#include <simulation.h>

Collaboration diagram for bdm::Simulation:

Public Member Functions
	Simulation (TRootIOCtor *p)

	Simulation (int argc, const char **argv, const std::vector< std::string > &config_files={})

	Simulation (CommandLineOptions *clo, const std::vector< std::string > &config_files={})

	Simulation (const std::string &simulation_name, const std::vector< std::string > &config_files={})

	Simulation (int argc, const char *argv, const std::function< void(Param )> &set_param, const std::vector< std::string > &config_files={})

	Simulation (CommandLineOptions clo, const std::function< void(Param )> &set_param, const std::vector< std::string > &config_files={})

	Simulation (const std::string &simulation_name, const std::function< void(Param *)> &set_param, const std::vector< std::string > &config_files={})

	~Simulation ()

void	Restore (Simulation &&restored)

void	Activate ()
	Activates this simulation. More...

ResourceManager *	GetResourceManager ()
	Returns the ResourceManager instance. More...

void	SetResourceManager (ResourceManager *rm)

const Param *	GetParam () const
	Returns the simulation parameters. More...

AgentUidGenerator *	GetAgentUidGenerator ()

Environment *	GetEnvironment ()

void	SetEnvironment (Environment *env)

Scheduler *	GetScheduler ()

void	Simulate (uint64_t steps)

Random *	GetRandom ()
	Returns a thread local random number generator. More...

std::vector< Random * > &	GetAllRandom ()
	Returns all thread local random number generator. More...

ExecutionContext *	GetExecutionContext ()
	Returns a thread local execution context. More...

std::vector< ExecutionContext * > &	GetAllExecCtxts ()
	Returns all thread local execution contexts. More...

void	SetAllExecCtxts (const std::vector< ExecutionContext * > &exec_ctxts)

MemoryManager *	GetMemoryManager ()

OpenCLState *	GetOpenCLState ()
	Return helper class for OpenCL environment. More...

const std::string &	GetUniqueName () const
	Returns the name of the simulation. More...

const std::string &	GetOutputDir () const
	Returns the output directory for this specific simulation. More...

experimental::TimeSeries *	GetTimeSeries ()

void	ReplaceScheduler (Scheduler *scheduler)

Static Public Member Functions
static Simulation *	GetActive ()
	This function returns the currently active Simulation simulation. More...

Private Member Functions
void	Initialize (CommandLineOptions clo, const std::function< void(Param )> &set_param, const std::vector< std::string > &config_files)
	Initialize Simulation. More...

void	InitializeMembers ()
	Initialize data members that have a dependency on Simulation. More...

void	InitializeRuntimeParams (CommandLineOptions clo, const std::function< void(Param )> &set_param, const std::vector< std::string > &ctor_config)
	This function parses command line parameters and the configuration file. More...

void	LoadConfigFiles (const std::vector< std::string > &ctor_configs, const std::vector< std::string > &cli_configs)

void	InitializeUniqueName (const std::string &simulation_name)
	This function initializes `unique_name_` More...

void	InitializeOutputDir ()
	Initializes `output_dir_` and creates dir if it does not exist. More...

	BDM_CLASS_DEF_NV (Simulation, 1)

Private Attributes
std::vector< Random * >	random_
	random number generator for each thread More...

std::vector< ExecutionContext * >	exec_ctxt_
	Execution Context for each thread. More...

ResourceManager *	rm_ = nullptr

Param *	param_ = nullptr

AgentUidGenerator *	agent_uid_generator_ = nullptr

std::string	name_

Environment *	environment_ = nullptr

Scheduler *	scheduler_ = nullptr

OpenCLState *	ocl_state_ = nullptr

bool	is_gpu_environment_initialized_ = false

uint64_t	id_ = 0
	This id is unique for each simulation within the same process. More...

std::string	unique_name_

std::string	output_dir_
	cached value where `unique_name_` is appended to `Param::output_dir` More...

std::string	command_line_parameter_str_

MemoryManager *	mem_mgr_ = nullptr
	BioDynaMo memory manager. If nullptr, default allocator will be used. More...

int64_t	ctor_ts_ = 0
	Timestep when constructor was called. More...

int64_t	dtor_ts_ = 0
	Timestep when destructor was called. More...

experimental::TimeSeries *	time_series_ = nullptr
	Collects time series information during the simulation. More...

friend	SimulationTest

friend	ParaviewAdaptorTest

Static Private Attributes
static Simulation *	active_ = nullptr
	Currently active simulation. More...

static std::atomic< uint64_t >	counter_
	Number of simulations in this process. More...

Friends
class	DiffusionTest_CopyOldData_Test

std::ostream &	operator<< (std::ostream &os, Simulation &sim)

Detailed Description

This is the central BioDynaMo object. It contains pointers to e.g. the ResourceManager, the scheduler, parameters, ...
It is possible to create multiple simulations, but only one can be active at the same time. Creating a new agent automatically activates it.

Definition at line 50 of file simulation.h.

Constructor & Destructor Documentation

◆ Simulation() [1/7]

bdm::Simulation::Simulation ( TRootIOCtor * p )

explicit

Definition at line 70 of file simulation.cc.

◆ Simulation() [2/7]

bdm::Simulation::Simulation	(	int	argc,
		const char **	argv,
		const std::vector< std::string > &	config_files = `{}`
	)

Constructor that takes the arguments from main to parse command line arguments. The simulation name is extracted from the executable name. Creation of a new simulation automatically activates it.

Definition at line 72 of file simulation.cc.

◆ Simulation() [3/7]

bdm::Simulation::Simulation	(	CommandLineOptions *	clo,
		const std::vector< std::string > &	config_files = `{}`
	)

explicit

Definition at line 82 of file simulation.cc.

◆ Simulation() [4/7]

bdm::Simulation::Simulation	(	const std::string &	simulation_name,
		const std::vector< std::string > &	config_files = `{}`
	)

explicit

Alternative constructor, if the arguments from function main are not available, or if a different simulation name should be chosen.
Command line arguments are not parsed!
Creation of a new simulation automatically activates it.

Parameters

config_file Use a different config file than the default bdm.toml or bdm.json

Definition at line 77 of file simulation.cc.

◆ Simulation() [5/7]

bdm::Simulation::Simulation	(	int	argc,
		const char **	argv,
		const std::function< void(Param *)> &	set_param,
		const std::vector< std::string > &	config_files = `{}`
	)

Definition at line 94 of file simulation.cc.

◆ Simulation() [6/7]

bdm::Simulation::Simulation	(	CommandLineOptions *	clo,
		const std::function< void(Param *)> &	set_param,
		const std::vector< std::string > &	config_files = `{}`
	)

Definition at line 88 of file simulation.cc.

◆ Simulation() [7/7]

bdm::Simulation::Simulation	(	const std::string &	simulation_name,
		const std::function< void(Param *)> &	set_param,
		const std::vector< std::string > &	config_files = `{}`
	)

Definition at line 101 of file simulation.cc.

◆ ~Simulation()

bdm::Simulation::~Simulation ( )

Definition at line 191 of file simulation.cc.

Member Function Documentation

◆ Activate()

void bdm::Simulation::Activate ( )

Activates this simulation.

Definition at line 241 of file simulation.cc.

◆ BDM_CLASS_DEF_NV()

bdm::Simulation::BDM_CLASS_DEF_NV	(	Simulation	,
		1
	)

private

◆ GetActive()

Simulation * bdm::Simulation::GetActive ( )

static

This function returns the currently active Simulation simulation.

Definition at line 68 of file simulation.cc.

◆ GetAgentUidGenerator()

AgentUidGenerator * bdm::Simulation::GetAgentUidGenerator ( )

Definition at line 256 of file simulation.cc.

◆ GetAllExecCtxts()

std::vector< ExecutionContext * > & bdm::Simulation::GetAllExecCtxts ( )

Returns all thread local execution contexts.

Definition at line 275 of file simulation.cc.

◆ GetAllRandom()

std::vector< Random * > & bdm::Simulation::GetAllRandom ( )

Returns all thread local random number generator.

Definition at line 269 of file simulation.cc.

◆ GetEnvironment()

Environment * bdm::Simulation::GetEnvironment ( )

Definition at line 260 of file simulation.cc.

◆ GetExecutionContext()

ExecutionContext * bdm::Simulation::GetExecutionContext ( )

Returns a thread local execution context.

Definition at line 271 of file simulation.cc.

◆ GetMemoryManager()

MemoryManager* bdm::Simulation::GetMemoryManager ( )

inline

Definition at line 127 of file simulation.h.

◆ GetOpenCLState()

OpenCLState * bdm::Simulation::GetOpenCLState ( )

Return helper class for OpenCL environment.

Definition at line 279 of file simulation.cc.

◆ GetOutputDir()

const std::string & bdm::Simulation::GetOutputDir ( ) const

Returns the output directory for this specific simulation.

Returns the path to the simulation's output directory.

Definition at line 285 of file simulation.cc.

◆ GetParam()

const Param * bdm::Simulation::GetParam ( ) const

Returns the simulation parameters.

Definition at line 254 of file simulation.cc.

◆ GetRandom()

Random * bdm::Simulation::GetRandom ( )

Returns a thread local random number generator.

Returns a random number generator (thread-specific)

Definition at line 267 of file simulation.cc.

◆ GetResourceManager()

ResourceManager * bdm::Simulation::GetResourceManager ( )

Returns the ResourceManager instance.

Definition at line 244 of file simulation.cc.

◆ GetScheduler()

Scheduler * bdm::Simulation::GetScheduler ( )

Definition at line 262 of file simulation.cc.

◆ GetTimeSeries()

experimental::TimeSeries * bdm::Simulation::GetTimeSeries ( )

Definition at line 287 of file simulation.cc.

◆ GetUniqueName()

const std::string & bdm::Simulation::GetUniqueName ( ) const

Returns the name of the simulation.

See also: unique_name_

Definition at line 282 of file simulation.cc.

◆ Initialize()

void bdm::Simulation::Initialize	(	CommandLineOptions *	clo,
		const std::function< void(Param *)> &	set_param,
		const std::vector< std::string > &	config_files
	)

private

Initialize Simulation.

Definition at line 294 of file simulation.cc.

◆ InitializeMembers()

void bdm::Simulation::InitializeMembers ( )

private

Initialize data members that have a dependency on Simulation.

Definition at line 314 of file simulation.cc.

◆ InitializeOutputDir()

void bdm::Simulation::InitializeOutputDir ( )

private

Initializes output_dir_ and creates dir if it does not exist.

Definition at line 540 of file simulation.cc.

◆ InitializeRuntimeParams()

void bdm::Simulation::InitializeRuntimeParams	(	CommandLineOptions *	clo,
		const std::function< void(Param *)> &	set_param,
		const std::vector< std::string > &	ctor_config
	)

private

This function parses command line parameters and the configuration file.

Definition at line 380 of file simulation.cc.

◆ InitializeUniqueName()

void bdm::Simulation::InitializeUniqueName ( const std::string & simulation_name )

private

This function initializes unique_name_

Definition at line 530 of file simulation.cc.

◆ LoadConfigFiles()

void bdm::Simulation::LoadConfigFiles	(	const std::vector< std::string > &	ctor_configs,
		const std::vector< std::string > &	cli_configs
	)

private

Definition at line 460 of file simulation.cc.

◆ ReplaceScheduler()

void bdm::Simulation::ReplaceScheduler ( Scheduler * scheduler )

Replaces the scheduler for this simulation. Existing scheduler will be deleted! Therefore, pointers to the old scheduler (obtained with GetScheduler()) will be invalidated.
Simulation will take ownership of the passed pointer

Definition at line 289 of file simulation.cc.

◆ Restore()

void bdm::Simulation::Restore ( Simulation && restored )

Copies / moves values from a restored simulation into this object. Thus, pointers to rm_, param_, ... are not invalidated.

Definition at line 109 of file simulation.cc.

◆ SetAllExecCtxts()

void bdm::Simulation::SetAllExecCtxts ( const std::vector< ExecutionContext * > & exec_ctxts )

Definition at line 363 of file simulation.cc.

◆ SetEnvironment()

void bdm::Simulation::SetEnvironment ( Environment * env )

Set a specific environment for the simulation. *env must point to an object instance of a subclass of Environment.

Definition at line 356 of file simulation.cc.

◆ SetResourceManager()

void bdm::Simulation::SetResourceManager ( ResourceManager * rm )

Definition at line 246 of file simulation.cc.

◆ Simulate()

void bdm::Simulation::Simulate ( uint64_t steps )

Definition at line 264 of file simulation.cc.

Friends And Related Function Documentation

◆ DiffusionTest_CopyOldData_Test

friend class DiffusionTest_CopyOldData_Test

friend

Definition at line 211 of file simulation.h.

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		Simulation &	sim
	)

friend

Definition at line 138 of file simulation.cc.

Member Data Documentation

◆ active_

Simulation * bdm::Simulation::active_ = nullptr

staticprivate

Currently active simulation.

Definition at line 148 of file simulation.h.

◆ agent_uid_generator_

AgentUidGenerator* bdm::Simulation::agent_uid_generator_ = nullptr

private

Definition at line 160 of file simulation.h.

◆ command_line_parameter_str_

std::string bdm::Simulation::command_line_parameter_str_

private

Stores command line arguments if (argc,argv) or CommandLineOptions are passed to the constructor.

Definition at line 177 of file simulation.h.

◆ counter_

std::atomic< uint64_t > bdm::Simulation::counter_

staticprivate

Number of simulations in this process.

Implementation for Simulation: It must be separate to avoid circular dependencies.

Definition at line 150 of file simulation.h.

◆ ctor_ts_

int64_t bdm::Simulation::ctor_ts_ = 0

private

Timestep when constructor was called.

Definition at line 181 of file simulation.h.

◆ dtor_ts_

int64_t bdm::Simulation::dtor_ts_ = 0

private

Timestep when destructor was called.

Definition at line 183 of file simulation.h.

◆ environment_

Environment* bdm::Simulation::environment_ = nullptr

private

Definition at line 162 of file simulation.h.

◆ exec_ctxt_

std::vector<ExecutionContext*> bdm::Simulation::exec_ctxt_

private

Execution Context for each thread.

Definition at line 156 of file simulation.h.

◆ id_

uint64_t bdm::Simulation::id_ = 0

private

This id is unique for each simulation within the same process.

Definition at line 167 of file simulation.h.

◆ is_gpu_environment_initialized_

bool bdm::Simulation::is_gpu_environment_initialized_ = false

private

Definition at line 165 of file simulation.h.

◆ mem_mgr_

MemoryManager* bdm::Simulation::mem_mgr_ = nullptr

private

BioDynaMo memory manager. If nullptr, default allocator will be used.

Definition at line 179 of file simulation.h.

◆ name_

std::string bdm::Simulation::name_

private

Definition at line 161 of file simulation.h.

◆ ocl_state_

OpenCLState* bdm::Simulation::ocl_state_ = nullptr

private

Definition at line 164 of file simulation.h.

◆ output_dir_

std::string bdm::Simulation::output_dir_

private

cached value where unique_name_ is appended to Param::output_dir

Definition at line 174 of file simulation.h.

◆ param_

Param* bdm::Simulation::param_ = nullptr

private

Definition at line 159 of file simulation.h.

◆ ParaviewAdaptorTest

friend bdm::Simulation::ParaviewAdaptorTest

private

Definition at line 210 of file simulation.h.

◆ random_

std::vector<Random*> bdm::Simulation::random_

private

random number generator for each thread

Definition at line 153 of file simulation.h.

◆ rm_

ResourceManager* bdm::Simulation::rm_ = nullptr

private

Definition at line 158 of file simulation.h.

◆ scheduler_

Scheduler* bdm::Simulation::scheduler_ = nullptr

private

Definition at line 163 of file simulation.h.

◆ SimulationTest

friend bdm::Simulation::SimulationTest

private

Definition at line 209 of file simulation.h.

◆ time_series_

experimental::TimeSeries* bdm::Simulation::time_series_ = nullptr

private

Collects time series information during the simulation.

Definition at line 185 of file simulation.h.

◆ unique_name_

std::string bdm::Simulation::unique_name_

private

cached value where id_ is appended to name_ if id_ is not zero.
e.g. name_ = "my-sim" and id_ = 0 -> "my-sim"
e.g. name_ = "my-sim" and id_ = 4 -> "my-sim4"

Definition at line 172 of file simulation.h.

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

core/simulation.h
core/simulation.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Simulation() [1/7]

◆ Simulation() [2/7]

◆ Simulation() [3/7]

◆ Simulation() [4/7]

◆ Simulation() [5/7]

◆ Simulation() [6/7]

◆ Simulation() [7/7]

◆ ~Simulation()

Member Function Documentation

◆ Activate()

◆ BDM_CLASS_DEF_NV()

◆ GetActive()

◆ GetAgentUidGenerator()

◆ GetAllExecCtxts()

◆ GetAllRandom()

◆ GetEnvironment()

◆ GetExecutionContext()

◆ GetMemoryManager()

◆ GetOpenCLState()

◆ GetOutputDir()

◆ GetParam()

◆ GetRandom()

◆ GetResourceManager()

◆ GetScheduler()

◆ GetTimeSeries()

◆ GetUniqueName()

◆ Initialize()

◆ InitializeMembers()

◆ InitializeOutputDir()

◆ InitializeRuntimeParams()

◆ InitializeUniqueName()

◆ LoadConfigFiles()

◆ ReplaceScheduler()

◆ Restore()

◆ SetAllExecCtxts()

◆ SetEnvironment()

◆ SetResourceManager()

◆ Simulate()

Friends And Related Function Documentation

◆ DiffusionTest_CopyOldData_Test

◆ operator<<

Member Data Documentation

◆ active_

◆ agent_uid_generator_

◆ command_line_parameter_str_

◆ counter_

◆ ctor_ts_

◆ dtor_ts_

◆ environment_

◆ exec_ctxt_

◆ id_

◆ is_gpu_environment_initialized_

◆ mem_mgr_

◆ name_

◆ ocl_state_

◆ output_dir_

◆ param_

◆ ParaviewAdaptorTest

◆ random_

◆ rm_

◆ scheduler_

◆ SimulationTest

◆ time_series_

◆ unique_name_