Public Member Functions
public	runWorker ()

public	cleanup_if_needed ()

protected	_update_resource_usage ()

Detailed Description

Definition at line 6 of file RunWorker.pm.

Member Function Documentation

◆ _update_resource_usage()

protected Bio::EnsEMBL::Hive::Scripts::RunWorker::_update_resource_usage ( )

Undocumented method

Code:

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sub _update_resource_usage {
    my ($worker, $worker_stopwatch, $exception_status) = @_;
 
    $worker_stopwatch->pause();
    my $resource_usage;
    eval {
        # Try BSD::Resource if present
        my $res_self;
        my $res_child;
        # NOTE: I couldn't find a way of require-ing the module and getting
        # the barewords RUSAGE_* imported
        eval q{
            use BSD::Resource;
            $res_self = BSD::Resource::getrusage(RUSAGE_SELF);
            $res_child = BSD::Resource::getrusage(RUSAGE_CHILDREN);
            };
        return 0 if $@;
        $resource_usage = {
            'exit_status'   => 'done',
            'mem_megs'      => ($res_self->maxrss + $res_child->maxrss) / 1024.,
            'swap_megs'     => undef,
            'pending_sec'   => 0,
            'cpu_sec'       => $res_self->utime + $res_self->stime + $res_child->utime + $res_child->stime,
            'lifespan_sec'  => $worker_stopwatch->get_elapsed(),
            'exception_status' => $exception_status,
            #'file_blocks_in'   => $res_self->inblock + $res_child->inblock,     # Only blocks physically read. Blocks cached by the OS are not counted
            #'file_blocks_out'  => $res_self->oublock + $res_child->oublock,
            #'net_msg_sent'     => $res_self->msgsnd + $res_child->msgsnd,       # IPC messages sent: not used in the context of eHive Runnables
            #'net_msg_rec'      => $res_self->msgrcv + $res_child->msgrcv,       # IPC messages received: not used in the context of eHive Runnables
        };
 
    } or eval {
        # Unix::Getrusage otherwise
        require Unix::Getrusage;
        my $res_self = Unix::Getrusage::getrusage();
        my $res_child = Unix::Getrusage::getrusage_children();
        $resource_usage = {
            'exit_status'   => 'done',
            'mem_megs'      => ($res_self->{ru_maxrss} + $res_child->{ru_maxrss}) / 1024.,
            'swap_megs'     => undef,
            'pending_sec'   => 0,
            'cpu_sec'       => $res_self->{ru_utime} + $res_self->{ru_stime} + $res_child->{ru_utime} + $res_child->{ru_stime},
            'lifespan_sec'  => $worker_stopwatch->get_elapsed(),
            'exception_status' => $exception_status,
        };
    };
 
    # Store the data if one of the above calls was successful
    if ($resource_usage) {
        $worker->adaptor->store_resource_usage(
            {$worker->process_id => $resource_usage},
            {$worker->process_id => $worker->dbID},
        );
    }
}

◆ cleanup_if_needed()

public Bio::EnsEMBL::Hive::Scripts::RunWorker::cleanup_if_needed ( )

Undocumented method

Code:

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◆ runWorker()

public Bio::EnsEMBL::Hive::Scripts::RunWorker::runWorker ( )

Undocumented method

Code:

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sub runWorker {
    my ($pipeline, $specialization_options, $life_options, $execution_options) = @_;
 
    my $worker_stopwatch = Bio::EnsEMBL::Hive::Utils::Stopwatch->new();
    $worker_stopwatch->_unit(1); # lifespan_sec is in seconds
    $worker_stopwatch->restart();
 
    my $hive_dba = $pipeline->hive_dba;
 
    die "Hive's DBAdaptor is not a defined Bio::EnsEMBL::Hive::DBSQL::DBAdaptor\n" unless $hive_dba and $hive_dba->isa('Bio::EnsEMBL::Hive::DBSQL::DBAdaptor');
 
    $specialization_options ||= {};
    $life_options ||= {};
    $execution_options ||= {};
 
    my $queen = $hive_dba->get_Queen();
    die "No Queen, God Bless Her\n" unless $queen and $queen->isa('Bio::EnsEMBL::Hive::Queen');
 
    # Create the worker
    my $worker = $queen->create_new_worker(
             -preregistered         => $specialization_options->{'preregistered'},
             -config_files          => $execution_options->{'config_files'},
 
          # Resource class:
             -resource_class_id     => $specialization_options->{'resource_class_id'},
             -resource_class_name   => $specialization_options->{'resource_class_name'},
             -beekeeper_id          => $specialization_options->{'beekeeper_id'},
 
          # Worker control parameters:
             -job_limit             => $life_options->{'job_limit'},
             -life_span             => $life_options->{'life_span'},
             -no_cleanup            => $execution_options->{'no_cleanup'},
             -no_write              => $execution_options->{'no_write'},
             -worker_base_temp_dir  => $execution_options->{'worker_base_temp_dir'},
             -worker_log_dir        => $execution_options->{'worker_log_dir'},
             -hive_log_dir          => $execution_options->{'hive_log_dir'},
             -retry_throwing_jobs   => $life_options->{'retry_throwing_jobs'},
             -can_respecialize      => $specialization_options->{'can_respecialize'},
             -worker_delay_startup_seconds  => $life_options->{'worker_delay_startup_seconds'},
             -worker_crash_on_startup_prob  => $life_options->{'worker_crash_on_startup_prob'},
 
          # Other parameters:
             -debug                 => $execution_options->{'debug'},
    );
    die "No worker !\n" unless $worker and $worker->isa('Bio::EnsEMBL::Hive::Worker');
 
    # Run the worker
    eval {
        $worker->run( {
             -analyses_pattern      => $specialization_options->{'analyses_pattern'},
             -job_id                => $specialization_options->{'job_id'},
             -force                 => $specialization_options->{'force'},
        } );
        cleanup_if_needed($worker);
        _update_resource_usage($worker, $worker_stopwatch);
        $hive_dba->dbc->disconnect_if_idle;
        1;

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

modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ _update_resource_usage()

◆ cleanup_if_needed()

◆ runWorker()