protocols::jd2 Namespace Reference

Namespaces
	archive
	JobInputterInputSource
	parser

Classes
class	AtomTreeDiffJobInputter
class	AtomTreeDiffJobInputterCreator
class	AtomTreeDiffJobOutputter
class	AtomTreeDiffJobOutputterCreator
class	BatchJobInputter
class	BOINCJobDistributor
class	CompareTags
class	DebugOut_MpiFileBuffer
class	FileJobOutputter
class	FileSystemJobDistributor
class	InnerJob
class	InnerMultiThreadingJob
class	JD2ResourceManager
	The JD2ResourceManager is the ResourceManager that should be used when running protocols under the jd2 JobDistributor. More...
class	JD2ResourceManagerCreator
	The JD2ResourceManagerCreator is responsible for instantiating the JD2ResourceManager for the ResourceManagerFactory. More...
class	JD2ResourceManagerJobInputter
	The JD2ResourceManagerJobInputter works with the JobDistributor to define the set of jobs that are to be executed. It reads the list of jobs and the set of resouces they require from one or more XML files. More...
class	JD2ResourceManagerJobInputterCreator
	the JD2ResourceManagerJobInputterCreator is responsible for instantiating the JD2ResourceManagerJobInputter for the JobDistributorFactory More...
class	Job
class	JobDistributor
class	JobDistributorFactory
class	JobInputter
class	JobInputterCreator
	Abstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class. More...
class	JobInputterFactory
class	JobInputterRegistrator
	This templated class will register an instance of an JobInputterCreator (class T) with the JobInputterFactory. It will ensure that no JobInputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	JobOutputter
class	JobOutputterCreator
	Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class. More...
class	JobOutputterFactory
class	JobOutputterObserver
class	JobOutputterRegistrator
	This templated class will register an instance of an JobOutputterCreator (class T) with the JobOutputterFactory. It will ensure that no JobOutputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	JobsContainer
class	LargeNstructJobInputter
class	LargeNstructJobInputterCreator
class	LazySilentFileJobInputter
class	LazySilentFileJobInputterCreator
class	MpiFileBuffer
class	MPIFileBufJobDistributor
class	MPIMultiCommJobDistributor
class	MPIWorkPartitionJobDistributor
class	MPIWorkPoolJobDistributor
class	MSDJobDistributor
class	MultiThreadingJob
class	NoOutputJobOutputter
class	NoOutputJobOutputterCreator
class	Parser
class	PDBJobInputter
class	PDBJobInputterCreator
class	PDBJobOutputter
class	PDBJobOutputterCreator
class	PoseInputStreamJobInputter
class	PoseInputStreamJobInputterCreator
class	ScoreMap
class	ScoreOnlyJobOutputter
class	ScoreOnlyJobOutputterCreator
class	ScreeningJobInputter
class	ScreeningJobInputterCreator
class	ShuffleFileSystemJobDistributor
class	SilentFileJobInputter
class	SilentFileJobInputterCreator
class	SilentFileJobOutputter
class	SilentFileJobOutputterCreator
class	SingleFileBuffer
class	WriteFileSFB
class	WriteOut_MpiFileBuffer

Typedefs
typedef utility::pointer::shared_ptr < GenericJobInputter >	GenericJobInputterOP
typedef utility::pointer::shared_ptr < AtomTreeDiffJobInputter >	AtomTreeDiffJobInputterOP
typedef utility::pointer::shared_ptr < AtomTreeDiffJobOutputter >	AtomTreeDiffJobOutputterOP
typedef utility::pointer::shared_ptr < AtomTreeDiffJobOutputter const >	AtomTreeDiffJobOutputterCOP
typedef utility::pointer::shared_ptr < BatchJobInputter >	BatchJobInputterOP
typedef utility::pointer::shared_ptr < FileJobOutputter >	FileJobOutputterOP
typedef utility::pointer::shared_ptr < InnerJob >	InnerJobOP
typedef utility::pointer::shared_ptr < InnerJob const >	InnerJobCOP
typedef utility::pointer::shared_ptr < InnerMultiThreadingJob >	InnerMultiThreadingJobOP
typedef utility::pointer::shared_ptr < InnerMultiThreadingJob const >	InnerMultiThreadingJobCOP
typedef utility::pointer::shared_ptr < Job >	JobOP
typedef utility::pointer::shared_ptr < Job const >	JobCOP
typedef utility::vector1< JobOP >	Jobs
typedef utility::pointer::weak_ptr < JobInputter >	JobInputterAP
typedef utility::pointer::weak_ptr < JobInputter const >	JobInputterCAP
typedef utility::pointer::shared_ptr < JobInputter >	JobInputterOP
typedef utility::pointer::shared_ptr < JobInputter const >	JobInputterCOP
typedef utility::pointer::shared_ptr < JobInputterCreator >	JobInputterCreatorOP
typedef utility::pointer::shared_ptr < JobInputterCreator const >	JobInputterCreatorCOP
typedef utility::pointer::shared_ptr < JobInputterFactory >	JobInputterFactoryOP
typedef utility::pointer::shared_ptr < JobInputterFactory const >	JobInputterFactoryCOP
typedef utility::pointer::shared_ptr < JobOutputter >	JobOutputterOP
typedef utility::pointer::shared_ptr < JobOutputter const >	JobOutputterCOP
typedef utility::pointer::shared_ptr < JobOutputterCreator >	JobOutputterCreatorOP
typedef utility::pointer::shared_ptr < JobOutputterCreator const >	JobOutputterCreatorCOP
typedef utility::pointer::shared_ptr < JobOutputterFactory >	JobOutputterFactoryOP
typedef utility::pointer::shared_ptr < JobOutputterFactory const >	JobOutputterFactoryCOP
typedef utility::pointer::weak_ptr < JobOutputterObserver const >	JobOutputterObserverAP
typedef utility::pointer::shared_ptr < JobOutputterObserver const >	JobOutputterObserverOP
typedef utility::pointer::shared_ptr < JobsContainer >	JobsContainerOP
typedef utility::pointer::shared_ptr < JobsContainer const >	JobsContainerCOP
typedef utility::pointer::weak_ptr < LargeNstructJobInputter >	LargeNstructJobInputterAP
typedef utility::pointer::weak_ptr < LargeNstructJobInputter const >	LargeNstructJobInputterCAP
typedef utility::pointer::shared_ptr < LargeNstructJobInputter >	LargeNstructJobInputterOP
typedef utility::pointer::shared_ptr < LargeNstructJobInputter const >	LargeNstructJobInputterCOP
typedef utility::pointer::owning_ptr < LazySilentFileJobInputter >	LazySilentFileJobInputterOP
typedef utility::pointer::shared_ptr < MpiFileBuffer >	MpiFileBufferOP
typedef utility::pointer::shared_ptr < MpiFileBuffer const >	MpiFileBufferCOP
typedef utility::pointer::shared_ptr < MSDJobDistributor >	MSDJobDistributorOP
typedef utility::pointer::shared_ptr < MSDJobDistributor const >	MSDJobDistributorCOP
typedef utility::pointer::shared_ptr < MTJob >	MTJobOP
typedef utility::pointer::shared_ptr < MTJob const >	MTJobCOP
typedef utility::pointer::shared_ptr < MTJobGroup >	MTJobGroupOP
typedef utility::pointer::shared_ptr < MTJobGroup const >	MTJobGroupCOP
typedef utility::pointer::shared_ptr < RunningJob >	RunningJobOP
typedef utility::pointer::shared_ptr < RunningJob const >	RunningJobCOP
typedef utility::pointer::shared_ptr < MultiThreadingJob >	MultiThreadingJobOP
typedef utility::pointer::shared_ptr < MultiThreadingJob const >	MultiThreadingJobCOP
typedef utility::pointer::shared_ptr < Parser >	ParserOP
typedef utility::pointer::shared_ptr < Parser const >	ParserCOP
typedef utility::pointer::shared_ptr < PDBJobInputter >	PDBJobInputterOP
typedef utility::pointer::shared_ptr < PDBJobOutputter >	PDBJobOutputterOP
typedef utility::pointer::shared_ptr < PoseInputStreamJobInputter >	PoseInputStreamJobInputterOP
typedef utility::pointer::shared_ptr < ScreeningJobInputter >	ScreeningJobInputterOP
typedef utility::pointer::shared_ptr < SilentFileJobInputter >	SilentFileJobInputterOP
typedef utility::pointer::shared_ptr < SilentFileJobOutputter >	SilentFileJobOutputterOP
typedef utility::pointer::shared_ptr < SingleFileBuffer >	SingleFileBufferOP
typedef utility::pointer::shared_ptr < SingleFileBuffer const >	SingleFileBufferCOP

Enumerations
enum	mpi_tags {   NEW_JOB_ID_TAG = 10, BAD_INPUT_TAG = 20, JOB_SUCCESS_TAG = 30, JOB_FAILURE_TAG = 40,   REQUEST_MESSAGE_TAG = 50, RECEIVE_MESSAGE_TAG = 60, JOB_GO_TAG = 70 }
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...

Functions
core::Size	get_min_nstruct_index_checkpoint_file ()
bool	operator== (InnerJob const &a, InnerJob const &b)
bool	operator!= (InnerJob const &a, InnerJob const &b)
std::ostream &	operator<< (std::ostream &out, const InnerJob &inner_job)
static thread_local basic::Tracer	tr ("protocols.jd2.JD2ResourceManagerJobInputter")
JobCOP const	JD2_BOGUS_JOB (JobOP(new Job(InnerJobOP(new InnerJob("EMPTY_JOB_use_jd2", 0)), 0)))
bool	operator== (Job const &a, Job const &b)
bool	operator!= (Job const &a, Job const &b)
std::ostream &	operator<< (std::ostream &out, const Job &job)
static thread_local basic::Tracer	tr ("protocols.jd2.JobDistributor")
static thread_local basic::Tracer	TR ("protocols.jd2.JobInputterFactory")
static thread_local basic::Tracer	TR ("protocols.jd2.JobOutputterFactory")
static thread_local basic::Tracer	tr ("protocols.jd2.MpiFileBuffer")
Size const	MPI_CLOSE_FILE (1004)
core::Size const	MPI_JOB_DIST_TAG (1542)
	this tag is used for all communication with JobDistributor ( use this tag to be received in the main MSG-loop of jd2 cf. process_message() ) More...
static thread_local basic::Tracer	TR ("protocols.jd2.ScreeningJobInputter")
static thread_local basic::Tracer	tr ("protocols.jd2.MpiFileBuffer")
std::string const	START_BLOCK ("MPI_FILE_BUFFER_BLOCK_START")
std::string const	END_BLOCK ("MPI_FILE_BUFFER_BLOCK_END")
void	register_options ()
static thread_local basic::Tracer	TR ("protocols.jd2.JobDistributor")
void	output_intermediate_pose (core::pose::Pose const &pose, std::string const &stage_tag, int copy_count, bool score_only)
	end parser interface, start Job Distributor interface///////////// More...
std::string	current_output_name ()
	gets used output name of pose ask jd for current-job —> ask jobOutputter for name of this job More...
std::string	current_batch ()
bool	jd2_used ()
	is this application running with jd2 — used for some code that yields backward compatability with old JobDistributor More...
std::string	current_output_filename ()
	call the 'filename' accessor of the current job-distributor with the current job More...
void	write_score_tracer (core::pose::Pose const &pose_in, std::string tracer_point)
JobOP	get_current_job ()
core::pose::PoseCOP	get_current_jobs_starting_pose ()
void	add_job_data_to_ss (core::io::silent::SilentStructOP ss, JobCOP job_op)
void	set_native_in_mover (protocols::moves::Mover &mover)
core::Size	current_replica ()
	returns 0 if no replicas (i.e., multiple processes per job ) otherwise it returns the sub-rank of the process within the job starting at 1 More...

Variables
static Tracer	TR ("protocols.resource_manager.planner.JD2ResourceManager")
JobCOP const	JD2_BOGUS_JOB
core::Size const	NEW_JOB_ID = 1
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...
core::Size const	BAD_INPUT = 2
core::Size const	JOB_SUCCESS = 3
core::Size const	JOB_FAILED_NO_RETRY = 4
static basic::Tracer	TR ("protocols.jd2.MSDJobDistributor")

Typedef Documentation

typedef utility::pointer::shared_ptr< AtomTreeDiffJobInputter > protocols::jd2::AtomTreeDiffJobInputterOP

typedef utility::pointer::shared_ptr< AtomTreeDiffJobOutputter const > protocols::jd2::AtomTreeDiffJobOutputterCOP

typedef utility::pointer::shared_ptr< AtomTreeDiffJobOutputter > protocols::jd2::AtomTreeDiffJobOutputterOP

typedef utility::pointer::shared_ptr< BatchJobInputter > protocols::jd2::BatchJobInputterOP

typedef utility::pointer::shared_ptr< FileJobOutputter > protocols::jd2::FileJobOutputterOP

typedef utility::pointer::shared_ptr< GenericJobInputter > protocols::jd2::GenericJobInputterOP

typedef utility::pointer::shared_ptr< InnerJob const > protocols::jd2::InnerJobCOP

typedef utility::pointer::shared_ptr< InnerJob > protocols::jd2::InnerJobOP

typedef utility::pointer::shared_ptr< InnerMultiThreadingJob const > protocols::jd2::InnerMultiThreadingJobCOP

typedef utility::pointer::shared_ptr< InnerMultiThreadingJob > protocols::jd2::InnerMultiThreadingJobOP

typedef utility::pointer::shared_ptr< Job const > protocols::jd2::JobCOP

typedef utility::pointer::weak_ptr< JobInputter > protocols::jd2::JobInputterAP

typedef utility::pointer::weak_ptr< JobInputter const > protocols::jd2::JobInputterCAP

typedef utility::pointer::shared_ptr< JobInputter const > protocols::jd2::JobInputterCOP

typedef utility::pointer::shared_ptr< JobInputterCreator const > protocols::jd2::JobInputterCreatorCOP

typedef utility::pointer::shared_ptr< JobInputterCreator > protocols::jd2::JobInputterCreatorOP

typedef utility::pointer::shared_ptr< JobInputterFactory const > protocols::jd2::JobInputterFactoryCOP

typedef utility::pointer::shared_ptr< JobInputterFactory > protocols::jd2::JobInputterFactoryOP

typedef utility::pointer::shared_ptr< JobInputter > protocols::jd2::JobInputterOP

typedef utility::pointer::shared_ptr< Job > protocols::jd2::JobOP

typedef utility::pointer::shared_ptr< JobOutputter const > protocols::jd2::JobOutputterCOP

typedef utility::pointer::shared_ptr< JobOutputterCreator const > protocols::jd2::JobOutputterCreatorCOP

typedef utility::pointer::shared_ptr< JobOutputterCreator > protocols::jd2::JobOutputterCreatorOP

typedef utility::pointer::shared_ptr< JobOutputterFactory const > protocols::jd2::JobOutputterFactoryCOP

typedef utility::pointer::shared_ptr< JobOutputterFactory > protocols::jd2::JobOutputterFactoryOP

typedef utility::pointer::weak_ptr< JobOutputterObserver const > protocols::jd2::JobOutputterObserverAP

typedef utility::pointer::shared_ptr< JobOutputterObserver const > protocols::jd2::JobOutputterObserverOP

typedef utility::pointer::shared_ptr< JobOutputter > protocols::jd2::JobOutputterOP

typedef utility::vector1< JobOP > protocols::jd2::Jobs

typedef utility::pointer::shared_ptr< JobsContainer const > protocols::jd2::JobsContainerCOP

typedef utility::pointer::shared_ptr< JobsContainer > protocols::jd2::JobsContainerOP

typedef utility::pointer::weak_ptr< LargeNstructJobInputter > protocols::jd2::LargeNstructJobInputterAP

typedef utility::pointer::weak_ptr< LargeNstructJobInputter const > protocols::jd2::LargeNstructJobInputterCAP

typedef utility::pointer::shared_ptr< LargeNstructJobInputter const > protocols::jd2::LargeNstructJobInputterCOP

typedef utility::pointer::shared_ptr< LargeNstructJobInputter > protocols::jd2::LargeNstructJobInputterOP

typedef utility::pointer::owning_ptr< LazySilentFileJobInputter > protocols::jd2::LazySilentFileJobInputterOP

typedef utility::pointer::shared_ptr< MpiFileBuffer const > protocols::jd2::MpiFileBufferCOP

typedef utility::pointer::shared_ptr< MpiFileBuffer > protocols::jd2::MpiFileBufferOP

typedef utility::pointer::shared_ptr< MSDJobDistributor const > protocols::jd2::MSDJobDistributorCOP

typedef utility::pointer::shared_ptr< MSDJobDistributor > protocols::jd2::MSDJobDistributorOP

typedef utility::pointer::shared_ptr< MTJob const > protocols::jd2::MTJobCOP

typedef utility::pointer::shared_ptr< MTJobGroup const > protocols::jd2::MTJobGroupCOP

typedef utility::pointer::shared_ptr< MTJobGroup > protocols::jd2::MTJobGroupOP

typedef utility::pointer::shared_ptr< MTJob > protocols::jd2::MTJobOP

typedef utility::pointer::shared_ptr< MultiThreadingJob const > protocols::jd2::MultiThreadingJobCOP

typedef utility::pointer::shared_ptr< MultiThreadingJob > protocols::jd2::MultiThreadingJobOP

typedef utility::pointer::shared_ptr< Parser const > protocols::jd2::ParserCOP

typedef utility::pointer::shared_ptr< Parser > protocols::jd2::ParserOP

typedef utility::pointer::shared_ptr< PDBJobInputter > protocols::jd2::PDBJobInputterOP

typedef utility::pointer::shared_ptr< PDBJobOutputter > protocols::jd2::PDBJobOutputterOP

typedef utility::pointer::shared_ptr< PoseInputStreamJobInputter > protocols::jd2::PoseInputStreamJobInputterOP

typedef utility::pointer::shared_ptr< RunningJob const > protocols::jd2::RunningJobCOP

typedef utility::pointer::shared_ptr< RunningJob > protocols::jd2::RunningJobOP

typedef utility::pointer::shared_ptr< ScreeningJobInputter > protocols::jd2::ScreeningJobInputterOP

typedef utility::pointer::shared_ptr< SilentFileJobInputter > protocols::jd2::SilentFileJobInputterOP

typedef utility::pointer::shared_ptr< SilentFileJobOutputter > protocols::jd2::SilentFileJobOutputterOP

typedef utility::pointer::shared_ptr< SingleFileBuffer const > protocols::jd2::SingleFileBufferCOP

typedef utility::pointer::shared_ptr< SingleFileBuffer > protocols::jd2::SingleFileBufferOP

Enumeration Type Documentation

enum protocols::jd2::mpi_tags

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

Enumerator
NEW_JOB_ID_TAG
BAD_INPUT_TAG
JOB_SUCCESS_TAG
JOB_FAILURE_TAG
REQUEST_MESSAGE_TAG
RECEIVE_MESSAGE_TAG
JOB_GO_TAG

Function Documentation

void protocols::jd2::add_job_data_to_ss	(	core::io::silent::SilentStructOP	ss,
		JobCOP	job_op
	)

References end.

Referenced by protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint(), and write_score_tracer().

std::string protocols::jd2::current_batch

(

)

References protocols::jd2::JobDistributor::get_current_batch(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::abinitio::AbrelaxMover::apply().

std::string protocols::jd2::current_output_filename

(

)

call the 'filename' accessor of the current job-distributor with the current job

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::job_outputter().

Referenced by protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), and protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint().

std::string protocols::jd2::current_output_name

(

)

gets used output name of pose ask jd for current-job —> ask jobOutputter for name of this job

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::job_outputter().

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::simple_filters::DdGScan::ddG_for_single_residue(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add(), protocols::protein_interface_design::filters::FilterScanFilter::FilterScanFilter(), protocols::canonical_sampling::BiasEnergy::finalize_simulation(), protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), protocols::relax::RelaxProtocolBase::output_debug_structure(), protocols::canonical_sampling::MetropolisHastingsMover::prepare_simulation(), protocols::simple_filters::print_nmer_svm_energy_data(), protocols::rotamer_recovery::RRReporterSQLite::report_predicted_features(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), and protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint().

core::Size protocols::jd2::current_replica

(

)

returns 0 if no replicas (i.e., multiple processes per job ) otherwise it returns the sub-rank of the process within the job starting at 1

References protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::MPIMultiCommJobDistributor::sub_rank().

Referenced by protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), protocols::canonical_sampling::MetropolisHastingsMover::output_file_name(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

std::string const protocols::jd2::END_BLOCK

(

"MPI_FILE_BUFFER_BLOCK_END"

)

JobOP protocols::jd2::get_current_job

(

)

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::job_inputter().

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::simple_filters::ConstraintScoreCutoffFilter::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::abinitio::KinematicTaskControl::apply(), protocols::canonical_sampling::TemperingBase::initialize_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and write_score_tracer().

core::pose::PoseCOP protocols::jd2::get_current_jobs_starting_pose

(

)

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::job_inputter(), and protocols::jd2::JobDistributor::job_outputter().

Referenced by protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::simple_filters::SelectGdtEvaluator::apply(), protocols::simple_filters::LoopRmsdEvaluator::apply(), protocols::toolbox::task_operations::JointSequenceOperation::parse_def(), and protocols::toolbox::task_operations::JointSequenceOperation::parse_tag().

core::Size protocols::jd2::get_min_nstruct_index_checkpoint_file

(

)

References begin, end, getline(), option, and user.

Referenced by protocols::jd2::FileSystemJobDistributor::get_new_job_id().

JobCOP const protocols::jd2::JD2_BOGUS_JOB

(

JobOP(new Job(InnerJobOP(new InnerJob("EMPTY_JOB_use_jd2", 0)), 0))

)

bool protocols::jd2::jd2_used

(

)

is this application running with jd2 — used for some code that yields backward compatability with old JobDistributor

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), JD2_BOGUS_JOB, and protocols::jd2::JobDistributor::job_outputter().

Referenced by protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::rosetta_scripts::ParsedProtocol::apply(), protocols::helical_bundle::BackboneGridSampler::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::helical_bundle::BundleGridSampler::apply(), protocols::simple_filters::SelectGdtEvaluator::apply(), protocols::simple_filters::LoopRmsdEvaluator::apply(), protocols::canonical_sampling::TemperingBase::initialize_simulation(), protocols::canonical_sampling::BiasEnergy::initialize_simulation(), protocols::analysis::PeptideDeriverPoseOutputter::output_pose(), protocols::canonical_sampling::SilentTrajectoryRecorder::parse_my_tag(), protocols::simple_filters::print_nmer_svm_energy_data(), protocols::analysis::PeptideDeriverFilter::report(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and protocols::canonical_sampling::BiasEnergy::~BiasEnergy().

Size const protocols::jd2::MPI_CLOSE_FILE

(

1004

)

Referenced by protocols::jd2::MpiFileBuffer::remote_close_file(), and protocols::jd2::MpiFileBuffer::run().

core::Size const protocols::jd2::MPI_JOB_DIST_TAG

(

1542

)

this tag is used for all communication with JobDistributor ( use this tag to be received in the main MSG-loop of jd2 cf. process_message() )

Referenced by protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::jd2::MPIFileBufJobDistributor::eat_signal(), protocols::jd2::MPIFileBufJobDistributor::master_go(), protocols::jd2::archive::ArchiveManager::queue_batch(), protocols::jd2::archive::MPIArchiveJobDistributor::receive_batch(), protocols::jd2::MPIFileBufJobDistributor::send_job_to_slave(), protocols::jd2::MPIFileBufJobDistributor::slave_to_master(), and protocols::jd2::archive::MPIArchiveJobDistributor::sync_batches().

bool protocols::jd2::operator!=	(	InnerJob const &	a,
		InnerJob const &	b
	)

References protocols::match::upstream::b.

bool protocols::jd2::operator!=	(	Job const &	a,
		Job const &	b
	)

References protocols::match::upstream::b.

std::ostream& protocols::jd2::operator<<	(	std::ostream &	out,
		const InnerJob &	inner_job
	)

References protocols::jd2::InnerJob::show().

std::ostream& protocols::jd2::operator<<	(	std::ostream &	out,
		const Job &	job
	)

References protocols::jd2::Job::show().

bool protocols::jd2::operator==	(	InnerJob const &	a,
		InnerJob const &	b
	)

Only compare the pointer value of the pose the inner job is referencing.

References protocols::jd2::InnerJob::bad_, protocols::jd2::InnerJob::input_tag_, protocols::jd2::InnerJob::nstruct_max_, and protocols::jd2::InnerJob::pose_.

bool protocols::jd2::operator==	(	Job const &	a,
		Job const &	b
	)

References protocols::jd2::Job::can_be_deleted_, protocols::jd2::Job::completed_, protocols::jd2::Job::inner_job_, protocols::jd2::Job::long_strings_, protocols::jd2::Job::nstruct_index_, protocols::jd2::Job::status_prefix_, protocols::jd2::Job::string_real_pairs_, and protocols::jd2::Job::string_string_pairs_.

void protocols::jd2::output_intermediate_pose	(	core::pose::Pose const &	pose,
		std::string const &	stage_tag,
		int	copy_count,
		bool	score_only
	)

end parser interface, start Job Distributor interface/////////////

writes pose to intermediate-scorefile using current Job and JobOutputter .. copy count is used if multiple poses with same job-tag are written as for instance into a trajectory. -1 indicates no copy count >=0 copy_count will be attached as zerofilled postfix to job-tag

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

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::FragmentSampler::apply(), protocols::abinitio::abscript::AbscriptMover::StageTracker::begin_stage(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::abinitio::FragmentSampler::do_stage1_cycles(), protocols::abinitio::FragmentSampler::do_stage2_cycles(), protocols::abinitio::FragmentSampler::do_stage3_cycles(), protocols::abinitio::FragmentSampler::do_stage4_cycles(), and protocols::abinitio::abscript::AbscriptMover::StageTracker::end_stage().

void protocols::jd2::register_options

(

)

References OPT, and protocols::evaluation::register_options().

void protocols::jd2::set_native_in_mover

(

protocols::moves::Mover &

mover

)

References option, core::import_pose::pose_from_pdb(), protocols::moves::Mover::set_native_pose(), and user.

Referenced by protocols::cryst::TagPoseWithRefinementStatsMover::apply(), and protocols::relax::Relax_main().

std::string const protocols::jd2::START_BLOCK

(

"MPI_FILE_BUFFER_BLOCK_START"

)

this is a implementation of Buffer for silent-file-based output.

static thread_local basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  )

static

static thread_local basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  )

static

static thread_local basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobOutputterFactory"  )

static

static thread_local basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobInputterFactory"  )

static

static thread_local basic::Tracer protocols::jd2::TR ( "protocols.jd2.ScreeningJobInputter"  )

static

static thread_local basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobDistributor"  )

static

static thread_local basic::Tracer protocols::jd2::tr ( "protocols.jd2.JobDistributor"  )

static

static thread_local basic::Tracer protocols::jd2::tr ( "protocols.jd2.JD2ResourceManagerJobInputter"  )

static

Referenced by protocols::jd2::archive::MPIArchiveJobDistributor::_notify_archive(), protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::jd2::archive::EvaluatedArchive::add_structure(), protocols::jd2::AtomTreeDiffJobInputter::AtomTreeDiffJobInputter(), protocols::jd2::archive::MPIArchiveJobDistributor::batch_underflow(), protocols::jd2::BatchJobInputter::BatchJobInputter(), protocols::jd2::SingleFileBuffer::block(), protocols::jd2::WriteFileSFB::block(), protocols::jd2::MpiFileBuffer::block_file(), protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::jd2::JobDistributor::check_for_parser_in_go_main(), protocols::jd2::JD2ResourceManagerJobInputter::cleanup_after_job_completion(), protocols::jd2::MpiFileBuffer::clear_channel_from_garbage_collector(), protocols::jd2::SingleFileBuffer::close(), protocols::jd2::MpiFileBuffer::close_channel(), protocols::jd2::MpiFileBuffer::close_file(), protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations(), protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::jd2::MPIFileBufJobDistributor::eat_signal(), protocols::jd2::archive::EvaluatedArchive::evaluate_pose(), protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(), protocols::jd2::LazySilentFileJobInputter::fill_jobs(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::jd2::LargeNstructJobInputter::fill_jobs(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), protocols::jd2::SilentFileJobInputter::fill_jobs(), protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs(), protocols::jd2::archive::BaseArchiveManager::finalize_batch(), protocols::jd2::MpiFileBuffer::flush_channel(), protocols::jd2::MpiFileBuffer::garbage_collection(), protocols::jd2::JobDistributor::get_job_time_estimate(), protocols::jd2::MPIFileBufJobDistributor::go(), protocols::jd2::archive::MPIArchiveJobDistributor::go(), protocols::jd2::archive::ArchiveManager::go(), protocols::jd2::JobDistributor::go_main(), protocols::jd2::archive::ArchiveManager::idle(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::jd2::JobDistributor::init_jd(), protocols::jd2::archive::ArchiveManager::jobs_completed(), protocols::jd2::LargeNstructJobInputter::LargeNstructJobInputter(), protocols::jd2::LazySilentFileJobInputter::LazySilentFileJobInputter(), protocols::jd2::JobDistributor::load_new_batch(), protocols::jd2::archive::MPIArchiveJobDistributor::mark_job_as_completed(), protocols::jd2::JobDistributor::mark_job_as_completed(), protocols::jd2::MPIFileBufJobDistributor::master_get_new_job_id(), protocols::jd2::MPIFileBufJobDistributor::master_go(), protocols::jd2::MPIFileBufJobDistributor::master_job_succeeded(), protocols::jd2::MPIFileBufJobDistributor::master_mark_current_job_id_for_repetition(), protocols::jd2::MPIFileBufJobDistributor::master_remove_bad_inputs_from_job_list(), protocols::jd2::JobDistributor::next_batch(), protocols::jd2::archive::MPIArchiveJobDistributor::notify_archive(), protocols::jd2::JD2ResourceManagerJobInputter::parse_jobs_table_tag(), protocols::jd2::LazySilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::pose_from_job(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::PoseInputStreamJobInputter(), protocols::jd2::MPIFileBufJobDistributor::process_message(), protocols::jd2::archive::MPIArchiveJobDistributor::process_message(), protocols::jd2::archive::ArchiveManager::queue_batch(), protocols::jd2::JD2ResourceManagerJobInputter::read_Data_for_subtag(), protocols::jd2::archive::ArchiveManager::read_existing_batches(), protocols::jd2::archive::BaseArchiveManager::read_returning_decoys(), protocols::jd2::archive::EvaluatedArchive::read_structures(), protocols::jd2::archive::ArchiveBase::read_structures(), protocols::jd2::archive::MPIArchiveJobDistributor::receive_batch(), protocols::jd2::MpiFileBuffer::release_file(), protocols::jd2::MpiFileBuffer::remote_close_file(), protocols::jd2::archive::EvaluatedArchive::remove_evaluation(), protocols::jd2::archive::EvaluatedArchive::rescore(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::jd2::MpiFileBuffer::run(), protocols::jd2::JobDistributor::run_one_job(), protocols::jd2::archive::ArchiveBase::save_to_file(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations(), protocols::jd2::archive::EvaluatedArchive::select_score(), protocols::jd2::MPIFileBufJobDistributor::send_job_to_slave(), protocols::jd2::archive::ArchiveManager::send_stop_to_jobdistributor(), protocols::jd2::JobDistributor::set_batch_id(), protocols::jd2::SilentFileJobOutputter::set_defaults(), protocols::jd2::archive::EvaluatedArchive::set_weight(), protocols::jd2::JobDistributor::setup_pymol_observer(), protocols::jd2::MPIMultiCommJobDistributor::setup_sub_communicators(), protocols::jd2::SilentFileJobInputter::SilentFileJobInputter(), protocols::jd2::MPIFileBufJobDistributor::slave_get_new_job_id(), protocols::jd2::MPIFileBufJobDistributor::slave_mark_current_job_id_for_repetition(), protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer(), protocols::jd2::archive::BaseArchiveManager::start_new_batch(), protocols::jd2::MpiFileBuffer::store_to_channel(), protocols::jd2::archive::MPIArchiveJobDistributor::sync_batches(), protocols::jd2::archive::ArchiveManager::unlock_file(), protocols::jd2::LargeNstructJobInputter::update_jobs_list(), protocols::jd2::SilentFileJobOutputter::write_all_structs(), protocols::jd2::archive::Batch::write_info_file(), protocols::jd2::WriteFileSFB::write_lines(), protocols::jd2::JobDistributor::write_output_from_job(), protocols::jd2::WriteFileSFB::WriteFileSFB(), and protocols::jd2::WriteFileSFB::~WriteFileSFB().

void protocols::jd2::write_score_tracer	(	core::pose::Pose const &	pose_in,
		std::string	tracer_point
	)

References add_job_data_to_ss(), get_current_job(), protocols::jd2::JobDistributor::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), protocols::jd2::JobDistributor::job_outputter(), basic::options::option, basic::t_info, and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::docking::DockMCMProtocol::apply(), and protocols::docking::DockingProtocol::apply().

Variable Documentation

core::Size const protocols::jd2::BAD_INPUT = 2

Referenced by protocols::jd2::MPIFileBufJobDistributor::process_message(), and protocols::jd2::MPIFileBufJobDistributor::slave_remove_bad_inputs_from_job_list().

JobCOP const protocols::jd2::JD2_BOGUS_JOB

Referenced by protocols::helical_bundle::BackboneGridSampler::apply(), protocols::helical_bundle::BundleGridSampler::apply(), jd2_used(), protocols::jd2::JobDistributor::load_new_batch(), and protocols::jd2::JobDistributor::restart().

core::Size const protocols::jd2::JOB_FAILED_NO_RETRY = 4

Referenced by protocols::jd2::MPIFileBufJobDistributor::job_failed(), and protocols::jd2::MPIFileBufJobDistributor::process_message().

core::Size const protocols::jd2::JOB_SUCCESS = 3

Referenced by protocols::jd2::MPIFileBufJobDistributor::process_message(), and protocols::jd2::MPIFileBufJobDistributor::slave_job_succeeded().

core::Size const protocols::jd2::NEW_JOB_ID = 1

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

Referenced by protocols::jd2::MPIFileBufJobDistributor::process_message(), and protocols::jd2::MPIFileBufJobDistributor::slave_get_new_job_id().

basic::Tracer protocols::jd2::TR("protocols.jd2.MSDJobDistributor")

static

Tracer protocols::jd2::TR("protocols.resource_manager.planner.JD2ResourceManager")

static

Referenced by protocols::jd2::MSDJobDistributor::apply_parsed_protocol(), protocols::jd2::AtomTreeDiffJobOutputter::dump_pose(), protocols::jd2::FileJobOutputter::file(), protocols::jd2::ScreeningJobInputter::fill_jobs(), protocols::jd2::PDBJobInputter::fill_jobs(), protocols::jd2::PDBJobOutputter::final_pose(), protocols::jd2::JobInputterFactory::get_JobInputter_from_string(), protocols::jd2::JobOutputterFactory::get_JobOutputter_from_string(), protocols::jd2::ShuffleFileSystemJobDistributor::get_new_job_id(), protocols::jd2::MSDJobDistributor::go(), protocols::jd2::MPIWorkPoolJobDistributor::job_failed(), protocols::jd2::FileSystemJobDistributor::mark_current_job_id_for_repetition(), protocols::jd2::MPIWorkPoolJobDistributor::master_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::master_go(), protocols::jd2::MPIWorkPoolJobDistributor::master_job_succeeded(), protocols::jd2::MPIWorkPoolJobDistributor::master_mark_current_job_id_for_repetition(), protocols::jd2::MPIWorkPoolJobDistributor::master_mark_job_as_completed(), protocols::jd2::MPIWorkPoolJobDistributor::master_mark_job_as_failed(), protocols::jd2::MPIWorkPoolJobDistributor::master_remove_bad_inputs_from_job_list(), protocols::jd2::MPIWorkPartitionJobDistributor::MPIWorkPartitionJobDistributor(), protocols::jd2::JobsContainer::operator[](), protocols::jd2::PDBJobOutputter::other_pose(), output_intermediate_pose(), protocols::jd2::PDBJobInputter::PDBJobInputter(), protocols::jd2::PDBJobOutputter::PDBJobOutputter(), protocols::jd2::ScreeningJobInputter::pose_from_job(), protocols::jd2::PDBJobInputter::pose_from_job(), protocols::jd2::JD2ResourceManager::read_resource_options_table_tag(), protocols::jd2::JD2ResourceManager::read_resource_table_tag(), protocols::jd2::FileSystemJobDistributor::remove_bad_inputs_from_job_list(), protocols::jd2::MPIWorkPartitionJobDistributor::remove_bad_inputs_from_job_list(), protocols::jd2::FileJobOutputter::scorefile(), protocols::jd2::FileJobOutputter::set_defaults(), protocols::jd2::MPIWorkPoolJobDistributor::slave_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::slave_job_succeeded(), and protocols::jd2::MPIWorkPoolJobDistributor::slave_mark_current_job_id_for_repetition().