#include <MPI_LoopHashRefine.hh>

Inheritance diagram for protocols::loophash::MPI_LoopHashRefine:

Collaboration diagram for protocols::loophash::MPI_LoopHashRefine:

Public Member Functions
	MPI_LoopHashRefine (char machine_letter)

void	set_defaults ()

virtual	~MPI_LoopHashRefine ()

Public Member Functions inherited from protocols::wum::MPI_WorkUnitManager
	MPI_WorkUnitManager (char machine_letter)

virtual	~MPI_WorkUnitManager ()

virtual void	go ()=0

Public Member Functions inherited from protocols::wum::WorkUnitManager
	WorkUnitManager ()

virtual	~WorkUnitManager ()

void	register_work_units (const protocols::wum::WorkUnitList &work_unit_list)

WorkUnitQueue &	outbound ()

WorkUnitQueue &	inbound ()

const WorkUnitQueue &	outbound () const

const WorkUnitQueue &	inbound () const

Protected Member Functions
void	load_structures_from_cmdline_into_library (core::Size structure_read_offset)

void	save_state (std::string prefix="default")

void	save_state_auto ()

void	load_state (std::string prefix="default")

void	print_stats ()
	Print a line with general run statistics, now. More...

void	print_library ()

virtual bool	add_structures_to_library (protocols::wum::SilentStructStore &new_structs, std::string add_algorithm="")

virtual bool	add_structure_to_library (core::io::silent::SilentStruct &pss, std::string add_algorithm="")

bool	add_structure_to_library_direct (core::io::silent::SilentStruct &pss)

bool	add_structure_to_library_add_n_replace (core::io::silent::SilentStruct &pss)

bool	add_structure_to_library_single_replace (core::io::silent::SilentStruct &pss)

void	send_random_library_struct (core::Size dest_rank, core::Size ssid) const

void	limit_library ()

void	dump_structures (const protocols::wum::SilentStructStore &new_structs, bool score_only=true) const

void	set_ident_string (std::string new_ident)

const std::string &	mpi_resume ()

core::Size &	totaltime_loophash ()

protocols::wum::SilentStructStore &	library_central ()

const std::string &	mpi_feedback ()

void	set_mpi_feedback (const std::string &mpi_feedback)

core::Size	max_lib_size ()

void	set_max_lib_size (core::Size max_lib_size)

core::Real	objective_function (const core::io::silent::SilentStructOP &ss) const

core::Real	score (const core::io::silent::SilentStructOP &ss) const

std::string	format_silent_struct (const core::io::silent::SilentStructOP &ss) const

core::Real	objective_function (const core::io::silent::SilentStruct &ss) const

core::Real	score (const core::io::silent::SilentStruct &ss) const

std::string	format_silent_struct (const core::io::silent::SilentStruct &ss) const

Protected Member Functions inherited from protocols::wum::MPI_WorkUnitManager
virtual void	init ()=0

virtual void	process_inbound_wus ()=0

virtual void	process_outbound_wus ()=0

virtual void	print_stats_auto ()
	Print a line with general run statistics, only if enough time has pased since the last statistics printout. More...

void	reset_timing_stats ()
	Reset all the stats counters. More...

void	process_incoming_msgs (bool wait_until_message=false)
	MPI Communication function. More...

void	send_MPI_workunit (const WorkUnitBaseOP &wu, int dest_rank) const
	Send a workunit to an arbitrary recipient. More...

void	receive_MPI_workunit (core::Size node_rank=MPI_ANY_SOURCE)
	Receive a workunit and add it to the inbound queue. By default accept any workunit or accept a specific source rank. Note that this function is blocking and will onyl return once a workunit has been received. More...

void	send_next_WU_on_request ()

char	get_machine_letter ()
	How many masters are there in total ? More...

core::Real	start_timer (MPI_TIMING timing_mode) const
	This initiates a new timer block. Note that there is no end_timer() function - you just keep calling start_timer, which automatically ends the previous block (and records times etc) More...

void	print_timing_stats ()
	Display the timing statistics. More...

long	wall_time () const
	Return the total life time of this class in seconds. More...

Protected Member Functions inherited from protocols::wum::WorkUnitManager
const protocols::wum::WorkUnitList &	work_unit_list () const

protocols::wum::WorkUnitList &	work_unit_list ()

void	write_queues_to_file (const std::string &prefix="default") const

void	write_work_unit (const WorkUnitBaseOP &wu, std::ostream &out) const

void	write_queue (const WorkUnitQueue &the_queue, std::ostream &out) const

void	read_queues_from_file (const std::string &prefix="default")

bool	read_work_unit (WorkUnitBaseOP &qualified_wu, std::istream &in)

void	read_queue (WorkUnitQueue &the_queue, std::istream &in)

core::Size	mem_foot_print () const
	return total memory foot print in bytes More...

Protected Attributes
core::Size	totaltime_loophash_

core::Size	n_loophash_

core::Size	totaltime_batchrelax_

core::Size	n_batchrelax_

core::Size	total_structures_

core::Size	total_structures_relax_

core::Size	total_metropolis_

core::Size	total_metropolis_accepts_

Private Attributes
core::Size	max_lib_size_

core::Size	save_state_interval_

std::string	mpi_feedback_

core::Real	mpi_metropolis_temp_

core::Real	rms_limit_

std::string	objective_function_

std::string	mpi_resume_

std::string	jobname_

protocols::wum::SilentStructStore	library_central_

core::Size	last_save_state_

std::string	ident_string_

Additional Inherited Members
Public Types inherited from protocols::wum::WorkUnitManager
typedef WorkUnitQueue::iterator	iterator

typedef WorkUnitQueue::const_iterator	const_iterator

Protected Types inherited from protocols::wum::MPI_WorkUnitManager
enum	MPI_TIMING { TIMING_WAIT =0, TIMING_TRANSFER_SEND, TIMING_TRANSFER_RECV, TIMING_CPU, TIMING_IO_WRITE, TIMING_IO_READ, TIMING_IDLE, TIMING_end }

Detailed Description

Definition at line 40 of file MPI_LoopHashRefine.hh.

Constructor & Destructor Documentation

protocols::loophash::MPI_LoopHashRefine::MPI_LoopHashRefine ( char machine_letter)

Definition at line 80 of file MPI_LoopHashRefine.cc.

References set_defaults().

virtual protocols::loophash::MPI_LoopHashRefine::~MPI_LoopHashRefine ( )

inlinevirtual

Definition at line 46 of file MPI_LoopHashRefine.hh.

Member Function Documentation

bool protocols::loophash::MPI_LoopHashRefine::add_structure_to_library	(	core::io::silent::SilentStruct &	pss,
		std::string	add_algorithm = `""`
	)

protectedvirtual

Reimplemented in protocols::loophash::MPI_LoopHashRefine_Master.

Definition at line 260 of file MPI_LoopHashRefine.cc.

References core::io::silent::SilentStruct::add_energy(), add_structure_to_library_add_n_replace(), add_structure_to_library_direct(), add_structure_to_library_single_replace(), and mpi_feedback_.

Referenced by add_structures_to_library().

bool protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace ( core::io::silent::SilentStruct & pss)

protected

bool protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_direct ( core::io::silent::SilentStruct & pss)

protected

Definition at line 280 of file MPI_LoopHashRefine.cc.

References protocols::wum::SilentStructStore::add(), and library_central_.

Referenced by add_structure_to_library(), and add_structure_to_library_add_n_replace().

bool protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace ( core::io::silent::SilentStruct & pss)

protected

Definition at line 361 of file MPI_LoopHashRefine.cc.

References protocols::wum::SilentStructStore::begin(), protocols::wum::SilentStructStore::end(), format_silent_struct(), core::io::silent::SilentStruct::get_energy(), library_central_, mpi_metropolis_temp_, objective_function(), print_library(), total_metropolis_, and total_metropolis_accepts_.

Referenced by add_structure_to_library().

bool protocols::loophash::MPI_LoopHashRefine::add_structures_to_library	(	protocols::wum::SilentStructStore &	new_structs,
		std::string	add_algorithm = `""`
	)

protectedvirtual

Reimplemented in protocols::loophash::MPI_LoopHashRefine_Emperor.

Definition at line 422 of file MPI_LoopHashRefine.cc.

References add_structure_to_library(), protocols::wum::SilentStructStore::begin(), protocols::wum::SilentStructStore::end(), format_silent_struct(), limit_library(), and print_library().

void protocols::loophash::MPI_LoopHashRefine::dump_structures	(	const protocols::wum::SilentStructStore &	new_structs,
		bool	score_only = `true`
	)		const

protected

Definition at line 451 of file MPI_LoopHashRefine.cc.

References protocols::wum::SilentStructStore::begin(), protocols::wum::SilentStructStore::end(), protocols::abinitio::filename(), jobname_, protocols::wum::mpi_rank(), protocols::wum::MPI_WorkUnitManager::start_timer(), protocols::wum::MPI_WorkUnitManager::TIMING_CPU, protocols::wum::MPI_WorkUnitManager::TIMING_IO_WRITE, and core::io::silent::SilentFileData::write_silent_struct().

std::string protocols::loophash::MPI_LoopHashRefine::format_silent_struct ( const core::io::silent::SilentStructOP & ss) const

protected

Definition at line 525 of file MPI_LoopHashRefine.cc.

Referenced by add_structure_to_library_add_n_replace(), add_structure_to_library_single_replace(), add_structures_to_library(), and print_library().

std::string protocols::loophash::MPI_LoopHashRefine::format_silent_struct ( const core::io::silent::SilentStruct & ss) const

protected

Definition at line 499 of file MPI_LoopHashRefine.cc.

References core::io::silent::SilentStruct::get_energy(), core::io::silent::SilentStruct::get_string_value(), and objective_function().

protocols::wum::SilentStructStore& protocols::loophash::MPI_LoopHashRefine::library_central ( )

inlineprotected

Definition at line 90 of file MPI_LoopHashRefine.hh.

References library_central_.

void protocols::loophash::MPI_LoopHashRefine::limit_library ( )

protected

Definition at line 441 of file MPI_LoopHashRefine.cc.

References library_central_, max_lib_size_, protocols::wum::SilentStructStore::size(), protocols::wum::SilentStructStore::sort_by(), and protocols::wum::SilentStructStore::store().

Referenced by add_structures_to_library().

void protocols::loophash::MPI_LoopHashRefine::load_state ( std::string prefix = "default")

protected

Definition at line 231 of file MPI_LoopHashRefine.cc.

References protocols::wum::WorkUnitQueue::clear(), protocols::wum::SilentStructStore::clear(), protocols::wum::WorkUnitManager::inbound(), library_central_, protocols::wum::mpi_rank(), protocols::wum::WorkUnitManager::outbound(), protocols::wum::SilentStructStore::read_from_file(), protocols::wum::WorkUnitManager::read_queues_from_file(), protocols::wum::MPI_WorkUnitManager::start_timer(), protocols::wum::MPI_WorkUnitManager::TIMING_CPU, and protocols::wum::MPI_WorkUnitManager::TIMING_IO_READ.

void protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library ( core::Size structure_read_offset)

protected

Definition at line 126 of file MPI_LoopHashRefine.cc.

References protocols::wum::SilentStructStore::add(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::pose::Pose::constraint_set(), core::scoring::constraints::get_cst_fa_file_option(), core::io::silent::SilentStructFactory::get_instance(), core::scoring::constraints::ConstraintIO::get_instance(), core::chemical::ChemicalManager::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), core::scoring::getScoreFunction(), library_central_, max_lib_size_, protocols::wum::mpi_rank(), core::scoring::constraints::ConstraintIO::read_constraints(), core::chemical::ChemicalManager::residue_type_set(), core::pose::set_ss_from_phipsi(), protocols::wum::SilentStructStore::size(), protocols::wum::MPI_WorkUnitManager::start_timer(), core::import_pose::pose_stream::streams_from_cmd_line(), protocols::wum::MPI_WorkUnitManager::TIMING_CPU, and protocols::wum::MPI_WorkUnitManager::TIMING_IO_READ.

core::Size protocols::loophash::MPI_LoopHashRefine::max_lib_size ( )

inlineprotected

Definition at line 98 of file MPI_LoopHashRefine.hh.

References max_lib_size_.

Referenced by set_max_lib_size().

const std::string& protocols::loophash::MPI_LoopHashRefine::mpi_feedback ( )

inlineprotected

Definition at line 93 of file MPI_LoopHashRefine.hh.

References mpi_feedback_.

Referenced by set_mpi_feedback().

const std::string& protocols::loophash::MPI_LoopHashRefine::mpi_resume ( )

inlineprotected

Definition at line 86 of file MPI_LoopHashRefine.hh.

References mpi_resume_.

core::Real protocols::loophash::MPI_LoopHashRefine::objective_function ( const core::io::silent::SilentStructOP & ss) const

protected

Definition at line 515 of file MPI_LoopHashRefine.cc.

Referenced by add_structure_to_library_add_n_replace(), add_structure_to_library_single_replace(), and format_silent_struct().

core::Real protocols::loophash::MPI_LoopHashRefine::objective_function ( const core::io::silent::SilentStruct & ss) const

protected

Definition at line 487 of file MPI_LoopHashRefine.cc.

References core::io::silent::SilentStruct::get_energy(), and objective_function_.

void protocols::loophash::MPI_LoopHashRefine::print_library ( )

protected

Definition at line 412 of file MPI_LoopHashRefine.cc.

References protocols::wum::SilentStructStore::begin(), protocols::wum::SilentStructStore::end(), format_silent_struct(), library_central_, and protocols::wum::SilentStructStore::store().

Referenced by add_structure_to_library_single_replace(), and add_structures_to_library().

void protocols::loophash::MPI_LoopHashRefine::print_stats ( )

protectedvirtual

Print a line with general run statistics, now.

Reimplemented from protocols::wum::MPI_WorkUnitManager.

Definition at line 242 of file MPI_LoopHashRefine.cc.

References library_central_, protocols::wum::SilentStructStore::mem_footprint(), n_batchrelax_, n_loophash_, total_metropolis_, total_metropolis_accepts_, total_structures_, total_structures_relax_, totaltime_batchrelax_, totaltime_loophash_, and protocols::wum::MPI_WorkUnitManager::wall_time().

void protocols::loophash::MPI_LoopHashRefine::save_state ( std::string prefix = "default")

protected

Definition at line 211 of file MPI_LoopHashRefine.cc.

References protocols::wum::WorkUnitManager::inbound(), library_central_, protocols::wum::mpi_rank(), protocols::wum::WorkUnitManager::outbound(), protocols::wum::SilentStructStore::serialize_to_file(), protocols::wum::WorkUnitQueue::size(), protocols::wum::SilentStructStore::size(), protocols::wum::MPI_WorkUnitManager::start_timer(), protocols::wum::MPI_WorkUnitManager::TIMING_CPU, protocols::wum::MPI_WorkUnitManager::TIMING_IO_WRITE, and protocols::wum::WorkUnitManager::write_queues_to_file().

Referenced by save_state_auto().

void protocols::loophash::MPI_LoopHashRefine::save_state_auto ( )

protected

Definition at line 222 of file MPI_LoopHashRefine.cc.

References ident_string_, last_save_state_, save_state(), and save_state_interval_.

core::Real protocols::loophash::MPI_LoopHashRefine::score ( const core::io::silent::SilentStructOP & ss) const

protected

Definition at line 520 of file MPI_LoopHashRefine.cc.

core::Real protocols::loophash::MPI_LoopHashRefine::score ( const core::io::silent::SilentStruct & ss) const

protected

Definition at line 493 of file MPI_LoopHashRefine.cc.

References core::io::silent::SilentStruct::get_energy().

void protocols::loophash::MPI_LoopHashRefine::send_random_library_struct	(	core::Size	dest_rank,
		core::Size	ssid
	)		const

protected

Definition at line 471 of file MPI_LoopHashRefine.cc.

References protocols::wum::SilentStructStore::get_struct_random(), library_central_, protocols::wum::MPI_WorkUnitManager::send_MPI_workunit(), and protocols::wum::SilentStructStore::size().

void protocols::loophash::MPI_LoopHashRefine::set_defaults ( )

Definition at line 99 of file MPI_LoopHashRefine.cc.

References ident_string_, jobname_, last_save_state_, max_lib_size_, mpi_feedback_, mpi_metropolis_temp_, mpi_resume_, objective_function_, rms_limit_, and save_state_interval_.

Referenced by MPI_LoopHashRefine().

void protocols::loophash::MPI_LoopHashRefine::set_ident_string ( std::string new_ident)

inlineprotected

Definition at line 83 of file MPI_LoopHashRefine.hh.

References ident_string_.

void protocols::loophash::MPI_LoopHashRefine::set_max_lib_size ( core::Size max_lib_size)

inlineprotected

Definition at line 100 of file MPI_LoopHashRefine.hh.

References max_lib_size(), and max_lib_size_.

void protocols::loophash::MPI_LoopHashRefine::set_mpi_feedback ( const std::string & mpi_feedback)

inlineprotected

Definition at line 95 of file MPI_LoopHashRefine.hh.

References mpi_feedback(), and mpi_feedback_.

core::Size& protocols::loophash::MPI_LoopHashRefine::totaltime_loophash ( )

inlineprotected

Definition at line 88 of file MPI_LoopHashRefine.hh.

References totaltime_loophash_.

Member Data Documentation

std::string protocols::loophash::MPI_LoopHashRefine::ident_string_

private

Definition at line 144 of file MPI_LoopHashRefine.hh.

Referenced by save_state_auto(), set_defaults(), and set_ident_string().

std::string protocols::loophash::MPI_LoopHashRefine::jobname_

private

Definition at line 126 of file MPI_LoopHashRefine.hh.

Referenced by dump_structures(), and set_defaults().

core::Size protocols::loophash::MPI_LoopHashRefine::last_save_state_

private

Definition at line 130 of file MPI_LoopHashRefine.hh.

Referenced by save_state_auto(), and set_defaults().

protocols::wum::SilentStructStore protocols::loophash::MPI_LoopHashRefine::library_central_

private

Definition at line 129 of file MPI_LoopHashRefine.hh.

Referenced by add_structure_to_library_add_n_replace(), add_structure_to_library_direct(), add_structure_to_library_single_replace(), library_central(), limit_library(), load_state(), load_structures_from_cmdline_into_library(), print_library(), print_stats(), save_state(), and send_random_library_struct().

core::Size protocols::loophash::MPI_LoopHashRefine::max_lib_size_

private

Definition at line 117 of file MPI_LoopHashRefine.hh.

Referenced by limit_library(), load_structures_from_cmdline_into_library(), max_lib_size(), set_defaults(), and set_max_lib_size().

std::string protocols::loophash::MPI_LoopHashRefine::mpi_feedback_

private

Definition at line 119 of file MPI_LoopHashRefine.hh.

Referenced by add_structure_to_library(), mpi_feedback(), set_defaults(), and set_mpi_feedback().

core::Real protocols::loophash::MPI_LoopHashRefine::mpi_metropolis_temp_

private

Definition at line 120 of file MPI_LoopHashRefine.hh.

Referenced by add_structure_to_library_single_replace(), and set_defaults().

std::string protocols::loophash::MPI_LoopHashRefine::mpi_resume_

private

Definition at line 125 of file MPI_LoopHashRefine.hh.

Referenced by mpi_resume(), and set_defaults().

core::Size protocols::loophash::MPI_LoopHashRefine::n_batchrelax_

protected

Definition at line 137 of file MPI_LoopHashRefine.hh.

Referenced by print_stats().

core::Size protocols::loophash::MPI_LoopHashRefine::n_loophash_

protected

Definition at line 135 of file MPI_LoopHashRefine.hh.

Referenced by print_stats().

std::string protocols::loophash::MPI_LoopHashRefine::objective_function_

private

Definition at line 122 of file MPI_LoopHashRefine.hh.

Referenced by objective_function(), and set_defaults().

core::Real protocols::loophash::MPI_LoopHashRefine::rms_limit_

private

Definition at line 121 of file MPI_LoopHashRefine.hh.

Referenced by add_structure_to_library_add_n_replace(), and set_defaults().

core::Size protocols::loophash::MPI_LoopHashRefine::save_state_interval_

private

Definition at line 118 of file MPI_LoopHashRefine.hh.

Referenced by save_state_auto(), and set_defaults().

core::Size protocols::loophash::MPI_LoopHashRefine::total_metropolis_

protected

Definition at line 140 of file MPI_LoopHashRefine.hh.

Referenced by add_structure_to_library_single_replace(), and print_stats().

core::Size protocols::loophash::MPI_LoopHashRefine::total_metropolis_accepts_

protected

Definition at line 141 of file MPI_LoopHashRefine.hh.

Referenced by add_structure_to_library_single_replace(), and print_stats().

core::Size protocols::loophash::MPI_LoopHashRefine::total_structures_

protected

Definition at line 138 of file MPI_LoopHashRefine.hh.

Referenced by print_stats().

core::Size protocols::loophash::MPI_LoopHashRefine::total_structures_relax_

protected

Definition at line 139 of file MPI_LoopHashRefine.hh.

Referenced by print_stats().

core::Size protocols::loophash::MPI_LoopHashRefine::totaltime_batchrelax_

protected

Definition at line 136 of file MPI_LoopHashRefine.hh.

Referenced by print_stats().

core::Size protocols::loophash::MPI_LoopHashRefine::totaltime_loophash_

protected

Definition at line 134 of file MPI_LoopHashRefine.hh.

Referenced by print_stats(), and totaltime_loophash().

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

src/protocols/loophash/MPI_LoopHashRefine.hh
src/protocols/loophash/MPI_LoopHashRefine.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation