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...

#include <ArchiveBase.hh>

Inheritance diagram for protocols::jd2::archive::AbstractArchiveBase:

[legend]

Public Member Functions
virtual	~AbstractArchiveBase ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	AbstractArchiveBase (BaseArchiveManagerAP ptr)

	AbstractArchiveBase ()

virtual bool	finished () const =0
	is archive converged ? More...

virtual void	initialize ()=0

virtual bool	still_interested (jd2::archive::Batch const &) const
	old-batches might be outdated and should not be computed anymore return true for this query if this is the case for old_batch More...

virtual void	generate_batch ()=0
	create a new batch with manager().start_new_batch() and manager().finalize_batch(); More...

virtual core::Size	generate_batch (jd2::archive::Batch &, core::Size)
	create a batch for the current stage, return ct != 0 if more batches should be created at current stage. (e.g., harvest_batches) More...

virtual void	idle ()=0
	do some computations on archive that can be done while we are waiting More...

virtual void	read_structures (core::io::silent::SilentFileData &returned_decoys, core::io::silent::SilentFileData &alternative_decoys, Batch const &batch)=0
	read 'returned_decoys' from 'batch' into archive. More...

virtual void	save_to_file (std::string suffix="")=0
	save archive to file .. you can put 'suffix' at end of dirname to save other snapshots than the 'current' More...

virtual void	save_status (std::ostream &) const =0

virtual bool	restore_from_file ()=0
	restore archive More...

virtual void	init_from_decoy_set (core::io::silent::SilentFileData const &sfd)=0

void	set_name (std::string const &set)
	set name of archive ( used also for save_to_file and restore_from_file ) More...

std::string const &	name () const

BaseArchiveManager &	manager ()
	access to the ArchiveManager (control of batches) More...

virtual void	set_manager (BaseArchiveManagerAP manager)

Protected Member Functions
BaseArchiveManagerAP	manager_ptr ()

Private Attributes
BaseArchiveManagerAP	manager_

std::string	name_

Detailed Description

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.

This job distributor is meant for running jobs where the machine you are using has a large number of processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs could vary greatly. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.

Constructor & Destructor Documentation

protocols::jd2::archive::AbstractArchiveBase::~AbstractArchiveBase ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::jd2::archive::AbstractArchiveBase::AbstractArchiveBase ( BaseArchiveManagerAP ptr )

inline

protocols::jd2::archive::AbstractArchiveBase::AbstractArchiveBase ( )

inline

Member Function Documentation

virtual bool protocols::jd2::archive::AbstractArchiveBase::finished ( ) const

pure virtual

is archive converged ?

Implemented in protocols::jd2::archive::ArchiveBase, protocols::abinitio::IterativeBase, and protocols::abinitio::IterativeAbrelax.

virtual void protocols::jd2::archive::AbstractArchiveBase::generate_batch ( )

pure virtual

create a new batch with manager().start_new_batch() and manager().finalize_batch();

Implemented in protocols::jd2::archive::ArchiveBase, protocols::abinitio::IterativeBase, protocols::abinitio::IterativeAbrelax, protocols::abinitio::HedgeArchive, protocols::abinitio::IterativeFullatom, and protocols::jd2::archive::VarianceStatisticsArchive.

Referenced by protocols::jd2::archive::ArchiveManager::go().

virtual core::Size protocols::jd2::archive::AbstractArchiveBase::generate_batch	(	jd2::archive::Batch &	,
		core::Size
	)

inlinevirtual

create a batch for the current stage, return ct != 0 if more batches should be created at current stage. (e.g., harvest_batches)

Reimplemented in protocols::abinitio::IterativeBase, protocols::abinitio::IterativeAbrelax, and protocols::abinitio::IterativeFullatom.

virtual void protocols::jd2::archive::AbstractArchiveBase::idle ( )

pure virtual

do some computations on archive that can be done while we are waiting

Implemented in protocols::jd2::archive::ArchiveBase, protocols::abinitio::IterativeBase, and protocols::abinitio::IterativeAbrelax.

Referenced by protocols::jd2::archive::ArchiveManager::idle().

virtual void protocols::jd2::archive::AbstractArchiveBase::init_from_decoy_set ( core::io::silent::SilentFileData const & sfd )

pure virtual

Implemented in protocols::jd2::archive::ArchiveBase, protocols::jd2::archive::EvaluatedArchive, protocols::abinitio::IterativeBase, protocols::abinitio::IterativeAbrelax, protocols::abinitio::HedgeArchive, and protocols::jd2::archive::VarianceStatisticsArchive.

Referenced by protocols::jd2::archive::ArchiveManager::go().

virtual void protocols::jd2::archive::AbstractArchiveBase::initialize ( )

pure virtual

Implemented in protocols::jd2::archive::ArchiveBase, protocols::abinitio::IterativeBase, protocols::jd2::archive::NormalizedEvaluatedArchive, protocols::abinitio::IterativeAbrelax, and protocols::abinitio::IterativeFullatom.

BaseArchiveManager& protocols::jd2::archive::AbstractArchiveBase::manager ( )

inline

access to the ArchiveManager (control of batches)

References manager_.

Referenced by protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), protocols::abinitio::IterativeBase::generate_batch(), protocols::abinitio::IterativeBase::increment_stage(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::abinitio::IterativeBase::rescore_nonlocal_archive(), and set_manager().

BaseArchiveManagerAP protocols::jd2::archive::AbstractArchiveBase::manager_ptr ( )

inlineprotected

References manager_.

Referenced by protocols::abinitio::IterativeBase::increment_stage().

std::string const& protocols::jd2::archive::AbstractArchiveBase::name ( ) const

inline

References name_.

virtual void protocols::jd2::archive::AbstractArchiveBase::read_structures	(	core::io::silent::SilentFileData &	returned_decoys,
		core::io::silent::SilentFileData &	alternative_decoys,
		Batch const &	batch
	)

pure virtual

read 'returned_decoys' from 'batch' into archive.

Implemented in protocols::jd2::archive::ArchiveBase, protocols::abinitio::IterativeBase, protocols::jd2::archive::EvaluatedArchive, and protocols::abinitio::IterativeAbrelax.

Referenced by protocols::jd2::archive::BaseArchiveManager::read_returning_decoys().

virtual bool protocols::jd2::archive::AbstractArchiveBase::restore_from_file ( )

pure virtual

restore archive

Implemented in protocols::jd2::archive::ArchiveBase, protocols::jd2::archive::EvaluatedArchive, protocols::jd2::archive::NormalizedEvaluatedArchive, protocols::abinitio::IterativeAbrelax, and protocols::abinitio::IterativeCentroid.

Referenced by protocols::jd2::archive::ArchiveManager::restore_archive().

virtual void protocols::jd2::archive::AbstractArchiveBase::save_status ( std::ostream & ) const

pure virtual

Implemented in protocols::jd2::archive::ArchiveBase, protocols::abinitio::IterativeBase, protocols::abinitio::IterativeAbrelax, and protocols::abinitio::HedgeArchive.

Referenced by protocols::jd2::archive::ArchiveManager::go().

virtual void protocols::jd2::archive::AbstractArchiveBase::save_to_file ( std::string suffix = "" )

pure virtual

save archive to file .. you can put 'suffix' at end of dirname to save other snapshots than the 'current'

Implemented in protocols::jd2::archive::EvaluatedArchive, protocols::jd2::archive::ArchiveBase, protocols::jd2::archive::NormalizedEvaluatedArchive, protocols::abinitio::IterativeAbrelax, and protocols::abinitio::IterativeCentroid.

Referenced by protocols::jd2::archive::ArchiveManager::save_archive().

virtual void protocols::jd2::archive::AbstractArchiveBase::set_manager ( BaseArchiveManagerAP manager )

inlinevirtual

Reimplemented in protocols::abinitio::IterativeAbrelax.

References manager(), and manager_.

Referenced by protocols::abinitio::IterativeAbrelax::set_manager().

void protocols::jd2::archive::AbstractArchiveBase::set_name ( std::string const & set )

inline

set name of archive ( used also for save_to_file and restore_from_file )

References name_.

Referenced by protocols::abinitio::HedgeArchive::HedgeArchive(), protocols::abinitio::IterativeBase::IterativeBase(), and protocols::jd2::archive::VarianceStatisticsArchive::VarianceStatisticsArchive().

virtual bool protocols::jd2::archive::AbstractArchiveBase::still_interested ( jd2::archive::Batch const & ) const

inlinevirtual

old-batches might be outdated and should not be computed anymore return true for this query if this is the case for old_batch

Reimplemented in protocols::abinitio::IterativeBase, and protocols::abinitio::IterativeAbrelax.

Referenced by protocols::jd2::archive::ArchiveBase::count_structure(), protocols::jd2::archive::BaseArchiveManager::finalize_batch(), and protocols::abinitio::IterativeBase::still_interested().

Member Data Documentation

BaseArchiveManagerAP protocols::jd2::archive::AbstractArchiveBase::manager_

private

Referenced by manager(), manager_ptr(), and set_manager().

std::string protocols::jd2::archive::AbstractArchiveBase::name_

private

Referenced by name(), and set_name().

The documentation for this class was generated from the following files:

src/protocols/jd2/archive/ArchiveBase.hh
src/protocols/jd2/archive/ArchiveBase.cc

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation