LOCAL.pm 3.64 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
=pod 

=head1 NAME

    Bio::EnsEMBL::Hive::Meadow::LOCAL

=head1 DESCRIPTION

    This is the 'Local' implementation of Meadow

=head1 LICENSE

    Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute

    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at

         http://www.apache.org/licenses/LICENSE-2.0

    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.

=head1 CONTACT

    Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.

=cut

30
31
32
33
34
35

package Bio::EnsEMBL::Hive::Meadow::LOCAL;

use strict;
use Sys::Hostname;

Leo Gordon's avatar
Leo Gordon committed
36
use base ('Bio::EnsEMBL::Hive::Meadow');
37

38

39
sub name {  # also called to check for availability; for the moment assume LOCAL meadow is always available
40

41
    return (split(/\./, hostname))[0];     # only take the first name
42
43
44
}


45
46
47
48
49
50
sub get_current_worker_process_id {
    my ($self) = @_;

    return $$;
}

51

52
53
54
55
56
57
58
sub count_pending_workers_by_rc_name {
    my ($self) = @_;

    return ({}, 0);     # LOCAL has no concept of pending workers
}


59
60
61
sub count_running_workers {
    my $self = shift @_;

Leo Gordon's avatar
Leo Gordon committed
62
    my $cmd = 'ps x | grep runWorker.pl | grep -v "grep runWorker.pl" | wc -l';
63
64
65
66
67
68
69
    my $run_count = qx/$cmd/;
    chomp($run_count);

    return $run_count;
}


70
sub status_of_all_our_workers { # returns a hashref
71
72
    my ($self) = @_;

Leo Gordon's avatar
Leo Gordon committed
73
    my $cmd = 'ps x -o state,pid,command -w -w | grep runWorker.pl | grep -v "grep runWorker.pl" ';
74
75
76
77
78
79
80
81
82
83
84

        # FIXME: if we want to incorporate Meadow->pipeline_name() filtering here,
        #        a dummy parameter to the runWorker.pl should probably be introduced
        #        for 'ps' to be able to externally differentiate between local workers
        #        working for different hives
        #        (but at the moment such a feature is unlikely to be be in demand).

    my %status_hash = ();
    foreach my $line (`$cmd`) {
        my ($pre_status, $worker_pid, $job_name) = split(/\s+/, $line);

85
86
87
88
89
90
91
92
93
94
95
        my $status = {
            'R' => 'RUN',   # running

            'S' => 'RUN',   # sleeping (sleeping for less than 20 sec on a Mac)
            'I' => 'RUN',   # Mac: idle (sleeping for more than 20 sec)

            'D' => 'RUN',   # Linux: uninterruptible sleep, usually IO
            'U' => 'RUN',   # Mac: uninterruptible wait

            'T' => 'SSUSP'  # stopped process
        }->{ substr($pre_status,0,1) }; # only take the first character because of Mac's additional modifiers
96
97
98
99
100
101
102
103

        # Note: you can locally 'kill -19' a worker to suspend it and 'kill -18' a worker to resume it

        $status_hash{$worker_pid} = $status;
    }
    return \%status_hash;
}

104

105
sub check_worker_is_alive_and_mine {
106
107
    my ($self, $worker) = @_;

108
109
110
111
112
    my $wpid = $worker->process_id();
    my $cmd = qq{ps x | grep $wpid | grep -v 'grep $wpid'};
    my $is_alive_and_mine = qx/$cmd/;

    return $is_alive_and_mine;
113
114
}

115

116
sub kill_worker {
117
    my $worker = pop @_;
118

119
120
    my $cmd = 'kill -9 '.$worker->process_id();
    system($cmd);
121
122
}

123

124
sub submit_workers {
125
    my ($self, $worker_cmd, $required_worker_count, $iteration, $rc_name, $rc_specific_submission_cmd_args, $submit_stdout_file, $submit_stderr_file) = @_;
126

Leo Gordon's avatar
Leo Gordon committed
127
    my $cmd = "$worker_cmd &";
128

129
130
    foreach (1..$required_worker_count) {
        print "SUBMITTING_CMD:\t\t$rc_specific_submission_cmd_args $cmd\n";
Leo Gordon's avatar
Leo Gordon committed
131
        system( $cmd );
132
133
134
135
    }
}

1;