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Commit 36053303 authored by Leo Gordon's avatar Leo Gordon
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pass either rc_name or logic_name or job_id from beekeeper.pl to runWorker.pl

parent 26e3e57a
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Showing with 31 additions and 28 deletions
scripts/beekeeper.pl
View file @ 36053303
......@@ -192,32 +192,32 @@ sub main {
$job->print_job();
}
if(my $logic_name_to_reset = $reset_all_jobs_for_analysis || $reset_failed_jobs_for_analysis) {
if(my $reset_logic_name = $reset_all_jobs_for_analysis || $reset_failed_jobs_for_analysis) {
my $analysis = $self->{'dba'}->get_AnalysisAdaptor->fetch_by_logic_name($logic_name_to_reset)
|| die( "Cannot AnalysisAdaptor->fetch_by_logic_name($logic_name_to_reset)");
my $reset_analysis = $self->{'dba'}->get_AnalysisAdaptor->fetch_by_logic_name($reset_logic_name)
|| die( "Cannot AnalysisAdaptor->fetch_by_logic_name($reset_logic_name)");
$self->{'dba'}->get_AnalysisJobAdaptor->reset_jobs_for_analysis_id($analysis->dbID, $reset_all_jobs_for_analysis);
$self->{'dba'}->get_Queen->synchronize_AnalysisStats($analysis->stats);
$self->{'dba'}->get_AnalysisJobAdaptor->reset_jobs_for_analysis_id($reset_analysis->dbID, $reset_all_jobs_for_analysis);
$self->{'dba'}->get_Queen->synchronize_AnalysisStats($reset_analysis->stats);
}
if($all_dead) { $queen->register_all_workers_dead(); }
if($check_for_dead) { $queen->check_for_dead_workers($valley, 1); }
if ($kill_worker_id) {
my $worker = $queen->fetch_by_dbID($kill_worker_id);
my $kill_worker = $queen->fetch_by_dbID($kill_worker_id);
unless( $worker->cause_of_death() ) {
if( my $meadow = $valley->find_available_meadow_responsible_for_worker( $worker ) ) {
unless( $kill_worker->cause_of_death() ) {
if( my $meadow = $valley->find_available_meadow_responsible_for_worker( $kill_worker ) ) {
if( $meadow->check_worker_is_alive_and_mine ) {
printf("Killing worker: %10d %35s %15s %20s(%d) : ",
$worker->dbID, $worker->host, $worker->process_id,
$worker->analysis->logic_name, $worker->analysis->dbID);
$kill_worker->dbID, $kill_worker->host, $kill_worker->process_id,
$kill_worker->analysis->logic_name, $kill_worker->analysis->dbID);
$meadow->kill_worker($worker);
$worker->cause_of_death('KILLED_BY_USER');
$queen->register_worker_death($worker);
$meadow->kill_worker($kill_worker);
$kill_worker->cause_of_death('KILLED_BY_USER');
$queen->register_worker_death($kill_worker);
# what about clean-up? Should we do it here or not?
} else {
die "According to the Meadow, the Worker (dbID=$kill_worker_id) is not running, so cannot kill";
......@@ -280,7 +280,7 @@ sub main {
sub generate_worker_cmd {
my ($self, $run_job_id) = @_;
my ($self, $run_analysis, $run_job_id) = @_;
my $worker_cmd = 'runWorker.pl';
......@@ -294,30 +294,33 @@ sub generate_worker_cmd {
$worker_cmd .= ' -url '. $self->{'url'};
}
if ($run_job_id) {
$worker_cmd .= " -job_id $run_job_id";
} else {
foreach my $worker_option ('job_limit', 'life_span', 'logic_name', 'retry_throwing_jobs', 'compile_module_once', 'hive_log_dir', 'debug') {
if(defined(my $value = $self->{$worker_option})) {
$worker_cmd .= " -${worker_option} $value";
}
foreach my $worker_option ('job_limit', 'life_span', 'retry_throwing_jobs', 'compile_module_once', 'hive_log_dir', 'debug') {
if(defined(my $value = $self->{$worker_option})) {
$worker_cmd .= " -${worker_option} $value";
}
}
# special task:
if ($run_analysis) {
$worker_cmd .= " -logic_name ".$run_analysis->logic_name;
} elsif ($run_job_id) {
$worker_cmd .= " -job_id $run_job_id";
}
return $worker_cmd;
}
sub run_autonomously {
my ($self, $max_loops, $keep_alive, $queen, $valley, $this_analysis, $run_job_id) = @_;
my ($self, $max_loops, $keep_alive, $queen, $valley, $run_analysis, $run_job_id) = @_;
unless(`runWorker.pl`) {
print("can't find runWorker.pl script. Please make sure it's in your path\n");
exit(1);
}
my $current_meadow = $valley->get_current_meadow();
my $worker_cmd = generate_worker_cmd($self, $run_job_id);
my $current_meadow = $valley->get_current_meadow();
my $worker_cmd = generate_worker_cmd($self, $run_analysis, $run_job_id);
my $special_task = $run_analysis || $run_job_id;
# first, fetch two resource-related mappings from the database:
my $rc_name2id = $self->{'dba'}->get_ResourceClassAdaptor->fetch_HASHED_FROM_name_TO_resource_class_id();
......@@ -345,7 +348,7 @@ sub run_autonomously {
$queen->print_analysis_status unless($self->{'no_analysis_stats'});
$queen->print_running_worker_counts;
my $workers_to_run_by_rc_name = $queen->schedule_workers_resync_if_necessary($valley, $this_analysis);
my $workers_to_run_by_rc_name = $queen->schedule_workers_resync_if_necessary($valley, $run_analysis);
if(keys %$workers_to_run_by_rc_name) {
foreach my $rc_name ( sort { $workers_to_run_by_rc_name->{$a}<=>$workers_to_run_by_rc_name->{$b} } keys %$workers_to_run_by_rc_name) {
......@@ -353,13 +356,13 @@ sub run_autonomously {
print "Submitting $this_rc_worker_count workers (rc_name=$rc_name) to ".$current_meadow->toString()."\n";
$current_meadow->submit_workers("$worker_cmd -rc_name $rc_name", $this_rc_worker_count, $iteration, $rc_name, $rc_name2xparams{ $rc_name } || '');
$current_meadow->submit_workers($worker_cmd.($special_task ? '' : " -rc_name $rc_name"), $this_rc_worker_count, $iteration, $rc_name, $rc_name2xparams{ $rc_name } || '');
}
} else {
print "Not submitting any workers this iteration\n";
}
$failed_analyses = $queen->get_num_failed_analyses($this_analysis);
$failed_analyses = $queen->get_num_failed_analyses($run_analysis);
$num_of_remaining_jobs = $queen->get_remaining_jobs_show_hive_progress();
} while( $keep_alive
......
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