CUDA-accelerated extended ByteLattice with particle size awareness. More...

#include <CudaByteLatticeExtended.h>

Inheritance diagram for lm::rdme::CudaByteLatticeExtended:

Collaboration diagram for lm::rdme::CudaByteLatticeExtended:

Public Member Functions
	CudaByteLatticeExtended (lattice_coord_t size, si_dist_t spacing, uint particlesPerSite, bool enableSizeChecking=true)
	Constructor with particle size support.
	CudaByteLatticeExtended (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite, bool enableSizeChecking=true)
	Constructor with particle size support.
virtual	~CudaByteLatticeExtended ()
	Destructor.
virtual void	copyToGPU () override
virtual void	copyFromGPU () override
virtual void *	getGPUMemorySiteSizes ()
virtual void *	getGPUMemoryParticleSizes ()
virtual void *	getGPUMemorySizeLattice ()
virtual void *	getGPUMemorySizeDest ()
virtual void	swapSizeSrcDest ()
void	setParticleSize (particle_t particleType, uint32_t size)
uint32_t	getParticleSize (particle_t particleType) const
uint32_t	getSizeBasedOccupancy (lattice_size_t x, lattice_size_t y, lattice_size_t z) const
uint32_t	getSizeBasedOccupancy (lattice_size_t subvolume) const
bool	canAddParticle (lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) const
bool	canAddParticle (lattice_size_t subvolume, particle_t particle) const
virtual void	addParticleWithSizeCheck (lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle)
virtual void	addParticleWithSizeCheck (lattice_size_t subvolume, particle_t particle)
virtual void	addParticle (lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) override
	Add a particle to the specified site.
virtual void	addParticle (lattice_size_t index, particle_t particle) override
	Add a particle to the specified site.
virtual void	removeParticles (lattice_size_t x, lattice_size_t y, lattice_size_t z) override
	Remove a particle to the specified site.
virtual void	removeParticles (lattice_size_t index) override
	Remove a particle to the specified site.
virtual void	removeAllParticles () override
	Empty all particles from the specified site.
void	setSizeCheckingEnabled (bool enable)
bool	isSizeCheckingEnabled () const
const ParticleSizeManager &	getParticleSizeManager () const
void	validateSizeConstraints () const
std::map< uint32_t, uint32_t >	getSizeBasedOccupancyStats () const
void	updateGPUSiteSizes ()
void	syncSiteSizesFromGPU ()
Public Member Functions inherited from lm::rdme::CudaByteLattice
	CudaByteLattice (lattice_coord_t size, si_dist_t spacing, uint particlesPerSite)
	CudaByteLattice (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite)
virtual	~CudaByteLattice ()
virtual void *	getGPUMemorySrc ()
virtual void *	getGPUMemoryDest ()
virtual void	swapSrcDest ()
virtual void *	getGPUMemorySiteTypes ()
virtual size_t	getParticleMemorySize () const
virtual void	setSiteType (lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site)
	Set the site type at the specified location.
virtual void	setSiteType (lattice_size_t index, site_t site)
	Set the site type at the specified location.
virtual void	setFromRowMajorByteData (void *buffer, size_t bufferSize)
virtual void	getSiteLatticeView (uint8_t *siteLattice, int Nz, int Ny, int Nx)
virtual void	getParticleLatticeView (uint8_t *particleLattice, int Nw, int Nz, int Ny, int Nx, int Np)
Public Member Functions inherited from lm::rdme::ByteLattice
virtual site_t	getMaxSiteType () const
	Get the maximum number of site types possible in the lattice.
virtual particle_t	getMaxParticle () const
	Get the maximum number of particle types possible in the lattice.
virtual site_size_t	getMaxOccupancy () const
	Get the maximum number of particles that can live in a site.
	ByteLattice (lattice_coord_t size, si_dist_t spacing, uint particlesPerSite)
	ByteLattice (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite)
virtual	~ByteLattice ()
virtual void	getNeighboringSites (lattice_size_t index, lattice_size_t *neighboringIndices)
	Get the sites that are neighbor to the indicated site.
virtual site_t	getSiteType (lattice_size_t x, lattice_size_t y, lattice_size_t z) const
	Get the site type at the specified location.
virtual site_t	getSiteType (lattice_size_t subvolume) const
	Get the site type at the specified location.
void	copySites (void *destBuffer, size_t latticeSize)
virtual site_size_t	getOccupancy (lattice_size_t x, lattice_size_t y, lattice_size_t z) const
	Get the number of particles in the specified lattice site.
virtual site_size_t	getOccupancy (lattice_size_t subvolume) const
	Get the number of particles in the specified lattice site.
virtual particle_t	getParticle (lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const
	Get the particle at the specified site with at the specified number in the particle list.
virtual particle_t	getParticle (lattice_size_t subvolume, site_size_t particleIndex) const
	Get the particle at the specified site with at the specified number in the particle list.
virtual std::map< particle_t, uint >	getParticleCounts ()
	Get the number of each particle type in the lattice.
virtual std::vector< particle_loc_t >	findParticles (particle_t minParticleType, particle_t maxParticleType)
	Get the number of the specified particles types in the lattice.
virtual void	setSitesFromRowMajorByteData (void *buffer, size_t bufferSize)
virtual size_t	getLatticeMemorySize () const
Public Member Functions inherited from lm::rdme::Lattice
	Lattice (lattice_coord_t size, si_dist_t spacing)
	Create a Lattice object.
	Lattice (lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing)
	Create a Lattice object.
virtual	~Lattice ()
	Destroy the Lattice object.
virtual lattice_coord_t	getSize () const
	Get size of the Lattice.
virtual lattice_size_t	getXSize () const
	Get x dimension of the Lattice.
virtual lattice_size_t	getYSize () const
	Get y dimension of the Lattice.
virtual lattice_size_t	getZSize () const
	Get z dimension of the Lattice.
virtual lattice_size_t	getNumberSites () const
	Get total number of sites in the Lattice.
virtual si_dist_t	getSpacing () const
	Get spacing between lattice sites.
std::vector< lattice_coord_t >	getNearbySites (lattice_size_t xc, lattice_size_t yc, lattice_size_t zc, uint minDistance, uint maxDistance)
	Get a list of sites near the specified site within a certain distance.
virtual void	print () const
	Print the lattice to the console.

Protected Member Functions
virtual void	allocateCudaMemory () override
virtual void	deallocateCudaMemory () override
void	updateSiteSize (lattice_size_t subvolume, particle_t particle, bool adding)
void	initializeGPUSiteSizes ()
void	recalculateAllSiteSizes ()
bool	canAddParticleGPU (lattice_size_t subvolume, particle_t particle) const
void	addParticleGPU (lattice_size_t subvolume, particle_t particle)
void	removeParticleGPU (lattice_size_t subvolume, particle_t particle)
site_size_t	getParticlesAtSite (lattice_size_t subvolume, particle_t *particles, site_size_t maxCount) const
Protected Member Functions inherited from lm::rdme::ByteLattice
virtual void	allocateMemory ()
virtual void	deallocateMemory ()
virtual uint32_t *	getParticlesMemory ()
virtual uint8_t *	getSitesMemory ()

Protected Attributes
std::unique_ptr< ParticleSizeManager >	sizeManager_
bool	sizeCheckingEnabled_
uint32_t	maxSiteCapacity_
std::vector< uint32_t >	siteSizes_
size_t	cudaSiteSizesSize_
void *	cudaSiteSizes_ [2]
uint	cudaSiteSizesCurrent_
size_t	cudaParticleSizesSize_
void *	cudaParticleSizes_
bool	isGPUSiteSizesSynched_
bool	isGPUParticleSizesSynched_
Protected Attributes inherited from lm::rdme::CudaByteLattice
uint	cudaParticlesCurrent
size_t	cudaParticlesSize
void *	cudaParticles [2]
size_t	cudaSiteTypesSize
void *	cudaSiteTypes
bool	isGPUMemorySynched
Protected Attributes inherited from lm::rdme::ByteLattice
size_t	wordsPerSite
uint32_t *	particles
uint8_t *	siteTypes
Protected Attributes inherited from lm::rdme::Lattice
lattice_coord_t	size
lattice_size_t	numberSites
si_dist_t	spacing

Friends
class	lm::MpdRdmeSolverExtended

Additional Inherited Members
Static Public Member Functions inherited from lm::rdme::ByteLattice
static void	nativeSerialize (void destBuffer, void lattice, size_t latticeSize)
static void	nativeSerializeSites (void destBuffer, void lattice, size_t latticeSize)
static void	copyNativeToRowMajorByte (void destBuffer, void sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, uint particlesPerSite, size_t bufferSize)
static void	copyRowMajorByteToNative (void destBuffer, void sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, uint particlesPerSite, size_t bufferSize)
static void	copySitesRowMajorByteToNative (void destBuffer, void sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, size_t bufferSize)
static void	copySitesNativeToRowMajorByte (void destBuffer, void sourceBuffer, lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, size_t bufferSize)
Static Public Member Functions inherited from lm::rdme::Lattice
static void	rowMajorByteSerialize (void destBuffer, void lattice, size_t bufferSize)
static void	rowMajorIntSerialize (void destBuffer, void lattice, size_t bufferSize)
static void	rowMajorByteSerializeSites (void destBuffer, void lattice, size_t bufferSize)

Detailed Description

CUDA-accelerated extended ByteLattice with particle size awareness.

This class extends CudaByteLattice to support particles with different sizes, providing GPU-accelerated capacity validation and site occupancy tracking. It maintains current site size = sum(particle * particle_size) for each site.

Constructor & Destructor Documentation

◆ CudaByteLatticeExtended() [1/2]

lm::rdme::CudaByteLatticeExtended::CudaByteLatticeExtended	(	lattice_coord_t	size,
		si_dist_t	spacing,
		uint	particlesPerSite,
		bool	enableSizeChecking = true )

Constructor with particle size support.

Parameters

size	Lattice dimensions
spacing	Lattice spacing
particlesPerSite	Maximum particles per site
enableSizeChecking	Enable particle size validation (default: true)

◆ CudaByteLatticeExtended() [2/2]

lm::rdme::CudaByteLatticeExtended::CudaByteLatticeExtended	(	lattice_size_t	xSize,
		lattice_size_t	ySize,
		lattice_size_t	zSize,
		si_dist_t	spacing,
		uint	particlesPerSite,
		bool	enableSizeChecking = true )

Constructor with particle size support.

Parameters

xSize	X dimension
ySize	Y dimension
zSize	Z dimension
spacing	Lattice spacing
particlesPerSite	Maximum particles per site
enableSizeChecking	Enable particle size validation (default: true)

◆ ~CudaByteLatticeExtended()

virtual lm::rdme::CudaByteLatticeExtended::~CudaByteLatticeExtended ( )

virtual

Destructor.

Member Function Documentation

◆ addParticle() [1/2]

virtual void lm::rdme::CudaByteLatticeExtended::addParticle	(	lattice_size_t	index,
		particle_t	particle )

overridevirtual

Add a particle to the specified site.

Reimplemented from lm::rdme::CudaByteLattice.

◆ addParticle() [2/2]

virtual void lm::rdme::CudaByteLatticeExtended::addParticle	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		particle_t	particle )

overridevirtual

Add a particle to the specified site.

Reimplemented from lm::rdme::CudaByteLattice.

◆ addParticleGPU()

void lm::rdme::CudaByteLatticeExtended::addParticleGPU	(	lattice_size_t	subvolume,
		particle_t	particle )

protected

◆ addParticleWithSizeCheck() [1/2]

virtual void lm::rdme::CudaByteLatticeExtended::addParticleWithSizeCheck	(	lattice_size_t	subvolume,
		particle_t	particle )

virtual

◆ addParticleWithSizeCheck() [2/2]

virtual void lm::rdme::CudaByteLatticeExtended::addParticleWithSizeCheck	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		particle_t	particle )

virtual

◆ allocateCudaMemory()

virtual void lm::rdme::CudaByteLatticeExtended::allocateCudaMemory ( )

overrideprotectedvirtual

Reimplemented from lm::rdme::CudaByteLattice.

◆ canAddParticle() [1/2]

bool lm::rdme::CudaByteLatticeExtended::canAddParticle	(	lattice_size_t	subvolume,
		particle_t	particle ) const

◆ canAddParticle() [2/2]

bool lm::rdme::CudaByteLatticeExtended::canAddParticle	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z,
		particle_t	particle ) const

◆ canAddParticleGPU()

bool lm::rdme::CudaByteLatticeExtended::canAddParticleGPU	(	lattice_size_t	subvolume,
		particle_t	particle ) const

protected

◆ copyFromGPU()

virtual void lm::rdme::CudaByteLatticeExtended::copyFromGPU ( )

overridevirtual

Reimplemented from lm::rdme::CudaByteLattice.

◆ copyToGPU()

virtual void lm::rdme::CudaByteLatticeExtended::copyToGPU ( )

overridevirtual

Reimplemented from lm::rdme::CudaByteLattice.

◆ deallocateCudaMemory()

virtual void lm::rdme::CudaByteLatticeExtended::deallocateCudaMemory ( )

overrideprotectedvirtual

Reimplemented from lm::rdme::CudaByteLattice.

◆ getGPUMemoryParticleSizes()

virtual void * lm::rdme::CudaByteLatticeExtended::getGPUMemoryParticleSizes ( )

virtual

◆ getGPUMemorySiteSizes()

virtual void * lm::rdme::CudaByteLatticeExtended::getGPUMemorySiteSizes ( )

virtual

◆ getGPUMemorySizeDest()

virtual void * lm::rdme::CudaByteLatticeExtended::getGPUMemorySizeDest ( )

virtual

◆ getGPUMemorySizeLattice()

virtual void * lm::rdme::CudaByteLatticeExtended::getGPUMemorySizeLattice ( )

virtual

◆ getParticlesAtSite()

site_size_t lm::rdme::CudaByteLatticeExtended::getParticlesAtSite	(	lattice_size_t	subvolume,
		particle_t *	particles,
		site_size_t	maxCount ) const

protected

◆ getParticleSize()

uint32_t lm::rdme::CudaByteLatticeExtended::getParticleSize ( particle_t particleType ) const

◆ getParticleSizeManager()

const ParticleSizeManager & lm::rdme::CudaByteLatticeExtended::getParticleSizeManager ( ) const

◆ getSizeBasedOccupancy() [1/2]

uint32_t lm::rdme::CudaByteLatticeExtended::getSizeBasedOccupancy ( lattice_size_t subvolume ) const

◆ getSizeBasedOccupancy() [2/2]

uint32_t lm::rdme::CudaByteLatticeExtended::getSizeBasedOccupancy	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z ) const

◆ getSizeBasedOccupancyStats()

std::map< uint32_t, uint32_t > lm::rdme::CudaByteLatticeExtended::getSizeBasedOccupancyStats ( ) const

◆ initializeGPUSiteSizes()

void lm::rdme::CudaByteLatticeExtended::initializeGPUSiteSizes ( )

protected

◆ isSizeCheckingEnabled()

bool lm::rdme::CudaByteLatticeExtended::isSizeCheckingEnabled ( ) const

◆ recalculateAllSiteSizes()

void lm::rdme::CudaByteLatticeExtended::recalculateAllSiteSizes ( )

protected

◆ removeAllParticles()

virtual void lm::rdme::CudaByteLatticeExtended::removeAllParticles ( )

overridevirtual

Empty all particles from the specified site.

Reimplemented from lm::rdme::CudaByteLattice.

◆ removeParticleGPU()

void lm::rdme::CudaByteLatticeExtended::removeParticleGPU	(	lattice_size_t	subvolume,
		particle_t	particle )

protected

◆ removeParticles() [1/2]

virtual void lm::rdme::CudaByteLatticeExtended::removeParticles ( lattice_size_t index )

overridevirtual

Remove a particle to the specified site.

Reimplemented from lm::rdme::CudaByteLattice.

◆ removeParticles() [2/2]

virtual void lm::rdme::CudaByteLatticeExtended::removeParticles	(	lattice_size_t	x,
		lattice_size_t	y,
		lattice_size_t	z )

overridevirtual

Remove a particle to the specified site.

Reimplemented from lm::rdme::CudaByteLattice.

◆ setParticleSize()

void lm::rdme::CudaByteLatticeExtended::setParticleSize	(	particle_t	particleType,
		uint32_t	size )

◆ setSizeCheckingEnabled()

void lm::rdme::CudaByteLatticeExtended::setSizeCheckingEnabled ( bool enable )

◆ swapSizeSrcDest()

virtual void lm::rdme::CudaByteLatticeExtended::swapSizeSrcDest ( )

virtual

◆ syncSiteSizesFromGPU()

void lm::rdme::CudaByteLatticeExtended::syncSiteSizesFromGPU ( )

◆ updateGPUSiteSizes()

void lm::rdme::CudaByteLatticeExtended::updateGPUSiteSizes ( )

◆ updateSiteSize()

void lm::rdme::CudaByteLatticeExtended::updateSiteSize	(	lattice_size_t	subvolume,
		particle_t	particle,
		bool	adding )

protected

◆ validateSizeConstraints()

void lm::rdme::CudaByteLatticeExtended::validateSizeConstraints ( ) const

◆ lm::MpdRdmeSolverExtended

friend class lm::MpdRdmeSolverExtended

friend

Member Data Documentation

◆ cudaParticleSizes_

void* lm::rdme::CudaByteLatticeExtended::cudaParticleSizes_

protected

◆ cudaParticleSizesSize_

size_t lm::rdme::CudaByteLatticeExtended::cudaParticleSizesSize_

protected

◆ cudaSiteSizes_

void* lm::rdme::CudaByteLatticeExtended::cudaSiteSizes_[2]

protected

◆ cudaSiteSizesCurrent_

uint lm::rdme::CudaByteLatticeExtended::cudaSiteSizesCurrent_

protected

◆ cudaSiteSizesSize_

size_t lm::rdme::CudaByteLatticeExtended::cudaSiteSizesSize_

protected

◆ isGPUParticleSizesSynched_

bool lm::rdme::CudaByteLatticeExtended::isGPUParticleSizesSynched_

protected

◆ isGPUSiteSizesSynched_

bool lm::rdme::CudaByteLatticeExtended::isGPUSiteSizesSynched_

protected

◆ maxSiteCapacity_

uint32_t lm::rdme::CudaByteLatticeExtended::maxSiteCapacity_

protected

◆ siteSizes_

std::vector<uint32_t> lm::rdme::CudaByteLatticeExtended::siteSizes_

protected

◆ sizeCheckingEnabled_

bool lm::rdme::CudaByteLatticeExtended::sizeCheckingEnabled_

protected

◆ sizeManager_

std::unique_ptr<ParticleSizeManager> lm::rdme::CudaByteLatticeExtended::sizeManager_

protected

The documentation for this class was generated from the following file:

/data2/LM_zls_github/Lattice-Microbes/src/rdme/CudaByteLatticeExtended.h

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CudaByteLatticeExtended() [1/2]

◆ CudaByteLatticeExtended() [2/2]

◆ ~CudaByteLatticeExtended()

Member Function Documentation

◆ addParticle() [1/2]

◆ addParticle() [2/2]

◆ addParticleGPU()

◆ addParticleWithSizeCheck() [1/2]

◆ addParticleWithSizeCheck() [2/2]

◆ allocateCudaMemory()

◆ canAddParticle() [1/2]

◆ canAddParticle() [2/2]

◆ canAddParticleGPU()

◆ copyFromGPU()

◆ copyToGPU()

◆ deallocateCudaMemory()

◆ getGPUMemoryParticleSizes()

◆ getGPUMemorySiteSizes()

◆ getGPUMemorySizeDest()

◆ getGPUMemorySizeLattice()

◆ getParticlesAtSite()

◆ getParticleSize()

◆ getParticleSizeManager()

◆ getSizeBasedOccupancy() [1/2]

◆ getSizeBasedOccupancy() [2/2]

◆ getSizeBasedOccupancyStats()

◆ initializeGPUSiteSizes()

◆ isSizeCheckingEnabled()

◆ recalculateAllSiteSizes()

◆ removeAllParticles()

◆ removeParticleGPU()

◆ removeParticles() [1/2]

◆ removeParticles() [2/2]

◆ setParticleSize()

◆ setSizeCheckingEnabled()

◆ swapSizeSrcDest()

◆ syncSiteSizesFromGPU()

◆ updateGPUSiteSizes()

◆ updateSiteSize()

◆ validateSizeConstraints()

Friends And Related Symbol Documentation

◆ lm::MpdRdmeSolverExtended

Member Data Documentation

◆ cudaParticleSizes_

◆ cudaParticleSizesSize_

◆ cudaSiteSizes_

◆ cudaSiteSizesCurrent_

◆ cudaSiteSizesSize_

◆ isGPUParticleSizesSynched_

◆ isGPUSiteSizesSynched_

◆ maxSiteCapacity_

◆ siteSizes_

◆ sizeCheckingEnabled_

◆ sizeManager_