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protocols::jd2::FileSystemJobDistributor Class Reference

#include <FileSystemJobDistributor.hh>

Inheritance diagram for protocols::jd2::FileSystemJobDistributor:
Inheritance graph
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Public Member Functions

 ~FileSystemJobDistributor () override
 
void restart () override
 
core::Size get_new_job_id () override
 Return 0 to signal that no available jobs remain. Otherwise return an index into the Jobs object. More...
 
void mark_current_job_id_for_repetition () override
 this function is called whenever a job "soft-fails" and needs to be retried. Generally it should ensure that the subsequent call to obtain_new_job returns this job over again. More...
 
void remove_bad_inputs_from_job_list () override
 
void current_job_finished () override
 
void go (protocols::moves::MoverOP mover) override
 This may be overridden by derived classes. Default implementation invokes go_main. More...
 
- Public Member Functions inherited from protocols::jd2::JobDistributor
virtual ~JobDistributor ()
 
void go (protocols::moves::MoverOP mover, JobOutputterOP jo)
 invokes go, after setting JobOutputter More...
 
void go (protocols::moves::MoverOP mover, JobInputterOP ji)
 invokes go, after setting JobInputter More...
 
void go (protocols::moves::MoverOP mover, JobInputterOP ji, JobOutputterOP jo)
 invokes go, after setting JobInputter and JobOutputter More...
 
virtual JobOP current_job () const
 Movers may ask their controlling job distributor for information about the current job. They may also write information to this job for later output, though this use is now discouraged as the addition of the MultiplePoseMover now means that a single job may include several separate trajectories. More...
 
virtual std::string current_output_name () const
 Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. More...
 
JobOutputterOP job_outputter () const
 Movers (or derived classes) may ask for the JobOutputter. More...
 
void set_job_outputter (const JobOutputterOP &new_job_outputter)
 Movers (or derived classes) may ask for the JobOutputter. More...
 
JobInputterOP job_inputter () const
 JobInputter access. More...
 
void set_job_inputter (JobInputterOP new_job_inputter)
 Set the JobInputter and reset the Job list – this is not something you want to do after go() has been called, but before it has returned. More...
 
virtual void mpi_finalize (bool finalize)
 should the go() function call MPI_finalize()? It probably should, this is true by default. More...
 
JobInputterInputSource::Enum job_inputter_input_source () const
 The input source for the current JobInputter. More...
 
core::Size total_nr_jobs () const
 
core::Size current_job_id () const
 integer access - which job are we on? More...
 
std::string get_current_batch () const
 what is the current batch ? — name refers to the flag-file used for this batch More...
 
virtual void add_batch (std::string const &, core::Size id=0)
 add a new batch ( name will be interpreted as flag_file ) More...
 
core::Size current_batch_id () const
 what is the current batch number ? — refers to position in batches_ More...
 

Protected Member Functions

 FileSystemJobDistributor ()
 
void job_succeeded (core::pose::Pose &pose, core::Real run_time, std::string const &tag) override
 This function is called upon a successful job completion; it has been virtualized so BOINC and MPI can delay/protect output base implementation is just a call to the job outputter. More...
 
void job_failed (core::pose::Pose &pose, bool will_retry) override
 This function is called when we five up on the job; it has been virtualized so BOINC and MPI can delay/protect output. More...
 
void handle_interrupt () override
 This function got called when job is not yet finished and got termitated abnormaly (ctrl-c, kill etc). when implimenting it in subclasses make sure to delete all in-progress-data that your job spawns. More...
 
- Protected Member Functions inherited from protocols::jd2::JobDistributor
 JobDistributor ()
 Singleton instantiation pattern; Derived classes will call default ctor, but their ctors, too must be protected (and the JDFactory must be their friend.) More...
 
 JobDistributor (bool empty)
 MPIArchiveJobDistributor starts with an empty job-list... More...
 
void go_main (protocols::moves::MoverOP mover)
 Non-virtual get-job, run it, & output loop. This function is pretty generic and your subclass may be able to use it. It is NOT virtual - this implementation can be shared by (at least) the simple FileSystemJobDistributor, the MPIWorkPoolJobDistributor, and the MPIWorkPartitionJobDistributor. Do not feel that you need to use it as-is in your class - but DO plan on implementing all its functionality! More...
 
JobsContainer const & get_jobs () const
 Read access to private data for derived classes. More...
 
JobsContainerget_jobs_nonconst ()
 Jobs is the container of Job objects. More...
 
void mark_job_as_completed (core::Size job_id, core::Real run_time)
 Jobs is the container of Job objects need non-const to mark Jobs as completed on Master in MPI-JobDistributor. More...
 
void mark_job_as_bad (core::Size job_id)
 
RosettaScriptsParserOP parser () const
 Parser access. More...
 
void begin_critical_section ()
 
void end_critical_section ()
 
void set_current_job_by_index (core::Size curr_job_index)
 For derived classes that wish to invoke JobDistributor functions which use the current_job_ and current_job_id_ member variables. Note that until those functions complete, it would be a bad idea for another thread to change current_job_. More...
 
bool obtain_new_job (bool re_consider_current_job=false)
 this function updates the current_job_id_ and current_job_ fields. The boolean return states whether or not a new job was obtained (if false, quit distributing!) More...
 
virtual void job_succeeded_additional_output (core::pose::Pose &pose, std::string const &tag)
 This function is called upon a successful job completion if there are additional poses generated by the mover base implementation is just a call to the job outputter. More...
 
virtual void note_all_jobs_finished ()
 Derived classes are allowed to perform some kind of action when the job distributor runs out of jobs to execute. Called inside go_main. Default implementation is a no-op. More...
 
void clear_current_job_output ()
 
void check_for_parser_in_go_main ()
 Send a message to the screen indicating that the parser is in use and that the mover that's been input to go_main will not be used, but instead will be replaced by the Mover created by the parser. More...
 
bool using_parser () const
 Is the parser in use? More...
 
bool run_one_job (protocols::moves::MoverOP &mover, time_t allstarttime, std::string &last_inner_job_tag, std::string &last_output_tag, core::Size &last_batch_id, core::Size &retries_this_job, bool first_job)
 
void setup_pymol_observer (core::pose::Pose &pose)
 After the construction of the pose for this job, check the command line to determine if the pymol observer should be attached to it. More...
 
void write_output_from_job (core::pose::Pose &pose, protocols::moves::MoverOP mover_copy, protocols::moves::MoverStatus status, core::Size jobtime, core::Size &retries_this_job)
 After a job has finished running, figure out from the MoverStatus whether the pose should be written to disk (or wherever) along with any other poses that the mover might have generated along the way. More...
 
void increment_failed_jobs ()
 Increment the number of failed jobs. More...
 
core::Size get_job_time_estimate () const
 Get an estimate of the time to run an additional job. If it can't be estimated, return a time of zero. More...
 
void write_citations_and_clear_citation_tracking () const
 Write out information about all modules that have been used that should be cited, then clear the list of citations from the CitationManager. More...
 
void set_batch_id (core::Size setting)
 set current_batch_id — eg for slave nodes in MPI framework More...
 
virtual bool next_batch ()
 switch current_batch_id_ to next batch More...
 
virtual void batch_underflow ()
 if end of batches_ reached via next_batch or set_batch_id ... More...
 
virtual void load_new_batch ()
 called by next_batch() or set_batch_id() to switch-over and restart JobDistributor on new batch More...
 
core::Size nr_batches () const
 how many batches are in our list ... this can change dynamically More...
 
std::string const & batch (core::Size batch_id)
 give name of batch with given id More...
 

Private Member Functions

void delete_in_progress_files ()
 delete all temporary files for this job More...
 
std::string const temporary_file_name (JobCOP job) const
 tacks an extension (.in_progress) on to filename - for multiple process/one directory behaviour More...
 

Private Attributes

std::string extension_
 
std::string path_
 
core::Size retry_count_
 

Friends

class JobDistributorFactory
 

Additional Inherited Members

- Static Public Member Functions inherited from protocols::jd2::JobDistributor
static bool has_been_instantiated ()
 Has the job distributor been instantiated? More...
 
static JobDistributorget_instance ()
 static function to get the instance of ( pointer to) this singleton class More...
 
- Static Protected Member Functions inherited from protocols::jd2::JobDistributor
static void setup_system_signal_handler (void(*prev_fn)(int)=jd2_signal_handler)
 Setting up callback function that will be call when our process is about to terminate. This will allow us to exit propely (clean up in_progress_files/tmp files if any). More...
 
static void remove_system_signal_handler ()
 Set signal handler back to default state. More...
 
static void jd2_signal_handler (int Signal)
 Default callback function for signal handling. More...
 

Constructor & Destructor Documentation

protocols::jd2::FileSystemJobDistributor::FileSystemJobDistributor ( )
protected
protocols::jd2::FileSystemJobDistributor::~FileSystemJobDistributor ( )
overridedefault

WARNING WARNING! SINGLETONS' DESTRUCTORS ARE NEVER CALLED IN MINI! DO NOT TRY TO PUT THINGS IN THIS FUNCTION! here's a nice link explaining why: http://www.research.ibm.com/designpatterns/pubs/ph-jun96.txt

Member Function Documentation

void protocols::jd2::FileSystemJobDistributor::current_job_finished ( )
overridevirtual

when multiple processes are writing to the same directory, then after a job completes, the "in_progress" file for the job must be deleted.

Reimplemented from protocols::jd2::JobDistributor.

References core::conformation::membrane::out.

void protocols::jd2::FileSystemJobDistributor::delete_in_progress_files ( )
private

delete all temporary files for this job

core::Size protocols::jd2::FileSystemJobDistributor::get_new_job_id ( )
overridevirtual

Return 0 to signal that no available jobs remain. Otherwise return an index into the Jobs object.

Implements protocols::jd2::JobDistributor.

Reimplemented in protocols::jd2::ShuffleFileSystemJobDistributor.

References protocols::jd2::get_min_nstruct_index_checkpoint_file(), protocols::mean_field::max(), protocols::jd2::JobsContainer::size(), and protocols::jd2::TR().

void protocols::jd2::FileSystemJobDistributor::go ( protocols::moves::MoverOP  mover)
overridevirtual

This may be overridden by derived classes. Default implementation invokes go_main.

Reimplemented from protocols::jd2::JobDistributor.

Reimplemented in protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor.

Referenced by protocols::jd2::BOINCJobDistributor::go().

void protocols::jd2::FileSystemJobDistributor::handle_interrupt ( )
overrideprotectedvirtual

This function got called when job is not yet finished and got termitated abnormaly (ctrl-c, kill etc). when implimenting it in subclasses make sure to delete all in-progress-data that your job spawns.

Implements protocols::jd2::JobDistributor.

Reimplemented in protocols::jd2::ShuffleFileSystemJobDistributor.

void protocols::jd2::FileSystemJobDistributor::job_failed ( core::pose::Pose pose,
bool  will_retry 
)
overrideprotectedvirtual

This function is called when we five up on the job; it has been virtualized so BOINC and MPI can delay/protect output.

Reimplemented from protocols::jd2::JobDistributor.

References protocols::jd2::JobDistributor::job_failed().

void protocols::jd2::FileSystemJobDistributor::job_succeeded ( core::pose::Pose pose,
core::Real  run_time,
std::string const &  tag 
)
overrideprotectedvirtual

This function is called upon a successful job completion; it has been virtualized so BOINC and MPI can delay/protect output base implementation is just a call to the job outputter.

Reimplemented from protocols::jd2::JobDistributor.

References protocols::jd2::JobDistributor::job_succeeded().

Referenced by protocols::jd2::BOINCJobDistributor::job_succeeded().

void protocols::jd2::FileSystemJobDistributor::mark_current_job_id_for_repetition ( )
overridevirtual

this function is called whenever a job "soft-fails" and needs to be retried. Generally it should ensure that the subsequent call to obtain_new_job returns this job over again.

Implements protocols::jd2::JobDistributor.

Reimplemented in protocols::jd2::ShuffleFileSystemJobDistributor.

References protocols::jd2::TR().

void protocols::jd2::FileSystemJobDistributor::remove_bad_inputs_from_job_list ( )
overridevirtual

this function handles the FAIL_BAD_INPUT mover status by removing other jobs with the same input from consideration

Reimplemented from protocols::jd2::JobDistributor.

References protocols::jd2::TR().

void protocols::jd2::FileSystemJobDistributor::restart ( )
overridevirtual

restart job-distribution from beginning – useful if you need a second pass over decoys...

Reimplemented from protocols::jd2::JobDistributor.

References protocols::jd2::JobDistributor::restart(), and retry_count_.

std::string const protocols::jd2::FileSystemJobDistributor::temporary_file_name ( JobCOP  job) const
private

tacks an extension (.in_progress) on to filename - for multiple process/one directory behaviour

Friends And Related Function Documentation

friend class JobDistributorFactory
friend

Member Data Documentation

std::string protocols::jd2::FileSystemJobDistributor::extension_
private
std::string protocols::jd2::FileSystemJobDistributor::path_
private
core::Size protocols::jd2::FileSystemJobDistributor::retry_count_
private

Referenced by restart().


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