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#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Hive::Queen
The Queen of the Hive based job control system
The Queen of the Hive based job control system is responsible to 'birthing' the
correct number of workers of the right type so that they can find jobs to do.
It will also free up jobs of Workers that died unexpectantly so that other workers
can claim them to do.
Hive based processing is a concept based on a more controlled version
of an autonomous agent type system. Each worker is not told what to do
(like a centralized control system - like the current pipeline system)
but rather queries a central database for jobs (give me jobs).
Each worker is linked to an analysis_id, registers its self on creation
into the Hive, creates a RunnableDB instance of the Analysis->module,
gets $runnable->batch_size() jobs from the analysis_job table, does its
work, creates the next layer of analysis_job entries by interfacing to
the DataflowRuleAdaptor to determine the analyses it needs to pass it's
output data to and creates jobs on the next analysis's database.
It repeats this cycle until it's lived it's lifetime or until there are no
more jobs left.
The lifetime limit is just a safety limit to prevent these from 'infecting'
a system.
The Queens job is to simply birth Workers of the correct analysis_id to get the
work down. The only other thing the Queen does is free up jobs that were
claimed by Workers that died unexpectantly so that other workers can take
over the work.
The Beekeeper is in charge of interfacing between the Queen and a compute resource
or 'compute farm'. It's job is to query Queens if they need any workers and to
send the requested number of workers to open machines via the runWorker.pl script.
It is also responsible for interfacing with the Queen to identify worker which died
unexpectantly.
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Hive::Queen;
use strict;
use strict;
use Bio::EnsEMBL::Hive::Worker;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Sys::Hostname;
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
#
# STORE METHODS
#
################
=head2 create_new_worker
Arg [1] : $analysis_id
Example :
Description:
Returntype : Bio::EnsEMBL::Hive::Worker
Exceptions :
Caller :
=cut
sub create_new_worker {
my ($self,$analysis_id) = @_;
my $analStatsDBA = $self->db->get_AnalysisStatsAdaptor;
return undef unless($analStatsDBA);
my $analysisStats = $analStatsDBA->fetch_by_analysis_id($analysis_id);
return undef unless($analysisStats);
$analysisStats->print_stats;
if($analysisStats->status eq 'BLOCKED') {
print("Analysis is BLOCKED, can't create workers\n");
return undef;
}
if($analysisStats->status eq 'DONE') {
print("Analysis is DONE, don't need to create workers\n");
return undef;
}
my $host = hostname;
my $ppid = getppid;
my $sql = "INSERT INTO hive SET born=now(), last_check_in=now()".
",process_id='$ppid' ".
",analysis_id='$analysis_id' ".
",host='$host'";
my $sth = $self->prepare($sql);
$sth->execute();
my $hive_id = $sth->{'mysql_insertid'};
$sth->finish;
my $worker = $self->_fetch_by_hive_id($hive_id);
$worker=undef unless($worker and $worker->analysis);
if($worker and $analysisStats) {
$analStatsDBA->update_status($analysis_id, 'WORKING');
}
return $worker;
}
sub register_worker_death {
my ($self, $worker) = @_;
return unless($worker);
# if called without a defined cause_of_death, assume catastrophic failure
$worker->cause_of_death('FATALITY') unless(defined($worker->cause_of_death));
my $sql = "UPDATE hive SET died=now(), last_check_in=now()";
$sql .= " ,work_done='" . $worker->work_done . "'";
$sql .= " ,cause_of_death='". $worker->cause_of_death ."'";
$sql .= " WHERE hive_id='" . $worker->hive_id ."'";
my $sth = $self->prepare($sql);
$sth->execute();
$sth->finish;
if($worker->cause_of_death eq "NO_WORK") {
$self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, "ALL_CLAIMED");
}
if($worker->cause_of_death eq "FATALITY") {
#print("FATAL DEATH Arrrrgggghhhhhhhh (hive_id=",$worker->hive_id,")\n");
$self->db->get_AnalysisJobAdaptor->reset_dead_jobs_for_worker($worker);
sub worker_check_in {
my ($self, $worker) = @_;
return unless($worker);
my $sql = "UPDATE hive SET last_check_in=now()";
$sql .= " WHERE hive_id='" . $worker->hive_id ."'";
my $sth = $self->prepare($sql);
$sth->execute();
$sth->finish;
}
sub fetch_overdue_workers {
my ($self,$overdue_secs) = @_;
$overdue_secs = 3600 unless(defined($overdue_secs));
my $constraint = "h.cause_of_death='' ".
"AND (UNIX_TIMESTAMP()-UNIX_TIMESTAMP(h.last_check_in))>$overdue_secs";
return $self->_generic_fetch($constraint);
}
sub update_analysis_stats {
my $self = shift;
my $sql = "SELECT analysis.analysis_id, status, count(*) ".
"FROM analysis_job, analysis ".
"WHERE analysis_job.analysis_id=analysis.analysis_id ".
"GROUP BY analysis_job.analysis_id, status";
my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
my $analysisStats = undef;
my $sth = $self->prepare($sql);
$sth->execute();
while (my ($analysis_id, $status, $count)=$sth->fetchrow_array()) {
unless(defined($analysisStats) and $analysisStats->analysis_id==$analysis_id) {
$analysisStats->determine_status->update() if($analysisStats);
$analysisStats = $statsDBA->fetch_by_analysis_id($analysis_id);
$analysisStats->total_job_count(0);
$analysisStats->unclaimed_job_count(0);
$analysisStats->done_job_count(0);
$analysisStats->num_required_workers(0);
}
my $total = $analysisStats->total_job_count();
$analysisStats->total_job_count($total + $count);
if($status eq 'READY') {
$analysisStats->unclaimed_job_count($count);
my $numWorkers = $count/$analysisStats->batch_size;
$numWorkers=1 if($numWorkers<1);
if($analysisStats->hive_capacity>0 and $numWorkers > $analysisStats->hive_capacity) {
$numWorkers=$analysisStats->hive_capacity;
}
$analysisStats->num_required_workers($numWorkers);
}
if($status eq 'DONE') { $analysisStats->done_job_count($count); }
}
$analysisStats->determine_status->update() if($analysisStats);
$sth->finish;
}
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#
# INTERNAL METHODS
#
###################
=head2 _fetch_by_hive_id
Arg [1] : int $id
the unique database identifier for the feature to be obtained
Example : $feat = $adaptor->fetch_by_dbID(1234);
Description: Returns the feature created from the database defined by the
the id $id.
Returntype : Bio::EnsEMBL::Hive::Worker
Exceptions : thrown if $id is not defined
Caller : general
=cut
sub _fetch_by_hive_id{
my ($self,$id) = @_;
unless(defined $id) {
$self->throw("fetch_by_dbID must have an id");
}
my @tabs = $self->_tables;
my $constraint = "h.hive_id = $id";
#return first element of _generic_fetch list
my ($obj) = @{$self->_generic_fetch($constraint)};
return $obj;
}
=head2 _generic_fetch
Arg [1] : (optional) string $constraint
An SQL query constraint (i.e. part of the WHERE clause)
Arg [2] : (optional) string $logic_name
the logic_name of the analysis of the features to obtain
Example : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
Description: Performs a database fetch and returns feature objects in
contig coordinates.
Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
Exceptions : none
Caller : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch
=cut
sub _generic_fetch {
my ($self, $constraint, $join) = @_;
my @tables = $self->_tables;
my $columns = join(', ', $self->_columns());
if ($join) {
foreach my $single_join (@{$join}) {
my ($tablename, $condition, $extra_columns) = @{$single_join};
if ($tablename && $condition) {
push @tables, $tablename;
if($constraint) {
$constraint .= " AND $condition";
} else {
$constraint = " $condition";
}
}
if ($extra_columns) {
$columns .= ", " . join(', ', @{$extra_columns});
}
}
}
#construct a nice table string like 'table1 t1, table2 t2'
my $tablenames = join(', ', map({ join(' ', @$_) } @tables));
my $sql = "SELECT $columns FROM $tablenames";
my $default_where = $self->_default_where_clause;
my $final_clause = $self->_final_clause;
#append a where clause if it was defined
if($constraint) {
$sql .= " WHERE $constraint ";
if($default_where) {
$sql .= " AND $default_where ";
}
} elsif($default_where) {
$sql .= " WHERE $default_where ";
}
#append additional clauses which may have been defined
$sql .= " $final_clause";
my $sth = $self->prepare($sql);
$sth->execute;
# print STDERR $sql,"\n";
return $self->_objs_from_sth($sth);
}
sub _tables {
my $self = shift;
return (['hive', 'h']);
}
sub _columns {
my $self = shift;
return qw (h.hive_id
h.analysis_id
h.host
h.process_id
h.work_done
h.born
h.last_check_in
h.died
h.cause_of_death
);
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my %column;
$sth->bind_columns( \( @column{ @{$sth->{NAME_lc} } } ));
my @workers = ();
while ($sth->fetch()) {
my $worker = new Bio::EnsEMBL::Hive::Worker;
$worker->init;
$worker->hive_id($column{'hive_id'});
$worker->host($column{'host'});
$worker->process_id($column{'process_id'});
$worker->work_done($column{'work_done'});
$worker->born($column{'born'});
$worker->last_check_in($column{'last_check_in'});
$worker->died($column{'died'});
$worker->cause_of_death($column{'cause_of_death'});
$worker->adaptor($self);
$worker->db($self->db);
if($column{'analysis_id'} and $self->db->get_AnalysisAdaptor) {
$worker->analysis($self->db->get_AnalysisAdaptor->fetch_by_dbID($column{'analysis_id'}));
}
push @workers, $worker;
}
$sth->finish;
return \@workers
}
sub _default_where_clause {
my $self = shift;
return '';
}
sub _final_clause {
my $self = shift;
return '';
}
1;