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Commit adf206b2 authored by Leo Gordon's avatar Leo Gordon
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cause_of_death="" no longer used for decision making, cause_of_death IS NULL... 

cause_of_death="" no longer used for decision making, cause_of_death IS NULL by default and FATALITY renamed UNKNOWN for clarity
parent 6f85948d
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Showing with 43 additions and 30 deletions
modules/Bio/EnsEMBL/Hive/Queen.pm
View file @ adf206b2
......@@ -283,7 +283,7 @@ sub register_worker_death {
return unless($worker);
my $cod = $worker->cause_of_death();
my $cod = $worker->cause_of_death() || 'UNKNOWN'; # make sure we do not attempt to insert a void
my $sql = "UPDATE worker SET died=CURRENT_TIMESTAMP, last_check_in=CURRENT_TIMESTAMP";
$sql .= " ,status='DEAD'";
......@@ -300,7 +300,7 @@ sub register_worker_death {
if($cod eq 'NO_WORK') {
$self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, 'ALL_CLAIMED');
}
if($cod eq 'FATALITY'
if($cod eq 'UNKNOWN'
or $cod eq 'MEMLIMIT'
or $cod eq 'RUNLIMIT'
or $cod eq 'KILLED_BY_USER') {
......@@ -372,7 +372,7 @@ sub check_for_dead_workers { # scans the whole Valley for lost Workers (but i
warn "GarbageCollector:\tReleasing the jobs\n";
while(my ($process_id, $worker) = each %$pid_to_lost_worker) {
$worker->cause_of_death( $wpid_to_cod->{$process_id} || 'FATALITY');
$worker->cause_of_death( $wpid_to_cod->{$process_id} || 'UNKNOWN');
$self->register_worker_death($worker);
}
}
......@@ -449,7 +449,7 @@ sub fetch_overdue_workers {
$overdue_secs = 3600 unless(defined($overdue_secs));
my $constraint = "cause_of_death='' AND ".
my $constraint = "status!='DEAD' AND ".
( ($self->dbc->driver eq 'sqlite')
? "(strftime('%s','now')-strftime('%s',last_check_in))>$overdue_secs"
: "(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(last_check_in))>$overdue_secs");
......@@ -676,8 +676,10 @@ sub get_hive_current_load {
my $self = shift;
my $sql = qq{
SELECT sum(1/hive_capacity)
FROM worker JOIN analysis_stats USING(analysis_id)
WHERE cause_of_death ='' AND hive_capacity>0
FROM worker w
JOIN analysis_stats USING(analysis_id)
WHERE w.status!='DEAD'
AND hive_capacity>0
};
my $sth = $self->prepare($sql);
$sth->execute();
......@@ -690,8 +692,11 @@ sub get_hive_current_load {
sub count_running_workers {
my ($self, $analysis_id) = @_;
my $sql = "SELECT count(*) FROM worker WHERE cause_of_death =''"
. ($analysis_id ? " AND analysis_id='$analysis_id'" : '');
my $sql = qq{
SELECT count(*)
FROM worker
WHERE status!='DEAD'
} . ($analysis_id ? " AND analysis_id='$analysis_id'" : '');
my $sth = $self->prepare($sql);
$sth->execute();
......@@ -852,25 +857,27 @@ sub print_analysis_status {
sub print_running_worker_counts {
my $self = shift;
my $self = shift;
print "\n===== Stats of live Workers according to the Queen: ======\n";
my $sql = qq{ SELECT logic_name, count(*)
FROM worker
JOIN analysis_base USING(analysis_id)
WHERE worker.cause_of_death=''
GROUP BY worker.analysis_id
};
my $sql = qq{
SELECT logic_name, count(*)
FROM worker w
JOIN analysis_base USING(analysis_id)
WHERE w.status!='DEAD'
GROUP BY analysis_id
};
my $total_workers = 0;
my $sth = $self->prepare($sql);
$sth->execute();
while((my $logic_name, my $worker_count)=$sth->fetchrow_array()) {
printf("%30s : %d workers\n", $logic_name, $worker_count);
$total_workers += $worker_count;
}
$sth->finish;
printf("%30s : %d workers\n\n", '======= TOTAL =======', $total_workers);
my $total_workers = 0;
my $sth = $self->prepare($sql);
$sth->execute();
print "\n===== Stats of live Workers according to the Queen: ======\n";
while((my $logic_name, my $worker_count)=$sth->fetchrow_array()) {
printf("%30s : %d workers\n", $logic_name, $worker_count);
$total_workers += $worker_count;
}
$sth->finish;
printf("%30s : %d workers\n\n", '======= TOTAL =======', $total_workers);
}
......@@ -899,8 +906,9 @@ sub monitor {
sum(work_done/(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(born)))/count(*), }
). qq{
group_concat(DISTINCT logic_name)
FROM worker left join analysis_base USING (analysis_id)
WHERE cause_of_death = ''
FROM worker w
LEFT JOIN analysis_base USING (analysis_id)
WHERE w.status!='DEAD'
};
my $sth = $self->prepare($sql);
......@@ -922,7 +930,7 @@ sub register_all_workers_dead {
my $overdueWorkers = $self->fetch_overdue_workers(0);
foreach my $worker (@{$overdueWorkers}) {
$worker->cause_of_death( 'FATALITY' ); # well, maybe we could have investigated further...
$worker->cause_of_death( 'UNKNOWN' ); # well, maybe we could have investigated further...
$self->register_worker_death($worker);
}
}
......
sql/patch_2012-10-06.sql 0 → 100644
View file @ adf206b2
# Adding the (default) NULL option and renaming 'FATALITY'-->'UNKNOWN'
ALTER TABLE worker MODIFY COLUMN cause_of_death enum('NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'UNKNOWN') DEFAULT NULL;
sql/tables.sql
View file @ adf206b2
......@@ -82,7 +82,7 @@ CREATE TABLE worker (
born timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
last_check_in datetime NOT NULL,
died datetime DEFAULT NULL,
cause_of_death enum('', 'NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'FATALITY') DEFAULT '' NOT NULL,
cause_of_death enum('NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'UNKNOWN') DEFAULT NULL,
log_dir varchar(80) DEFAULT NULL,
PRIMARY KEY (worker_id),
......
sql/tables.sqlite
View file @ adf206b2
......@@ -75,7 +75,7 @@ CREATE TABLE worker (
born timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
last_check_in datetime NOT NULL,
died datetime DEFAULT NULL,
cause_of_death TEXT DEFAULT '' NOT NULL, /* enum('', 'NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'FATALITY') DEFAULT '' NOT NULL */
cause_of_death TEXT DEFAULT NULL, /* enum('NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'UNKNOWN') DEFAULT NULL */
log_dir varchar(80) DEFAULT NULL
);
......
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