Commit ba5578d5 authored by Jessica Severin's avatar Jessica Severin
Browse files

implemented a proper 'dead worker on lsf' checking system. Workers are

created registered to the LSF beekeeper, and the 'dead' check is done only
where the beekeeper is LSF and it's 15minutes overdue for it's checkin.
The check is done with an ssh to the workers registered host machine and
a 'ps' command to see if the registered process_id of the worker is still
running.  This allows jobs to be submitted via lsf arrays (which only give
a single LSF job id for the entire array), but still allows each worker
to be checked separately.
parent 81e809d5
......@@ -150,7 +150,7 @@ sub run_next_worker_clutch
my $hive_capacity = $analysis_stats->hive_capacity;
my $cmd;
my $worker_cmd = "./runWorker.pl -logic_name " . $analysis->logic_name;
my $worker_cmd = "./runWorker.pl -bk LSF -logic_name " . $analysis->logic_name;
$worker_cmd .= " -conf $conf_file" if($conf_file);
$worker_cmd .= " -url $url" if($url);
......@@ -177,19 +177,23 @@ sub check_for_dead_workers {
my $self = shift;
my $queen = shift;
my $host = hostname;
my $overdueWorkers = $queen->fetch_overdue_workers(5*60); #overdue by 5 minutes
my $overdueWorkers = $queen->fetch_overdue_workers(15*60); #overdue by 15 minutes
print(scalar(@{$overdueWorkers}), " overdue workers\n");
foreach my $worker (@{$overdueWorkers}) {
printf("%10d %20s analysis_id=%d\n", $worker->hive_id,$worker->host, $worker->analysis->dbID);
#if(($worker->beekeeper eq '') and ($worker->host eq $host)) {
#print(" is one of mine\n");
my $cmd = "ps -p ". $worker->process_id;
if($worker->beekeeper eq 'LSF') {
printf("%10d %20s analysis_id=%d : ", $worker->hive_id,$worker->host, $worker->analysis->dbID);
my $cmd = "ssh -x ". $worker->host . " ps -p ". $worker->process_id . "|grep -v PID";
#print(" check worker with : $cmd\n");
my $check = qx/$cmd/;
$queen->register_worker_death($worker);
#}
unless($check) {
print("worker is missing => it DIED!!\n");
$queen->register_worker_death($worker);
}
else {
print("ALIVE and running\n");
}
}
}
}
......
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