pnm Namespace Reference

Namespaces
namespace	detail_mpi
namespace	kernels
namespace	test

Classes
struct	BlockGeo
	Extended-block geometry policy (the MPI pipeline): ghost-inclusive local box <-> global periodic grid. More...
struct	GridGeo
	Single-rank geometry policy: the field IS the whole periodic grid, owned == field coords, gid == index. More...
struct	I3
struct	MpiPoreNetwork
	Result of one distributed extraction. More...
struct	NetworkFlow
struct	Pore
struct	PoreNetwork
	The full pore network from one extraction: pores, the per-voxel segmentation (flat), and the label-adjacency connections. More...
struct	PoreRec
	One owned pore-peak record of the distributed network-flow extraction (namespace-scope: nvcc forbids function-local types in extended-lambda captures). More...

Typedefs
using	Exec = Kokkos::DefaultExecutionSpace
using	Mem = Exec::memory_space
using	Index = std::int64_t
	Global voxel / face id (== peclet::core::Index; asserted where core is included).

Functions
std::vector< Pore >	extractPoresView (const Kokkos::View< float *, Mem > &sdf, std::array< int, 3 > resolution, std::array< float, 3 > origin, std::array< float, 3 > spacing)
std::vector< Pore >	extract_pores_k (const std::vector< float > &sdf_h, std::array< int, 3 > resolution, std::array< float, 3 > origin, std::array< float, 3 > spacing)
Kokkos::View< int *, Mem >	segmentVolumeView (const Kokkos::View< float *, Mem > &sdf, std::array< int, 3 > resolution, std::array< float, 3 > spacing, Kokkos::View< int *, Mem > *rootsOut=nullptr)
std::vector< int >	segment_volume_k (const std::vector< float > &sdf_h, std::array< int, 3 > resolution, std::array< float, 3 > spacing)
std::vector< std::pair< int, int > >	extractTopologyView (const Kokkos::View< int *, Mem > &seg, std::array< int, 3 > resolution)
std::vector< std::pair< int, int > >	extract_topology_k (const int *seg_h, std::size_t n, std::array< int, 3 > resolution)
std::vector< std::pair< int, int > >	extract_topology_k (const std::vector< int > &seg_h, std::array< int, 3 > resolution)
NetworkFlow	extract_network_flow_k (const std::vector< float > &sdf_h, std::array< int, 3 > resolution, std::array< float, 3 > origin, std::array< float, 3 > spacing, const std::vector< double > &u_h, const std::vector< double > &v_h, const std::vector< double > &w_h, const std::vector< double > &p_h, const std::vector< double > &ox_h, const std::vector< double > &oy_h, const std::vector< double > &oz_h, std::array< double, 3 > grad_p)
PoreNetwork	extract_pore_network_k (const std::vector< float > &sdf_h, std::array< int, 3 > resolution, std::array< float, 3 > origin, std::array< float, 3 > spacing)
void	mpi_block_of (std::array< int, 3 > gdims, MPI_Comm comm, std::array< int, 3 > &offset, std::array< int, 3 > &size)
	This rank's ORB block of the global grid (deterministic; same partition as flow/dem): offset = the block's first voxel index per axis (an integer grid offset, not a physical origin), size = its voxel count per axis.
MpiPoreNetwork	extract_pore_network_mpi (const std::vector< float > &sdf_local, std::array< int, 3 > gdims, std::array< float, 3 > origin, std::array< float, 3 > spacing, MPI_Comm comm)
	Distributed fused extraction.
NetworkFlow	extract_network_flow_mpi (const std::vector< float > &sdf_local, std::array< int, 3 > gdims, std::array< float, 3 > origin, std::array< float, 3 > spacing, const std::vector< double > &u_h, const std::vector< double > &v_h, const std::vector< double > &w_h, const std::vector< double > &p_h, const std::vector< double > &ox_h, const std::vector< double > &oy_h, const std::vector< double > &oz_h, std::array< double, 3 > grad_p, MPI_Comm comm)
template<class T >
void	uploadVec (const std::vector< T > &h, const Kokkos::View< T *, Mem > &d)
	Bulk host->device upload of a whole std::vector via one deep_copy over an unmanaged host view.
template<class V >
std::vector< typename V::value_type >	downloadN (const V &d, std::size_t count)
	Download the first count elements of a device view into a fresh std::vector via one deep_copy — only moves what is used.
template<class V >
V::value_type	readScalar (const V &d)
	Read a device scalar (the changed / counter flags) back to the host.
int	get_idx (int x, int y, int z, I3 res)
int	wrapc (int a, int n)

Typedef Documentation

Exec

using pnm::Exec = typedef Kokkos::DefaultExecutionSpace

Definition at line 51 of file pore_kernels.hpp.

Mem

using pnm::Mem = typedef Exec::memory_space

Definition at line 52 of file pore_kernels.hpp.

Index

using pnm::Index = typedef std::int64_t

Global voxel / face id (== peclet::core::Index; asserted where core is included).

Definition at line 54 of file pore_kernels.hpp.

Function Documentation

extractPoresView()

std::vector< Pore > pnm::extractPoresView ( const Kokkos::View< float *, Mem > &  sdf, std::array< int, 3 >  resolution, std::array< float, 3 >  origin, std::array< float, 3 >  spacing  )

inline

Definition at line 29 of file pore_extraction.hpp.

References pnm::kernels::detectPores(), downloadN(), pnm::GridGeo::of(), and readScalar().

Referenced by extract_pore_network_k(), and extract_pores_k().

extract_pores_k()

std::vector< Pore > pnm::extract_pores_k ( const std::vector< float > &  sdf_h, std::array< int, 3 >  resolution, std::array< float, 3 >  origin, std::array< float, 3 >  spacing  )

inline

Definition at line 45 of file pore_extraction.hpp.

References extractPoresView(), and uploadVec().

Referenced by NB_MODULE().

segmentVolumeView()

Kokkos::View< int *, Mem > pnm::segmentVolumeView ( const Kokkos::View< float *, Mem > &  sdf, std::array< int, 3 >  resolution, std::array< float, 3 >  spacing, Kokkos::View< int *, Mem > *  rootsOut = nullptr  )

inline

Definition at line 59 of file pore_extraction.hpp.

References pnm::kernels::cclFixpoint(), pnm::kernels::cclMergeMarkers(), pnm::kernels::floodFixpoint(), pnm::kernels::gradientWalk(), pnm::kernels::initMarkers(), and pnm::GridGeo::of().

Referenced by extract_network_flow_k(), extract_pore_network_k(), and segment_volume_k().

segment_volume_k()

std::vector< int > pnm::segment_volume_k ( const std::vector< float > &  sdf_h, std::array< int, 3 >  resolution, std::array< float, 3 >  spacing  )

inline

Definition at line 169 of file pore_extraction.hpp.

References downloadN(), segmentVolumeView(), and uploadVec().

Referenced by NB_MODULE().

extractTopologyView()

std::vector< std::pair< int, int > > pnm::extractTopologyView ( const Kokkos::View< int *, Mem > &  seg, std::array< int, 3 >  resolution  )

inline

Definition at line 181 of file pore_extraction.hpp.

References pnm::kernels::boundaryPairs(), pnm::GridGeo::of(), readScalar(), and pnm::kernels::uniquePairs().

Referenced by extract_pore_network_k(), and extract_topology_k().

extract_topology_k() [1/2]

std::vector< std::pair< int, int > > pnm::extract_topology_k ( const int *  seg_h, std::size_t  n, std::array< int, 3 >  resolution  )

inline

Definition at line 198 of file pore_extraction.hpp.

References extractTopologyView().

Referenced by extract_topology_k(), and NB_MODULE().

extract_topology_k() [2/2]

std::vector< std::pair< int, int > > pnm::extract_topology_k ( const std::vector< int > &  seg_h, std::array< int, 3 >  resolution  )

inline

Definition at line 209 of file pore_extraction.hpp.

References extract_topology_k().

extract_network_flow_k()

NetworkFlow pnm::extract_network_flow_k ( const std::vector< float > &  sdf_h, std::array< int, 3 >  resolution, std::array< float, 3 >  origin, std::array< float, 3 >  spacing, const std::vector< double > &  u_h, const std::vector< double > &  v_h, const std::vector< double > &  w_h, const std::vector< double > &  p_h, const std::vector< double > &  ox_h, const std::vector< double > &  oy_h, const std::vector< double > &  oz_h, std::array< double, 3 >  grad_p  )

inline

Definition at line 244 of file pore_extraction.hpp.

References downloadN(), pnm::GridGeo::of(), pnm::NetworkFlow::pore_pressure, pnm::NetworkFlow::pore_residual, pnm::NetworkFlow::pores, readScalar(), segmentVolumeView(), pnm::NetworkFlow::throat_area, pnm::NetworkFlow::throat_dp, pnm::NetworkFlow::throat_flow, pnm::NetworkFlow::throats, uploadVec(), pnm::Pore::x, pnm::Pore::y, and pnm::Pore::z.

Referenced by NB_MODULE().

extract_pore_network_k()

PoreNetwork pnm::extract_pore_network_k ( const std::vector< float > &  sdf_h, std::array< int, 3 >  resolution, std::array< float, 3 >  origin, std::array< float, 3 >  spacing  )

inline

Definition at line 466 of file pore_extraction.hpp.

References pnm::PoreNetwork::connections, downloadN(), extractPoresView(), extractTopologyView(), pnm::PoreNetwork::pores, pnm::PoreNetwork::seg, segmentVolumeView(), and uploadVec().

Referenced by NB_MODULE().

mpi_block_of()

void pnm::mpi_block_of ( std::array< int, 3 >  gdims, MPI_Comm  comm, std::array< int, 3 > &  offset, std::array< int, 3 > &  size  )

inline

This rank's ORB block of the global grid (deterministic; same partition as flow/dem): offset = the block's first voxel index per axis (an integer grid offset, not a physical origin), size = its voxel count per axis.

Definition at line 327 of file pore_extraction_mpi.hpp.

Referenced by NB_MODULE().

extract_pore_network_mpi()

MpiPoreNetwork pnm::extract_pore_network_mpi ( const std::vector< float > &  sdf_local, std::array< int, 3 >  gdims, std::array< float, 3 >  origin, std::array< float, 3 >  spacing, MPI_Comm  comm  )

inline

Distributed fused extraction.

sdf_local is this rank's INNER block (x-fastest, no ghosts), sized to the ORB block from mpi_block_of. Bit-exact to the single-rank extract_pore_network_k on the gathered grid (pores as a set; seg per voxel; connections).

Definition at line 343 of file pore_extraction_mpi.hpp.

References pnm::MpiPoreNetwork::block_origin, pnm::MpiPoreNetwork::block_size, downloadN(), pnm::BlockGeo::ex, pnm::BlockGeo::ey, pnm::BlockGeo::ez, pnm::BlockGeo::numExt(), pnm::BlockGeo::numOwned(), pnm::BlockGeo::nx, pnm::BlockGeo::ny, pnm::BlockGeo::nz, pnm::BlockGeo::ox, pnm::BlockGeo::oy, pnm::BlockGeo::oz, pnm::MpiPoreNetwork::pores, readScalar(), and uploadVec().

Referenced by extract_network_flow_mpi(), NB_MODULE(), and state_hash::run_case_mpi().

extract_network_flow_mpi()

NetworkFlow pnm::extract_network_flow_mpi ( const std::vector< float > &  sdf_local, std::array< int, 3 >  gdims, std::array< float, 3 >  origin, std::array< float, 3 >  spacing, const std::vector< double > &  u_h, const std::vector< double > &  v_h, const std::vector< double > &  w_h, const std::vector< double > &  p_h, const std::vector< double > &  ox_h, const std::vector< double > &  oy_h, const std::vector< double > &  oz_h, std::array< double, 3 >  grad_p, MPI_Comm  comm  )

inline

Definition at line 639 of file pore_extraction_mpi.hpp.

References downloadN(), extract_network_flow_mpi(), extract_pore_network_mpi(), pnm::PoreRec::id, pnm::BlockGeo::numExt(), pnm::BlockGeo::numOwned(), pnm::PoreRec::pgx, pnm::PoreRec::pgy, pnm::PoreRec::pgz, pnm::PoreRec::po, pnm::NetworkFlow::pore_pressure, pnm::NetworkFlow::pore_residual, pnm::NetworkFlow::pores, pnm::PoreRec::press, readScalar(), pnm::MpiPoreNetwork::seg, pnm::NetworkFlow::throat_area, pnm::NetworkFlow::throat_dp, pnm::NetworkFlow::throat_flow, pnm::NetworkFlow::throats, uploadVec(), pnm::Pore::x, pnm::Pore::y, and pnm::Pore::z.

Referenced by extract_network_flow_mpi(), NB_MODULE(), and state_hash::run_case_mpi().

uploadVec()

template<class T >

void pnm::uploadVec ( const std::vector< T > &  h, const Kokkos::View< T *, Mem > &  d  )

inline

Bulk host->device upload of a whole std::vector via one deep_copy over an unmanaged host view.

d must already be sized to h.

Definition at line 59 of file pore_kernels.hpp.

Referenced by extract_network_flow_k(), extract_network_flow_mpi(), extract_pore_network_k(), extract_pore_network_mpi(), extract_pores_k(), pnm::detail_mpi::globalMerge(), segment_volume_k(), and pnm::detail_mpi::stageInner().

downloadN()

template<class V >

std::vector< typename V::value_type > pnm::downloadN ( const V &  d, std::size_t  count  )

inline

Download the first count elements of a device view into a fresh std::vector via one deep_copy — only moves what is used.

Definition at line 70 of file pore_kernels.hpp.

Referenced by extract_network_flow_k(), extract_network_flow_mpi(), extract_pore_network_k(), extract_pore_network_mpi(), extractPoresView(), pnm::detail_mpi::localPairs(), pnm::detail_mpi::minByKey(), pnm::detail_mpi::packInner(), segment_volume_k(), and pnm::kernels::uniquePairs().

readScalar()

template<class V >

V::value_type pnm::readScalar ( const V &  d )

inline

Read a device scalar (the changed / counter flags) back to the host.

Definition at line 81 of file pore_kernels.hpp.

Referenced by pnm::kernels::cclFixpoint(), extract_network_flow_k(), extract_network_flow_mpi(), extract_pore_network_mpi(), extractPoresView(), extractTopologyView(), and pnm::kernels::floodFixpoint().

get_idx()

int pnm::get_idx	(	int	x,
		int	y,
		int	z,
		I3	res
	)

Definition at line 87 of file pore_kernels.hpp.

wrapc()

int pnm::wrapc	(	int	a,
		int	n
	)

Definition at line 94 of file pore_kernels.hpp.

Referenced by pnm::GridGeo::cell(), pnm::GridGeo::gcoord(), and pnm::BlockGeo::wrapc().