protocols::wum::WorkUnitBase Class Reference

The base class for all work units. More...

#include <WorkUnitBase.hh>

Inheritance diagram for protocols::wum::WorkUnitBase:

Classes
struct	WU_Header
	this structure can contain any non-dynamicly allocated data. Any simple data types can be used here, ints, real, floats, char, etc.. More...

Public Member Functions
	WorkUnitBase ()
	~WorkUnitBase () override=default
virtual protocols::wum::WorkUnitBaseOP	clone () const
virtual void	clear_serial_data ()
	Remove all data, make sure that the memory is also cleared, hence the cals to reserve. More...
virtual void	run ()
	Run the workunit - overloaded by children of this class. More...
void	print (std::ostream &out, bool verbose=false) const
	Print header information to the stream, single line by default or verbose if verbose is set to true. More...
core::Size	id ()
	Accessor to the ID of the WorkUnit. More...
core::Size	extra_data_1 ()
	Accessor to the extra_data_1 and 3 field of the header. More...
core::Size	extra_data_2 ()
core::Size	extra_data_3 ()
void	set_extra_data_1 (core::Size const value)
void	set_extra_data_2 (core::Size const value)
void	set_extra_data_3 (core::Size const value)
void	add_blacklist (int mpi_rank)
	Adds to the blacklist. More...
void	clear_blacklist ()
	Erases the blacklist. More...
bool	in_blacklist (int mpi_rank)
	Finds in blacklist, true if is, false if it isn't. More...
void	set_options (const std::string &text)
	Accesor to the "options" text field. More...
core::Size	get_run_time ()
	Returns the differrence between unix start and stop times. More...
std::string	get_wu_type () const
	Accessor to header structure, return the WorkUnit Type. More...
void	set_wu_type (const std::string &text)
	Accessor to header structure, sets the WorkUnit Type. More...
std::string	get_options () const
	Optain the options string from the header. More...
virtual core::Size	mem_footprint () const
	Return the memory usage of this WorkUnit. More...
core::Size	last_received_from ()

Protected Member Functions
virtual void	serialize ()
	Make ready for sending. More...
virtual void	deserialize ()
	Make ready for working - i.o.w. take information in serial_data_ and turn it into whatever real data the derivative class has. More...
void	create_unique_id ()
	Make a unique number out of Processor Number and unix timestamp ? More...
std::string &	serial_data ()
	Accessor to the serial data field. More...
const std::string &	serial_data () const
	Accessor to the serial data field. More...
void	set_run_start ()
	Set the unixtime of the start of the execution of this WorkUnit. More...
void	set_run_stop ()
	Set the unixtime of the stop of the execution of this WorkUnit. More...

Protected Attributes
WU_Header	header
	The header data. More...
core::Size	last_received_from_
	Contains the serial number of whatever Rank/Node this WU was last receeived from. More...
std::vector< int >	blacklist_
	Contains blacklist of nodes. This data is NOT sent, and is only used on the sending side to determine where not to send a workunit. More...

Private Member Functions
unsigned int	raw_data_size () const
unsigned int	raw_data_dump (unsigned char **raw_data_ptr) const
	This allocates and returns a pointer to a block of memory with the workunit data totally serialized. Note that it is that callers responsibility to call delete [] on this memory when they're done with it. More...
void	raw_data_load (const unsigned char *raw_data_ptr, unsigned int size)
	Read in Header and serial data from a raw block of memeory, like one you'd get from a lowlevel network communication. More...

Private Attributes
std::string	serial_data_
	Contains more data, such as decoys, silent structucts, .. whatever really. Must be serialized, i.e. in plain text form read for transmission. More...

Friends
class	MPI_WorkUnitManager
class	MPI_WorkUnitManager_Slave
class	WorkUnitManager
class	WorkUnitQueue

Detailed Description

The base class for all work units.

Constructor & Destructor Documentation

protocols::wum::WorkUnitBase::WorkUnitBase

(

)

References create_unique_id(), protocols::wum::WorkUnitBase::WU_Header::extra_data_1_, protocols::wum::WorkUnitBase::WU_Header::extra_data_2_, protocols::wum::WorkUnitBase::WU_Header::extra_data_3_, protocols::wum::WorkUnitBase::WU_Header::extra_data_4_, header, protocols::wum::WorkUnitBase::WU_Header::id_, last_received_from_, set_options(), set_wu_type(), protocols::wum::TR(), protocols::wum::WorkUnitBase::WU_Header::unixtime_creation_, protocols::wum::WorkUnitBase::WU_Header::unixtime_start_, and protocols::wum::WorkUnitBase::WU_Header::unixtime_stop_.

protocols::wum::WorkUnitBase::~WorkUnitBase ( )

overridedefault

Member Function Documentation

void protocols::wum::WorkUnitBase::add_blacklist

(

int

mpi_rank

)

Adds to the blacklist.

References blacklist_.

void protocols::wum::WorkUnitBase::clear_blacklist

(

)

Erases the blacklist.

References blacklist_.

virtual void protocols::wum::WorkUnitBase::clear_serial_data ( )

inlinevirtual

Remove all data, make sure that the memory is also cleared, hence the cals to reserve.

References serial_data_.

virtual protocols::wum::WorkUnitBaseOP protocols::wum::WorkUnitBase::clone ( ) const

inlinevirtual

Reimplemented in protocols::wum::WorkUnit_MoverWrapper, protocols::wum::WorkUnit_SilentStructStore, protocols::wum::WorkUnit_Wait, protocols::mpi_refinement::WorkUnit_PartialAbinitio, protocols::mpi_refinement::WorkUnit_RamaPerturber, protocols::mpi_refinement::WorkUnit_KicCloser, protocols::mpi_refinement::WorkUnit_Relax, protocols::mpi_refinement::WorkUnit_NormalMode, protocols::mpi_refinement::WorkUnit_FragInsert, protocols::mpi_refinement::WorkUnit_MD, protocols::relax::WorkUnit_BatchRelax_and_PostRescore, protocols::wum::DatabaseEntryWorkUnit, protocols::relax::WorkUnit_BatchRelax, protocols::loophash::WorkUnit_LoopHash, protocols::mpi_refinement::WorkUnit_CombinePose, protocols::mpi_refinement::WorkUnit_LoopHash, and protocols::mpi_refinement::WorkUnit_bbGauss.

void protocols::wum::WorkUnitBase::create_unique_id ( )

inlineprotected

Make a unique number out of Processor Number and unix timestamp ?

Referenced by WorkUnitBase().

virtual void protocols::wum::WorkUnitBase::deserialize ( )

inlineprotectedvirtual

Make ready for working - i.o.w. take information in serial_data_ and turn it into whatever real data the derivative class has.

Reimplemented in protocols::wum::WorkUnit_SilentStructStore, and protocols::wum::DatabaseEntryWorkUnit.

core::Size protocols::wum::WorkUnitBase::extra_data_1 ( )

inline

Accessor to the extra_data_1 and 3 field of the header.

References protocols::wum::WorkUnitBase::WU_Header::extra_data_1_, and header.

core::Size protocols::wum::WorkUnitBase::extra_data_2 ( )

inline

References protocols::wum::WorkUnitBase::WU_Header::extra_data_2_, and header.

core::Size protocols::wum::WorkUnitBase::extra_data_3 ( )

inline

References protocols::wum::WorkUnitBase::WU_Header::extra_data_3_, and header.

std::string protocols::wum::WorkUnitBase::get_options

(

)

const

Optain the options string from the header.

References header, and protocols::wum::WorkUnitBase::WU_Header::options_.

Referenced by protocols::mpi_refinement::WorkUnit_KicCloser::run().

core::Size protocols::wum::WorkUnitBase::get_run_time

(

)

Returns the differrence between unix start and stop times.

References header, protocols::wum::WorkUnitBase::WU_Header::unixtime_start_, and protocols::wum::WorkUnitBase::WU_Header::unixtime_stop_.

std::string protocols::wum::WorkUnitBase::get_wu_type

(

)

const

Accessor to header structure, return the WorkUnit Type.

References header, and protocols::wum::WorkUnitBase::WU_Header::wu_type_.

Referenced by protocols::wum::WorkUnitList::get_work_unit(), and protocols::wum::WorkUnitList::get_work_unit_clone().

core::Size protocols::wum::WorkUnitBase::id ( )

inline

Accessor to the ID of the WorkUnit.

References header, and protocols::wum::WorkUnitBase::WU_Header::id_.

bool protocols::wum::WorkUnitBase::in_blacklist

(

int

mpi_rank

)

Finds in blacklist, true if is, false if it isn't.

References blacklist_, and protocols::wum::mpi_rank().

core::Size protocols::wum::WorkUnitBase::last_received_from ( )

inline

References last_received_from_.

virtual core::Size protocols::wum::WorkUnitBase::mem_footprint ( ) const

inlinevirtual

Return the memory usage of this WorkUnit.

References serial_data().

void protocols::wum::WorkUnitBase::print	(	std::ostream &	out,
		bool	verbose = false
	)		const

Print header information to the stream, single line by default or verbose if verbose is set to true.

References protocols::wum::WorkUnitBase::WU_Header::extra_data_1_, protocols::wum::WorkUnitBase::WU_Header::extra_data_2_, protocols::wum::WorkUnitBase::WU_Header::extra_data_3_, protocols::wum::WorkUnitBase::WU_Header::extra_data_4_, header, protocols::wum::WorkUnitBase::WU_Header::id_, protocols::mean_field::max(), protocols::wum::WorkUnitBase::WU_Header::options_, serial_data(), protocols::wum::WorkUnitBase::WU_Header::unixtime_creation_, protocols::wum::WorkUnitBase::WU_Header::unixtime_start_, protocols::wum::WorkUnitBase::WU_Header::unixtime_stop_, and protocols::wum::WorkUnitBase::WU_Header::wu_type_.

Referenced by protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus(), protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus(), protocols::mpi_refinement::MPI_Refine_Emperor::process_inbound_wus(), and protocols::loophash::MPI_LoopHashRefine_Emperor::process_inbound_wus().

unsigned int protocols::wum::WorkUnitBase::raw_data_dump ( unsigned char **  raw_data_ptr ) const

private

This allocates and returns a pointer to a block of memory with the workunit data totally serialized. Note that it is that callers responsibility to call delete [] on this memory when they're done with it.

References header, raw_data_size(), serial_data(), and protocols::wum::TR().

void protocols::wum::WorkUnitBase::raw_data_load ( const unsigned char *  raw_data_ptr, unsigned int  size  )

private

Read in Header and serial data from a raw block of memeory, like one you'd get from a lowlevel network communication.

References header, serial_data(), and protocols::wum::TR().

unsigned int protocols::wum::WorkUnitBase::raw_data_size ( ) const

private

References serial_data(), and protocols::wum::TR().

Referenced by raw_data_dump().

void protocols::wum::WorkUnitBase::run ( )

virtual

Run the workunit - overloaded by children of this class.

Reimplemented in protocols::wum::WorkUnit_MoverWrapper, protocols::wum::WorkUnit_SilentStructStore, protocols::wum::WorkUnit_Wait, protocols::mpi_refinement::WorkUnit_PartialAbinitio, protocols::mpi_refinement::WorkUnit_RamaPerturber, protocols::mpi_refinement::WorkUnit_KicCloser, protocols::mpi_refinement::WorkUnit_Relax, protocols::mpi_refinement::WorkUnit_NormalMode, protocols::mpi_refinement::WorkUnit_FragInsert, protocols::mpi_refinement::WorkUnit_MD, protocols::mpi_refinement::WorkUnit_CombinePose, protocols::mpi_refinement::WorkUnit_LoopHash, protocols::mpi_refinement::WorkUnit_bbGauss, protocols::mpi_refinement::WorkUnit_Sampler, protocols::loophash::WorkUnit_LoopHash, and protocols::relax::WorkUnit_BatchRelax.

References protocols::wum::TR().

std::string& protocols::wum::WorkUnitBase::serial_data ( )

inlineprotected

Accessor to the serial data field.

References serial_data_.

Referenced by protocols::wum::DatabaseEntryWorkUnit::deserialize(), protocols::wum::WorkUnit_SilentStructStore::deserialize(), mem_footprint(), print(), raw_data_dump(), raw_data_load(), raw_data_size(), protocols::wum::DatabaseEntryWorkUnit::serialize(), and protocols::wum::WorkUnit_SilentStructStore::serialize().

const std::string& protocols::wum::WorkUnitBase::serial_data ( ) const

inlineprotected

Accessor to the serial data field.

References serial_data_.

virtual void protocols::wum::WorkUnitBase::serialize ( )

inlineprotectedvirtual

Make ready for sending.

Reimplemented in protocols::wum::WorkUnit_SilentStructStore, and protocols::wum::DatabaseEntryWorkUnit.

void protocols::wum::WorkUnitBase::set_extra_data_1 ( core::Size const  value )

inline

References protocols::wum::WorkUnitBase::WU_Header::extra_data_1_, and header.

void protocols::wum::WorkUnitBase::set_extra_data_2 ( core::Size const  value )

inline

References protocols::wum::WorkUnitBase::WU_Header::extra_data_2_, and header.

void protocols::wum::WorkUnitBase::set_extra_data_3 ( core::Size const  value )

inline

References protocols::wum::WorkUnitBase::WU_Header::extra_data_3_, and header.

void protocols::wum::WorkUnitBase::set_options

(

const std::string &

text

)

Accesor to the "options" text field.

References protocols::wum::WorkUnitBase::WU_Header::BUFFER_SIZE, header, and protocols::wum::WorkUnitBase::WU_Header::options_.

Referenced by protocols::mpi_refinement::WorkUnit_KicCloser::WorkUnit_KicCloser(), protocols::mpi_refinement::WorkUnit_MD::WorkUnit_MD(), and WorkUnitBase().

void protocols::wum::WorkUnitBase::set_run_start ( )

protected

Set the unixtime of the start of the execution of this WorkUnit.

References header, and protocols::wum::WorkUnitBase::WU_Header::unixtime_start_.

void protocols::wum::WorkUnitBase::set_run_stop ( )

protected

Set the unixtime of the stop of the execution of this WorkUnit.

References header, and protocols::wum::WorkUnitBase::WU_Header::unixtime_stop_.

void protocols::wum::WorkUnitBase::set_wu_type

(

const std::string &

text

)

Accessor to header structure, sets the WorkUnit Type.

References protocols::wum::WorkUnitBase::WU_Header::BUFFER_SIZE, header, and protocols::wum::WorkUnitBase::WU_Header::wu_type_.

Referenced by WorkUnitBase().

Friends And Related Function Documentation

friend class MPI_WorkUnitManager

friend

friend class MPI_WorkUnitManager_Slave

friend

friend class WorkUnitManager

friend

friend class WorkUnitQueue

friend

Member Data Documentation

std::vector< int > protocols::wum::WorkUnitBase::blacklist_

protected

Contains blacklist of nodes. This data is NOT sent, and is only used on the sending side to determine where not to send a workunit.

Referenced by add_blacklist(), clear_blacklist(), and in_blacklist().

WU_Header protocols::wum::WorkUnitBase::header

protected

The header data.

Referenced by extra_data_1(), extra_data_2(), extra_data_3(), protocols::mpi_refinement::WorkUnit_CombinePose::get_cartesian(), protocols::mpi_refinement::WorkUnit_bbGauss::get_centroid(), protocols::mpi_refinement::WorkUnit_MD::get_cstweight(), protocols::mpi_refinement::WorkUnit_Relax::get_cstweight(), protocols::loophash::WorkUnit_LoopHash::get_end(), protocols::mpi_refinement::WorkUnit_LoopHash::get_end(), protocols::mpi_refinement::WorkUnit_LoopHash::get_global(), protocols::mpi_refinement::WorkUnit_bbGauss::get_kT(), protocols::mpi_refinement::WorkUnit_RamaPerturber::get_kT(), protocols::mpi_refinement::WorkUnit_NormalMode::get_maxscale(), protocols::mpi_refinement::WorkUnit_NormalMode::get_nmodes(), protocols::mpi_refinement::WorkUnit_NormalMode::get_nmtype(), protocols::mpi_refinement::WorkUnit_Relax::get_nrepeat(), protocols::mpi_refinement::WorkUnit_FragInsert::get_nsteps(), protocols::mpi_refinement::WorkUnit_KicCloser::get_nsteps(), protocols::mpi_refinement::WorkUnit_RamaPerturber::get_nsteps(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::get_nsteps(), protocols::mpi_refinement::WorkUnit_bbGauss::get_nstruct(), protocols::mpi_refinement::WorkUnit_CombinePose::get_nstruct(), protocols::mpi_refinement::WorkUnit_MD::get_nstruct(), get_options(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::get_reconstruct(), protocols::mpi_refinement::WorkUnit_MD::get_relaxtype(), protocols::mpi_refinement::WorkUnit_NormalMode::get_relaxtype(), protocols::mpi_refinement::WorkUnit_Relax::get_relaxtype(), protocols::mpi_refinement::WorkUnit_FragInsert::get_res1(), protocols::mpi_refinement::WorkUnit_KicCloser::get_res1(), protocols::mpi_refinement::WorkUnit_RamaPerturber::get_res1(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::get_res1(), protocols::mpi_refinement::WorkUnit_FragInsert::get_res2(), protocols::mpi_refinement::WorkUnit_KicCloser::get_res2(), protocols::mpi_refinement::WorkUnit_RamaPerturber::get_res2(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::get_res2(), get_run_time(), protocols::mpi_refinement::WorkUnit_MD::get_scoretype(), protocols::mpi_refinement::WorkUnit_FragInsert::get_scoretype(), protocols::mpi_refinement::WorkUnit_Relax::get_scoretype(), protocols::mpi_refinement::WorkUnit_KicCloser::get_scoretype(), protocols::mpi_refinement::WorkUnit_bbGauss::get_segdef(), protocols::loophash::WorkUnit_LoopHash::get_ssid(), protocols::mpi_refinement::WorkUnit_LoopHash::get_ssid(), protocols::loophash::WorkUnit_LoopHash::get_start(), protocols::mpi_refinement::WorkUnit_LoopHash::get_start(), get_wu_type(), id(), print(), raw_data_dump(), raw_data_load(), protocols::wum::WorkUnit_Wait::run(), protocols::mpi_refinement::WorkUnit_CombinePose::set_cartesian(), protocols::mpi_refinement::WorkUnit_bbGauss::set_centroid(), protocols::mpi_refinement::WorkUnit_MD::set_cstweight(), protocols::mpi_refinement::WorkUnit_Relax::set_cstweight(), protocols::loophash::WorkUnit_LoopHash::set_end(), protocols::mpi_refinement::WorkUnit_LoopHash::set_end(), set_extra_data_1(), set_extra_data_2(), set_extra_data_3(), protocols::mpi_refinement::WorkUnit_LoopHash::set_global(), protocols::mpi_refinement::WorkUnit_bbGauss::set_kT(), protocols::mpi_refinement::WorkUnit_RamaPerturber::set_kT(), protocols::mpi_refinement::WorkUnit_NormalMode::set_maxscale(), protocols::mpi_refinement::WorkUnit_NormalMode::set_nmodes(), protocols::mpi_refinement::WorkUnit_NormalMode::set_nmtype(), protocols::mpi_refinement::WorkUnit_Relax::set_nrepeat(), protocols::mpi_refinement::WorkUnit_FragInsert::set_nsteps(), protocols::mpi_refinement::WorkUnit_KicCloser::set_nsteps(), protocols::mpi_refinement::WorkUnit_RamaPerturber::set_nsteps(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::set_nsteps(), protocols::mpi_refinement::WorkUnit_bbGauss::set_nstruct(), protocols::mpi_refinement::WorkUnit_CombinePose::set_nstruct(), protocols::mpi_refinement::WorkUnit_MD::set_nstruct(), set_options(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::set_reconstruct(), protocols::mpi_refinement::WorkUnit_MD::set_relaxtype(), protocols::mpi_refinement::WorkUnit_NormalMode::set_relaxtype(), protocols::mpi_refinement::WorkUnit_Relax::set_relaxtype(), protocols::mpi_refinement::WorkUnit_FragInsert::set_res1(), protocols::mpi_refinement::WorkUnit_KicCloser::set_res1(), protocols::mpi_refinement::WorkUnit_RamaPerturber::set_res1(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::set_res1(), protocols::mpi_refinement::WorkUnit_FragInsert::set_res2(), protocols::mpi_refinement::WorkUnit_KicCloser::set_res2(), protocols::mpi_refinement::WorkUnit_RamaPerturber::set_res2(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::set_res2(), set_run_start(), set_run_stop(), protocols::mpi_refinement::WorkUnit_MD::set_scoretype(), protocols::mpi_refinement::WorkUnit_FragInsert::set_scoretype(), protocols::mpi_refinement::WorkUnit_Relax::set_scoretype(), protocols::mpi_refinement::WorkUnit_KicCloser::set_scoretype(), protocols::mpi_refinement::WorkUnit_bbGauss::set_segdef(), protocols::loophash::WorkUnit_LoopHash::set_ssid(), protocols::mpi_refinement::WorkUnit_LoopHash::set_ssid(), protocols::loophash::WorkUnit_LoopHash::set_start(), protocols::mpi_refinement::WorkUnit_LoopHash::set_start(), set_wu_type(), protocols::wum::WorkUnit_Wait::WorkUnit_Wait(), and WorkUnitBase().

core::Size protocols::wum::WorkUnitBase::last_received_from_

protected

Contains the serial number of whatever Rank/Node this WU was last receeived from.

Referenced by last_received_from(), and WorkUnitBase().

std::string protocols::wum::WorkUnitBase::serial_data_

private

Contains more data, such as decoys, silent structucts, .. whatever really. Must be serialized, i.e. in plain text form read for transmission.

Referenced by clear_serial_data(), and serial_data().

---

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

• src/protocols/wum/WorkUnitBase.hh
• src/protocols/wum/WorkUnitBase.cc