Job Queen for MultiStage Rosetta Scripts (MRS) More...

#include <MRSJobQueen.hh>

Inheritance diagram for protocols::multistage_rosetta_scripts::MRSJobQueen:

Public Member Functions
	MRSJobQueen ()

	~MRSJobQueen () override

jd3::JobDigraphOP	create_initial_job_dag () override
	The job dag encodes which job nodes are independent or dependant on each other. If you have a applicationwhere all inputs are independant and only a single run of a protocol is needed, Then do not override this method. More...

std::list< jd3::LarvalJobOP >	determine_job_list (jd3::JobDAGNodeID job_dag_node_index, Size max_njobs) override
	Create a list of LarvalJobs for each Node Index. Only can create max_njobs to save memory. More...

jd3::JobOP	complete_larval_job_maturation (jd3::LarvalJobCOP larval_job, utility::options::OptionCollectionCOP job_options, utility::vector1< jd3::JobResultCOP > const &input_job_results) override
	The derived JobQueen must define the method that takes a larval job and the job-specific options and matures the larval job into a full job. More...

void	note_job_completed (jd3::GlobalJobID job_id, jd3::JobStatus status, core::Size nresults, bool are_you_a_unit_test)
	this was only created for the unit test. Please do not call this. More...

void	note_job_completed (core::Size, jd3::JobStatus, core::Size)

void	note_job_completed (jd3::LarvalJobCOP job, jd3::JobStatus status, core::Size nresults) override
	The JD calls this function on completion of a LarvalJob, after updating the JobTracker. More...

void	completed_job_summary (jd3::GlobalJobID job_id, jd3::ResultIndex result_index, jd3::JobSummaryOP summary)

void	completed_job_summary (jd3::LarvalJobCOP job, jd3::ResultIndex result_index, jd3::JobSummaryOP summary) override
	As each job completes, this function is called for each result coming from a LarvalJob. More...

jd3::JobDAGNodeID	stage_for_global_job_id (jd3::GlobalJobID global_job_id) const

std::list< jd3::JobResultID >	job_results_that_should_be_discarded () override
	The IDs of jobs that should be discarded, IE not kept in memory for the next set of job nodes. More...

std::list < jd3::output::OutputSpecificationOP >	jobs_that_should_be_output () override
	By default outputs all recently finished jobs for JD output (stored in recent_successes_). Override this method if you want to cull these lists. More...

TagManager const &	tag_manager () const

void	determine_validity_of_stage_tags ()

core::Size	num_input_structs () const

core::Size	num_stages () const

core::Size	num_results_to_keep_for_stage (core::Size stage) const

Public Member Functions inherited from protocols::jd3::standard::StandardJobQueen
	StandardJobQueen ()
	The StandardJobQueen constructor asks the PoseInputterFactory for a PoseInputter and creates a ResourceManager. More...

	~StandardJobQueen () override

void	update_job_dag (JobDigraphUpdater &updater) override
	Starting the Job ///. More...

protocols::jd3::JobOP	mature_larval_job (protocols::jd3::LarvalJobCOP job, utility::vector1< JobResultCOP > const &input_job_results) override
	Mature the LarvalJob into a full Job that will be run on a processor. Calls complete_larval_job_maturation, which you will need to override. More...

output::ResultOutputterOP	result_outputter (output::OutputSpecification const &spec) override
	Return the bag of of PoseOutputters (in the form of a MultipleOutputter) for the Pose that has been requested and specified by a particular OutputSpecification;. More...

bool	has_job_previously_been_output (protocols::jd3::LarvalJobCOP job) override
	Checks the outputter to see if the job already has been output. Used for JD override behavior. More...

std::list < deallocation::DeallocationMessageOP >	deallocation_messages () override
	Resource Management ///. More...

void	process_deallocation_message (deallocation::DeallocationMessageOP message) override
	A deallocation message first sent to the JobDistributor on this host originating from a remote JobQueen. If a derived JobQueen has deallocation messages she needs to recieve, she should override derived_process_deallocation_message. More...

void	flush () override
	Send all buffered output to disk – called by the JobDistributor right before it shuts down if it hits an error or catches an exception that it cannot ignore. More...

std::string	job_definition_xsd () const override
	XSD Functions ///. More...

std::string	resource_definition_xsd () const override
	JobQueens may optionally define an XSD for their resource definition file which is fed to their resource manager (if they control one). If the JobDistributor is awakened with the flag "jd3::output_resource_xsd <output file>" on the command line, and if the derived JobQueen defines an XSD for resources she uses, then the JobDistributor will write out the resource definition XSD to the output file. The derived queen may return an empty string to indicate that no resources are definable for the resource manager. More...

void	determine_preliminary_job_list_from_xml_file (std::string const &job_def_string)
	Read from an input string representing the contents of the job-definiton XML file and construct a set of PreliminaryLarvalJobs; this function is primarily useful for testing, but could be used to organize jobs by an enterprising job distributor or by another JobQueen. More...

Public Member Functions inherited from protocols::jd3::JobQueen
	JobQueen ()

	~JobQueen () override

JobDigraphOP	create_and_set_initial_job_dag ()
	Creates the initial job dag using create_initial_job_dag function and sets it to the JQ. More...

void	note_job_completed_and_track (LarvalJobCOP job, JobStatus status, Size nresults)
	Call note_job_completed in derived classes and track the job using the JobTracker. More...

LarvalJobs	determine_job_list_and_track (JobDAGNodeID job_dag_node_index, Size max_njobs)
	Call determine_job_list in derived classes and track the jobs using the JobTracker. More...

Protected Member Functions
core::pose::PoseOP	pose_for_job_derived (jd3::LarvalJobCOP job, utility::options::OptionCollection const &options)

core::pose::PoseOP	pose_for_inner_job_derived (jd3::InnerLarvalJobCOP inner_job, utility::options::OptionCollection const &options)

void	all_settings_to_defualt ()

jd3::LarvalJobOP	get_nth_job_for_initial_stage (jd3::LocalJobID local_job_id)

jd3::LarvalJobOP	get_nth_job_for_noninitial_stage (jd3::JobDAGNodeID stage, jd3::LocalJobID local_job_id)

void	append_common_tag_subelements (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaComplexTypeGenerator &ct_gen) const override
	Here, you specify which tags that are defined in the <common> element. More...

void	parse_job_definition_tags (utility::tag::TagCOP common_block_tags, utility::vector1< jd3::standard::PreliminaryLarvalJob > const &) override
	This gives the derived JobQueen a chance to read any relevant information from the job-definition file. The second argument holds a PreliminaryLarvalJob for every job block and the PreliminaryLarvalJob itself has all of the information given in its corresponding block. More...

void	parse_common_tag (utility::tag::TagCOP common_tag)

void	parse_single_stage_tag (utility::tag::TagCOP subprotocol_tag)

void	append_job_tag_subelements (utility::tag::XMLSchemaDefinition &job_definition_xsd, utility::tag::XMLSchemaComplexTypeGenerator &job_ct_gen) const override
	XML Schema ///. More...

void	parse_single_job_tag (jd3::standard::PreliminaryLarvalJob const &prelim_larval_job, jd3::PrelimJobNodeID input_pose_id)

jd3::PrelimJobNodeID	input_pose_id_for_jobid (jd3::GlobalJobID global_jobid) const

void	print_job_lineage () const

void	assign_output_index (jd3::LarvalJobCOP larval_job, jd3::ResultIndex result_index_for_job, core::Size n_results_for_job, jd3::JobOutputIndex &output_index) override
	The derived job queen may assign her own numbering to output Poses if she chooses. More...

void	assign_output_index (jd3::GlobalJobID global_job_id, jd3::ResultIndex result_id, jd3::JobOutputIndex &output_index)

void	cluster (jd3::JobDAGNodeID stage_about_to_start)

Protected Member Functions inherited from protocols::jd3::standard::StandardJobQueen
virtual LarvalJobs	next_batch_of_larval_jobs_for_job_node (JobDAGNodeID job_dag_node_index, Size max_njobs)
	Called during the SJQs determine_job_list function. Override this function to create LarvalJobs for nodes other than preliminary job nodes. More...

GlobalJobID	current_job_index () const
	Get the current larval job index from the JobTracker. More...

virtual void	determine_preliminary_job_list ()
	Preliminary Larval Jobs ///. More...

bool	get_preliminary_larval_jobs_determined () const
	Has determine_preliminary_job_list been called? More...

PreliminaryLarvalJobTracker &	get_prelim_larval_job_tracker ()
	Get write access to the PreliminaryLarvalJobTracker. More...

PreliminaryLarvalJobTracker const &	get_prelim_larval_job_tracker () const
	Get read access to the PreliminaryLarvalJobTracker. More...

utility::vector1 < PreliminaryLarvalJob > const &	get_preliminary_larval_jobs () const
	Read access to derived JobQueens to the preliminary job list. More...

virtual void	note_preliminary_job_node_is_complete (PrelimJobNodeID pjn_index)
	Respond to the completion of a preliminary job node in derived SJQs. More...

virtual InnerLarvalJobs	refine_preliminary_job (PreliminaryLarvalJob const &prelim_job)
	Optional Larval Job Creation ///. More...

virtual LarvalJobs	expand_job_list (InnerLarvalJobOP inner_job, core::Size max_larval_jobs_to_create)
	Expand an InnerLarvalJob into a full set of LarvalJobs, creating nstruct LarvalJob objects Increments larval_job_counter_. More...

virtual StandardInnerLarvalJobOP	create_inner_larval_job (core::Size nstruct, JobDAGNodeID job_node, PrelimJobNodeID preliminary_job_node) const
	Factory method for derived classes if they wish to rely on classes derived from StandardInnerLarvalJob. This is invoked by the StandardJobQueen in her determine_job_list method just as jobs are prepared. If the base StandardInnerLarvalJob class is desired, then do not override this method. More...

virtual LarvalJobOP	create_larval_job (InnerLarvalJobOP job, NStructIndex nstruct_index, core::Size larval_job_index)
	Factory method for derived classes if they wish to rely on classes derived from LarvalJob. This is invoked by the StandardJobQueen in the expand_job_list method. If the base LarvalJob class is desired, then do not override this method. More...

InnerLarvalJobOP	create_and_init_inner_larval_job_from_preliminary (core::Size nstruct, PrelimJobNodeID prelim_job_node, JobDAGNodeID job_node) const
	Adds information regarding the job definition (job tag, input source, jobdef tag, and outputter). Uses the PreliminaryInnerLarvalJob to do so. More...

void	create_and_store_output_specification_for_job_result (LarvalJobCOP job, ResultIndex result_index, core::Size nresults)
	Output Specifications and Ouputters ///. More...

void	create_and_store_output_specification_for_job_result (LarvalJobCOP job, utility::options::OptionCollection const &job_options, ResultIndex result_index, core::Size nresults)
	Create an output specification for a given job + result index and store it in the recent_successes_ list, which will be given to the JobDistributor upon request. More...

virtual output::OutputSpecificationOP	create_output_specification_for_job_result (LarvalJobCOP job, utility::options::OptionCollection const &job_options, ResultIndex result_index, core::Size nresults)
	Construct the OutputSpecification for a completed successful job. More...

JobOutputIndex	build_output_index (protocols::jd3::LarvalJobCOP larval_job, ResultIndex result_index_for_job, Size n_results_for_job)
	Construct a JobOutputIndex for a given job based on "the obvious", but giving derived classes the chance to assign their own indices via the assign_output_index function. More...

virtual void	derived_process_deallocation_message (deallocation::DeallocationMessageOP message)
	If the derived class has deallocation messages that it needs to broadcast to remote nodes and then to process on those remote nodes, then the StanardJobQueen will pass them along to the derived job queen using this function. More...

pose_outputters::PoseOutputterOP	pose_outputter_for_job (InnerLarvalJob const &innerJob)
	Create or get the PoseOutputter from the job. Cache the Outputter in the SJQ. More...

pose_outputters::PoseOutputterOP	pose_outputter_for_job (InnerLarvalJob const &innerJob, utility::options::OptionCollection const &job_options)
	Create or get the PoseOutputter from the job. Cache the Outputter in the SJQ. More...

pose_outputters::PoseOutputterOP	pose_outputter_for_job (pose_outputters::PoseOutputSpecification const &spec)
	Find the PoseOutputter for a job specification, respecting the Job-distributor provided output file suffix. More...

utility::vector1 < pose_outputters::SecondaryPoseOutputterOP >	secondary_outputters_for_job (InnerLarvalJob const &innerJob, utility::options::OptionCollection const &job_options)

core::pose::PoseOP	pose_for_inner_job (InnerLarvalJobCOP inner_job)

core::pose::PoseOP	pose_for_inner_job (InnerLarvalJobCOP inner_job, utility::options::OptionCollection const &options)
	Return a copy of the Pose to be used with the given inner job. More...

core::pose::PoseOP	pose_for_job (LarvalJobCOP job, utility::options::OptionCollection const &options)
	Return a copy of the Pose to be used with the given job. Wrapper for pose_for_inner_job() More...

utility::options::OptionCollectionOP	options_for_job (InnerLarvalJob const &inner_job) const
	Options Collection ///. More...

utility::options::OptionCollectionOP	options_from_tag (utility::tag::TagCOP job_options_tags) const
	Create an OptionCollection from tags and OptionKeys stored in the SJQ. More...

pose_inputters::PoseInputterOP	pose_inputter_for_job (InnerLarvalJob const &inner_job) const
	Access the pose inputter. More...

void	add_options (utility::options::OptionKeyList const &opts)

void	add_option (utility::options::OptionKey const &key)

void	remove_default_input_element ()
	Override the basic specification of input elements as either PDBs, Silent Structures, or ResourceManager defined structures. This should be called during the derived class's constructor if it is to be used. More...

utility::tag::TagCOP	common_block_tags () const
	Return the set of subtags that are common to the whole set of jobs in the Job definition file, if any are given. This set of tags is read from disk at most once per execution. More...

void	set_common_block_precedes_job_blocks (bool setting)
	By default, the common block is given before the job blocks in the job definition file. Setting this value to false reverses the order and the common block goes at the end of the file. More...

void	do_not_accept_all_pose_inputters_from_factory ()
	Expert Override Input/Output behavior ///. More...

void	allow_pose_inputter (pose_inputters::PoseInputterCreatorOP creator)

void	do_not_accept_all_pose_outputters_from_factory ()

void	allow_pose_outputter (pose_outputters::PoseOutputterCreatorOP creator)

void	set_default_outputter (pose_outputters::PoseOutputterCreatorOP creator)

Protected Member Functions inherited from protocols::jd3::JobQueen
JobDigraph const &	get_job_graph () const
	Get read access to the current job graph. More...

JobTracker &	get_job_tracker ()
	Get write access to the current job tracker. More...

JobTracker const &	get_job_tracker () const
	Get read access to the current job tracker. More...

Static Protected Member Functions
static std::string	protocols_subelement_mangler (std::string const &name)

static std::string	job_subelement_mangler (std::string const &name)

Private Attributes
bool	has_been_initialized_

SortByLowEnergy	sorter_

core::Size	num_input_structs_

core::Size	num_stages_

utility::vector1< core::Size >	num_total_jobs_for_stage_

utility::vector1< core::Size >	num_results_to_keep_for_stage_

utility::vector1< core::Size >	max_num_results_to_keep_per_instance_for_stage_

utility::vector1< core::Size >	max_num_results_to_keep_per_input_struct_for_stage_

utility::vector1< core::Size >	num_jobs_per_input_for_stage_

utility::vector1< core::Size >	result_cutoffs_for_stage_

utility::vector1< core::Size >	job_results_have_been_discarded_for_stage_

utility::vector1 < jd3::dag_node_managers::NodeManagerOP >	node_managers_

utility::vector1 < utility::tag::TagCOP >	tag_for_stage_

TagManager	tag_manager_

utility::vector1< std::string >	outputters_

utility::vector1< std::string >	input_job_tags_

utility::vector1< core::Size >	num_structs_output_for_input_job_tag_

utility::vector1< std::pair < jd3::InnerLarvalJobOP, core::Size > >	current_inner_larval_job_for_stage_

jd3::JobGenealogistOP	job_genealogist_

std::map< jd3::JobResultID, jd3::output::OutputSpecificationOP >	pose_output_specification_for_job_result_id_

PoseForPoseID	most_recent_pose_id_

utility::vector1< std::pair < core::Size, utility::tag::TagCOP > >	checkpoints_

utility::vector1 < utility::tag::TagCOP >	cluster_metric_tag_for_stage_

utility::vector1< core::Size >	num_results_to_keep_after_clustering_for_stage_

utility::vector1 < std::unordered_map < jd3::JobResultID, cluster::ClusterMetricCOP, JobResultID_hash > >	cluster_data_for_results_of_stage_

utility::vector1 < jd3::JobResultID >	most_recent_cluster_results_
	No need to store this data for more than one stage at a time. More...

Additional Inherited Members
Static Public Member Functions inherited from protocols::jd3::standard::StandardJobQueen
static std::string	job_def_complex_type_name (std::string const &type)
	Naming function for the complexTypes in the job-definition XSD. More...

Detailed Description

Job Queen for MultiStage Rosetta Scripts (MRS)

Constructor & Destructor Documentation

protocols::multistage_rosetta_scripts::MRSJobQueen::MRSJobQueen ( )

References protocols::rosetta_scripts::RosettaScriptsParser::register_factory_prototypes(), and protocols::jd3::standard::StandardJobQueen::set_common_block_precedes_job_blocks().

protocols::multistage_rosetta_scripts::MRSJobQueen::~MRSJobQueen ( )

override

Member Function Documentation

void protocols::multistage_rosetta_scripts::MRSJobQueen::all_settings_to_defualt ( )

protected

void protocols::multistage_rosetta_scripts::MRSJobQueen::append_common_tag_subelements	(	utility::tag::XMLSchemaDefinition &	xsd,
		utility::tag::XMLSchemaComplexTypeGenerator &	ct_gen
	)		const

overrideprotectedvirtual

Here, you specify which tags that are defined in the <common> element.

The derived JobQueen must inform the StandardJobQueen of any additional tags that belong as sub elements of the <Common> tag. The StandardJobQueen will have already appended the <Options> subtag before this function executes, so the only functions that the derived class should invoke of the XMLSchemaComplexTypeGenerator are its add_ordered_subelement_set_* functions, if you have additional subelements to add. Adding additional subelements to the complexType generator may require writing additional complexTypes to the XML Schema for the job definition file, and so that job definition xsd is passed in as well. The Tags in the <Common> block should be parsed for each Job in the mature_larval_job step; these tags are available to the derived class through the common_block_tags method. This is where data that is not constant over the course of the job can be declared (e.g. ScoreFunctions, the weights of which are often modified during the course of protocol execution), but data that is constant and that can be shared between multiple jobs ought to be initialized and held by the ResourceManager. Options provided in the <Common> block will supercede the command line, but will be overriden by any options provided for a particular job. (This is logic the StandardJobQueen manages).

Derived classes may choose to not override this method as a way to indicate that they have no common-block data that needs to be defined.

Reimplemented from protocols::jd3::standard::StandardJobQueen.

References protocols::multistage_rosetta_scripts::cluster::complex_type_name_for_cluster_metric(), protocols::filters::complex_type_name_for_filter(), protocols::moves::complex_type_name_for_mover(), protocols::parser::DataLoaderFactory::data_loader_ct_namer(), and protocols_subelement_mangler().

void protocols::multistage_rosetta_scripts::MRSJobQueen::append_job_tag_subelements	(	utility::tag::XMLSchemaDefinition &	job_definition_xsd,
		utility::tag::XMLSchemaComplexTypeGenerator &	ct_gen
	)		const

overrideprotectedvirtual

XML Schema ///.

Here you can specify Schema's to use when creating your XSD for a specific JOB. AKA - you can add elements such as ResidueSelectors, task operations, etc. to parse.

The derived JobQueen must inform the StandardJobQueen of any additional tags that belong as sub elements of the <Job> tag. The StandardJobQueen will have already appended the <Input>, <Output>, and <Options> subtags before this function executes, so the only functions that the derived class should invoke of the XMLSchemaComplexTypeGenerator are its add_ordered_subelement_set_* functions, if you have additional subelements to add. Adding additional subelements to the complexType generator may require writing additional complexTypes to the XML Schema for the job definition file, and so that job definition xsd is passed in as well.

Derived classes may choose to not override this method as a way to indicate that they have no additional subtags of the <Job> tag they wish to add. This is a no-op implementation.

Reimplemented from protocols::jd3::standard::StandardJobQueen.

References protocols::parser::DataLoaderFactory::data_loader_ct_namer(), protocols::parser::ResidueSelectorLoader::loader_name(), and protocols::parser::ResidueSelectorLoader::res_selector_loader_ct_namer().

void protocols::multistage_rosetta_scripts::MRSJobQueen::assign_output_index	(	jd3::LarvalJobCOP	larval_job,
		jd3::ResultIndex	result_index_for_job,
		core::Size	n_results_for_job,
		jd3::JobOutputIndex &	output_index
	)

overrideprotectedvirtual

The derived job queen may assign her own numbering to output Poses if she chooses.

No-op implementation – leave the indices the way they were initialized.

Just before a job result is written to disk, the StandardJobQueen asks the derived job queen what indices should be used to identify the soon-to-be-output Pose. The default behavior is to use the nstruct index for the primary output index, and if there are multiple result Poses from a job, to use the result index (as is) for the secondary output index. These values will already have been loaded into the output_index before this function is called. This function will possibly be invoked more than a single time for a single job result, so it is important that the derived JobQueen not assume that it only happens once. This function will only be called on JQ0; it will not be called on any other JQs, so it is welcome to use information that would only be known on the "head node"

Reimplemented from protocols::jd3::standard::StandardJobQueen.

Referenced by jobs_that_should_be_output().

void protocols::multistage_rosetta_scripts::MRSJobQueen::assign_output_index	(	jd3::GlobalJobID	global_job_id,
		jd3::ResultIndex	result_id,
		jd3::JobOutputIndex &	output_index
	)

protected

References max_num_results_to_keep_per_instance_for_stage_, protocols::jd3::JobOutputIndex::n_primary_outputs, protocols::jd3::JobOutputIndex::n_secondary_outputs, num_total_jobs_for_stage_, protocols::jd3::JobOutputIndex::primary_output_index, and protocols::jd3::JobOutputIndex::secondary_output_index.

void protocols::multistage_rosetta_scripts::MRSJobQueen::cluster ( jd3::JobDAGNodeID stage_about_to_start )

protected

References cluster_data_for_results_of_stage_, protocols::jd3::dag_node_managers::ResultElements::job_result_id(), protocols::multistage_rosetta_scripts::cluster::k_medoids_on_the_fly(), most_recent_cluster_results_, node_managers_, and num_results_to_keep_after_clustering_for_stage_.

Referenced by determine_job_list().

JobOP protocols::multistage_rosetta_scripts::MRSJobQueen::complete_larval_job_maturation	(	jd3::LarvalJobCOP	larval_job,
		utility::options::OptionCollectionCOP	job_options,
		utility::vector1< jd3::JobResultCOP > const &	input_job_results
	)

overridevirtual

The derived JobQueen must define the method that takes a larval job and the job-specific options and matures the larval job into a full job.

Implements protocols::jd3::standard::StandardJobQueen.

References cluster_metric_tag_for_stage_, protocols::jd3::JobQueen::create_and_set_initial_job_dag(), protocols::multistage_rosetta_scripts::TagManager::generate_data_for_input_pose_id(), protocols::jd3::standard::StandardJobQueen::get_preliminary_larval_jobs(), has_been_initialized_, max_num_results_to_keep_per_instance_for_stage_, protocols::jd3::standard::StandardJobQueen::options_for_job(), protocols::jd3::job_results::PoseJobResult::pose(), pose_for_inner_job_derived(), protocols::jd3::standard::StandardInnerLarvalJob::preliminary_job_node(), stage_for_global_job_id(), tag_for_stage_, and tag_manager_.

void protocols::multistage_rosetta_scripts::MRSJobQueen::completed_job_summary	(	jd3::GlobalJobID	job_id,
		jd3::ResultIndex	result_index,
		jd3::JobSummaryOP	summary
	)

References cluster_data_for_results_of_stage_, protocols::multistage_rosetta_scripts::MRSJobSummary::cluster_metric(), cluster_metric_tag_for_stage_, protocols::jd3::job_summaries::EnergyJobSummary::energy(), input_pose_id_for_jobid(), job_genealogist_, max_num_results_to_keep_per_input_struct_for_stage_, node_managers_, num_stages_, stage_for_global_job_id(), and protocols::TR().

Referenced by completed_job_summary().

void protocols::multistage_rosetta_scripts::MRSJobQueen::completed_job_summary	(	jd3::LarvalJobCOP	job,
		jd3::ResultIndex	result_index,
		jd3::JobSummaryOP	summary
	)

inlineoverridevirtual

As each job completes, this function is called for each result coming from a LarvalJob.

Override this method to store any results you need.

Reimplemented from protocols::jd3::standard::StandardJobQueen.

References completed_job_summary().

JobDigraphOP protocols::multistage_rosetta_scripts::MRSJobQueen::create_initial_job_dag ( )

overridevirtual

The job dag encodes which job nodes are independent or dependant on each other. If you have a applicationwhere all inputs are independant and only a single run of a protocol is needed, Then do not override this method.

The StandardJobQueen provides an implementation of this function which returns the most straight-forward DAG representing a set of jobs that have no interdependencies: a DAG with a single node and no edges.

Override this method if you have a need for any more job nodes other than what is created from input structures and the Job Definition file.

The base class provides a digraph with a single node – that is, all the jobs are independent of each other. This is equivalent to the kind of jobs that could be run in JD2.

Reimplemented from protocols::jd3::standard::StandardJobQueen.

Reimplemented in protocols::multistage_rosetta_scripts::MRSJobQueenChecker.

References protocols::jd3::standard::StandardJobQueen::determine_preliminary_job_list(), has_been_initialized_, and num_stages_.

Referenced by protocols::multistage_rosetta_scripts::MRSJobQueenChecker::create_initial_job_dag().

std::list< LarvalJobOP > protocols::multistage_rosetta_scripts::MRSJobQueen::determine_job_list	(	jd3::JobDAGNodeID	job_dag_node_index,
		Size	max_njobs
	)

overridevirtual

Create a list of LarvalJobs for each Node Index. Only can create max_njobs to save memory.

The StandardJobQueen manages the process of creating the list of LarvalJobs that will later be matured into actual jobs and run by the JobDistributor. It is not recommended that derived job queens override this method; doing so will mean that some of the data the SJQ relies on will not be initialized – see comments on the SJQs data members below to understand the consequences of overriding this method.

It is recommended to override next_batch_of_larval_jobs_for_job_node instead of this method However, if you do override this - especially for more complicated protocols - be sure to call similar functions here

The process begins by first constructing the job definition and resource definition XSDs. With these schemas, the StandardJobQueen validates the input XML files (if present). The StandardJobQueen then populates preliminary versions of LarvalJob objects./ If the XSD includes "command line options" (which may be specified either from the command line or in the <options> sections of the Job XML file), the StandardJobQueen loads the preliminary LarvalJob objects with the options. These preliminary LarvalJob objects will not have been nstruct expanded (i.e. if there are 100 nstruct for each of 5 different jobs, then there will only be 5 preliminary larval jobs created). It then passes the preliminary LarvalJob list and the TagOP objects for each preliminary LarvalJob to the derived class through the refine_job_list method.

Reimplemented from protocols::jd3::standard::StandardJobQueen.

Reimplemented in protocols::multistage_rosetta_scripts::MRSJobQueenChecker.

References cluster(), cluster_data_for_results_of_stage_, cluster_metric_tag_for_stage_, current_inner_larval_job_for_stage_, protocols::jd3::JobQueen::get_job_tracker(), get_nth_job_for_initial_stage(), get_nth_job_for_noninitial_stage(), protocols::jd3::JobTracker::increment_current_job_index(), node_managers_, num_jobs_per_input_for_stage_, num_total_jobs_for_stage_, and protocols::TR().

void protocols::multistage_rosetta_scripts::MRSJobQueen::determine_validity_of_stage_tags ( )

References protocols::multistage_rosetta_scripts::TagManager::generate_data_for_input_pose_id(), protocols::jd3::standard::StandardJobQueen::get_preliminary_larval_jobs(), protocols::filters::FilterFactory::newFilter(), protocols::moves::MoverFactory::newMover(), num_input_structs_, pose_for_inner_job_derived(), tag_for_stage_, tag_manager_, core::id::to_string(), and protocols::TR().

Referenced by protocols::multistage_rosetta_scripts::MRSJobQueenChecker::create_initial_job_dag().

LarvalJobOP protocols::multistage_rosetta_scripts::MRSJobQueen::get_nth_job_for_initial_stage ( jd3::LocalJobID local_job_id )

protected

References current_inner_larval_job_for_stage_, job_genealogist_, num_input_structs_, and num_jobs_per_input_for_stage_.

Referenced by determine_job_list().

LarvalJobOP protocols::multistage_rosetta_scripts::MRSJobQueen::get_nth_job_for_noninitial_stage	(	jd3::JobDAGNodeID	stage,
		jd3::LocalJobID	local_job_id
	)

protected

References cluster_metric_tag_for_stage_, current_inner_larval_job_for_stage_, input_pose_id_for_jobid(), job_genealogist_, most_recent_cluster_results_, node_managers_, and num_jobs_per_input_for_stage_.

Referenced by determine_job_list().

jd3::PrelimJobNodeID protocols::multistage_rosetta_scripts::MRSJobQueen::input_pose_id_for_jobid ( jd3::GlobalJobID global_jobid ) const

inlineprotected

References job_genealogist_, and stage_for_global_job_id().

Referenced by completed_job_summary(), and get_nth_job_for_noninitial_stage().

std::list< jd3::JobResultID > protocols::multistage_rosetta_scripts::MRSJobQueen::job_results_that_should_be_discarded ( )

overridevirtual

The IDs of jobs that should be discarded, IE not kept in memory for the next set of job nodes.

Override this method to note which jobs we don't need for the next set of Job Nodes.

Default implementation does not discard any job results.

Reimplemented from protocols::jd3::standard::StandardJobQueen.

References cluster_data_for_results_of_stage_, job_genealogist_, job_results_have_been_discarded_for_stage_, node_managers_, num_stages_, and pose_output_specification_for_job_result_id_.

static std::string protocols::multistage_rosetta_scripts::MRSJobQueen::job_subelement_mangler ( std::string const & name )

inlinestaticprotected

std::list< output::OutputSpecificationOP > protocols::multistage_rosetta_scripts::MRSJobQueen::jobs_that_should_be_output ( )

overridevirtual

By default outputs all recently finished jobs for JD output (stored in recent_successes_). Override this method if you want to cull these lists.

Reimplemented from protocols::jd3::standard::StandardJobQueen.

References assign_output_index(), node_managers_, num_input_structs_, num_structs_output_for_input_job_tag_, pose_output_specification_for_job_result_id_, and protocols::TR().

void protocols::multistage_rosetta_scripts::MRSJobQueen::note_job_completed	(	jd3::GlobalJobID	job_id,
		jd3::JobStatus	status,
		core::Size	nresults,
		bool	are_you_a_unit_test
	)

this was only created for the unit test. Please do not call this.

References protocols::jd3::jd3_job_status_success, job_genealogist_, node_managers_, and stage_for_global_job_id().

void protocols::multistage_rosetta_scripts::MRSJobQueen::note_job_completed	(	core::Size	,
		jd3::JobStatus	,
		core::Size
	)

inline

void protocols::multistage_rosetta_scripts::MRSJobQueen::note_job_completed	(	jd3::LarvalJobCOP	job,
		jd3::JobStatus	status,
		core::Size	nresults
	)

overridevirtual

The JD calls this function on completion of a LarvalJob, after updating the JobTracker.

If you override this method, call the SJQs version first for PJN tracking and output.

Prepare this job for output by building an OutputSpecification for it and storing this specification in the list of recent successes. Note that tracking of completion of jobs from preliminary job nodes can only occur if the DerivedJobQueen invoked the SJQ's version of next_batch_of_larval_jobs_from_prelim in its determine_job_list method.

Reimplemented from protocols::jd3::standard::StandardJobQueen.

References protocols::jd3::standard::StandardJobQueen::create_output_specification_for_job_result(), protocols::jd3::jd3_job_status_success, job_genealogist_, node_managers_, num_stages_, protocols::jd3::standard::StandardJobQueen::options_for_job(), pose_output_specification_for_job_result_id_, stage_for_global_job_id(), and protocols::TR().

core::Size protocols::multistage_rosetta_scripts::MRSJobQueen::num_input_structs ( ) const

inline

References num_input_structs_.

Referenced by protocols::multistage_rosetta_scripts::MRSJobQueenChecker::estimate_number_of_bytes_needed_for_archiving().

core::Size protocols::multistage_rosetta_scripts::MRSJobQueen::num_results_to_keep_for_stage ( core::Size stage ) const

inline

References num_results_to_keep_for_stage_.

Referenced by protocols::multistage_rosetta_scripts::MRSJobQueenChecker::estimate_number_of_bytes_needed_for_archiving().

core::Size protocols::multistage_rosetta_scripts::MRSJobQueen::num_stages ( ) const

inline

References num_stages_.

Referenced by protocols::multistage_rosetta_scripts::MRSJobQueenChecker::estimate_number_of_bytes_needed_for_archiving().

void protocols::multistage_rosetta_scripts::MRSJobQueen::parse_common_tag ( utility::tag::TagCOP common_tag )

protected

References checkpoints_, cluster_data_for_results_of_stage_, cluster_metric_tag_for_stage_, job_genealogist_, max_num_results_to_keep_per_input_struct_for_stage_, node_managers_, num_input_structs_, num_results_to_keep_after_clustering_for_stage_, num_results_to_keep_for_stage_, num_stages_, num_total_jobs_for_stage_, parse_single_stage_tag(), result_cutoffs_for_stage_, protocols::multistage_rosetta_scripts::TagManager::set_common_data_tags(), tag_manager_, and protocols::TR().

Referenced by parse_job_definition_tags().

void protocols::multistage_rosetta_scripts::MRSJobQueen::parse_job_definition_tags	(	utility::tag::TagCOP	,
		utility::vector1< jd3::standard::PreliminaryLarvalJob > const &
	)

overrideprotectedvirtual

This gives the derived JobQueen a chance to read any relevant information from the job-definition file. The second argument holds a PreliminaryLarvalJob for every job block and the PreliminaryLarvalJob itself has all of the information given in its corresponding block.

Author: Jack Maguire, jackm.nosp@m.agui.nosp@m.re144.nosp@m.4@gm.nosp@m.ail.c.nosp@m.om

Reimplemented from protocols::jd3::standard::StandardJobQueen.

References input_job_tags_, job_results_have_been_discarded_for_stage_, num_input_structs_, num_stages_, num_structs_output_for_input_job_tag_, outputters_, parse_common_tag(), parse_single_job_tag(), protocols::multistage_rosetta_scripts::TagManager::set_num_input_pose_ids(), and tag_manager_.

void protocols::multistage_rosetta_scripts::MRSJobQueen::parse_single_job_tag	(	jd3::standard::PreliminaryLarvalJob const &	prelim_larval_job,
		jd3::PrelimJobNodeID	input_pose_id
	)

protected

References protocols::jd3::standard::PreliminaryLarvalJob::job_tag, num_stages_, protocols::multistage_rosetta_scripts::TagManager::register_data_tags_for_input_pose_id(), tag_manager_, and protocols::TR().

Referenced by parse_job_definition_tags().

void protocols::multistage_rosetta_scripts::MRSJobQueen::parse_single_stage_tag ( utility::tag::TagCOP subprotocol_tag )

protected

References max_num_results_to_keep_per_input_struct_for_stage_, max_num_results_to_keep_per_instance_for_stage_, num_input_structs_, num_jobs_per_input_for_stage_, num_results_to_keep_for_stage_, num_stages_, num_total_jobs_for_stage_, result_cutoffs_for_stage_, and tag_for_stage_.

Referenced by parse_common_tag().

core::pose::PoseOP protocols::multistage_rosetta_scripts::MRSJobQueen::pose_for_inner_job_derived	(	jd3::InnerLarvalJobCOP	inner_job,
		utility::options::OptionCollection const &	options
	)

protected

References protocols::jd3::InputSource::input_tag(), most_recent_pose_id_, protocols::multistage_rosetta_scripts::PoseForPoseID::pose, protocols::multistage_rosetta_scripts::PoseForPoseID::pose_id, protocols::jd3::standard::StandardJobQueen::pose_inputter_for_job(), protocols::jd3::InputSource::source_id(), and protocols::TR().

Referenced by complete_larval_job_maturation(), determine_validity_of_stage_tags(), and pose_for_job_derived().

core::pose::PoseOP protocols::multistage_rosetta_scripts::MRSJobQueen::pose_for_job_derived	(	jd3::LarvalJobCOP	job,
		utility::options::OptionCollection const &	options
	)

protected

References pose_for_inner_job_derived().

void protocols::multistage_rosetta_scripts::MRSJobQueen::print_job_lineage ( ) const

protected

References job_genealogist_, and protocols::TR().

static std::string protocols::multistage_rosetta_scripts::MRSJobQueen::protocols_subelement_mangler ( std::string const & name )

inlinestaticprotected

Referenced by append_common_tag_subelements().

jd3::JobDAGNodeID protocols::multistage_rosetta_scripts::MRSJobQueen::stage_for_global_job_id ( jd3::GlobalJobID global_job_id ) const

inline

References node_managers_, and num_stages_.

Referenced by complete_larval_job_maturation(), completed_job_summary(), input_pose_id_for_jobid(), and note_job_completed().

TagManager const& protocols::multistage_rosetta_scripts::MRSJobQueen::tag_manager ( ) const

inline

References tag_manager_.

Member Data Documentation

utility::vector1< std::pair< core::Size, utility::tag::TagCOP > > protocols::multistage_rosetta_scripts::MRSJobQueen::checkpoints_

private

Referenced by parse_common_tag().

utility::vector1< std::unordered_map< jd3::JobResultID, cluster::ClusterMetricCOP, JobResultID_hash > > protocols::multistage_rosetta_scripts::MRSJobQueen::cluster_data_for_results_of_stage_

private

Referenced by cluster(), completed_job_summary(), determine_job_list(), job_results_that_should_be_discarded(), and parse_common_tag().

utility::vector1< utility::tag::TagCOP > protocols::multistage_rosetta_scripts::MRSJobQueen::cluster_metric_tag_for_stage_

private

Referenced by complete_larval_job_maturation(), completed_job_summary(), determine_job_list(), get_nth_job_for_noninitial_stage(), and parse_common_tag().

utility::vector1< std::pair< jd3::InnerLarvalJobOP, core::Size > > protocols::multistage_rosetta_scripts::MRSJobQueen::current_inner_larval_job_for_stage_

private

Referenced by determine_job_list(), get_nth_job_for_initial_stage(), and get_nth_job_for_noninitial_stage().

bool protocols::multistage_rosetta_scripts::MRSJobQueen::has_been_initialized_

private

Referenced by complete_larval_job_maturation(), and create_initial_job_dag().

utility::vector1< std::string > protocols::multistage_rosetta_scripts::MRSJobQueen::input_job_tags_

private

Referenced by parse_job_definition_tags().

jd3::JobGenealogistOP protocols::multistage_rosetta_scripts::MRSJobQueen::job_genealogist_

private

Referenced by completed_job_summary(), get_nth_job_for_initial_stage(), get_nth_job_for_noninitial_stage(), input_pose_id_for_jobid(), job_results_that_should_be_discarded(), note_job_completed(), parse_common_tag(), and print_job_lineage().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::job_results_have_been_discarded_for_stage_

private

Referenced by job_results_that_should_be_discarded(), and parse_job_definition_tags().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::max_num_results_to_keep_per_input_struct_for_stage_

private

Referenced by completed_job_summary(), parse_common_tag(), and parse_single_stage_tag().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::max_num_results_to_keep_per_instance_for_stage_

private

Referenced by assign_output_index(), complete_larval_job_maturation(), and parse_single_stage_tag().

utility::vector1< jd3::JobResultID > protocols::multistage_rosetta_scripts::MRSJobQueen::most_recent_cluster_results_

private

No need to store this data for more than one stage at a time.

Referenced by cluster(), and get_nth_job_for_noninitial_stage().

PoseForPoseID protocols::multistage_rosetta_scripts::MRSJobQueen::most_recent_pose_id_

private

Referenced by pose_for_inner_job_derived().

utility::vector1< jd3::dag_node_managers::NodeManagerOP > protocols::multistage_rosetta_scripts::MRSJobQueen::node_managers_

private

Referenced by cluster(), completed_job_summary(), determine_job_list(), get_nth_job_for_noninitial_stage(), job_results_that_should_be_discarded(), jobs_that_should_be_output(), note_job_completed(), parse_common_tag(), and stage_for_global_job_id().

core::Size protocols::multistage_rosetta_scripts::MRSJobQueen::num_input_structs_

private

Referenced by determine_validity_of_stage_tags(), get_nth_job_for_initial_stage(), jobs_that_should_be_output(), num_input_structs(), parse_common_tag(), parse_job_definition_tags(), and parse_single_stage_tag().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::num_jobs_per_input_for_stage_

private

Referenced by determine_job_list(), get_nth_job_for_initial_stage(), get_nth_job_for_noninitial_stage(), and parse_single_stage_tag().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::num_results_to_keep_after_clustering_for_stage_

private

Referenced by cluster(), and parse_common_tag().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::num_results_to_keep_for_stage_

private

Referenced by num_results_to_keep_for_stage(), parse_common_tag(), and parse_single_stage_tag().

core::Size protocols::multistage_rosetta_scripts::MRSJobQueen::num_stages_

private

Referenced by completed_job_summary(), create_initial_job_dag(), job_results_that_should_be_discarded(), note_job_completed(), num_stages(), parse_common_tag(), parse_job_definition_tags(), parse_single_job_tag(), parse_single_stage_tag(), and stage_for_global_job_id().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::num_structs_output_for_input_job_tag_

private

Referenced by jobs_that_should_be_output(), and parse_job_definition_tags().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::num_total_jobs_for_stage_

private

Referenced by assign_output_index(), determine_job_list(), parse_common_tag(), and parse_single_stage_tag().

utility::vector1< std::string > protocols::multistage_rosetta_scripts::MRSJobQueen::outputters_

private

Referenced by parse_job_definition_tags().

std::map< jd3::JobResultID, jd3::output::OutputSpecificationOP > protocols::multistage_rosetta_scripts::MRSJobQueen::pose_output_specification_for_job_result_id_

private

Referenced by job_results_that_should_be_discarded(), jobs_that_should_be_output(), and note_job_completed().

utility::vector1< core::Size > protocols::multistage_rosetta_scripts::MRSJobQueen::result_cutoffs_for_stage_

private

Referenced by parse_common_tag(), and parse_single_stage_tag().

SortByLowEnergy protocols::multistage_rosetta_scripts::MRSJobQueen::sorter_

private

utility::vector1< utility::tag::TagCOP > protocols::multistage_rosetta_scripts::MRSJobQueen::tag_for_stage_

private

Referenced by complete_larval_job_maturation(), determine_validity_of_stage_tags(), and parse_single_stage_tag().

TagManager protocols::multistage_rosetta_scripts::MRSJobQueen::tag_manager_

private