From e47201c5d2f0726091e2b827b83726ae90635c74 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 1 May 2012 14:55:02 +0000
Subject: [PATCH] bugfix: make sure runtime_msec is stored even when a job dies
---
modules/Bio/EnsEMBL/Hive/Worker.pm | 57 ++++++++++++++----------------
1 file changed, 26 insertions(+), 31 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/Worker.pm b/modules/Bio/EnsEMBL/Hive/Worker.pm
index bf0b27f4b..a4f8fa31d 100755
--- a/modules/Bio/EnsEMBL/Hive/Worker.pm
+++ b/modules/Bio/EnsEMBL/Hive/Worker.pm
@@ -582,11 +582,24 @@ sub run_one_batch {
foreach my $job (@{$jobs}) {
$job->print_job if($self->debug);
+ my $job_stopwatch = Bio::EnsEMBL::Hive::Utils::Stopwatch->new();
+
$self->start_job_output_redirection($job); # switch logging into job's STDERR
eval { # capture any throw/die
- $self->run_module_with_job($job);
+
+ $self->enter_status('COMPILATION', $job); # ToDo: when Runnables are ready, switch to compiling once per batch (saves time)
+ my $runnable_db = $self->analysis->process or die "Unknown compilation error";
+
+ $self->queen->dbc->query_count(0);
+ $job_stopwatch->restart();
+
+ $self->run_module_with_job($runnable_db, $job);
};
my $msg_thrown = $@;
+
+ $job->runtime_msec( $job_stopwatch->get_elapsed );
+ $job->query_count( $self->queen->dbc->query_count );
+
my $job_id = $job->dbID();
my $job_completion_line = "\njob $job_id : complete\n";
@@ -638,50 +651,34 @@ sub run_one_batch {
sub run_module_with_job {
- my ($self, $job) = @_;
+ my ($self, $runnable_db, $job) = @_;
- $job->incomplete(1);
- $job->autoflow(1);
-
- $self->enter_status('COMPILATION', $job);
- my $runObj = $self->analysis->process or die "Unknown compilation error";
-
- my $job_stopwatch = Bio::EnsEMBL::Hive::Utils::Stopwatch->new()->restart();
- $self->queen->dbc->query_count(0);
+ $runnable_db->input_job($job);
+ $runnable_db->queen($self->queen);
+ $runnable_db->worker($self);
+ $runnable_db->debug($self->debug);
- #pass the input_id from the job into the Process object
- if( $runObj->isa('Bio::EnsEMBL::Hive::Process') ) {
- $runObj->input_job($job);
- $runObj->queen($self->queen);
- $runObj->worker($self);
- $runObj->debug($self->debug);
-
- $job->param_init( $runObj->strict_hash_format(), $runObj->param_defaults(), $self->db->get_MetaContainer->get_param_hash(), $self->analysis->parameters(), $job->input_id() );
-
- } else {
- $runObj->input_id($job->input_id);
- $runObj->db($self->db);
-
- $job->param_init( 0, $self->db->get_MetaContainer->get_param_hash(), $self->analysis->parameters(), $job->input_id() ); # Well, why not?
- }
+ $job->param_init( $runnable_db->strict_hash_format(), $runnable_db->param_defaults(), $self->db->get_MetaContainer->get_param_hash(), $self->analysis->parameters(), $job->input_id() );
+ $job->incomplete(1);
+ $job->autoflow(1);
$self->enter_status('GET_INPUT', $job);
$self->{'fetching_stopwatch'}->continue();
- $runObj->fetch_input;
+ $runnable_db->fetch_input;
$self->{'fetching_stopwatch'}->pause();
$self->enter_status('RUN', $job);
$self->{'running_stopwatch'}->continue();
- $runObj->run;
+ $runnable_db->run;
$self->{'running_stopwatch'}->pause();
if($self->execute_writes) {
$self->enter_status('WRITE_OUTPUT', $job);
$self->{'writing_stopwatch'}->continue();
- $runObj->write_output;
+ $runnable_db->write_output;
$self->{'writing_stopwatch'}->pause();
if( $job->autoflow ) {
@@ -698,12 +695,10 @@ sub run_module_with_job {
die "There are cached semaphored fans for which a funnel job (dataflow_rule_id(s) ".join(',',@zombie_funnel_dataflow_rule_ids).") has never been dataflown";
}
- $job->query_count($self->queen->dbc->query_count);
- $job->runtime_msec( $job_stopwatch->get_elapsed );
-
$job->incomplete(0);
}
+
sub enter_status {
my ($self, $status, $job) = @_;
--
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