = Kokkos::View<double* [3][3], typename Mesh::memory_space>(
Kokkos::ViewAllocateWithoutInitializing( "facets" ), 0 );
Expand Down Expand Up @@ -944,6 +942,39 @@ struct Data
Kokkos::Array<short, 3>{ 5, 0, 9 },
Kokkos::Array<short, 3>{ 0, 4, 8 } };
}

// Return the number of facets (not necessarily equal to the size of the
// facet View).
std::size_t numFacet() const { return num_facet; }

// Return the number of facets allocated.
std::size_t facetCapacity() const { return facets.extent( 0 ); }

// Set number of facets.
void resetNumFacet( const std::size_t new_num_facet,
const bool reset_data_memory = false )
{
num_facet = new_num_facet;

// Allocate facet data if necessary.
if ( numFacet() > facetCapacity() || reset_data_memory )
{
Kokkos::realloc( facets, numFacet() );
}
}

template <class CellSpace>
void resetCellIdsAndOffsets( CellSpace cell_space )
{
// Resize the IDs and offsets if needed (without copying).
if ( cell_space.extent( 0 ) > cell_case_ids_and_offsets.extent( 0 ) ||
cell_space.extent( 1 ) > cell_case_ids_and_offsets.extent( 1 ) ||
cell_space.extent( 2 ) > cell_case_ids_and_offsets.extent( 2 ) )
Kokkos::realloc( cell_case_ids_and_offsets, cell_space.extent( 0 ),
cell_space.extent( 1 ), cell_space.extent( 2 ) );
// Reset IDs and offsets.
Kokkos::deep_copy( cell_case_ids_and_offsets, 0 );
}
};

//---------------------------------------------------------------------------//
Expand Down Expand Up @@ -1145,11 +1176,14 @@ void build( const ExecutionSpace& exec_space, const Mesh& mesh,
auto cell_space = signed_distance.layout()->localGrid()->indexSpace(
Cajita::Own{}, Cajita::Cell{}, Cajita::Local{} );

data.resetCellIdsAndOffsets( cell_space );

// Get the case id and number of facets for each cell.
data.num_facet = 0;
std::size_t new_num_facet = 0;
Cajita::grid_parallel_reduce(
"marching_cubes_facet_count", exec_space, cell_space,
KOKKOS_LAMBDA( const int i, const int j, const int k, int& result ) {
KOKKOS_LAMBDA( const int i, const int j, const int k,
std::size_t& result ) {
Kokkos::Array<double, 8> vertex_data;
Impl::vertexData( distance_view, i, j, k, vertex_data );
Kokkos::Array<int, 8> vertex_signs;
Expand All @@ -1160,14 +1194,8 @@ void build( const ExecutionSpace& exec_space, const Mesh& mesh,
data.cell_case_ids_and_offsets( i, j, k, 1 ) = num_facet;
result += num_facet;
},
data.num_facet );

// Allocate facet data if necessary.
if ( data.num_facet > static_cast<int>( data.facets.extent( 0 ) ) ||
reset_data_memory )
{
Kokkos::realloc( data.facets, data.num_facet );
}
new_num_facet );
data.resetNumFacet( new_num_facet, reset_data_memory );

// Compute cell offsets into facet data via exclusive scan.
Kokkos::parallel_scan(
Expand Down Expand Up @@ -1261,8 +1289,8 @@ void writeDataToSTL( const Data<MemorySpace>& data, MPI_Comm comm,
{
if ( r == comm_rank )
{
int num_facet = facets.extent( 0 );
for ( int f = 0; f < num_facet; ++f )
std::size_t num_facet = data.numFacet();
for ( std::size_t f = 0; f < num_facet; ++f )
{
file << " facet normal 0.000000e+00 0.000000e+00 0.000000e+00"
<< std::endl;
Expand Down
2 changes: 1 addition & 1 deletion unit_test/tstMarchingCubes.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ void runTest( const Phi0& phi_0, const std::string& stl_filename )

auto facets = Kokkos::create_mirror_view_and_copy( Kokkos::HostSpace{},
mc_data->facets );
for ( std::size_t f = 0; f < facets.extent( 0 ); ++f )
for ( std::size_t f = 0; f < mc_data->numFacet(); ++f )
{
Vec3<double> ab = { facets( f, 1, 0 ) - facets( f, 0, 0 ),
facets( f, 1, 1 ) - facets( f, 0, 1 ),
Expand Down