LOCAL.pm 3.95 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
=pod 

=head1 NAME

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

=head1 DESCRIPTION

    This is the 'Local' implementation of Meadow

=head1 LICENSE

13
    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
14
15
16
17
18
19
20
21
22
23
24
25

    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

26
    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
27
28
29

=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
62
63
64
65
66
sub _command_line_to_extract_all_running_workers {
    my ($self) = @_;

        # Make sure we have excluded both 'awk' itself and commands like "less runWorker.pl" :
    return q{ps x -o state,pid,command -w -w | awk '(/runWorker.pl/ && ($3 ~ /perl$/) )'};
}


67
68
69
sub count_running_workers {
    my $self = shift @_;

70
    my $cmd = $self->_command_line_to_extract_all_running_workers . ' | wc -l';
71
72
73
74
75
76
77
    my $run_count = qx/$cmd/;
    chomp($run_count);

    return $run_count;
}


78
sub status_of_all_our_workers { # returns a hashref
79
80
    my ($self) = @_;

81
    my $cmd = $self->_command_line_to_extract_all_running_workers;
82
83
84
85
86
87
88
89
90
91
92

        # 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);

93
94
95
96
97
98
99
100
101
102
103
        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
104
105
106
107
108
109
110
111

        # 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;
}

112

113
sub check_worker_is_alive_and_mine {
114
115
    my ($self, $worker) = @_;

116
117
118
119
120
    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;
121
122
}

123

124
sub kill_worker {
125
    my $worker = pop @_;
126

127
128
    my $cmd = 'kill -9 '.$worker->process_id();
    system($cmd);
129
130
}

131

132
sub submit_workers {
133
    my ($self, $worker_cmd, $required_worker_count, $iteration, $rc_name, $rc_specific_submission_cmd_args, $submit_stdout_file, $submit_stderr_file) = @_;
134

Leo Gordon's avatar
Leo Gordon committed
135
    my $cmd = "$worker_cmd &";
136

137
138
    foreach (1..$required_worker_count) {
        print "SUBMITTING_CMD:\t\t$rc_specific_submission_cmd_args $cmd\n";
Leo Gordon's avatar
Leo Gordon committed
139
        system( $cmd );
140
141
142
143
    }
}

1;