#include <MPI_Refine_Master.hh>

Inheritance diagram for protocols::mpi_refinement::MPI_Refine_Master:

Public Member Functions
	MPI_Refine_Master (core::Size my_emperor, core::Size master_rank)

	~MPI_Refine_Master () override=default

void	set_defaults ()

void	go () override

Public Member Functions inherited from protocols::mpi_refinement::MPI_Refinement
	MPI_Refinement (char machine_letter)

void	set_defaults ()

	~MPI_Refinement () override=default

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

	~MPI_WorkUnitManager () override=default

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

	~WorkUnitManager () override=default

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	init () override

void	process_inbound_wus () override
	figure out what to do with incoming WUs. Some will be returning WUs that need to be resent others will be finished and will need reintegration into the library this may send something to Emperor too More...

void	process_outbound_wus () override

bool	process_round ()

bool	process_termination ()

void	create_WUs (const core::io::silent::SilentStructOP &start_struct, core::Size const i_ss)

void	assign_loop_info (core::io::silent::SilentStructOP ss) const

void	add_relax_simple (protocols::wum::SilentStructStore &start_decoys, core::Size const rerelax_type)

void	check_library_expiry_dates ()
	hpark - let's not use this for now More...

void	load_sample_weight ()

bool	add_structure_to_library (core::io::silent::SilentStructOP ss, std::string add_algorithm="") override

void	feedback_structures_to_emperor (bool get_feedback, std::string const pick_strategy, std::string const objfunction)

void	feedback_structure_to_emperor (core::io::silent::SilentStructOP &ss)

void	feedback_structure_to_emperor (core::io::silent::SilentStruct &pss)

core::Size	n_to_gen () const

core::Size	master_rank ()

core::Size	my_emperor ()

Protected Member Functions inherited from protocols::mpi_refinement::MPI_Refinement
void	load_structures_from_cmdline_into_library (protocols::wum::SilentStructStore &library)

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

void	save_state_auto ()

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

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

void	print_summary (std::string const prefix="SUMM ")

void	print_library (protocols::wum::SilentStructStore &library, std::string const prefix="LIB ")

virtual bool	add_structures_to_library (protocols::wum::SilentStructStore &new_structs, 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	update_library_NSGAII (protocols::wum::SilentStructStore &new_structs)

void	setup_multi_objective ()

void	send_sortedpick_library_structs (core::Size dest_rank, core::Size nsend, std::string const scorename, bool const weighted, bool const inverse=false, core::Real const kT=0.2)

void	send_random_library_structs (core::Size dest_rank, core::Size nsend)

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

void	limit_library ()

void	shave_library (protocols::wum::SilentStructStore &new_structs, std::string const scorename, core::Real const frac) const

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

void	set_ident_string (std::string new_ident)

void	report_time () const

const std::string &	mpi_resume ()

core::Size &	totaltime_loophash ()

protocols::wum::SilentStructStore &	library_central ()

protocols::wum::SilentStructStore &	library_ref ()

const std::string &	mpi_feedback ()

void	set_mpi_feedback (const std::string &mpi_feedback)

core::Size	max_lib_size ()

core::Size	max_ref_lib_size ()

void	set_max_lib_size (core::Size max_lib_size)

void	set_max_ref_lib_size (core::Size max_ref_lib_size)

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

void	retag_library (protocols::wum::SilentStructStore &store, std::string const prefix) const

std::string	format_silent_struct (const core::io::silent::SilentStructOP &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	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...

Private Member Functions
core::pose::Pose	get_average_structure (protocols::wum::SilentStructStore &decoys, utility::vector1< core::Size > const touse, std::string const columnname, bool const minimize, bool const calcdev=false) const

Private Attributes
core::Size	max_sample_per_structure_

core::Size	batch_relax_chunks_

core::Size	batch_relax_absolute_max_

core::Size	outbound_wu_buffer_size_

core::Size	loophash_split_size_

core::Size	library_expiry_time_

core::Size	expire_after_rounds_

bool	mpi_master_save_score_only_

std::string	loophash_scan_type_

core::Size	ngen_serial_per_structure_

core::Real	prob_terminus_ramapert_

utility::vector1< int >	myslaves_

std::map< int, bool >	slaves_finished_

Scheduler	scheduler_

bool	sent_termination_

bool	got_termination_signal_

bool	asked_for_feedback_

core::Size	sch_stage_

std::string	sample_weight_str_

const core::Size	my_emperor_

const core::Size	master_rank_

core::Size	n_lib_modified_

core::Size	nchange_emperor_call_

std::map< std::string, core::Size >	ssids_by_name_

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 }

Protected Attributes inherited from protocols::mpi_refinement::MPI_Refinement
MultiObjectiveOP	fobj_

core::Size	starttime_

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_

bool	native_given_

core::pose::Pose	native_pose_

core::pose::Pose	pose0_

Constructor & Destructor Documentation

protocols::mpi_refinement::MPI_Refine_Master::MPI_Refine_Master	(	core::Size	my_emperor,
		core::Size	master_rank
	)

inline

References set_defaults().

protocols::mpi_refinement::MPI_Refine_Master::~MPI_Refine_Master ( )

overridedefault

Member Function Documentation

void protocols::mpi_refinement::MPI_Refine_Master::add_relax_simple	(	protocols::wum::SilentStructStore &	start_decoys,
		core::Size const	rerelax_type
	)

protected

References core::sequence::end, protocols::wum::SilentStructStore::get_struct(), protocols::wum::SilentStructStore::size(), and protocols::loops::start.

bool protocols::mpi_refinement::MPI_Refine_Master::add_structure_to_library	(	core::io::silent::SilentStructOP	ss,
		std::string	add_algorithm = `""`
	)

overrideprotectedvirtual

This is a virtual over load of the base class MPI_Refinement:: add_structure_to_library with an extra behavioural step that reports any successful library add-ons to the emperor. This behaviour is master specific and thus should not be in the base class.

Reimplemented from protocols::mpi_refinement::MPI_Refinement.

void protocols::mpi_refinement::MPI_Refine_Master::assign_loop_info ( core::io::silent::SilentStructOP ss ) const

protected

References protocols::kinmatch::str().

void protocols::mpi_refinement::MPI_Refine_Master::check_library_expiry_dates ( )

protected

hpark - let's not use this for now

References core::sequence::end, protocols::noesy_assign::round(), and TRDEBUG.

void protocols::mpi_refinement::MPI_Refine_Master::create_WUs	(	const core::io::silent::SilentStructOP &	start_struct,
		core::Size const	i_ss
	)

protected

References protocols::mpi_refinement::CA_Sscore(), protocols::mpi_refinement::get_loop_info(), protocols::mean_field::max(), protocols::wum::mpi_rank(), core::scoring::rg, and protocols::noesy_assign::round().

void protocols::mpi_refinement::MPI_Refine_Master::feedback_structure_to_emperor ( core::io::silent::SilentStructOP & ss )

protected

void protocols::mpi_refinement::MPI_Refine_Master::feedback_structure_to_emperor ( core::io::silent::SilentStruct & pss )

protected

void protocols::mpi_refinement::MPI_Refine_Master::feedback_structures_to_emperor	(	bool	get_feedback,
		std::string const	pick_strategy,
		std::string const	objfunction
	)

protected

References core::sequence::end, and TRDEBUG.

core::pose::Pose protocols::mpi_refinement::MPI_Refine_Master::get_average_structure	(	protocols::wum::SilentStructStore &	decoys,
		utility::vector1< core::Size > const	touse,
		std::string const	columnname,
		bool const	minimize,
		bool const	calcdev = `false`
	)		const

private

References protocols::mpi_refinement::StructAvrgMover::apply(), protocols::wum::SilentStructStore::begin(), protocols::wum::SilentStructStore::end(), protocols::wum::SilentStructStore::get_struct(), protocols::mpi_refinement::StructAvrgMover::report_dev(), and protocols::wum::SilentStructStore::size().

void protocols::mpi_refinement::MPI_Refine_Master::go ( )

overridevirtual

Implements protocols::wum::MPI_WorkUnitManager.

References core::init::init(), protocols::wum::mpi_rank(), and TRDEBUG.

void protocols::mpi_refinement::MPI_Refine_Master::init ( void )

overrideprotectedvirtual

Implements protocols::wum::MPI_WorkUnitManager.

References protocols::mpi_refinement::get_loop_info_full(), and protocols::wum::mpi_rank().

void protocols::mpi_refinement::MPI_Refine_Master::load_sample_weight ( )

protected

References protocols::sparta::split(), and protocols::hybridization::t.

core::Size protocols::mpi_refinement::MPI_Refine_Master::master_rank ( )

inlineprotected

References master_rank_.

core::Size protocols::mpi_refinement::MPI_Refine_Master::my_emperor ( )

inlineprotected

References my_emperor_.

core::Size protocols::mpi_refinement::MPI_Refine_Master::n_to_gen ( ) const

inlineprotected

References protocols::mpi_refinement::Scheduler::n_to_gen(), and scheduler_.

void protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus ( )

overrideprotectedvirtual

figure out what to do with incoming WUs. Some will be returning WUs that need to be resent others will be finished and will need reintegration into the library this may send something to Emperor too

Implements protocols::wum::MPI_WorkUnitManager.

References protocols::wum::SilentStructStore::all_add_energy(), protocols::wum::SilentStructStore::clear(), protocols::mpi_refinement::MethodParams::fshave1, protocols::mpi_refinement::MethodParams::fshave2, protocols::wum::SilentStructStore::get_struct(), protocols::wum::WorkUnitBase::print(), protocols::mpi_refinement::MethodParams::rerelax_type, protocols::wum::SilentStructStore::size(), protocols::wum::SilentStructStore::sort_by(), and TRDEBUG.

void protocols::mpi_refinement::MPI_Refine_Master::process_outbound_wus ( )

overrideprotectedvirtual

Implements protocols::wum::MPI_WorkUnitManager.

References core::sequence::end, protocols::mpi_refinement::MethodParams::name, protocols::mpi_refinement::MethodParams::nrun, protocols::mpi_refinement::MethodParams::roundtype, and TRDEBUG.

bool protocols::mpi_refinement::MPI_Refine_Master::process_round ( )

protected

References protocols::wum::SilentStructStore::add(), protocols::mpi_refinement::Clusterer::apply(), and protocols::wum::mpi_rank().

bool protocols::mpi_refinement::MPI_Refine_Master::process_termination ( )

protected

void protocols::mpi_refinement::MPI_Refine_Master::set_defaults ( )

Referenced by MPI_Refine_Master().

Member Data Documentation

bool protocols::mpi_refinement::MPI_Refine_Master::asked_for_feedback_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::batch_relax_absolute_max_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::batch_relax_chunks_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::expire_after_rounds_

private

bool protocols::mpi_refinement::MPI_Refine_Master::got_termination_signal_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::library_expiry_time_

private

std::string protocols::mpi_refinement::MPI_Refine_Master::loophash_scan_type_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::loophash_split_size_

private

const core::Size protocols::mpi_refinement::MPI_Refine_Master::master_rank_

private

Referenced by master_rank().

core::Size protocols::mpi_refinement::MPI_Refine_Master::max_sample_per_structure_

private

bool protocols::mpi_refinement::MPI_Refine_Master::mpi_master_save_score_only_

private

const core::Size protocols::mpi_refinement::MPI_Refine_Master::my_emperor_

private

Referenced by my_emperor().

utility::vector1< int > protocols::mpi_refinement::MPI_Refine_Master::myslaves_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::n_lib_modified_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::nchange_emperor_call_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::ngen_serial_per_structure_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::outbound_wu_buffer_size_

private

core::Real protocols::mpi_refinement::MPI_Refine_Master::prob_terminus_ramapert_

private

std::string protocols::mpi_refinement::MPI_Refine_Master::sample_weight_str_

private

core::Size protocols::mpi_refinement::MPI_Refine_Master::sch_stage_

private

Scheduler protocols::mpi_refinement::MPI_Refine_Master::scheduler_

private

Referenced by n_to_gen().

bool protocols::mpi_refinement::MPI_Refine_Master::sent_termination_

private

std::map< int, bool > protocols::mpi_refinement::MPI_Refine_Master::slaves_finished_

private

std::map< std::string, core::Size > protocols::mpi_refinement::MPI_Refine_Master::ssids_by_name_

private

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

src/protocols/mpi_refinement/MPI_Refine_Master.hh
src/protocols/mpi_refinement/MPI_Refine_Master.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation