#include <UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.hh>

Inheritance diagram for protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor:

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Public Types
typedef std::map< std::string, utility::vector1 < core::scoring::EMapVector > >::iterator	uem_iter

Public Member Functions
	UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor ()
	ctor is protected; singleton pattern More...

	~UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor () override
	dtor (don't put anything in here) More...

void	add_unfolded_energy_data (std::string tlc, core::scoring::EMapVector const &scores)
	dummy for master/slave version More...

void	set_energy_terms (core::scoring::EMapVector const &weights)
	dummy for master/slave version More...

Public Member Functions inherited from protocols::jd2::MPIWorkPoolJobDistributor
	~MPIWorkPoolJobDistributor () override
	dtor WARNING WARNING! SINGLETONS' DESTRUCTORS ARE NEVER CALLED IN MINI! DO NOT TRY TO PUT THINGS IN THIS FUNCTION! here's a nice link explaining why: http://www.research.ibm.com/designpatterns/pubs/ph-jun96.txt More...

void	go (protocols::moves::MoverOP mover) override
	dummy for master/slave version More...

core::Size	get_new_job_id () override
	dummy for master/slave version More...

void	mark_current_job_id_for_repetition () override
	dummy for master/slave version More...

void	remove_bad_inputs_from_job_list () override
	dummy for master/slave version More...

void	job_succeeded (core::pose::Pose &pose, core::Real run_time, std::string const &tag) override
	dummy for master/slave version More...

void	job_failed (core::pose::Pose &pose, bool will_retry) override
	Called if job fails. More...

void	mpi_finalize (bool finalize) override
	should the go() function call MPI_finalize()? It probably should, this is true by default. More...

Public Member Functions inherited from protocols::jd2::JobDistributor
virtual	~JobDistributor ()

void	go (protocols::moves::MoverOP mover, JobOutputterOP jo)
	invokes go, after setting JobOutputter More...

void	go (protocols::moves::MoverOP mover, JobInputterOP ji)
	invokes go, after setting JobInputter More...

void	go (protocols::moves::MoverOP mover, JobInputterOP ji, JobOutputterOP jo)
	invokes go, after setting JobInputter and JobOutputter More...

virtual JobOP	current_job () const
	Movers may ask their controlling job distributor for information about the current job. They may also write information to this job for later output, though this use is now discouraged as the addition of the MultiplePoseMover now means that a single job may include several separate trajectories. More...

virtual std::string	current_output_name () const
	Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. More...

JobOutputterOP	job_outputter () const
	Movers (or derived classes) may ask for the JobOutputter. More...

void	set_job_outputter (const JobOutputterOP &new_job_outputter)
	Movers (or derived classes) may ask for the JobOutputter. More...

JobInputterOP	job_inputter () const
	JobInputter access. More...

void	set_job_inputter (JobInputterOP new_job_inputter)
	Set the JobInputter and reset the Job list – this is not something you want to do after go() has been called, but before it has returned. More...

JobInputterInputSource::Enum	job_inputter_input_source () const
	The input source for the current JobInputter. More...

virtual void	restart ()

core::Size	total_nr_jobs () const

core::Size	current_job_id () const
	integer access - which job are we on? More...

std::string	get_current_batch () const
	what is the current batch ? — name refers to the flag-file used for this batch More...

virtual void	add_batch (std::string const &, core::Size id=0)
	add a new batch ( name will be interpreted as flag_file ) More...

core::Size	current_batch_id () const
	what is the current batch number ? — refers to position in batches_ More...

Protected Member Functions
void	master_go (protocols::moves::MoverOP mover) override
	unforntunatly this is pretty much copied from the MPIWorkPoolJobDistributor, I should make that more compartmentalized More...

Protected Member Functions inherited from protocols::jd2::MPIWorkPoolJobDistributor
	MPIWorkPoolJobDistributor ()
	ctor is protected; singleton pattern More...

void	handle_interrupt () override
	This function got called when job is not yet finished and got termitated abnormaly (ctrl-c, kill etc). when implimenting it in subclasses make sure to delete all in-progress-data that your job spawns. More...

virtual void	slave_go (protocols::moves::MoverOP mover)
	Proceeds to the parent class go_main() as usual. More...

virtual core::Size	master_get_new_job_id ()
	Always returns zero, simply increments next_job_to_assign_ to the next job that should be run based on what has been completeted and the overwrite flags. More...

virtual core::Size	slave_get_new_job_id ()
	requests, receives, and returns a new job id from the master node or returns the current job id if the repeat_job_ flag is set to true More...

virtual void	master_mark_current_job_id_for_repetition ()
	This should never be called as this is handled internally by the slave nodes, it utility_exits. More...

virtual void	slave_mark_current_job_id_for_repetition ()
	Sets the repeat_job_ flag to true. More...

virtual void	master_remove_bad_inputs_from_job_list ()
	Simply increments next_job_to_assign_ to the next job that should be run based on what has been completed and if the input job tag of the job marked as having bad input. More...

virtual void	slave_remove_bad_inputs_from_job_list ()
	Sends a message to the head node that contains the id of a job that had bad input. More...

virtual void	master_job_succeeded (core::pose::Pose &pose, std::string const &tag)
	This should never be called as this is handled internally by the slave nodes, it utility_exits. More...

virtual void	slave_job_succeeded (core::pose::Pose &pose, std::string const &tag)
	Sends a message to the head node upon successful job completion to avoid output interleaving. More...

virtual void	master_mark_job_as_completed (core::Size const job_index)
	Mark the job as completed/deletable in the jobs list on the master process. More...

virtual void	master_mark_job_as_failed (core::Size const job_index)
	Mark the job as deletable in the jobs list on the master process. More...

virtual void	set_sequential_distribution (bool const val)
	Set whether the JobDistributor sends jobs to each slave in sequence (1, 2, 3, etc.) More...

virtual bool	sequential_distribution () const
	Get whether the JobDistributor sends jobs to each slave in sequence (1, 2, 3, etc.)? More...

virtual void	set_starter_for_sequential_distribution (bool const val)
	Set whether this is the process that should start requesting jobs (be the first for sequential distribution). More...

virtual bool	starter_for_sequential_distribution () const
	Is this the process that should start requesting jobs (be the first for sequential distribution)? More...

virtual void	wait_for_go_signal () const
	Wait for a signal from the n-1 process saying that I can proceed. More...

virtual void	send_go_signal ()
	Send a signal to the n+1 process saying that it can proceed. More...

Protected Member Functions inherited from protocols::jd2::JobDistributor
	JobDistributor ()
	Singleton instantiation pattern; Derived classes will call default ctor, but their ctors, too must be protected (and the JDFactory must be their friend.) More...

	JobDistributor (bool empty)
	MPIArchiveJobDistributor starts with an empty job-list... More...

void	go_main (protocols::moves::MoverOP mover)
	Non-virtual get-job, run it, & output loop. This function is pretty generic and your subclass may be able to use it. It is NOT virtual - this implementation can be shared by (at least) the simple FileSystemJobDistributor, the MPIWorkPoolJobDistributor, and the MPIWorkPartitionJobDistributor. Do not feel that you need to use it as-is in your class - but DO plan on implementing all its functionality! More...

JobsContainer const &	get_jobs () const
	Read access to private data for derived classes. More...

JobsContainer &	get_jobs_nonconst ()
	Jobs is the container of Job objects. More...

void	mark_job_as_completed (core::Size job_id, core::Real run_time)
	Jobs is the container of Job objects need non-const to mark Jobs as completed on Master in MPI-JobDistributor. More...

void	mark_job_as_bad (core::Size job_id)

RosettaScriptsParserOP	parser () const
	Parser access. More...

void	begin_critical_section ()

void	end_critical_section ()

void	set_current_job_by_index (core::Size curr_job_index)
	For derived classes that wish to invoke JobDistributor functions which use the current_job_ and current_job_id_ member variables. Note that until those functions complete, it would be a bad idea for another thread to change current_job_. More...

bool	obtain_new_job (bool re_consider_current_job=false)
	this function updates the current_job_id_ and current_job_ fields. The boolean return states whether or not a new job was obtained (if false, quit distributing!) More...

virtual void	job_succeeded_additional_output (core::pose::Pose &pose, std::string const &tag)
	This function is called upon a successful job completion if there are additional poses generated by the mover base implementation is just a call to the job outputter. More...

virtual void	current_job_finished ()
	Derived classes are allowed to clean up any temporary files or data relating to the current job after the current job has completed. Called inside go_main loop. Default implementation is a no-op. More...

virtual void	note_all_jobs_finished ()
	Derived classes are allowed to perform some kind of action when the job distributor runs out of jobs to execute. Called inside go_main. Default implementation is a no-op. More...

void	clear_current_job_output ()

void	check_for_parser_in_go_main ()
	Send a message to the screen indicating that the parser is in use and that the mover that's been input to go_main will not be used, but instead will be replaced by the Mover created by the parser. More...

bool	using_parser () const
	Is the parser in use? More...

bool	run_one_job (protocols::moves::MoverOP &mover, time_t allstarttime, std::string &last_inner_job_tag, std::string &last_output_tag, core::Size &last_batch_id, core::Size &retries_this_job, bool first_job)

void	setup_pymol_observer (core::pose::Pose &pose)
	After the construction of the pose for this job, check the command line to determine if the pymol observer should be attached to it. More...

void	write_output_from_job (core::pose::Pose &pose, protocols::moves::MoverOP mover_copy, protocols::moves::MoverStatus status, core::Size jobtime, core::Size &retries_this_job)
	After a job has finished running, figure out from the MoverStatus whether the pose should be written to disk (or wherever) along with any other poses that the mover might have generated along the way. More...

void	increment_failed_jobs ()
	Increment the number of failed jobs. More...

core::Size	get_job_time_estimate () const
	Get an estimate of the time to run an additional job. If it can't be estimated, return a time of zero. More...

void	write_citations_and_clear_citation_tracking () const
	Write out information about all modules that have been used that should be cited, then clear the list of citations from the CitationManager. More...

void	set_batch_id (core::Size setting)
	set current_batch_id — eg for slave nodes in MPI framework More...

virtual bool	next_batch ()
	switch current_batch_id_ to next batch More...

virtual void	batch_underflow ()
	if end of batches_ reached via next_batch or set_batch_id ... More...

virtual void	load_new_batch ()
	called by next_batch() or set_batch_id() to switch-over and restart JobDistributor on new batch More...

core::Size	nr_batches () const
	how many batches are in our list ... this can change dynamically More...

std::string const &	batch (core::Size batch_id)
	give name of batch with given id More...

Private Member Functions
void	master_add_unfolded_energy_data (std::string tlc, core::scoring::EMapVector const &scores)
	dummy for master/slave version More...

void	slave_add_unfolded_energy_data (std::string tlc, core::scoring::EMapVector const &scores)
	dummy for master/slave version More...

void	master_set_energy_terms (core::scoring::EMapVector const &weights)
	dummy for master/slave version More...

void	slave_set_energy_terms (core::scoring::EMapVector const &weights)
	dummy for master/slave version More...

Private Attributes
core::scoring::EMapVector	energy_terms_

utility::vector1 < core::scoring::EMapVector >	unweighted_energies_

std::map< std::string, utility::vector1 < core::scoring::EMapVector > >	unweighted_energies_map_

Additional Inherited Members
Static Public Member Functions inherited from protocols::jd2::JobDistributor
static bool	has_been_instantiated ()
	Has the job distributor been instantiated? More...

static JobDistributor *	get_instance ()
	static function to get the instance of ( pointer to) this singleton class More...

Static Protected Member Functions inherited from protocols::jd2::JobDistributor
static void	setup_system_signal_handler (void(*prev_fn)(int)=jd2_signal_handler)
	Setting up callback function that will be call when our process is about to terminate. This will allow us to exit propely (clean up in_progress_files/tmp files if any). More...

static void	remove_system_signal_handler ()
	Set signal handler back to default state. More...

static void	jd2_signal_handler (int Signal)
	Default callback function for signal handling. More...

Protected Attributes inherited from protocols::jd2::MPIWorkPoolJobDistributor
core::Size	npes_
	total number of processing elements More...

core::Size	rank_
	rank of the "local" instance More...

core::Size	current_job_id_
	where slave jobs store current job id More...

core::Size	next_job_to_assign_
	where master stores next job to assign (in a good state after get_new_job_id up until it's used) More...

core::Size	bad_job_id_
	where master temporarily stores id of jobs with bad input More...

bool	repeat_job_
	where slave stores whether it should repeat its current job id More...

bool	finalize_MPI_
	should the go() function call MPI_finalize? There are very few cases where this should be false More...

bool	sequential_distribution_
	Should the JobDistributor send jobs to each slave in sequence (1, 2, 3, etc.)? Default false – slaves request jobs as they become available. More...

bool	starter_for_sequential_distribution_
	Is this the process that should start requesting jobs (be the first for sequential distribution)? More...

Member Typedef Documentation

typedef std::map<std::string, utility::vector1< core::scoring::EMapVector > >::iterator protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::uem_iter

Constructor & Destructor Documentation

protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor ( )

ctor is protected; singleton pattern

ctor

protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::~UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor ( )

overridedefault

dtor (don't put anything in here)

WARNING WARNING! SINGLETONS' DESTRUCTORS ARE NEVER CALLED IN MINI! DO NOT TRY TO PUT THINGS IN THIS FUNCTION! here's a nice link explaining why: http://www.research.ibm.com/designpatterns/pubs/ph-jun96.txt

Member Function Documentation

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::add_unfolded_energy_data	(	std::string	tlc,
		core::scoring::EMapVector const &	scores
	)

dummy for master/slave version

References master_add_unfolded_energy_data(), protocols::jd2::MPIWorkPoolJobDistributor::rank_, and slave_add_unfolded_energy_data().

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_add_unfolded_energy_data	(	std::string	tlc,
		core::scoring::EMapVector const &	scores
	)

private

dummy for master/slave version

References unweighted_energies_map_.

Referenced by add_unfolded_energy_data(), and master_go().

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go ( protocols::moves::MoverOP mover )

overrideprotectedvirtual

unforntunatly this is pretty much copied from the MPIWorkPoolJobDistributor, I should make that more compartmentalized

Reimplemented from protocols::jd2::MPIWorkPoolJobDistributor.

References protocols::jd2::MPIWorkPoolJobDistributor::bad_job_id_, protocols::unfolded_state_energy_calculator::calc_all_averages(), energy_terms_, protocols::unfolded_state_energy_calculator::LENGTH_TLC(), master_add_unfolded_energy_data(), protocols::jd2::MPIWorkPoolJobDistributor::master_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::master_remove_bad_inputs_from_job_list(), master_set_energy_terms(), MPI_ANY_SOURCE, core::scoring::n_score_types, protocols::jd2::MPIWorkPoolJobDistributor::next_job_to_assign_, protocols::jd2::MPIWorkPoolJobDistributor::npes_, protocols::jd2::MPIWorkPoolJobDistributor::rank_, protocols::TR(), protocols::unfolded_state_energy_calculator::UNFOLDED_ENERGY_DATA_TAG(), protocols::unfolded_state_energy_calculator::UNFOLDED_ENERGY_TERMS_TAG(), and unweighted_energies_map_.

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_set_energy_terms ( core::scoring::EMapVector const & weights )

private

dummy for master/slave version

References energy_terms_, and core::scoring::n_score_types.

Referenced by master_go(), and set_energy_terms().

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::set_energy_terms ( core::scoring::EMapVector const & weights )

dummy for master/slave version

References master_set_energy_terms(), protocols::jd2::MPIWorkPoolJobDistributor::rank_, and slave_set_energy_terms().

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::slave_add_unfolded_energy_data	(	std::string	tlc,
		core::scoring::EMapVector const &	scores
	)

private

dummy for master/slave version

References protocols::jd2::MPIWorkPoolJobDistributor::current_job_id_, protocols::unfolded_state_energy_calculator::LENGTH_TLC(), core::scoring::n_score_types, protocols::jd2::MPIWorkPoolJobDistributor::rank_, protocols::TR(), and protocols::unfolded_state_energy_calculator::UNFOLDED_ENERGY_DATA_TAG().

Referenced by add_unfolded_energy_data().

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::slave_set_energy_terms ( core::scoring::EMapVector const & weights )

private

dummy for master/slave version

References protocols::jd2::MPIWorkPoolJobDistributor::current_job_id_, core::scoring::n_score_types, protocols::jd2::MPIWorkPoolJobDistributor::rank_, protocols::TR(), and protocols::unfolded_state_energy_calculator::UNFOLDED_ENERGY_TERMS_TAG().

Referenced by set_energy_terms().

Member Data Documentation

core::scoring::EMapVector protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::energy_terms_

private

Referenced by master_go(), and master_set_energy_terms().

utility::vector1< core::scoring::EMapVector > protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::unweighted_energies_

private

std::map<std::string, utility::vector1< core::scoring::EMapVector > > protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::unweighted_energies_map_

private

Referenced by master_add_unfolded_energy_data(), and master_go().

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

src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.hh
src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation