Inheritance diagram for Bio::EnsEMBL::Hive::Meadow::LSF:

Public Member Functions
public String	name ()

public	get_current_worker_process_id ()

public	deregister_local_process ()

public	status_of_all_our_workers ()

public	check_worker_is_alive_and_mine ()

public	kill_worker ()

protected	_convert_to_datetime ()

public	parse_report_source_line ()

public	get_report_entries_for_process_ids ()

public	get_report_entries_for_time_interval ()

public	submit_workers_return_meadow_pids ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::Meadow
public	get_meadow_major_version ()

public	get_meadow_version ()

public	check_version_compatibility ()

public	new ()

protected	_init_meadow ()

public	cached_name ()

public	type ()

public	get_current_hostname ()

public	signature ()

public	pipeline_name ()

public	runWorker_path ()

public	job_name_prefix ()

public	job_array_common_name ()

public	name ()

public	get_current_worker_process_id ()

public	status_of_all_our_workers ()

public	check_worker_is_alive_and_mine ()

public	kill_worker ()

public	parse_report_source_line ()

public	get_report_entries_for_process_ids ()

public	get_report_entries_for_time_interval ()

public	submit_workers_return_meadow_pids ()

public	run_on_host ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::Configurable
public	config ()

public	context ()

public	config_get ()

public	config_set ()

Detailed Description

Description

    This is the 'LSF' implementation of Meadow

Definition at line 13 of file LSF.pm.

Member Function Documentation

◆ _convert_to_datetime()

protected Bio::EnsEMBL::Hive::Meadow::LSF::_convert_to_datetime ( )

Undocumented method

Code:

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◆ check_worker_is_alive_and_mine()

public Bio::EnsEMBL::Hive::Meadow::LSF::check_worker_is_alive_and_mine ( )

Undocumented method

Code:

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◆ deregister_local_process()

public Bio::EnsEMBL::Hive::Meadow::LSF::deregister_local_process ( )

Undocumented method

Code:

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◆ get_current_worker_process_id()

public Bio::EnsEMBL::Hive::Meadow::LSF::get_current_worker_process_id ( )

Undocumented method

Code:

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◆ get_report_entries_for_process_ids()

public Bio::EnsEMBL::Hive::Meadow::LSF::get_report_entries_for_process_ids ( )

Undocumented method

Code:

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◆ get_report_entries_for_time_interval()

public Bio::EnsEMBL::Hive::Meadow::LSF::get_report_entries_for_time_interval ( )

Undocumented method

Code:

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◆ kill_worker()

public Bio::EnsEMBL::Hive::Meadow::LSF::kill_worker ( )

Undocumented method

Code:

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◆ name()

public String Bio::EnsEMBL::Hive::Meadow::LSF::name ( )

   Args:       : None
   Description : Determine the LSF cluster_name, if an LSF meadow is available.
   Returntype  : String

Code:

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◆ parse_report_source_line()

public Bio::EnsEMBL::Hive::Meadow::LSF::parse_report_source_line ( )

Undocumented method

Code:

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sub parse_report_source_line {
    my ($self, $bacct_source_line) = @_;
    print "LSF::parse_report_source_line( \"$bacct_source_line\" )\n";
    # Conplete list of exit codes is available at
    # https://www.ibm.com/support/knowledgecenter/SSETD4_9.1.3/lsf_admin/termination_reasons_lsf.html
    my %status_2_cod = (
        'TERM_MEMLIMIT'     => 'MEMLIMIT',
        'TERM_RUNLIMIT'     => 'RUNLIMIT',
        'TERM_OWNER'        => 'KILLED_BY_USER',    # bkill     (wait until it dies)
        'TERM_FORCE_OWNER'  => 'KILLED_BY_USER',    # bkill -r  (quick remove)
        'TERM_BUCKET_KILL'  => 'KILLED_BY_USER',    # bkill -b  (kills large numbers of jobs as soon as possible)
        'TERM_REQUEUE_OWNER'=> 'KILLED_BY_USER',    # Job killed and requeued by owner
    );
    my %units_2_megs = (
        'K' => 1.0/1024,
        'M' => 1,
        'G' => 1024,
        'T' => 1024*1024,
    );
    local $/ = "------------------------------------------------------------------------------\n\n";
    open(my $bacct_fh, '-|', $bacct_source_line);
    my $record = <$bacct_fh>; # skip the header
    my %report_entry = ();
    for my $record (<$bacct_fh>) {
        chomp $record;
        # warn "RECORD:\n$record";
        my @lines = split(/\n/, $record);
        if( my ($process_id) = $lines[0]=~/^Job <(\d+(?:\[\d+\])?)>/) {
            my ($exit_status, $exception_status) = ('' x 2);
            my ($when_born, $meadow_host);
            my ($when_died, $cause_of_death);
            my (@keys, @values);
            my $line_has_key_values = 0;
            foreach (@lines) {
                if( /^(\w+)\s+(\w+\s+\d+\s+\d+:\d+:\d+)(?:\s+(\d{4}))?:\s+(?:\[\d+\]\s+)?[Dd]ispatched to\s<([\w\-\.]+)>/ ) {
                    $when_born      = _convert_to_datetime($1, $2, $3);
                    $meadow_host    = $4;
                }
                elsif( /^(\w+)\s+(\w+\s+\d+\s+\d+:\d+:\d+)(?:\s+(\d{4}))?:\s+Completed\s<(\w+)>(?:\.|;\s+(\w+))/ ) {
                    $when_died      = _convert_to_datetime($1, $2, $3);
                    $cause_of_death = $5 && ($status_2_cod{$5} || 'SEE_EXIT_STATUS');
                    $exit_status = $4 . ($5 ? "/$5" : '');
                }
                elsif(/^\s*EXCEPTION STATUS:\s*(.*?)\s*$/) {
                    $exception_status = $1;
                    $exception_status =~s/\s+/;/g;
                }
                elsif(/^\s*CPU_T/) {
                    @keys = split(/\s+/, ' '.$_);
                    $line_has_key_values = 1;
                }
                elsif($line_has_key_values) {
                    @values = split(/\s+/, ' '.$_);
                    $line_has_key_values = 0;
                }
            }
            my %usage;  @usage{@keys} = @values;
            #warn join(', ', map {sprintf('%s=%s', $_, $usage{$_})} (sort keys %usage)), "\n";
            my ($mem_in_units, $mem_unit)   = $usage{'MEM'}  =~ /^([\d\.]+)([KMGT])$/;
            my ($swap_in_units, $swap_unit) = $usage{'SWAP'} =~ /^([\d\.]+)([KMGT])$/;
            $report_entry{ $process_id } = {
                    # entries for 'worker' table:
                'meadow_host'       => $meadow_host,
                'when_born'         => $when_born,
                'when_died'         => $when_died,
                'cause_of_death'    => $cause_of_death,
                    # entries for 'worker_resource_usage' table:
                'exit_status'       => $exit_status,
                'exception_status'  => $exception_status,
                'mem_megs'          => $mem_in_units  * $units_2_megs{$mem_unit},
                'swap_megs'         => $swap_in_units * $units_2_megs{$swap_unit},
                'pending_sec'       => $usage{'WAIT'},
                'cpu_sec'           => $usage{'CPU_T'},
                'lifespan_sec'      => $usage{'TURNAROUND'},
            };
        }
    }
    close $bacct_fh;
    my $exit = $? >> 8;
    die "Could not read from '$bacct_source_line'. Received the error $exit\n" if $exit;
    return \%report_entry;
}

◆ status_of_all_our_workers()

public Bio::EnsEMBL::Hive::Meadow::LSF::status_of_all_our_workers ( )

Undocumented method

Code:

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◆ submit_workers_return_meadow_pids()

public Bio::EnsEMBL::Hive::Meadow::LSF::submit_workers_return_meadow_pids ( )

Undocumented method

Code:

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

modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm

Public Member Functions

Detailed Description

Description

Member Function Documentation

◆ _convert_to_datetime()

◆ check_worker_is_alive_and_mine()

◆ deregister_local_process()

◆ get_current_worker_process_id()

◆ get_report_entries_for_process_ids()

◆ get_report_entries_for_time_interval()

◆ kill_worker()

◆ name()

◆ parse_report_source_line()

◆ status_of_all_our_workers()

◆ submit_workers_return_meadow_pids()