protocols::jd2 Namespace Reference

Namespaces
	archive
	JobInputterInputSource
	parser

Classes
class	AtomTreeDiffJobInputter
class	AtomTreeDiffJobInputterCreator
class	AtomTreeDiffJobOutputter
class	AtomTreeDiffJobOutputterCreator
class	BatchJobInputter
class	BOINCJobDistributor
class	DockDesignParser
	Reading the xml file and generating the mover. More...
class	FileJobOutputter
class	FileSystemJobDistributor
class	InnerJob
class	InnerMultiThreadingJob
class	JD2ResourceManager
class	JD2ResourceManagerCreator
class	JD2ResourceManagerJobInputter
class	JD2ResourceManagerJobInputterCreator
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	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	JobInputterFactory
class	JobOutputter
class	JobOutputterCreator
	Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class. More...
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	JobOutputterFactory
class	LazySilentFileJobInputter
class	LazySilentFileJobInputterCreator
class	MpiFileBuffer
class	WriteOut_MpiFileBuffer
class	DebugOut_MpiFileBuffer
class	MPIFileBufJobDistributor
class	MPIMultiCommJobDistributor
class	MPIWorkPartitionJobDistributor
class	MPIWorkPoolJobDistributor
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	ShuffleFileSystemJobDistributor
class	SilentFileJobInputter
class	SilentFileJobInputterCreator
class	SilentFileJobOutputter
class	CompareTags
class	SilentFileJobOutputterCreator
class	SingleFileBuffer
class	WriteFileSFB

Typedefs
typedef utility::pointer::owning_ptr < GenericJobInputter >	GenericJobInputterOP
typedef utility::pointer::owning_ptr < AtomTreeDiffJobInputter >	AtomTreeDiffJobInputterOP
typedef utility::pointer::owning_ptr < AtomTreeDiffJobOutputter >	AtomTreeDiffJobOutputterOP
typedef utility::pointer::owning_ptr < AtomTreeDiffJobOutputter const >	AtomTreeDiffJobOutputterCOP
typedef utility::pointer::owning_ptr < BatchJobInputter >	BatchJobInputterOP
typedef utility::tag::TagPtr	TagPtr
typedef utility::vector0< TagPtr >	TagPtrs
typedef utility::pointer::owning_ptr < FileJobOutputter >	FileJobOutputterOP
typedef utility::pointer::owning_ptr < InnerJob >	InnerJobOP
typedef utility::pointer::owning_ptr < InnerJob const >	InnerJobCOP
typedef utility::pointer::owning_ptr < InnerMultiThreadingJob >	InnerMultiThreadingJobOP
typedef utility::pointer::owning_ptr < InnerMultiThreadingJob const >	InnerMultiThreadingJobCOP
typedef utility::pointer::owning_ptr < Job >	JobOP
typedef utility::pointer::owning_ptr < Job const >	JobCOP
typedef utility::vector1< JobOP >	Jobs
typedef utility::pointer::access_ptr < JobInputter >	JobInputterAP
typedef utility::pointer::access_ptr < JobInputter const >	JobInputterCAP
typedef utility::pointer::owning_ptr < JobInputter >	JobInputterOP
typedef utility::pointer::owning_ptr < JobInputter const >	JobInputterCOP
typedef utility::pointer::owning_ptr < JobInputterCreator >	JobInputterCreatorOP
typedef utility::pointer::owning_ptr < JobInputterCreator const >	JobInputterCreatorCOP
typedef utility::pointer::owning_ptr < JobInputterFactory >	JobInputterFactoryOP
typedef utility::pointer::owning_ptr < JobInputterFactory const >	JobInputterFactoryCOP
typedef utility::pointer::owning_ptr < JobOutputter >	JobOutputterOP
typedef utility::pointer::owning_ptr < JobOutputter const >	JobOutputterCOP
typedef utility::pointer::owning_ptr < JobOutputterCreator >	JobOutputterCreatorOP
typedef utility::pointer::owning_ptr < JobOutputterCreator const >	JobOutputterCreatorCOP
typedef utility::pointer::owning_ptr < JobOutputterFactory >	JobOutputterFactoryOP
typedef utility::pointer::owning_ptr < JobOutputterFactory const >	JobOutputterFactoryCOP
typedef utility::pointer::owning_ptr < LazySilentFileJobInputter >	LazySilentFileJobInputterOP
typedef utility::pointer::owning_ptr < MpiFileBuffer >	MpiFileBufferOP
typedef utility::pointer::owning_ptr < MpiFileBuffer const >	MpiFileBufferCOP
typedef utility::pointer::owning_ptr < MultiThreadingJob >	MultiThreadingJobOP
typedef utility::pointer::owning_ptr < MultiThreadingJob const >	MultiThreadingJobCOP
typedef utility::pointer::owning_ptr < Parser >	ParserOP
typedef utility::pointer::owning_ptr < Parser const >	ParserCOP
typedef utility::pointer::owning_ptr < PDBJobInputter >	PDBJobInputterOP
typedef utility::pointer::owning_ptr < PDBJobOutputter >	PDBJobOutputterOP
typedef utility::pointer::owning_ptr < PoseInputStreamJobInputter >	PoseInputStreamJobInputterOP
typedef utility::pointer::owning_ptr < SilentFileJobInputter >	SilentFileJobInputterOP
typedef utility::pointer::owning_ptr < SilentFileJobOutputter >	SilentFileJobOutputterOP
typedef utility::pointer::owning_ptr < SingleFileBuffer >	SingleFileBufferOP
typedef utility::pointer::owning_ptr < SingleFileBuffer const >	SingleFileBufferCOP

Enumerations
enum	mpi_tags {   NEW_JOB_ID_TAG = 10, BAD_INPUT_TAG = 20, JOB_SUCCESS_TAG = 30, REQUEST_MESSAGE_TAG = 40,   RECEIVE_MESSAGE_TAG = 50 }
	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
static basic::Tracer	TR ("protocols.jd2.DockDesignParser")
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 Tracer	TR ("protocols.resource_manager.planner.JD2ResourceManager")
static basic::Tracer	tr ("protocols.jd2.JD2ResourceManagerJobInputter")
JobOP const	JD2_BOGUS_JOB (new Job((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 basic::Tracer	tr ("protocols.jd2.JobDistributor")
static basic::Tracer	TR ("protocols.jd2.JobInputterFactory")
static basic::Tracer	TR ("protocols.jd2.JobOutputterFactory")
static basic::Tracer	tr ("protocols.jd2.MpiFileBuffer")
Size const	MPI_WIND_DOWN (1001)
Size const	MPI_BLOCK_FILE (1002)
Size const	MPI_RELEASE_FILE (1003)
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 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 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
JobOP 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

Typedef Documentation

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

Definition at line 22 of file AtomTreeDiffJobInputter.fwd.hh.

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

Definition at line 24 of file AtomTreeDiffJobOutputter.fwd.hh.

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

Definition at line 22 of file AtomTreeDiffJobOutputter.fwd.hh.

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

Definition at line 22 of file BatchJobInputter.fwd.hh.

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

Definition at line 22 of file FileJobOutputter.fwd.hh.

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

Definition at line 22 of file GenericJobInputter.fwd.hh.

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

Definition at line 25 of file InnerJob.fwd.hh.

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

Definition at line 23 of file InnerJob.fwd.hh.

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

Definition at line 24 of file InnerMultiThreadingJob.fwd.hh.

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

Definition at line 22 of file InnerMultiThreadingJob.fwd.hh.

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

Definition at line 32 of file Job.fwd.hh.

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

Definition at line 23 of file JobInputter.fwd.hh.

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

Definition at line 25 of file JobInputter.fwd.hh.

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

Definition at line 27 of file JobInputter.fwd.hh.

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

Definition at line 42 of file JobInputterCreator.hh.

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

Definition at line 41 of file JobInputterCreator.hh.

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

Definition at line 25 of file JobInputterFactory.fwd.hh.

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

Definition at line 22 of file JobInputterFactory.fwd.hh.

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

Definition at line 26 of file JobInputter.fwd.hh.

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

Definition at line 30 of file Job.fwd.hh.

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

Definition at line 24 of file JobOutputter.fwd.hh.

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

Definition at line 42 of file JobOutputterCreator.hh.

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

Definition at line 41 of file JobOutputterCreator.hh.

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

Definition at line 25 of file JobOutputterFactory.fwd.hh.

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

Definition at line 22 of file JobOutputterFactory.fwd.hh.

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

Definition at line 22 of file JobOutputter.fwd.hh.

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

Definition at line 34 of file Job.fwd.hh.

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

Definition at line 22 of file LazySilentFileJobInputter.fwd.hh.

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

Definition at line 25 of file MpiFileBuffer.fwd.hh.

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

Definition at line 23 of file MpiFileBuffer.fwd.hh.

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

Definition at line 24 of file MultiThreadingJob.fwd.hh.

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

Definition at line 22 of file MultiThreadingJob.fwd.hh.

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

Definition at line 24 of file Parser.fwd.hh.

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

Definition at line 22 of file Parser.fwd.hh.

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

Definition at line 22 of file PDBJobInputter.fwd.hh.

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

Definition at line 22 of file PDBJobOutputter.fwd.hh.

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

Definition at line 22 of file PoseInputStreamJobInputter.fwd.hh.

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

Definition at line 22 of file SilentFileJobInputter.fwd.hh.

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

Definition at line 22 of file SilentFileJobOutputter.fwd.hh.

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

Definition at line 26 of file SingleFileBuffer.fwd.hh.

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

Definition at line 24 of file SingleFileBuffer.fwd.hh.

typedef utility::tag::TagPtr protocols::jd2::TagPtr

Definition at line 107 of file DockDesignParser.cc.

typedef utility::vector0< TagPtr > protocols::jd2::TagPtrs

Definition at line 108 of file DockDesignParser.cc.

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
REQUEST_MESSAGE_TAG
RECEIVE_MESSAGE_TAG

Definition at line 72 of file MPIWorkPoolJobDistributor.hh.

Function Documentation

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

Definition at line 188 of file util.cc.

References core::sequence::end.

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

std::string protocols::jd2::current_batch

(

)

Definition at line 106 of file util.cc.

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

Definition at line 120 of file util.cc.

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

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation().

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

Definition at line 98 of file util.cc.

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::abinitio::AbrelaxMover::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add(), protocols::protein_interface_design::filters::FilterScanFilter::FilterScanFilter(), OPT_1GRP_KEY(), protocols::relax::RelaxProtocolBase::output_debug_structure(), protocols::canonical_sampling::MetropolisHastingsMover::prepare_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), and protocols::canonical_sampling::SimulatedTempering::temperature_move().

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

Definition at line 249 of file util.cc.

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

Referenced by protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::canonical_sampling::MetropolisHastingsMover::output_file_name(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), 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

(

)

Definition at line 166 of file util.cc.

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::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::simple_filters::ConstraintScoreCutoffFilter::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(), and write_score_tracer().

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

(

)

Definition at line 175 of file util.cc.

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().

JobOP const protocols::jd2::JD2_BOGUS_JOB

(

new

Job(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

Definition at line 114 of file util.cc.

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

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::simple_filters::SelectGdtEvaluator::apply(), protocols::simple_filters::LoopRmsdEvaluator::apply(), protocols::canonical_sampling::TemperingBase::initialize_simulation(), and protocols::canonical_sampling::SilentTrajectoryRecorder::write_model().

Size const protocols::jd2::MPI_BLOCK_FILE

(

1002

)

Referenced by protocols::jd2::MpiFileBuffer::run().

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().

Size const protocols::jd2::MPI_RELEASE_FILE

(

1003

)

Referenced by protocols::jd2::MpiFileBuffer::release_file().

Size const protocols::jd2::MPI_WIND_DOWN

(

1001

)

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

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

Definition at line 84 of file InnerJob.cc.

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

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

Definition at line 186 of file Job.cc.

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

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

Definition at line 109 of file InnerJob.cc.

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

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

Definition at line 239 of file Job.cc.

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.

Definition at line 71 of file InnerJob.cc.

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
	)

Definition at line 170 of file Job.cc.

References 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

Definition at line 83 of file util.cc.

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::FragmentSampler::checkpointed_cycle_block(), protocols::abinitio::FragmentSampler::do_stage1_cycles(), and protocols::canonical_sampling::SilentTrajectoryRecorder::write_model().

void protocols::jd2::register_options

(

)

Definition at line 64 of file util.cc.

References protocols::evaluation::register_options().

void protocols::jd2::set_native_in_mover

(

protocols::moves::Mover &

mover)

Definition at line 209 of file util.cc.

References core::chemical::ChemicalManager::get_instance(), core::import_pose::pose_from_pdb(), core::chemical::ChemicalManager::residue_type_set(), and protocols::moves::Mover::set_native_pose().

Referenced by 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 basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobInputterFactory"  )

static

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

static

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

static

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

static

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

static

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

static

static 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::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::JD2ResourceManagerJobInputter::fill_jobs(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), protocols::jd2::SilentFileJobInputter::fill_jobs(), protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::jd2::MpiFileBuffer::flush_channel(), protocols::jd2::MpiFileBuffer::garbage_collection(), protocols::jd2::archive::DebugArchive::generate_batch(), 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::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::JD2ResourceManagerJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::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::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::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::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::ArchiveManager::start_new_batch(), protocols::jd2::MpiFileBuffer::store_to_channel(), protocols::jd2::archive::MPIArchiveJobDistributor::sync_batches(), protocols::jd2::SilentFileJobOutputter::write_all_structs(), protocols::jd2::archive::Batch::write_info_file(), protocols::jd2::WriteFileSFB::write_lines(), protocols::jd2::WriteFileSFB::WriteFileSFB(), and protocols::jd2::WriteFileSFB::~WriteFileSFB().

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

static

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.DockDesignParser"  )

static

Referenced by protocols::jd2::AtomTreeDiffJobOutputter::dump_pose(), protocols::jd2::FileJobOutputter::file(), protocols::jd2::FileJobOutputter::FileJobOutputter(), 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::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_remove_bad_inputs_from_job_list(), protocols::jd2::MPIWorkPartitionJobDistributor::MPIWorkPartitionJobDistributor(), protocols::jd2::PDBJobOutputter::other_pose(), output_intermediate_pose(), protocols::jd2::PDBJobInputter::PDBJobInputter(), protocols::jd2::PDBJobOutputter::PDBJobOutputter(), protocols::jd2::PDBJobInputter::pose_from_job(), protocols::jd2::FileSystemJobDistributor::remove_bad_inputs_from_job_list(), protocols::jd2::MPIWorkPartitionJobDistributor::remove_bad_inputs_from_job_list(), protocols::jd2::FileJobOutputter::scorefile(), 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().

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

Definition at line 132 of file util.cc.

References add_job_data_to_ss(), get_current_job(), core::io::silent::SilentStructFactory::get_instance(), protocols::jd2::JobDistributor::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), protocols::jd2::JobDistributor::job_outputter(), 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

Definition at line 47 of file MPIFileBufJobDistributor.hh.

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

JobOP const protocols::jd2::JD2_BOGUS_JOB

Referenced by jd2_used(), protocols::jd2::JobDistributor::load_new_batch(), and protocols::jd2::JobDistributor::restart().

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

Definition at line 49 of file MPIFileBufJobDistributor.hh.

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

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

Definition at line 48 of file MPIFileBufJobDistributor.hh.

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.

Definition at line 46 of file MPIFileBufJobDistributor.hh.

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