Distributor for use with silent files. More...

#include <JobDistributors.hh>

Inheritance diagram for protocols::jobdist::PlainSilentFileJobDistributor:

Public Types
typedef BaseJobDistributor	parent

Public Member Functions
	PlainSilentFileJobDistributor (JobVector jobs)

	~PlainSilentFileJobDistributor () override

virtual void	dump_pose (BasicJobOP const &job, int const &nstruct, bool const &fullatom, core::pose::Pose &pose)
	Writes pose and basic score data to a standard silent file. More...

void	dump_silent (int const &struct_n, core::io::silent::SilentStruct &silent_struct)
	Writes the silent_struct to a silen file. More...

void	dump_silent (core::io::silent::SilentFileData const &silent_file)

virtual std::string	get_output_tag (BasicJobOP const &job, int const &struct_n) const

std::string	get_current_output_tag () override

std::string	get_output_filename () override

void	startup () override
	Must be called by client before first call to next_job(). If overriden by a subclass, it MUST call the superclass implementation. More...

void	shutdown () override
	Must be called by client after last call to next_job(). If overriden by a subclass, it MUST call the superclass implementation. More...

Public Member Functions inherited from protocols::jobdist::BaseJobDistributor
	BaseJobDistributor (JobVector const &jobs)

	BaseJobDistributor (BaseJobDistributor const &)

	~BaseJobDistributor () override

bool	next_job (BasicJobOP &job, int &struct_n)
	If true, sets the next Job and nstruct number to be processed. Deliberately not virtual: should not be overriden. Uses the "find_available_job" method, which is common to both MPI and standard protocols, but used in slightly different manners. More...

virtual void	begin_critical_section ()
	Signal that if at all possible, we would like to not be killed while in the critical section. If overriden by a subclass, it MUST call the superclass implementation. More...

virtual void	end_critical_section ()
	Signal that if at all possible, we would like to not be killed while in the critical section. If overriden by a subclass, it MUST call the superclass implementation. More...

virtual void	dump_pose_and_map (std::string const &, core::pose::Pose &)
	Virtual function for dump_pose that is needed for main_plain_mover. More...

virtual void	temp_file (std::string const &)
	Virtual function for temp_file main_plain_mover. More...

virtual void	score_map (std::map< std::string, core::Real > &)
	Virtual function for score_map that is needed for main_plain_mover sets the score_map. More...

void	disable_ignorefinished ()

void	enable_ignorefinished ()

void	disable_output ()

void	enable_output ()

void	disable_inprogress ()

void	enable_inprogress ()

bool	ignorefinished () const

bool	nooutput () const

bool	inprogress () const

void	set_proc_id (core::Size proc_id, core::Size nproc)

Protected Types
typedef utility::vector1 < BasicJobOP >	JobVector

Protected Types inherited from protocols::jobdist::BaseJobDistributor
typedef utility::vector1 < BasicJobOP >	JobVector

Protected Member Functions
bool	is_finished (BasicJobOP const &job, int struct_n) override
	Is the given nstruct number of the given input job already finished by the local process? To be implemented by subclasses. More...

Protected Member Functions inherited from protocols::jobdist::BaseJobDistributor
virtual void	checkpoint_read ()
	Restore state from checkpoint file, if it exists. More...

virtual void	checkpoint_write ()
	Save state to checkpoint file, overwriting previous. More...

virtual void	checkpoint_clear ()
	Remove checkpoint file (at end of batch) More...

int	current_nstruct ()
	accessor for current_nstruct_ More...

BasicJobOP	current_job ()
	accessor for current_job owning pointer More...

int	get_next_random_range (int low, int high)

Private Attributes
utility::vector1< std::string >	used_tags_

Additional Inherited Members
Protected Attributes inherited from protocols::jobdist::BaseJobDistributor
bool	ignorefinished_
	ignore already done jobs - redo everything ! More...

bool	nooutput_
	do not write files - useful such things as statistics or rescoring ! More...

bool	inprogress_
	write .in_progress files for multiple processor runs More...

int	start_time_
	starttime More...

int	random_counter_
	RandomStore - needed for. More...

utility::vector1< core::Real >	random_store_

Detailed Description

Distributor for use with silent files.

This class is deliberately designed for each process to work on its own silent file (and preferrably in its own directory); unlike Rosetta++, we DO NOT share silent files among multiple processes. First, true atomic file locking is impossible on most distributed file systems (e.g. NFS), meaning that files may be corrupted by multiple simultaneous writes. For long-running processes, collisions may be rare, but as we scale to more processors it becomes increasingly dangerous. Second, many processes writing to the same file (or even directory) can cause tremendous file system bottlenecks, possibly bringing down the cluster; ask Keith or Chance in the Baker lab for details.

Member Typedef Documentation

typedef utility::vector1< BasicJobOP > protocols::jobdist::PlainSilentFileJobDistributor::JobVector

protected

typedef BaseJobDistributor protocols::jobdist::PlainSilentFileJobDistributor::parent

Constructor & Destructor Documentation

protocols::jobdist::PlainSilentFileJobDistributor::PlainSilentFileJobDistributor ( JobVector jobs )

protocols::jobdist::PlainSilentFileJobDistributor::~PlainSilentFileJobDistributor ( )

overridedefault

Member Function Documentation

void protocols::jobdist::PlainSilentFileJobDistributor::dump_pose	(	BasicJobOP const &	job,
		int const &	nstruct,
		bool const &	fullatom,
		core::pose::Pose &	pose
	)

virtual

Writes pose and basic score data to a standard silent file.

References protocols::jobdist::BaseJobDistributor::begin_critical_section(), protocols::jobdist::BaseJobDistributor::end_critical_section(), get_output_filename(), get_output_tag(), and protocols::jobdist::BaseJobDistributor::nooutput().

void protocols::jobdist::PlainSilentFileJobDistributor::dump_silent	(	int const &	struct_n,
		core::io::silent::SilentStruct &	silent_struct
	)

Writes the silent_struct to a silen file.

References protocols::jobdist::BaseJobDistributor::begin_critical_section(), protocols::jobdist::BaseJobDistributor::end_critical_section(), and get_output_filename().

Referenced by protocols::jobdist::universal_main().

void protocols::jobdist::PlainSilentFileJobDistributor::dump_silent ( core::io::silent::SilentFileData const & silent_file )

References protocols::jobdist::BaseJobDistributor::begin_critical_section(), protocols::jobdist::BaseJobDistributor::end_critical_section(), get_output_filename(), and core::io::silent::SilentFileData::write_all().

std::string protocols::jobdist::PlainSilentFileJobDistributor::get_current_output_tag ( )

overridevirtual

override base class function to

Reimplemented from protocols::jobdist::BaseJobDistributor.

References protocols::jobdist::BaseJobDistributor::current_job(), protocols::jobdist::BaseJobDistributor::current_nstruct(), and get_output_tag().

std::string protocols::jobdist::PlainSilentFileJobDistributor::get_output_filename ( )

overridevirtual

Reimplemented from protocols::jobdist::BaseJobDistributor.

References protocols::wum::mpi_rank(), and core::id::to_string().

Referenced by dump_pose(), dump_silent(), and startup().

std::string protocols::jobdist::PlainSilentFileJobDistributor::get_output_tag	(	BasicJobOP const &	job,
		int const &	struct_n
	)		const

virtual

returns an output tag generated as follows "S_" + the current jobs tag + "option[ user_tag ]" + nstruct

References TAG_NUM_FORMAT_LENGTH.

Referenced by dump_pose(), get_current_output_tag(), and is_finished().

bool protocols::jobdist::PlainSilentFileJobDistributor::is_finished	(	BasicJobOP const &	job,
		int	struct_n
	)

overrideprotectedvirtual

Is the given nstruct number of the given input job already finished by the local process? To be implemented by subclasses.

Implements protocols::jobdist::BaseJobDistributor.

References get_output_tag(), and used_tags_.

void protocols::jobdist::PlainSilentFileJobDistributor::shutdown ( )

overridevirtual

Must be called by client after last call to next_job(). If overriden by a subclass, it MUST call the superclass implementation.

If overriden by a subclass, it MUST call the superclass implementation.

Reimplemented from protocols::jobdist::BaseJobDistributor.

References core::io::silent::gzip(), and protocols::jobdist::BaseJobDistributor::shutdown().

void protocols::jobdist::PlainSilentFileJobDistributor::startup ( )

overridevirtual

Must be called by client before first call to next_job(). If overriden by a subclass, it MUST call the superclass implementation.

If overriden by a subclass, it MUST call the superclass implementation.

Reimplemented from protocols::jobdist::BaseJobDistributor.

References get_output_filename(), core::io::silent::SilentFileData::read_tags_fast(), protocols::jobdist::BaseJobDistributor::startup(), and used_tags_.

Member Data Documentation

utility::vector1< std::string > protocols::jobdist::PlainSilentFileJobDistributor::used_tags_

private

Referenced by is_finished(), and startup().

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

src/protocols/jobdist/JobDistributors.hh
src/protocols/jobdist/JobDistributors.cc

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation