Main-MPMPD.cpp File Reference

#include <iostream>
#include <string>
#include <map>
#include <cstdio>
#include <cstring>
#include <ctime>
#include "config.h"
#include <csignal>
#include <cerrno>
#include <unistd.h>
#include <sys/wait.h>
#include <pthread.h>
#include <google/protobuf/stubs/common.h>
#include "core/Print.h"
#include "core/Exceptions.h"
#include "core/Types.h"
#include "core/Math.h"
#include "mpi/lm_mpi.h"
#include "io/lm_hdf5.h"
#include "io/SimulationFile.h"
#include "DiffusionModel.pb.h"
#include "ReactionModel.pb.h"
#include "SimulationParameters.h"
#include "core/CheckpointSignaler.h"
#include "core/DataOutputQueue.h"
#include "core/LocalDataOutputWorker.h"
#include "core/MPIRemoteDataOutputQueue.h"
#include "cmd/common.h"
#include "core/Globals.h"
#include "core/SignalHandler.h"
#include "core/ReplicateRunner.h"
#include "core/ResourceAllocator.h"
#include "SimulationParameters.pb.h"
#include "thread/Thread.h"
#include "thread/WorkerManager.h"
#include "lptf/Profile.h"
#include "me/MESolverFactory.h"
#include "rdme/RDMESolver.h"

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Classes
class	ReplicateRunner
	A thread that launches all the various replicates requested. More...
class	ResourceAllocator
	An object that tracks the available resources for the main simulation runner. More...
class	MESolverFactory
	A factory object used to create Master Equation simulation instances. More...
class	PthreadException
	An Exception class for handling pthread exceptions. More...

Functions
void	listDevicesMPI ()
void	executeSimulationMPI ()
void	executeSimulationMPISingleMaster ()
void	executeSimulationMPISingleSlave ()
void	broadcastSimulationParameters (void *staticDataBuffer, map< string, string > &simulationParameters)
void	broadcastReactionModel (void *staticDataBuffer, lm::io::ReactionModel *reactionModel)
void	broadcastDiffusionModel (void *staticDataBuffer, lm::io::DiffusionModel *diffusionModel, uint8_t *lattice, size_t latticeSize, uint8_t *latticeSites, size_t latticeSitesSize)
map< string, string >	receiveSimulationParameters (void *staticDataBuffer)
void	receiveReactionModel (void *staticDataBuffer, lm::io::ReactionModel *reactionModel)
void	receiveDiffusionModel (void *staticDataBuffer, lm::io::DiffusionModel *diffusionModel, uint8_t **lattice, size_t *latticeSize, uint8_t **latticeSites, size_t *latticeSitesSize)
int	runReplicateNOW (int replicate, MESolverFactory solverFactory, std::map< std::string, string > &simulationParameters, lm::io::ReactionModel *reactionModel, lm::io::DiffusionModel *diffusionModel, uint8_t *lattice, size_t latticeSize, uint8_t *latticeSites, size_t latticeSitesSize, ResourceAllocator &resourceAllocator)
int	main (int argc, char **argv)

Variables
	PROF_ALLOC

Function Documentation

broadcastDiffusionModel()

void broadcastDiffusionModel	(	void *	staticDataBuffer,
		lm::io::DiffusionModel *	diffusionModel,
		uint8_t *	lattice,
		size_t	latticeSize,
		uint8_t *	latticeSites,
		size_t	latticeSitesSize )

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broadcastReactionModel()

void broadcastReactionModel	(	void *	staticDataBuffer,
		lm::io::ReactionModel *	reactionModel )

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broadcastSimulationParameters()

void broadcastSimulationParameters	(	void *	staticDataBuffer,
		map< string, string > &	simulationParameters )

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executeSimulationMPI()

void executeSimulationMPI

(

)

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executeSimulationMPISingleMaster()

void executeSimulationMPISingleMaster

(

)

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executeSimulationMPISingleSlave()

void executeSimulationMPISingleSlave

(

)

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listDevicesMPI()

void listDevicesMPI

(

)

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main()

int main	(	int	argc,
		char **	argv )

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receiveDiffusionModel()

void receiveDiffusionModel	(	void *	staticDataBuffer,
		lm::io::DiffusionModel *	diffusionModel,
		uint8_t **	lattice,
		size_t *	latticeSize,
		uint8_t **	latticeSites,
		size_t *	latticeSitesSize )

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receiveReactionModel()

void receiveReactionModel	(	void *	staticDataBuffer,
		lm::io::ReactionModel *	reactionModel )

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receiveSimulationParameters()

map< string, string > receiveSimulationParameters

(

void *

staticDataBuffer

)

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runReplicateNOW()

int runReplicateNOW	(	int	replicate,
		MESolverFactory	solverFactory,
		std::map< std::string, string > &	simulationParameters,
		lm::io::ReactionModel *	reactionModel,
		lm::io::DiffusionModel *	diffusionModel,
		uint8_t *	lattice,
		size_t	latticeSize,
		uint8_t *	latticeSites,
		size_t	latticeSitesSize,
		ResourceAllocator &	resourceAllocator )

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Variable Documentation

PROF_ALLOC

PROF_ALLOC