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protocols::jd2::MPIMultiCommJobDistributor Class Reference

#include <MPIMultiCommJobDistributor.hh>

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

core::Size get_new_job_id () override
 dummy for master/slave version More...
 
void job_succeeded (core::pose::Pose &pose, core::Real run_timei, std::string const &tag) override
 overloaded to suppress message from higher-rank replicas More...
 
void job_failed (core::pose::Pose &pose, bool) override
 overloaded to suppress message from higher-rank replicas More...
 
core::Size sub_rank ()
 
- Public Member Functions inherited from protocols::jd2::MPIFileBufJobDistributor
 ~MPIFileBufJobDistributor () override
 dtor 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 More...
 
core::Size increment_client_rank ()
 
core::Size min_client_rank () const
 return rank of first worker process (there might be more dedicated processes, e.g., ArchiveManager...) More...
 
void go (protocols::moves::MoverOP mover) override
 dummy for master/slave version More...
 
void mark_current_job_id_for_repetition () override
 dummy for master/slave version More...
 
void remove_bad_inputs_from_job_list () override
 dummy for master/slave version 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...
 
virtual void restart ()
 
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

 MPIMultiCommJobDistributor (core::Size sub_size)
 ctor is protected; singleton pattern 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::MPIFileBufJobDistributor
 MPIFileBufJobDistributor ()
 ctor is protected; singleton pattern More...
 
 MPIFileBufJobDistributor (core::Size master_rank, core::Size file_buf_rank, core::Size min_client_rank, bool start_empty=false)
 protected ctor for child-classes More...
 
virtual bool process_message (core::Size msg_tag, core::Size slave_rank, core::Size slave_job_id, core::Size slave_batch_id, core::Real runtime)
 
bool next_batch () override
 switch current_batch_id_ to next batch More...
 
void master_go (protocols::moves::MoverOP mover)
 Handles the receiving of job requests and the sending of job ids to and from slaves. More...
 
core::Size master_get_new_job_id ()
 Always returns zero, simply increments next_job_to_assign_ to the next job that should be run based on what has been completeted and the overwrite flags. More...
 
core::Size slave_get_new_job_id ()
 requests, receives, and returns a new job id from the master node or returns the current job id if the repeat_job_ flag is set to true More...
 
void master_mark_current_job_id_for_repetition ()
 This should never be called as this is handled internally by the slave nodes, it utility_exits. More...
 
void slave_mark_current_job_id_for_repetition ()
 Sets the repeat_job_ flag to true. More...
 
void master_remove_bad_inputs_from_job_list ()
 Simply increments next_job_to_assign_ to the next job that should be run based on what has been completed and if the input job tag of the job marked as having bad input. More...
 
void slave_remove_bad_inputs_from_job_list ()
 Sends a message to the head node that contains the id of a job that had bad input. More...
 
void master_job_succeeded (core::pose::Pose &pose, std::string const &tag)
 This should never be called as this is handled internally by the slave nodes, it utility_exits. More...
 
void slave_job_succeeded (core::pose::Pose &pose, std::string const &tag)
 Sends a message to the head node upon successful job completion to avoid output interleaving. More...
 
void slave_to_master (core::Size tag)
 send a message to master More...
 
void send_job_to_slave (core::Size slave_rank)
 called by master to send and by slave to receive job More...
 
core::Size rank () const
 return rank of this process More...
 
core::Size master_rank () const
 return rank of master process ( where JobDistributor is running ) More...
 
core::Size file_buf_rank () const
 return rank of file-buffer process ( where output data (via ozstream )is handled ) More...
 
core::Size number_of_processors ()
 how many processes — this includes dedicated processes More...
 
core::Size n_rank ()
 how many processes — this includes dedicated processes More...
 
core::Size n_worker ()
 how many workers — important to keep track during spin-down process More...
 
void set_n_worker (core::Size setting)
 how many workers — important to keep track during spin-down process More...
 
virtual void mark_job_as_completed (core::Size job_id, core::Size batch_id, core::Real runtime)
 marks job as completed in joblist More...
 
virtual void mark_job_as_bad (core::Size job_id, core::Size batch_id)
 marks job as bad in joblist More...
 
void eat_signal (core::Size signal, int source)
 receive a certain signal and ignore it.... this is needed, for instance, when MPIArchiveJobDistributor triggers an ADD_BATCH signal by sending QUEUE_EMPTY to the ArchiveManager... 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 current_job_finished ()
 Derived classes are allowed to clean up any temporary files or data relating to the current job after the current job has completed. Called inside go_main loop. Default implementation is a no-op. 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 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 Types

typedef MPIFileBufJobDistributor Parent
 

Private Member Functions

void setup_sub_communicators (core::Size sub_size)
 

Private Attributes

core::Size n_comm_
 
int sub_rank_
 
core::Size communicator_handle_
 

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...
 

Detailed Description

This JobDistributor is intended for JD2 controlled runs of multiple parallel simulations that use multiple replicas: e.g., N trajectories of M replicas on N*M+2 processes. (2 processes for central JD2 and MPIFileBuf ) derived from MPIFileBufJobDistributor: two dedicated processes are used to handle JobDistribution and File-IO. all other processes (higher rank ) are used for computation.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::jd2::MPIMultiCommJobDistributor::MPIMultiCommJobDistributor ( core::Size  sub_size)
protected

ctor is protected; singleton pattern

constructor. Notice it calls the parent class! It also builds some internal variables for determining which processor it is in MPI land.

Member Function Documentation

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

dummy for master/slave version

master-job distributes job-ids as usual. sub-masters obtain a new job from master all processes within a single communication context work on the same job-id. ( Bcast )

Reimplemented from protocols::jd2::MPIFileBufJobDistributor.

References protocols::jd2::current_batch_id().

void protocols::jd2::MPIMultiCommJobDistributor::handle_interrupt ( )
inlineoverrideprotectedvirtual

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.

Reimplemented from protocols::jd2::MPIFileBufJobDistributor.

void protocols::jd2::MPIMultiCommJobDistributor::job_failed ( core::pose::Pose pose,
bool  retry 
)
overridevirtual

overloaded to suppress message from higher-rank replicas

dummy for master/slave version

Reimplemented from protocols::jd2::MPIFileBufJobDistributor.

void protocols::jd2::MPIMultiCommJobDistributor::job_succeeded ( core::pose::Pose pose,
core::Real  run_timei,
std::string const &  tag 
)
overridevirtual

overloaded to suppress message from higher-rank replicas

dummy for master/slave version

Reimplemented from protocols::jd2::MPIFileBufJobDistributor.

void protocols::jd2::MPIMultiCommJobDistributor::setup_sub_communicators ( core::Size  sub_size)
private

References protocols::jd2::tr().

core::Size protocols::jd2::MPIMultiCommJobDistributor::sub_rank ( )
inline

References sub_rank_.

Referenced by protocols::jd2::current_replica().

Friends And Related Function Documentation

friend class JobDistributorFactory
friend

Member Data Documentation

core::Size protocols::jd2::MPIMultiCommJobDistributor::communicator_handle_
private
core::Size protocols::jd2::MPIMultiCommJobDistributor::n_comm_
private
int protocols::jd2::MPIMultiCommJobDistributor::sub_rank_
private

Referenced by sub_rank().


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