=pod =head1 NAME Bio::EnsEMBL::Hive::Meadow::LOCAL =head1 DESCRIPTION This is the 'Local' implementation of Meadow =head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2017] 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 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 =cut package Bio::EnsEMBL::Hive::Meadow::LOCAL; use strict; use Sys::Hostname; use base ('Bio::EnsEMBL::Hive::Meadow'); our $VERSION = '1.0'; # Semantic version of the Meadow interface: # change the Major version whenever an incompatible change is introduced, # change the Minor version whenever the interface is extended, but compatibility is retained. sub name { # also called to check for availability; for the moment assume LOCAL meadow is always available return (split(/\./, hostname))[0]; # only take the first name } sub get_current_worker_process_id { my ($self) = @_; return $$; } sub count_pending_workers_by_rc_name { my ($self) = @_; return ({}, 0); # LOCAL has no concept of pending workers } sub _command_line_to_extract_all_running_workers { my ($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/ && ($3 ~ /perl$/) )'}; } sub count_running_workers { my $self = shift @_; my $cmd = $self->_command_line_to_extract_all_running_workers . ' | wc -l'; my $run_count = qx/$cmd/; chomp($run_count); return $run_count; } sub status_of_all_our_workers { # returns a hashref my ($self) = @_; my $cmd = $self->_command_line_to_extract_all_running_workers; # 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); 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 # Note: you can locally 'kill -19' a worker to suspend it and 'kill -18' a worker to resume it $status_hash{$worker_pid} = $status; } return \%status_hash; } sub check_worker_is_alive_and_mine { my ($self, $worker) = @_; 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; } sub kill_worker { my $worker = pop @_; my $cmd = 'kill -9 '.$worker->process_id(); system($cmd); } sub submit_workers { my ($self, $worker_cmd, $required_worker_count, $iteration, $rc_name, $rc_specific_submission_cmd_args, $submit_stdout_file, $submit_stderr_file) = @_; my $cmd = "$worker_cmd &"; foreach (1..$required_worker_count) { print "SUBMITTING_CMD:\t\t$rc_specific_submission_cmd_args $cmd\n"; system( $cmd ); } } 1;