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Commit 5380b9d8 authored by Thomas Steinreiter's avatar Thomas Steinreiter
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Merge branch 'master' into refactor_bhtree_mpi

parents 8cce5175 ee0fb174
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CMakeLists.txt
View file @ 5380b9d8
......@@ -26,6 +26,7 @@ add_subdirectory(hermite4)
add_subdirectory(dynamic_sparse_data_exchange)
add_subdirectory(naive)
add_subdirectory(bhtree_mpi)
add_subdirectory(bhtree_pthread)
#
## BHTree requies gcc compiler, so we create it as a separate projectg
......
bhtree_pthread/CMakeLists.txt 0 → 100644
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# ==================================================================================================
# This file is part of the CodeVault project. The project is licensed under Apache Version 2.0.
# CodeVault is part of the EU-project PRACE-4IP (WP7.3.C).
#
# Author(s):
# Paul Heinzlreiter <paul.heinzlreiter@risc-software.at>
#
# ==================================================================================================
cmake_minimum_required(VERSION 3.0)
project ("bhtree_pthread")
include(${CMAKE_CURRENT_SOURCE_DIR}/../../cmake/common.cmake)
# ==================================================================================================
if ("${DWARF_PREFIX}" STREQUAL "")
set(DWARF_PREFIX 4_nbody)
endif()
set(NAME ${DWARF_PREFIX}_bhtree_pthread)
enable_language(CXX)
message("** Enabling '${NAME}'")
include(CheckCXXCompilerFlag)
CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
set(CXX11 ${COMPILER_SUPPORTS_CXX11})
set(CXX11_FLAGS -std=c++11)
set(CMAKE_CXX_FLAGS "-std=c++11")
set(GCC_DEBUG_COMPILE_FLAGS "-g")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GCC_DEBUG_COMPILE_FLAGS}")
find_package(Threads)
include_directories(src/datastructures src/simulation)
add_subdirectory(src/datastructures)
add_subdirectory(src/simulation)
add_executable(${NAME} src/pthreadmain.cpp)
target_link_libraries(${NAME} datastructures simulation ${CMAKE_THREAD_LIBS_INIT})
bhtree_pthread/src/data/dubinski.tab 0 → 100644
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bhtree_pthread/src/data/tab1024.dat 0 → 100644
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bhtree_pthread/src/data/tab128.dat 0 → 100644
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bhtree_pthread/src/data/tab65536.dat 0 → 100644
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bhtree_pthread/src/data/tab8096.dat 0 → 100644
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bhtree_pthread/src/datastructures/BarnesHutTree.cpp 0 → 100644
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#include "BarnesHutTree.hpp"
#include "Node.hpp"
#include "Box.hpp"
#include <iostream>
#include <climits>
#include <cfloat>
namespace nbody {
using namespace std;
BarnesHutTree::BarnesHutTree(int parallelId) : Tree(parallelId) {
}
BarnesHutTree::~BarnesHutTree() {
}
//determine octree subboxes
vector<Box> BarnesHutTree::splitBB(Node* node) {
return octreeSplit(node->getBB());
}
int BarnesHutTree::numberOfChildren() {
return 8;
}
//update upper tree nodes according to moved particles
void BarnesHutTree::update() {
//iterate for updating representatives
Node* current = this->nodes->prev;
while (current != this->nodes) {
current->representative.id = ULONG_MAX;
current->representative.mass = 0.0;
current->representative.position[0] = 0.0;
current->representative.position[1] = 0.0;
current->representative.position[2] = 0.0;
if (current->leaf) {
for (unsigned int i = 0; i < current->bodies.size(); i++) {
current->representative.mass += current->bodies[i].mass;
for (int j = 0; j < 3; j++) {
current->representative.position[j] += current->bodies[i].position[j] * current->bodies[i].mass;
}
}
} else {
Node* child = current->next;
do {
current->representative.mass += child->representative.mass;
for (int j = 0; j < 3; j++) {
current->representative.position[j] += child->representative.position[j] * child->representative.mass;
}
child = child->nextSibling;
} while (child != nullptr);
}
for (int j = 0; j < 3; j++) {
if (current->representative.mass > FLT_EPSILON) {
current->representative.position[j] /= current->representative.mass;
} else {
current->representative.position[j] = 0.0;
}
}
current = current->prev;
}
}
//split tree node into sub-boxes during tree build
void BarnesHutTree::split(Node* current) {
vector<Box> subboxes = BarnesHutTree::splitBB(current);
current->leaf = false;
Node* after = current->next;
for (vector<Box>::iterator it = subboxes.begin(); it != subboxes.end(); it++) {
Node* child = new Node(current->tree);
child->parent = current;
child->bb = *it;
child->bodies = copyBodies(*it, current->bodies);
child->nextSibling = nullptr;
child->prevSibling = nullptr;
after->insertBefore(child);
if (it != subboxes.begin()) {
child->prev->nextSibling = child;
child->prevSibling = child->prev;
child->prev->afterSubtree = child;
}
}
after->prev->afterSubtree = current->afterSubtree;
current->bodies.clear();
}
//initialize tree for build process
void BarnesHutTree::init(vector<Body> bodies, Box domain) {
Node* current;
this->clean();
if (bodies.empty()) return;
//insert root node
this->nodes->insertAfter(new Node(this));
current = this->nodes->next;
//assign bodies to root node
current->bodies = bodies;
//setup proper bounding box
current->bb = domain;
current->extendBBforBodies();
current->extendBBtoCube();
current->afterSubtree = current->next;
}
//check if split is required and perform it
bool BarnesHutTree::splitNode(Node* current) {
bool result = current->isSplitable();
if (result) {
split(current);
}
return result;
}
//build tree with given domain
void BarnesHutTree::build(vector<Body> bodies, Box domain) {
this->init(bodies, domain);
//iterate over existing boxes and split if it contains too much bodies
BarnesHutTree::splitSubtree(this->nodes->next);
this->update();
}
//build tree
void BarnesHutTree::build(vector<Body> bodies) {
Box bb;
initBox(bb);
extendForBodies(bb, bodies);
this->build(bodies, bb);
}
//merge remote refinement particles into local tree
//(this are remote particles from other processes needed for force computation on local particles)
void BarnesHutTree::mergeLET(vector<Body> bodies) {
//put all new bodies into fitting leaves, walk through tree and split
Node* current;
for (vector<Body>::iterator it = bodies.begin(); it != bodies.end(); it++) {
current = this->nodes->next;
while (!current->leaf) {
Node* child = current->next;
while (child != nullptr && !contained(child->getBB(), it->position)) {
child = child->nextSibling;
}
if (child != nullptr) {
current = child;
}
current = child;
}
current->bodies.push_back(*it);
current->bodies.back().refinement = true;
}
current = this->nodes->next;
while (current != this->nodes) {
this->splitNode(current);
current = current->next;
}
this->update();
}
//node splitting if required
void BarnesHutTree::splitSubtree(Node* root) {
bool toSplitLeft;
Node* current = root;
do {
toSplitLeft = false;
while (current != root->afterSubtree) {
if (current->isSplitable()) {
split(current);
toSplitLeft = true;
}
current = current->next;
}
} while (toSplitLeft);
}
//checking for tree validity
bool BarnesHutTree::isCorrect() {
for (Node* current = this->nodes->next; current != this->nodes; current = current->next) {
if (!current->isCorrect()) {
return false;
}
}
return true;
}
}
bhtree_pthread/src/datastructures/BarnesHutTree.hpp 0 → 100644
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#ifndef BARNES_HUT_TREE_HPP
#define BARNES_HUT_TREE_HPP
#include "Tree.hpp"
#include "Box.hpp"
namespace nbody {
using namespace std;
class Node;
class BarnesHutTree : public Tree {
protected:
static vector<Box> splitBB(Node* node);
static bool splitNode(Node* current);
virtual void update();
virtual void init(vector<Body> bodies, Box domain);
static void split(Node* current);
public:
BarnesHutTree(int parallelId);
virtual ~BarnesHutTree();
virtual void build(vector<Body> bodies);
virtual void build(vector<Body> bodies, Box domain);
virtual void mergeLET(vector<Body> bodies);
virtual int numberOfChildren();
static void splitSubtree(Node* root);
virtual bool isCorrect();
};
}
#endif
bhtree_pthread/src/datastructures/BarnesHutTreeThreaded.cpp 0 → 100644
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#include <climits>
#include <cfloat>
#include <algorithm>
#include <iostream>
#include "BarnesHutTreeThreaded.hpp"
#include "Node.hpp"
#include "PthreadSimulation.hpp"
namespace nbody {
using namespace std;
BarnesHutTreeThreaded::BarnesHutTreeThreaded(int parallelId) : BarnesHutTree(parallelId) {
pthread_mutex_init(&this->nodesToProcess.mutex, nullptr);
}
BarnesHutTreeThreaded::~BarnesHutTreeThreaded() {
pthread_mutex_destroy(&this->nodesToProcess.mutex);
}
void BarnesHutTreeThreaded::addNodeToProcess(Node* node, NodesToProcess* store) {
pthread_mutex_lock(&store->mutex);
store->toProcess.push_back(node);
pthread_mutex_unlock(&store->mutex);
}
Node* BarnesHutTreeThreaded::getNodeToProcess(NodesToProcess* store) {
Node* result;
pthread_mutex_lock(&store->mutex);
if (store->toProcess.empty()) {
result = nullptr;
} else {
result = store->toProcess.back();
store->toProcess.pop_back();
vector<pthread_t>::iterator it = std::find(store->processing.begin(), store->processing.end(), pthread_self());
if (it == store->processing.end()) {
store->processing.push_back(pthread_self());
}
}
pthread_mutex_unlock(&store->mutex);
return result;
}
void BarnesHutTreeThreaded::checkNodeProcessingFinished(NodesToProcess* store) {
pthread_mutex_lock(&store->mutex);
if (store->toProcess.empty()) {
vector<pthread_t>::iterator it = std::find(store->processing.begin(), store->processing.end(), pthread_self());
if (it != store->processing.end()) {
store->processing.erase(it);
}
}
pthread_mutex_unlock(&store->mutex);
}
bool BarnesHutTreeThreaded::hasNodeProcessingFinished(NodesToProcess* store) {
bool finished;
pthread_mutex_lock(&store->mutex);
finished = store->processing.empty() && store->toProcess.empty();
pthread_mutex_unlock(&store->mutex);
return finished;
}
void BarnesHutTreeThreaded::updateNode(Node* current) {
current->representative.id = ULONG_MAX;
current->representative.mass = 0.0;
current->representative.position[0] = 0.0;
current->representative.position[1] = 0.0;
current->representative.position[2] = 0.0;
for (size_t i = 0; i < current->bodies.size(); i++) {
current->representative.mass += current->bodies[i].mass;
for (size_t j = 0; j < 3; j++) {
current->representative.position[j] += current->bodies[i].position[j] * current->bodies[i].mass;
}
}
for (size_t j = 0; j < 3; j++) {
if (current->representative.mass > FLT_EPSILON) {
current->representative.position[j] /= current->representative.mass;
} else {
current->representative.position[j] = 0.0;
}
}
}
void* BarnesHutTreeThreaded::build(void* data) {
NodesToProcess* toProcess = (NodesToProcess*) data;
while (!BarnesHutTreeThreaded::hasNodeProcessingFinished(toProcess)) {
Node* current = BarnesHutTreeThreaded::getNodeToProcess(toProcess);
if (current != nullptr) {
BarnesHutTreeThreaded::updateNode(current);
if (BarnesHutTree::splitNode(current)) {
Node* child = current->next;
while (child != nullptr) {
BarnesHutTreeThreaded::addNodeToProcess(child, toProcess);
child = child->nextSibling;
}
}
}
BarnesHutTreeThreaded::checkNodeProcessingFinished(toProcess);
}
pthread_exit(nullptr);
}
void* BarnesHutTreeThreaded::computeMove(void* data) {
NodesToProcess* toProcess = (NodesToProcess*) data;
vector<Body*> localBodies;
while (!BarnesHutTreeThreaded::hasNodeProcessingFinished(toProcess)) {
Node* current = BarnesHutTreeThreaded::getNodeToProcess(toProcess);
if (current != nullptr) {
for (vector<Body>::iterator it = current->bodies.begin(); it != current->bodies.end(); it++) {
if (!it->refinement) {
toProcess->tree->accumulateForceOnto(*it);
localBodies.push_back(&(*it));
}
}
}
BarnesHutTreeThreaded::checkNodeProcessingFinished(toProcess);
}
while (!localBodies.empty()) {
integrate(*(localBodies.back()));
localBodies.pop_back();
}
pthread_exit(nullptr);
}
void BarnesHutTreeThreaded::clearNodesToProcess() {
this->nodesToProcess.processing.clear();
this->nodesToProcess.toProcess.clear();
}
void BarnesHutTreeThreaded::build(vector<Body> bodies, Box domain) {
this->init(bodies, domain);
this->clearNodesToProcess();
this->nodesToProcess.toProcess.push_back(this->nodes->next);
for (int i = 0; i < this->simulation->getNumberOfProcesses(); i++) {
pthread_create((&((PthreadSimulation*) this->simulation)->threads[i]), nullptr, BarnesHutTreeThreaded::build, &this->nodesToProcess);
}
for (int i = 0; i < this->simulation->getNumberOfProcesses(); i++) {
void* retVal;
pthread_join(((PthreadSimulation*) this->simulation)->threads[i], &retVal);
}
if (this->isCorrect()) {
cout << "correct" << endl;
}
}
void BarnesHutTreeThreaded::computeMove() {
//accumulate forces for whole tree (local particles) and move particles
this->nodesToProcess.tree = this;
for (Node* n = this->nodes->next; n != this->nodes; n = n->next) {
if (n->leaf && !n->bodies.empty()) {
this->nodesToProcess.toProcess.push_back(n);
}
}
for (int i = 0; i < this->simulation->getNumberOfProcesses(); i++) {
pthread_create((&((PthreadSimulation*) this->simulation)->threads[i]), nullptr, BarnesHutTreeThreaded::computeMove, &this->nodesToProcess);
}
for (int i = 0; i < this->simulation->getNumberOfProcesses(); i++) {
void* retVal;
pthread_join(((PthreadSimulation*) this->simulation)->threads[i], &retVal);
}
}
}
bhtree_pthread/src/datastructures/BarnesHutTreeThreaded.hpp 0 → 100644
View file @ 5380b9d8
#ifndef BARNES_HUT_TREE_THREADED_HPP
#define BARNES_HUT_TREE_THREADED_HPP
#include <vector>