#include <MPIWorkPartitionJobDistributor.hh>

Inheritance diagram for protocols::jd2::MPIWorkPartitionJobDistributor:

Public Member Functions
virtual	~MPIWorkPartitionJobDistributor ()
	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...

virtual void	go (protocols::moves::MoverOP mover)
	This may be overridden by derived classes. Default implementation invokes go_main. More...

virtual core::Size	get_new_job_id ()

virtual void	mark_current_job_id_for_repetition ()
	this function is called whenever a job "soft-fails" and needs to be retried. Generally it should ensure that the subsequent call to obtain_new_job returns this job over again. More...

virtual void	remove_bad_inputs_from_job_list ()

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

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

virtual void	mpi_finalize (bool finalize)
	should the go() function call MPI_finalize()? It probably should, this is true by default. 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
	MPIWorkPartitionJobDistributor ()
	ctor is protected; singleton pattern More...

virtual void	handle_interrupt ()
	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...

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)

ParserOP	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 (core::pose::Pose &pose, core::Real run_time, std::string const &tag)
	This function is called upon a successful job completion; it has been virtualized so BOINC and MPI can delay/protect output base implementation is just a call to the job outputter. 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	job_failed (core::pose::Pose &, bool will_retry)
	This function is called when we give up on the job; it has been virtualized so BOINC and MPI can delay/protect output. 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	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	determine_job_ids_to_run ()
	ctor helper function splits up job list More...

Private Attributes
core::Size	npes_
	total number of processing elements More...

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

core::Size	job_id_start_

core::Size	job_id_end_

core::Size	next_job_to_try_assigning_

Friends
class	JobDistributorFactory

Additional Inherited Members
Static Public Member Functions inherited from protocols::jd2::JobDistributor
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. 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...

Detailed Description

This job distributor is meant for running jobs where the number of jobs is equal to the number of processors (or, similarly, the jobs % processors calculation is very close to the number of processors and NOT a small number). It will blindly divide up jobs across processors and then start running them; it will NOT attempt load-balancing by giving more jobs to the processors that finished their original jobs. This is intended for use on smaller numbers of processors, and/or where the jobs are known to be equal in runtime. (The WorkPool implementation is meant for when runtimes are uncertain, or you have many many processors). It does not "waste" a processor as a master node, instead all processors run jobs.

Constructor & Destructor Documentation

protocols::jd2::MPIWorkPartitionJobDistributor::MPIWorkPartitionJobDistributor ( )

protected

ctor is protected; singleton pattern

constructor. Notice it calls the parent class! It also builds some internal variables for determining which processor it is in MPI land (later used in job determination). Note that all processors will have the same internal Jobs object (set by the parent class); this class merely iterates over it differently.

References determine_job_ids_to_run(), protocols::jd2::JobDistributor::get_jobs(), job_id_end_, job_id_start_, next_job_to_try_assigning_, npes_, rank_, protocols::jd2::JobsContainer::size(), and protocols::jd2::TR().

protocols::jd2::MPIWorkPartitionJobDistributor::~MPIWorkPartitionJobDistributor ( )

virtual

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

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::jd2::MPIWorkPartitionJobDistributor::determine_job_ids_to_run ( )

private

ctor helper function splits up job list

All processors will get the same Jobs object; this function determines which slice belongs to a particular processor determined solely by its mpi rank and the number of processors, no communication needed EXAMPLE CASE: 18 jobs, 4 processors processor rank number of jobs assigned range in Jobs vector 0 5 1-5 1 5 6-10 2 4 11-14 3 4 15-18

References protocols::jd2::JobDistributor::get_jobs(), job_id_end_, job_id_start_, npes_, rank_, and protocols::jd2::JobsContainer::size().

Referenced by MPIWorkPartitionJobDistributor().

core::Size protocols::jd2::MPIWorkPartitionJobDistributor::get_new_job_id ( )

virtual

determine which job to assign next: increment until we run out of available jobs

Implements protocols::jd2::JobDistributor.

References protocols::jd2::JobDistributor::get_jobs(), job_id_end_, protocols::jd2::JobDistributor::job_outputter(), and next_job_to_try_assigning_.

void protocols::jd2::MPIWorkPartitionJobDistributor::go ( protocols::moves::MoverOP mover )

virtual

This may be overridden by derived classes. Default implementation invokes go_main.

Reimplemented from protocols::jd2::JobDistributor.

References protocols::jd2::JobDistributor::go_main().

virtual void protocols::jd2::MPIWorkPartitionJobDistributor::handle_interrupt ( )

inlineprotectedvirtual

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.

Implements protocols::jd2::JobDistributor.

void protocols::jd2::MPIWorkPartitionJobDistributor::mark_current_job_id_for_repetition ( )

virtual

this function is called whenever a job "soft-fails" and needs to be retried. Generally it should ensure that the subsequent call to obtain_new_job returns this job over again.

Implements protocols::jd2::JobDistributor.

References protocols::jd2::JobDistributor::clear_current_job_output(), protocols::jd2::JobDistributor::current_job_id(), and next_job_to_try_assigning_.

void protocols::jd2::MPIWorkPartitionJobDistributor::remove_bad_inputs_from_job_list ( )

virtual

this function handles the FAIL_BAD_INPUT mover status by removing other jobs with the same input from consideration. This function DOES NOT percolate across processors - so if multiple processors have jobs starting with the same bad input, you will get multiple hits through this function. This is less efficient than it theoretically could be (but it's good enough).

Reimplemented from protocols::jd2::JobDistributor.

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_jobs(), job_id_end_, protocols::jd2::JobDistributor::job_outputter(), next_job_to_try_assigning_, and protocols::jd2::TR().