#include <MPI_LoopHashRefine_Master.hh>

Inheritance diagram for protocols::loophash::MPI_LoopHashRefine_Master:

Collaboration diagram for protocols::loophash::MPI_LoopHashRefine_Master:

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

virtual	~MPI_LoopHashRefine_Master ()

void	set_defaults ()

virtual void	go ()

Public Member Functions inherited from protocols::loophash::MPI_LoopHashRefine
	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 ()

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
virtual void	init ()

virtual void	process_inbound_wus ()
	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 More...

virtual void	process_outbound_wus ()

void	create_loophash_WUs (const core::io::silent::SilentStructOP &start_struct)

void	add_relax_batch (protocols::wum::SilentStructStore &start_decoys)

void	check_library_expiry_dates ()

void	load_sample_weight ()

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

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

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

core::Real	ev_objective_function (core::io::silent::SilentStructOP &ss)

core::Size	master_rank ()

core::Size	my_emperor ()

Protected Member Functions inherited from protocols::loophash::MPI_LoopHashRefine
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="")

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	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...

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::loophash::MPI_LoopHashRefine
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_

Detailed Description

Definition at line 35 of file MPI_LoopHashRefine_Master.hh.

Constructor & Destructor Documentation

protocols::loophash::MPI_LoopHashRefine_Master::MPI_LoopHashRefine_Master	(	core::Size	my_emperor,
		core::Size	master_rank
	)

inline

Definition at line 37 of file MPI_LoopHashRefine_Master.hh.

References set_defaults().

virtual protocols::loophash::MPI_LoopHashRefine_Master::~MPI_LoopHashRefine_Master ( )

inlinevirtual

Definition at line 46 of file MPI_LoopHashRefine_Master.hh.

Member Function Documentation

void protocols::loophash::MPI_LoopHashRefine_Master::add_relax_batch ( protocols::wum::SilentStructStore & start_decoys)

protected

Definition at line 327 of file MPI_LoopHashRefine_Master.cc.

References protocols::wum::SilentStructStore::get_struct(), RG(), protocols::wum::SilentStructStore::size(), and TRDEBUG.

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

protectedvirtual

This is a virtual over load of the base class MPI_LoopHashRefine:: 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::loophash::MPI_LoopHashRefine.

Definition at line 459 of file MPI_LoopHashRefine_Master.cc.

void protocols::loophash::MPI_LoopHashRefine_Master::check_library_expiry_dates ( )

protected

Definition at line 379 of file MPI_LoopHashRefine_Master.cc.

References protocols::noesy_assign::round(), and TRDEBUG.

void protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs ( const core::io::silent::SilentStructOP & start_struct)

protected

Definition at line 270 of file MPI_LoopHashRefine_Master.cc.

References core::pose::add_comment(), core::chemical::CENTROID, core::pose::delete_comment(), core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), protocols::wum::mpi_rank(), protocols::noesy_assign::round(), core::pose::set_ss_from_phipsi(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and TRDEBUG.

core::Real protocols::loophash::MPI_LoopHashRefine_Master::ev_objective_function ( core::io::silent::SilentStructOP & ss)

protected

void protocols::loophash::MPI_LoopHashRefine_Master::go ( )

virtual

Implements protocols::wum::MPI_WorkUnitManager.

Definition at line 118 of file MPI_LoopHashRefine_Master.cc.

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

void protocols::loophash::MPI_LoopHashRefine_Master::init ( void )

protectedvirtual

Implements protocols::wum::MPI_WorkUnitManager.

Definition at line 100 of file MPI_LoopHashRefine_Master.cc.

void protocols::loophash::MPI_LoopHashRefine_Master::load_sample_weight ( )

protected

Definition at line 486 of file MPI_LoopHashRefine_Master.cc.

References core::io::pdb::split(), and core::scoring::hbonds::t().

core::Size protocols::loophash::MPI_LoopHashRefine_Master::master_rank ( )

inlineprotected

Definition at line 81 of file MPI_LoopHashRefine_Master.hh.

References master_rank_.

core::Size protocols::loophash::MPI_LoopHashRefine_Master::my_emperor ( )

inlineprotected

Definition at line 83 of file MPI_LoopHashRefine_Master.hh.

References my_emperor_.

void protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus ( )

protectedvirtual

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

Implements protocols::wum::MPI_WorkUnitManager.

Definition at line 149 of file MPI_LoopHashRefine_Master.cc.

References protocols::wum::SilentStructStore::all_add_energy(), protocols::wum::SilentStructStore::all_sort_silent_scores(), core::io::serialization::size(), protocols::wum::SilentStructStore::size(), and TRDEBUG.

void protocols::loophash::MPI_LoopHashRefine_Master::process_outbound_wus ( )

protectedvirtual

Implements protocols::wum::MPI_WorkUnitManager.

Definition at line 238 of file MPI_LoopHashRefine_Master.cc.

References core::io::serialization::size(), and TRDEBUG.

void protocols::loophash::MPI_LoopHashRefine_Master::report_structure_to_emperor ( core::io::silent::SilentStructOP & ss)

protected

Definition at line 467 of file MPI_LoopHashRefine_Master.cc.

void protocols::loophash::MPI_LoopHashRefine_Master::report_structure_to_emperor ( core::io::silent::SilentStruct & pss)

protected

Definition at line 476 of file MPI_LoopHashRefine_Master.cc.

void protocols::loophash::MPI_LoopHashRefine_Master::set_defaults ( )

Definition at line 85 of file MPI_LoopHashRefine_Master.cc.

Referenced by MPI_LoopHashRefine_Master().

Member Data Documentation

core::Size protocols::loophash::MPI_LoopHashRefine_Master::batch_relax_absolute_max_

private

Definition at line 89 of file MPI_LoopHashRefine_Master.hh.

core::Size protocols::loophash::MPI_LoopHashRefine_Master::batch_relax_chunks_

private

Definition at line 88 of file MPI_LoopHashRefine_Master.hh.

core::Size protocols::loophash::MPI_LoopHashRefine_Master::expire_after_rounds_

private

Definition at line 93 of file MPI_LoopHashRefine_Master.hh.

core::Size protocols::loophash::MPI_LoopHashRefine_Master::library_expiry_time_

private

Definition at line 92 of file MPI_LoopHashRefine_Master.hh.

core::Size protocols::loophash::MPI_LoopHashRefine_Master::loophash_split_size_

private

Definition at line 91 of file MPI_LoopHashRefine_Master.hh.

const core::Size protocols::loophash::MPI_LoopHashRefine_Master::master_rank_

private

Definition at line 103 of file MPI_LoopHashRefine_Master.hh.

Referenced by master_rank().

core::Size protocols::loophash::MPI_LoopHashRefine_Master::max_loophash_per_structure_

private

Definition at line 87 of file MPI_LoopHashRefine_Master.hh.

bool protocols::loophash::MPI_LoopHashRefine_Master::mpi_master_save_score_only_

private

Definition at line 94 of file MPI_LoopHashRefine_Master.hh.

const core::Size protocols::loophash::MPI_LoopHashRefine_Master::my_emperor_

private

Definition at line 102 of file MPI_LoopHashRefine_Master.hh.

Referenced by my_emperor().

std::string protocols::loophash::MPI_LoopHashRefine_Master::objective_function

private

Definition at line 105 of file MPI_LoopHashRefine_Master.hh.

core::Size protocols::loophash::MPI_LoopHashRefine_Master::outbound_wu_buffer_size_

private

Definition at line 90 of file MPI_LoopHashRefine_Master.hh.

std::string protocols::loophash::MPI_LoopHashRefine_Master::sample_weight_str_

private

Definition at line 99 of file MPI_LoopHashRefine_Master.hh.

protocols::wum::SilentStructStore protocols::loophash::MPI_LoopHashRefine_Master::to_be_relaxed_

private

Definition at line 96 of file MPI_LoopHashRefine_Master.hh.

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

src/protocols/loophash/MPI_LoopHashRefine_Master.hh
src/protocols/loophash/MPI_LoopHashRefine_Master.cc

Private Attributes
core::Size	max_loophash_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_

protocols::wum::SilentStructStore	to_be_relaxed_

std::string	sample_weight_str_

const core::Size	my_emperor_

const core::Size	master_rank_

std::string	objective_function

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation