Bio::EnsEMBL::Hive::Queen Class Reference

Class Summary
Synopsis
The Queen of the Hive based job control system
Description
The Queen of the Hive based job control system is responsible to 'birthing' the correct number of workers of the right type so that they can find jobs to do. It will also free up jobs of Workers that died unexpectantly so that other workers can claim them to do.
Hive based processing is a concept based on a more controlled version of an autonomous agent type system. Each worker is not told what to do (like a centralized control system - like the current pipeline system) but rather queries a central database for jobs (give me jobs).
Each worker is linked to an analysis_id, registers its self on creation into the Hive, creates a RunnableDB instance of the Analysis->module, gets $analysis->stats->batch_size jobs from the job table, does its work, creates the next layer of job entries by interfacing to the DataflowRuleAdaptor to determine the analyses it needs to pass its output data to and creates jobs on the next analysis database. It repeats this cycle until it has lived its lifetime or until there are no more jobs left. The lifetime limit is just a safety limit to prevent these from 'infecting' a system.
The Queens job is to simply birth Workers of the correct analysis_id to get the work down. The only other thing the Queen does is free up jobs that were claimed by Workers that died unexpectantly so that other workers can take over the work.
The Beekeeper is in charge of interfacing between the Queen and a compute resource or 'compute farm'. Its job is to query Queens if they need any workers and to send the requested number of workers to open machines via the runWorker.pl script. It is also responsible for interfacing with the Queen to identify worker which died unexpectantly.
Method Documentation
protected Bio::EnsEMBL::Hive::Queen::_columns | ( | ) |
protected Bio::EnsEMBL::Hive::Queen::_default_where_clause | ( | ) |
protected Bio::EnsEMBL::Hive::Queen::_final_clause | ( | ) |
protected Listref Bio::EnsEMBL::Hive::Queen::_generic_fetch | ( | ) |
Arg [1] : (optional) string $constraint An SQL query constraint (i.e. part of the WHERE clause) Arg [2] : (optional) string $logic_name the logic_name of the analysis of the features to obtain Example : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall'); Description: Performs a database fetch and returns feature objects in contig coordinates. Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates Exceptions : none Caller : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch

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protected Bio::EnsEMBL::Hive::Queen::_objs_from_sth | ( | ) |
protected Bio::EnsEMBL::Hive::Queen::_pick_best_analysis_for_new_worker | ( | ) |
Undocumented method

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protected Bio::EnsEMBL::Hive::Queen::_tables | ( | ) |
public Bio::EnsEMBL::Hive::Queen::check_for_dead_workers | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::check_in_worker | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::count_running_workers | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Worker Bio::EnsEMBL::Hive::Queen::create_new_worker | ( | ) |
Arg [1] : $analysis_id (optional) Example : Description: If analysis_id is specified it will try to create a worker based on that analysis. If not specified the queen will analyze the hive and pick the analysis that has the most amount of work to be done. It creates an entry in the worker table, and returns a Worker object based on that insert. This guarantees that each worker registered in this queens hive is properly registered. Returntype : Bio::EnsEMBL::Hive::Worker Exceptions : Caller :

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public Bio::EnsEMBL::Hive::Queen::fetch_all_dead_workers_with_jobs | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Worker Bio::EnsEMBL::Hive::Queen::fetch_by_dbID | ( | ) |
Arg [1] : int $id the unique database identifier for the feature to be obtained Example : $feat = $queen->fetch_by_dbID(1234); Description: Returns the feature created from the database defined by the the id $id. Returntype : Bio::EnsEMBL::Hive::Worker Exceptions : thrown if $worker_id is not defined Caller : general

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.
public Bio::EnsEMBL::Hive::Queen::fetch_failed_workers | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::fetch_overdue_workers | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::get_hive_current_load | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::get_num_failed_analyses | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::get_remaining_jobs_show_hive_progress | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::monitor | ( | ) |
Arg[1] : --none-- Example : $queen->monitor(); Description: Monitors current throughput and store the result in the monitor table Exceptions : none Caller : beekeepers and other external processes

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public Bio::EnsEMBL::Hive::Queen::print_analysis_status | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::print_running_worker_status | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::register_all_workers_dead | ( | ) |
Example : $queen->register_all_workers_dead(); Description: Registers all workers dead Exceptions : none Caller : beekeepers and other external processes

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public Bio::EnsEMBL::Hive::Queen::register_worker_death | ( | ) |
Undocumented method

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public Bio::EnsEMBL::Hive::Queen::reset_and_fetch_job_by_dbID | ( | ) |
Arg [1]: int $job_id Example: my $job = $queen->reset_and_fetch_job_by_dbID($job_id); Description: For the specified job_id it will fetch just that job, reset it completely as if it has never run, and return it. Specifying a specific job bypasses the safety checks, thus multiple workers could be running the same job simultaneously (use only for debugging). Returntype : Bio::EnsEMBL::Hive::AnalysisJob object Exceptions : Caller : beekeepers, runWorker.pl scripts

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public Bio::EnsEMBL::Hive::Queen::safe_synchronize_AnalysisStats | ( | ) |
Arg [1] : Bio::EnsEMBL::Hive::AnalysisStats object Example : $self->synchronize($analysisStats); Description: Prewrapper around synchronize_AnalysisStats that does checks and grabs sync_lock before proceeding with sync. Used by distributed worker sync system to avoid contention. Exceptions : none Caller : general

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public Bio::EnsEMBL::Hive::Queen::schedule_workers | ( | ) |
Arg[1] : Bio::EnsEMBL::Analysis object (optional) Example : $count = $queen->schedule_workers(); Description: Runs through the analyses in the system which are waiting for workers to be created for them. Calculates the maximum number of workers needed to fill the current needs of the system If Arg[1] is defined, does it only for the given analysis. Exceptions : none Caller : beekeepers and other external processes

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public Bio::EnsEMBL::Hive::Queen::schedule_workers_resync_if_necessary | ( | ) |
Undocumented method

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public Newly Bio::EnsEMBL::Hive::Queen::synchronize_AnalysisStats | ( | ) |
Arg [1] : Bio::EnsEMBL::Hive::AnalysisStats object Example : $self->synchronize($analysisStats); Description: Queries the job and worker tables to get summary counts and rebuilds the AnalysisStats object. Then updates the analysis_stats table with the new summary info Returntype : newly synced Bio::EnsEMBL::Hive::AnalysisStats object Exceptions : none Caller : general

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public Bio::EnsEMBL::Hive::Queen::synchronize_hive | ( | ) |
Arg [1] : $filter_analysis (optional) Example : $queen->synchronize_hive(); Description: Runs through all analyses in the system and synchronizes the analysis_stats summary with the states in the job and worker tables. Then follows by checking all the blocking rules and blocks/unblocks analyses as needed. Exceptions : none Caller : general

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The documentation for this class was generated from the following file:
- Hive/Queen.pm