Skip to content

GitLab

Commit ff694cc1 authored by Leo Gordon's avatar Leo Gordon
Browse files

if runWorker.pl is run manually, rc_name may stay NULL in the database

parent 9397978c
Hide whitespace changes
Inline Side-by-side
Showing with 27 additions and 22 deletions
modules/Bio/EnsEMBL/Hive/Queen.pm
View file @ ff694cc1
......@@ -113,13 +113,12 @@ sub create_new_worker {
rearrange([qw(meadow_type meadow_name process_id exec_host resource_class_id resource_class_name
no_write debug worker_log_dir hive_log_dir job_limit life_span no_cleanup retry_throwing_jobs compile_module_once) ], @args);
if($resource_class_name) {
if( defined($resource_class_name) ) {
my $rc = $self->db->get_ResourceClassAdaptor->fetch_by_name($resource_class_name)
or die "resource_class with name='$resource_class_name' could not be fetched from the database";
$resource_class_id = $rc->dbID;
}
$resource_class_id ||= 1;
my $sql = q{INSERT INTO worker (born, last_check_in, meadow_type, meadow_name, host, process_id, resource_class_id)
VALUES (CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, ?, ?, ?, ?, ?)};
......@@ -190,7 +189,7 @@ sub specialize_new_worker {
my ($job, $analysis, $stats);
my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor;
if($job_id or $analysis_id or $logic_name) { # probably pre-specialized by running a runWorker.pl by hand
if($job_id or $analysis_id or $logic_name) { # probably pre-specialized from command-line
if($job_id) {
print "resetting and fetching job for job_id '$job_id'\n";
......@@ -215,8 +214,9 @@ sub specialize_new_worker {
or die "analysis with dbID='$analysis_id' could not be fetched from the database";
}
if($worker->resource_class_id != $analysis->resource_class_id) {
die "resource_class of analysis ".$analysis->logic_name." is incompatible with this Worker's resource_class";
if( $worker->resource_class_id
and $worker->resource_class_id != $analysis->resource_class_id) {
die "resource_class of analysis ".$analysis->logic_name." is incompatible with this Worker's resource_class";
}
$stats = $analysis_stats_adaptor->fetch_by_analysis_id($analysis_id);
......@@ -224,16 +224,16 @@ sub specialize_new_worker {
unless($job or $force) { # do we really need to run this analysis?
if($self->get_hive_current_load() >= 1.1) {
die "Hive is overloaded, can't create a worker";
die "Hive is overloaded, can't specialize a worker";
}
if($stats->status eq 'BLOCKED') {
die "Analysis is BLOCKED, can't create workers";
die "Analysis is BLOCKED, can't specialize a worker";
}
if($stats->num_required_workers <= 0) {
die "Analysis does not require workers at the moment";
die "Analysis requires 0 workers at the moment";
}
if($stats->status eq 'DONE') {
die "Analysis is DONE, don't need to create workers";
die "Analysis is DONE, and doesn't require workers";
}
}
......@@ -251,9 +251,16 @@ sub specialize_new_worker {
$worker->analysis_id( $analysis_id );
my $sth_update_analysis_id = $self->prepare( "UPDATE worker SET analysis_id=? WHERE worker_id=?" );
$sth_update_analysis_id->execute($worker->analysis_id, $worker->dbID);
$sth_update_analysis_id->finish;
if($job) {
$worker->_specific_job($job);
} else { # count it as autonomous worker sharing the load of that analysis:
$stats->update_status('WORKING');
$analysis_stats_adaptor->decrease_required_workers($worker->analysis_id);
}
......@@ -267,12 +274,6 @@ sub specialize_new_worker {
$analysis_stats_adaptor->increase_running_workers($worker->analysis_id);
}
my $sth_update_analysis_id = $self->prepare( "UPDATE worker SET analysis_id=? WHERE worker_id=?" );
$sth_update_analysis_id->execute($worker->analysis_id, $worker->dbID);
$sth_update_analysis_id->finish;
$stats->update_status('WORKING');
return $worker;
}
......
scripts/runWorker.pl
View file @ ff694cc1
......@@ -20,7 +20,7 @@ my $db_conf = {
};
my ($reg_conf, $reg_alias, $url); # Connection parameters
my ($rc_id, $rc_name, $analysis_id, $logic_name, $job_id); # Task specification parameters
my ($resource_class_id, $resource_class_name, $analysis_id, $logic_name, $job_id); # Task specification parameters
my ($job_limit, $life_span, $no_cleanup, $no_write, $hive_log_dir, $worker_log_dir, $retry_throwing_jobs, $compile_module_once, $force); # Worker control parameters
my ($help, $debug);
......@@ -37,8 +37,8 @@ GetOptions(
'database|dbname=s' => \$db_conf->{'-dbname'},
# Task specification parameters:
'rc_id=i' => \$rc_id,
'rc_name=s' => \$rc_name,
'rc_id=i' => \$resource_class_id,
'rc_name=s' => \$resource_class_name,
'analysis_id=i' => \$analysis_id,
'logic_name=s' => \$logic_name,
'job_id=i' => \$job_id,
......@@ -100,8 +100,8 @@ eval {
-meadow_name => $meadow_name,
-process_id => $process_id,
-exec_host => $exec_host,
-rc_id => $rc_id,
-rc_name => $rc_name,
-resource_class_id => $resource_class_id,
-resource_class_name => $resource_class_name,
# Worker control parameters:
-job_limit => $job_limit,
......
sql/patch_2012-10-13.sql 0 → 100644
View file @ ff694cc1
# In case of running runWorker.pl manually it is better not to set the resource_class_id in the Worker:
ALTER TABLE worker ADD COLUMN resource_class_id int(10) unsigned DEFAULT NULL;
sql/tables.sql
View file @ ff694cc1
......@@ -76,7 +76,7 @@ CREATE TABLE worker (
meadow_name varchar(40) NOT NULL,
host varchar(40) NOT NULL,
process_id varchar(40) NOT NULL,
resource_class_id int(10) unsigned NOT NULL,
resource_class_id int(10) unsigned DEFAULT NULL,
analysis_id int(10) unsigned DEFAULT NULL,
work_done int(11) DEFAULT '0' NOT NULL,
......
sql/tables.sqlite
View file @ ff694cc1
......@@ -69,7 +69,7 @@ CREATE TABLE worker (
meadow_name varchar(40) NOT NULL,
host varchar(40) NOT NULL,
process_id varchar(40) NOT NULL,
resource_class_id INTEGER NOT NULL,
resource_class_id INTEGER DEFAULT NULL,
analysis_id INTEGER DEFAULT NULL,
work_done int(11) DEFAULT '0' NOT NULL,
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment