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Commit 4f562f57 authored by BRAMAS Berenger's avatar BRAMAS Berenger
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Continue to work on the MPI Starpu

parent 5199e5b7
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Showing with 178 additions and 33 deletions
Src/GroupTree/FGroupOfCells.hpp
View file @ 4f562f57
......@@ -5,6 +5,7 @@
#define FGROUPOFCELLS_HPP
#include "../Utils/FAssert.hpp"
#include "../Utils/FAlignedMemory.hpp"
#include "../Containers/FTreeCoordinate.hpp"
#include <list>
......@@ -39,15 +40,34 @@ protected:
//< This value is for not used cells
static const MortonIndex CellIsEmptyFlag = -1;
//< To kown if the object has to delete the memory
bool deleteBuffer;
public:
/**
* Init from a given buffer
* @param inBuffer
* @param inAllocatedMemoryInByte
*/
FGroupOfCells(unsigned char* inBuffer, const size_t inAllocatedMemoryInByte)
: allocatedMemoryInByte(inAllocatedMemoryInByte), memoryBuffer(inBuffer),
blockHeader(nullptr), blockIndexesTable(nullptr), blockCells(nullptr),
deleteBuffer(false){
// Move the pointers to the correct position
blockHeader = reinterpret_cast<BlockHeader*>(memoryBuffer);
blockIndexesTable = reinterpret_cast<int*>(memoryBuffer+sizeof(BlockHeader));
blockCells = reinterpret_cast<CellClass*>(memoryBuffer+sizeof(BlockHeader)+(blockHeader->blockIndexesTableSize*sizeof(int)));
}
/**
* @brief FGroupOfCells
* @param inStartingIndex first cell morton index
* @param inEndingIndex last cell morton index + 1
* @param inNumberOfCells total number of cells in the interval (should be <= inEndingIndex-inEndingIndex)
*/
FGroupOfCells(const MortonIndex inStartingIndex, const MortonIndex inEndingIndex, const int inNumberOfCells)
: allocatedMemoryInByte(0), memoryBuffer(nullptr), blockHeader(nullptr), blockIndexesTable(nullptr), blockCells(nullptr) {
: allocatedMemoryInByte(0), memoryBuffer(nullptr), blockHeader(nullptr), blockIndexesTable(nullptr), blockCells(nullptr),
deleteBuffer(true){
// Find the number of cell to allocate in the blocks
const int blockIndexesTableSize = int(inEndingIndex-inStartingIndex);
FAssertLF(inNumberOfCells <= blockIndexesTableSize);
......@@ -57,7 +77,7 @@ public:
// Allocate
FAssertLF(0 <= int(memoryToAlloc) && int(memoryToAlloc) < std::numeric_limits<int>::max());
allocatedMemoryInByte = memoryToAlloc;
memoryBuffer = new unsigned char[memoryToAlloc];
memoryBuffer = (unsigned char*)FAlignedMemory::Allocate32BAligned(memoryToAlloc);
FAssertLF(memoryBuffer);
memset(memoryBuffer, 0, memoryToAlloc);
......@@ -80,12 +100,19 @@ public:
/** Call the destructor of cells and dealloc block memory */
~FGroupOfCells(){
for(int idxCellPtr = 0 ; idxCellPtr < blockHeader->blockIndexesTableSize ; ++idxCellPtr){
if(blockIndexesTable[idxCellPtr] != CellIsEmptyFlag){
(&blockCells[blockIndexesTable[idxCellPtr]])->~CellClass();
if(deleteBuffer){
for(int idxCellPtr = 0 ; idxCellPtr < blockHeader->blockIndexesTableSize ; ++idxCellPtr){
if(blockIndexesTable[idxCellPtr] != CellIsEmptyFlag){
(&blockCells[blockIndexesTable[idxCellPtr]])->~CellClass();
}
}
FAlignedMemory::Dealloc32BAligned(memoryBuffer);
}
delete[] memoryBuffer;
}
/** Give access to the buffer to send the data */
const unsigned char* getRawBuffer() const{
return memoryBuffer;
}
/** The the size of the allocated buffer */
......@@ -93,6 +120,11 @@ public:
return allocatedMemoryInByte;
}
/** To know if the object will delete the memory block */
bool getDeleteMemory() const{
return deleteBuffer;
}
/** The index of the fist cell (set from the constructor) */
MortonIndex getStartingIndex() const {
return blockHeader->startingIndex;
......
Src/GroupTree/FGroupOfParticles.hpp
View file @ 4f562f57
......@@ -41,6 +41,7 @@ class FGroupOfParticles {
size_t offSet;
};
protected:
static const int MemoryAlignementBytes = 32;
static const int MemoryAlignementParticles = MemoryAlignementBytes/sizeof(FReal);
......@@ -78,15 +79,49 @@ protected:
//< Pointers to the particles data inside the block memory
AttributeClass* particleAttributes[NbAttributesPerParticle];
/** To know if we have to delete the buffer */
bool deleteBuffer;
public:
/**
* Init from a given buffer
* @param inBuffer
* @param inAllocatedMemoryInByte
*/
FGroupOfParticles(unsigned char* inBuffer, const size_t inAllocatedMemoryInByte)
: allocatedMemoryInByte(inAllocatedMemoryInByte), memoryBuffer(inBuffer),
blockHeader(nullptr), blockIndexesTable(nullptr), leafHeader(nullptr), nbParticlesInGroup(0),
deleteBuffer(false){
// Move the pointers to the correct position
blockHeader = reinterpret_cast<BlockHeader*>(memoryBuffer);
blockIndexesTable = reinterpret_cast<int*>(memoryBuffer+sizeof(BlockHeader));
leafHeader = reinterpret_cast<LeafHeader*>(memoryBuffer+sizeof(BlockHeader)+(blockHeader->blockIndexesTableSize*sizeof(int)));
// Init particle pointers
blockHeader->positionOffset = (sizeof(FReal) * blockHeader->nbParticlesAllocatedInGroup);
particlePosition[0] = reinterpret_cast<FReal*>((reinterpret_cast<size_t>(leafHeader + blockHeader->numberOfLeavesInBlock)
+MemoryAlignementBytes-1) & ~(MemoryAlignementBytes-1));
particlePosition[1] = (particlePosition[0] + blockHeader->nbParticlesAllocatedInGroup);
particlePosition[2] = (particlePosition[1] + blockHeader->nbParticlesAllocatedInGroup);
// Redirect pointer to data
blockHeader->attributeOffset = (sizeof(AttributeClass) * blockHeader->nbParticlesAllocatedInGroup);
unsigned char* previousPointer = reinterpret_cast<unsigned char*>(particlePosition[2] + blockHeader->nbParticlesAllocatedInGroup);
for(unsigned idxAttribute = 0 ; idxAttribute < NbAttributesPerParticle ; ++idxAttribute){
particleAttributes[idxAttribute] = reinterpret_cast<AttributeClass*>(previousPointer);
previousPointer += sizeof(AttributeClass)*blockHeader->nbParticlesAllocatedInGroup;
}
}
/**
* @brief FGroupOfParticles
* @param inStartingIndex first leaf morton index
* @param inEndingIndex last leaf morton index + 1
* @param inNumberOfLeaves total number of leaves in the interval (should be <= inEndingIndex-inEndingIndex)
*/
FGroupOfParticles(const MortonIndex inStartingIndex, const MortonIndex inEndingIndex, const int inNumberOfLeaves, const int inNbParticles)
: allocatedMemoryInByte(0), memoryBuffer(nullptr), blockHeader(nullptr), blockIndexesTable(nullptr), leafHeader(nullptr), nbParticlesInGroup(inNbParticles) {
: allocatedMemoryInByte(0), memoryBuffer(nullptr), blockHeader(nullptr), blockIndexesTable(nullptr), leafHeader(nullptr), nbParticlesInGroup(inNbParticles),
deleteBuffer(true){
memset(particlePosition, 0, sizeof(particlePosition));
memset(particleAttributes, 0, sizeof(particleAttributes));
......@@ -144,7 +179,14 @@ public:
/** Call the destructor of leaves and dealloc block memory */
~FGroupOfParticles(){
FAlignedMemory::Dealloc32BAligned(memoryBuffer);
if(deleteBuffer){
FAlignedMemory::Dealloc32BAligned(memoryBuffer);
}
}
/** Give access to the buffer to send the data */
const unsigned char* getRawBuffer() const{
return memoryBuffer;
}
/** The the size of the allocated buffer */
......@@ -152,6 +194,11 @@ public:
return allocatedMemoryInByte;
}
/** To know if the object will delete the memory block */
bool getDeleteMemory() const{
return deleteBuffer;
}
/** The index of the fist leaf (set from the constructor) */
MortonIndex getStartingIndex() const {
return blockHeader->startingIndex;
......
Src/GroupTree/FGroupTaskStarpuMpiAlgorithm.hpp
View file @ 4f562f57
......@@ -10,6 +10,7 @@
#include "../Utils/FLog.hpp"
#include "../Utils/FTic.hpp"
#include "../Utils/FAssert.hpp"
#include "../Utils/FAlignedMemory.hpp"
#include "../Utils/FMpi.hpp"
......@@ -230,6 +231,18 @@ protected:
std::vector< std::vector< std::vector<BlockInteractions<CellContainerClass>>>> externalInteractionsAllLevelMpi;
std::vector< std::vector<BlockInteractions<ParticleGroupClass>>> externalInteractionsLeafLevelMpi;
struct RemoteHandle{
RemoteHandle() : ptr(nullptr){
memset(&handle, 0, sizeof(handle));
}
unsigned char * ptr;
starpu_data_handle_t handle;
};
std::vector<std::vector<RemoteHandle>> remoteCellGroups;
std::vector<RemoteHandle> remoteParticleGroupss;
void buildRemoteInteractionsAndHandles(){
// We need to have information about all other blocks
std::unique_ptr<int[]> nbBlocksPerLevel(new int[tree->getHeight()]);
......@@ -290,6 +303,13 @@ protected:
processesBlockInfos[idxLevel].data(), recvBlocksCount.get(), recvBlockDispl.get(), MPI_BYTE,
comm.getComm()), __LINE__);
}
// Prepare remate ptr and handles
remoteCellGroups.resize( tree->getHeight() );
for(int idxLevel = 1 ; idxLevel < tree->getHeight() ; ++idxLevel){
remoteCellGroups[idxLevel].resize( processesBlockInfos[idxLevel].size());
}
remoteParticleGroupss.resize(processesBlockInfos[tree->getHeight()-1].size());
// From now we have the number of blocks for all process
// we also have the size of the blocks therefor we can
// create the handles we need
......@@ -409,9 +429,22 @@ protected:
// Create interactions
const int nbInteractionsBetweenBlocks = (lastOutInteraction-currentOutInteraction);
if(nbInteractionsBetweenBlocks){
if(remoteCellGroups[idxLevel][idxOtherGroup].ptr == nullptr){
#pragma omp critical(CreateM2LRemotes)
{
if(remoteCellGroups[idxLevel][idxOtherGroup].ptr == nullptr){
const int nbBytesInBlock = processesBlockInfos[tree->getHeight()-1][idxOtherGroup].leavesBufferSize;
unsigned char* memoryBlock = (unsigned char*)FAlignedMemory::Allocate32BAligned(nbBytesInBlock);
remoteCellGroups[idxLevel][idxOtherGroup].ptr = memoryBlock;
starpu_variable_data_register(&remoteCellGroups[idxLevel][idxOtherGroup].handle, 0,
(uintptr_t)remoteCellGroups[idxLevel][idxOtherGroup].ptr, nbBytesInBlock);
}
}
}
externalInteractions->emplace_back();
BlockInteractions<CellContainerClass>* interactions = &externalInteractions->back();
//interactions->otherBlock = leftCells;
//interactions->otherBlock = remoteCellGroups[idxLevel][idxOtherGroup].ptr;
interactions->otherBlockId = idxOtherGroup;
interactions->interactions.resize(nbInteractionsBetweenBlocks);
std::copy(outsideInteractions.begin() + currentOutInteraction,
......@@ -493,9 +526,22 @@ protected:
const int nbInteractionsBetweenBlocks = (lastOutInteraction-currentOutInteraction);
if(nbInteractionsBetweenBlocks){
if(remoteParticleGroupss[idxOtherGroup].ptr == nullptr){
#pragma omp critical(CreateM2LRemotes)
{
if(remoteParticleGroupss[idxOtherGroup].ptr == nullptr){
const int nbBytesInBlock = processesBlockInfos[tree->getHeight()-1][idxOtherGroup].leavesBufferSize;
unsigned char* memoryBlock = (unsigned char*)FAlignedMemory::Allocate32BAligned(nbBytesInBlock);
remoteParticleGroupss[idxOtherGroup].ptr = memoryBlock;
starpu_variable_data_register(&remoteParticleGroupss[idxOtherGroup].handle, 0,
(uintptr_t)remoteParticleGroupss[idxOtherGroup].ptr, nbBytesInBlock);
}
}
}
externalInteractions->emplace_back();
BlockInteractions<ParticleGroupClass>* interactions = &externalInteractions->back();
//interactions->otherBlock = leftContainers;
//interactions->otherBlock = remoteParticleGroupss[idxOtherGroup].ptr;
interactions->otherBlockId = idxOtherGroup;
interactions->interactions.resize(nbInteractionsBetweenBlocks);
std::copy(outsideInteractions.begin() + currentOutInteraction,
......@@ -522,7 +568,7 @@ protected:
for(int idxGroup = 0 ; idxGroup < tree->getNbCellGroupAtLevel(idxLevel) ; ++idxGroup){
const CellContainerClass* currentCells = tree->getCellGroup(idxLevel, idxGroup);
starpu_variable_data_register(&handles[idxLevel][idxGroup], 0, (uintptr_t)currentCells, sizeof(*currentCells)); // TODO
starpu_variable_data_register(&handles[idxLevel][idxGroup], 0, (uintptr_t)currentCells->getRawBuffer(), currentCells->getBufferSizeInByte()); // TODO
}
}
{
......@@ -530,7 +576,7 @@ protected:
handles[idxLevel].resize(tree->getNbParticleGroup());
for(int idxGroup = 0 ; idxGroup < tree->getNbParticleGroup() ; ++idxGroup){
ParticleGroupClass* containers = tree->getParticleGroup(idxGroup);
starpu_variable_data_register(&handles[idxLevel][idxGroup], 0, (uintptr_t)containers, sizeof(*containers)); // TODO
starpu_variable_data_register(&handles[idxLevel][idxGroup], 0, (uintptr_t)containers->getRawBuffer(), containers->getBufferSizeInByte()); // TODO
}
}
}
......@@ -730,12 +776,14 @@ protected:
}
static void bottomPassCallback(void *buffers[], void *cl_arg){
CellContainerClass* leafCells = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[0]));
ParticleGroupClass* containers = reinterpret_cast<ParticleGroupClass*>(STARPU_VARIABLE_GET_PTR(buffers[1]));
CellContainerClass leafCells((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[0]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[0]));
ParticleGroupClass containers((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[1]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[1]));
ThisClass* worker = nullptr;
starpu_codelet_unpack_args(cl_arg, &worker);
worker->bottomPassPerform(leafCells, containers);
worker->bottomPassPerform(&leafCells, &containers);
}
void bottomPassPerform(CellContainerClass* leafCells, ParticleGroupClass* containers){
......@@ -808,7 +856,8 @@ protected:
}
static void upwardPassCallback(void *buffers[], void *cl_arg){
CellContainerClass* currentCells = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[0]));
CellContainerClass currentCells((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[0]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[0]));
ThisClass* worker = nullptr;
int nbSubCellGroups = 0;
......@@ -818,10 +867,15 @@ protected:
CellContainerClass* subCellGroups[9];
memset(subCellGroups, 0, 9*sizeof(CellContainerClass*));
for(int idxSubGroup = 0; idxSubGroup < nbSubCellGroups ; ++idxSubGroup){
subCellGroups[idxSubGroup] = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[idxSubGroup+1]));
subCellGroups[idxSubGroup] = new CellContainerClass((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[idxSubGroup+1]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[idxSubGroup+1]));
}
worker->upwardPassPerform(currentCells, subCellGroups, nbSubCellGroups, idxLevel);
worker->upwardPassPerform(&currentCells, subCellGroups, nbSubCellGroups, idxLevel);
for(int idxSubGroup = 0; idxSubGroup < nbSubCellGroups ; ++idxSubGroup){
delete subCellGroups[idxSubGroup];
}
}
void upwardPassPerform(CellContainerClass*const currentCells,
......@@ -895,13 +949,14 @@ protected:
}
static void transferInPassCallback(void *buffers[], void *cl_arg){
CellContainerClass* currentCells = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[0]));
CellContainerClass currentCells((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[0]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[0]));
ThisClass* worker = nullptr;
int idxLevel = 0;
starpu_codelet_unpack_args(cl_arg, &worker, &idxLevel);
worker->transferInPassPerform(currentCells, idxLevel);
worker->transferInPassPerform(&currentCells, idxLevel);
}
void transferInPassPerform(CellContainerClass*const currentCells, const int idxLevel){
......@@ -940,8 +995,8 @@ protected:
}
static void transferInoutPassCallback(void *buffers[], void *cl_arg){
CellContainerClass* currentCells = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[0]));
CellContainerClass* externalCells = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[1]));
CellContainerClass* currentCells = reinterpret_cast<CellContainerClass*>((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[0]));
CellContainerClass* externalCells = reinterpret_cast<CellContainerClass*>((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[1]));
ThisClass* worker = nullptr;
int idxLevel = 0;
......@@ -1033,7 +1088,8 @@ protected:
}
static void downardPassCallback(void *buffers[], void *cl_arg){
CellContainerClass* currentCells = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[0]));
CellContainerClass currentCells((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[0]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[0]));
ThisClass* worker = nullptr;
int nbSubCellGroups = 0;
......@@ -1043,10 +1099,15 @@ protected:
CellContainerClass* subCellGroups[9];
memset(subCellGroups, 0, 9*sizeof(CellContainerClass*));
for(int idxSubGroup = 0; idxSubGroup < nbSubCellGroups ; ++idxSubGroup){
subCellGroups[idxSubGroup] = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[idxSubGroup+1]));
subCellGroups[idxSubGroup] = new CellContainerClass((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[idxSubGroup+1]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[idxSubGroup+1]));
}
worker->downardPassPerform(currentCells, subCellGroups, nbSubCellGroups, idxLevel);
worker->downardPassPerform(&currentCells, subCellGroups, nbSubCellGroups, idxLevel);
for(int idxSubGroup = 0; idxSubGroup < nbSubCellGroups ; ++idxSubGroup){
delete subCellGroups[idxSubGroup];
}
}
void downardPassPerform(CellContainerClass*const currentCells,
......@@ -1116,12 +1177,13 @@ protected:
}
static void directInPassCallback(void *buffers[], void *cl_arg){
ParticleGroupClass* containers = reinterpret_cast<ParticleGroupClass*>(STARPU_VARIABLE_GET_PTR(buffers[0]));
ParticleGroupClass containers((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[0]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[0]));
ThisClass* worker = nullptr;
starpu_codelet_unpack_args(cl_arg, &worker);
worker->directInPassPerform(containers);
worker->directInPassPerform(&containers);
}
void directInPassPerform(ParticleGroupClass* containers){
......@@ -1159,14 +1221,16 @@ protected:
}
static void directInoutPassCallback(void *buffers[], void *cl_arg){
ParticleGroupClass* containers = reinterpret_cast<ParticleGroupClass*>(STARPU_VARIABLE_GET_PTR(buffers[0]));
ParticleGroupClass* externalContainers = reinterpret_cast<ParticleGroupClass*>(STARPU_VARIABLE_GET_PTR(buffers[1]));
ParticleGroupClass containers((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[0]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[0]));
ParticleGroupClass externalContainers((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[1]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[1]));
ThisClass* worker = nullptr;
const std::vector<OutOfBlockInteraction>* outsideInteractions = nullptr;
starpu_codelet_unpack_args(cl_arg, &worker, &outsideInteractions);
worker->directInoutPassPerform(containers, externalContainers, outsideInteractions);
worker->directInoutPassPerform(&containers, &externalContainers, outsideInteractions);
}
void directInoutPassPerform(ParticleGroupClass* containers, ParticleGroupClass* containersOther,
......@@ -1209,12 +1273,14 @@ protected:
}
static void mergePassCallback(void *buffers[], void *cl_arg){
CellContainerClass* leafCells = reinterpret_cast<CellContainerClass*>(STARPU_VARIABLE_GET_PTR(buffers[0]));
ParticleGroupClass* containers = reinterpret_cast<ParticleGroupClass*>(STARPU_VARIABLE_GET_PTR(buffers[1]));
CellContainerClass leafCells((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[0]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[0]));
ParticleGroupClass containers((unsigned char*)STARPU_VARIABLE_GET_PTR(buffers[1]),
STARPU_VARIABLE_GET_ELEMSIZE(buffers[1]));
ThisClass* worker = nullptr;
starpu_codelet_unpack_args(cl_arg, &worker);
worker->mergePassPerform(leafCells, containers);
worker->mergePassPerform(&leafCells, &containers);
}
void mergePassPerform(CellContainerClass* leafCells, ParticleGroupClass* containers){
......
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