#include <FileSystemJobDistributor.hh>

Inheritance diagram for protocols::jd2::FileSystemJobDistributor:

Collaboration diagram for protocols::jd2::FileSystemJobDistributor:

Public Member Functions
virtual	~FileSystemJobDistributor ()

virtual void	restart ()

virtual core::Size	get_new_job_id ()
	Return 0 to signal that no available jobs remain. Otherwise return an index into the Jobs object. More...

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 ()

virtual void	current_job_finished ()

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

JobOP	current_job () const
	Movers may ask their controlling job distributor for information about the current job. They may also load information into this job for later output. More...

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...

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
	FileSystemJobDistributor ()

virtual void	job_succeeded (core::pose::Pose &pose, core::Real run_time)
	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_failed (core::pose::Pose &pose, bool will_retry)
	This function is called when we five up on the job; 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	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 spawn. 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...

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

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	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	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	delete_in_progress_files ()
	delete all temporary files for this job More...

std::string const	temporary_file_name (JobCOP job) const
	tacks an extension (.in_progress) on to filename - for multiple process/one directory behaviour More...

Private Attributes
std::string	extension_

std::string	path_

core::Size	retry_count_

Friends
class	JobDistributorFactory

Additional Inherited Members
Static Public Member Functions inherited from protocols::jd2::JobDistributor
static JobDistributor *	get_instance ()

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...

Constructor & Destructor Documentation

protocols::jd2::FileSystemJobDistributor::FileSystemJobDistributor ( )

protected

References path_.

protocols::jd2::FileSystemJobDistributor::~FileSystemJobDistributor ( )

virtual

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::FileSystemJobDistributor::current_job_finished ( )

virtual

when multiple processes are writing to the same directory, then after a job completes, the "in_progress" file for the job must be deleted.

Reimplemented from protocols::jd2::JobDistributor.

References delete_in_progress_files().

void protocols::jd2::FileSystemJobDistributor::delete_in_progress_files ( )

private

delete all temporary files for this job

References protocols::jd2::JobDistributor::current_job_id(), protocols::jd2::JobDistributor::get_jobs(), protocols::jd2::JobDistributor::job_outputter(), and temporary_file_name().

Referenced by current_job_finished(), and handle_interrupt().

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

virtual

Return 0 to signal that no available jobs remain. Otherwise return an index into the Jobs object.

Implements protocols::jd2::JobDistributor.

Reimplemented in protocols::jd2::BOINCJobDistributor, and protocols::jd2::ShuffleFileSystemJobDistributor.

References protocols::jd2::JobDistributor::current_job_id(), protocols::swa::rna::file_exists(), protocols::jd2::JobDistributor::get_jobs(), protocols::jd2::JobDistributor::job_outputter(), retry_count_, and temporary_file_name().

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

virtual

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

Reimplemented from protocols::jd2::JobDistributor.

Reimplemented in protocols::jd2::BOINCJobDistributor, and protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor.

References protocols::jd2::JobDistributor::go_main(), protocols::jd2::JobDistributor::remove_system_signal_handler(), and protocols::jd2::JobDistributor::setup_system_signal_handler().

Referenced by protocols::jd2::BOINCJobDistributor::go().

void protocols::jd2::FileSystemJobDistributor::handle_interrupt ( )

protectedvirtual

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 spawn.

Implements protocols::jd2::JobDistributor.

Reimplemented in protocols::jd2::ShuffleFileSystemJobDistributor.

References delete_in_progress_files().

void protocols::jd2::FileSystemJobDistributor::job_failed	(	core::pose::Pose &	pose,
		bool	will_retry
	)

protectedvirtual

This function is called when we five up on the job; it has been virtualized so BOINC and MPI can delay/protect output base implementation is just a call to the job outputter.

Reimplemented from protocols::jd2::JobDistributor.

Reimplemented in protocols::jd2::BOINCJobDistributor.

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::job_failed(), job_succeeded(), and retry_count_.

void protocols::jd2::FileSystemJobDistributor::job_succeeded	(	core::pose::Pose &	pose,
		core::Real	run_time
	)

protectedvirtual

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.

Reimplemented from protocols::jd2::JobDistributor.

Reimplemented in protocols::jd2::BOINCJobDistributor.

References protocols::jd2::JobDistributor::job_succeeded(), and retry_count_.

Referenced by job_failed(), and protocols::jd2::BOINCJobDistributor::job_succeeded().

void protocols::jd2::FileSystemJobDistributor::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.

Reimplemented in protocols::jd2::ShuffleFileSystemJobDistributor, and protocols::jd2::BOINCJobDistributor.

References protocols::jd2::JobDistributor::clear_current_job_output(), retry_count_, and protocols::jd2::TR().

void protocols::jd2::FileSystemJobDistributor::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

Reimplemented from protocols::jd2::JobDistributor.

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::current_job_id(), protocols::jd2::JobDistributor::job_outputter(), protocols::jd2::JobDistributor::mark_job_as_bad(), and protocols::jd2::TR().

void protocols::jd2::FileSystemJobDistributor::restart ( )

virtual

restart job-distribution from beginning – useful if you need a second pass over decoys...

Reimplemented from protocols::jd2::JobDistributor.