an attempt to allow multiple users' beekeepers to keep one hive (needs more testing)

modules/Bio/EnsEMBL/Hive/Meadow.pm

@@ -34,12 +34,18 @@ sub meadow_options {    # general options that different Meadows can plug into t
     return $self->{'_meadow_options'} || '';
 }
 
+sub job_name_prefix {
+    my $self = shift @_;
+
+    return ($self->pipeline_name() ? $self->pipeline_name().'-' : '') . 'Hive';
+}
+
 sub generate_job_name {
     my ($self, $worker_count, $iteration, $rc_id) = @_;
     $rc_id ||= 0;
 
-    return ($self->pipeline_name() ? $self->pipeline_name().'-' : '')
-        ."Hive${rc_id}_${iteration}"
+    return $self->job_name_prefix()
+        ."${rc_id}_${iteration}"
         . (($worker_count > 1) ? "[1-${worker_count}]" : '');
 }
 
@@ -49,7 +55,7 @@ sub responsible_for_worker {
     return $worker->beekeeper() eq $self->type();
 }
 
-sub check_worker_is_alive {
+sub check_worker_is_alive_and_mine {
     my ($self, $worker) = @_;
 
     die "Please use a derived method";

modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm

@@ -29,7 +29,7 @@ sub responsible_for_worker {
     return ( $self->SUPER::responsible_for_worker($worker) && ($worker->host eq hostname()) );
 }
 
-sub status_of_all_my_workers { # returns a hashref
+sub status_of_all_our_workers { # returns a hashref
     my ($self) = @_;
 
     my $cmd = 'ps x -o state,pid,command -w -w | grep runWorker.pl | grep -v "grep runWorker.pl" ';
@@ -53,19 +53,21 @@ sub status_of_all_my_workers { # returns a hashref
     return \%status_hash;
 }
 
-sub check_worker_is_alive {
+sub check_worker_is_alive_and_mine {
     my ($self, $worker) = @_;
 
-    my $cmd = 'ps '. $worker->process_id . ' 2>&1 | grep ' . $worker->process_id;
-    my $is_alive = qx/$cmd/;
-    return $is_alive;
+    my $wpid = $worker->process_id();
+    my $cmd = qq{ps x | grep $wpid | grep -v 'grep $wpid'};
+    my $is_alive_and_mine = qx/$cmd/;
+
+    return $is_alive_and_mine;
 }
 
 sub kill_worker {
     my ($self, $worker) = @_;
 
     if( $self->responsible_for_worker($worker) ) {
-        if($self->check_worker_is_alive($worker)) {
+        if($self->check_worker_is_alive_and_mine($worker)) {
             my $cmd = 'kill -9 '.$worker->process_id();
             system($cmd);
         } else {

modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm

@@ -26,13 +26,8 @@ sub get_current_worker_process_id {
 sub count_pending_workers {
     my ($self) = @_;
 
-    my $cmd = "bjobs -w ";
-    if(my $pipeline_name = $self->pipeline_name()) {
-        $cmd .= " | grep '${pipeline_name}-Hive'";
-    } else {
-        $cmd .= " | grep Hive";
-    }
-    $cmd .= " | grep -c PEND";
+    my $jnp = $self->job_name_prefix();
+    my $cmd = qq{bjobs -w -J '${jnp}*' -u all | grep -c PEND};
 
     my $pend_count = qx/$cmd/;
     chomp($pend_count);
@@ -40,15 +35,11 @@ sub count_pending_workers {
     return $pend_count;
 }
 
-sub status_of_all_my_workers { # returns a hashref
+sub status_of_all_our_workers { # returns a hashref
     my ($self) = @_;
 
-    my $cmd = 'bjobs -w 2>&1 | grep -v "No unfinished job found" | grep -v JOBID | grep -v DONE | grep -v EXIT';
-    if(my $pipeline_name = $self->pipeline_name()) {
-        $cmd .= " | grep '${pipeline_name}-Hive'";
-    } else {
-        $cmd .= " | grep Hive";
-    }
+    my $jnp = $self->job_name_prefix();
+    my $cmd = qq{bjobs -w -J '${jnp}*' -u all 2>&1 | grep -v 'No unfinished job found' | grep -v JOBID | grep -v DONE | grep -v EXIT};
 
     my %status_hash = ();
     foreach my $line (`$cmd`) {
@@ -64,18 +55,21 @@ sub status_of_all_my_workers { # returns a hashref
     return \%status_hash;
 }
 
-sub check_worker_is_alive {
+sub check_worker_is_alive_and_mine {
     my ($self, $worker) = @_;
 
-    my $cmd = 'bjobs '. $worker->process_id . ' 2>&1 | grep -v "not found" | grep -v JOBID | grep -v EXIT';
-    my $is_alive = qx/$cmd/;
-    return $is_alive;
+    my $wpid = $worker->process_id();
+    my $this_user = $ENV{'USER'};
+    my $cmd = qq{bjobs $wpid -u $this_user 2>&1 | grep -v 'not found' | grep -v JOBID | grep -v EXIT};
+
+    my $is_alive_and_mine = qx/$cmd/;
+    return $is_alive_and_mine;
 }
 
 sub kill_worker {
     my ($self, $worker) = @_;
 
-    if($self->check_worker_is_alive($worker)) {
+    if($self->check_worker_is_alive_and_mine($worker)) {
         my $cmd = 'bkill '.$worker->process_id();
         system($cmd);
     } else {

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -201,7 +201,7 @@ sub register_worker_death {
 sub check_for_dead_workers {
     my ($self, $meadow, $check_buried_in_haste) = @_;
 
-    my $worker_status_hash    = $meadow->status_of_all_my_workers();
+    my $worker_status_hash    = $meadow->status_of_all_our_workers();
     my %worker_status_summary = ();
     my $queen_worker_list     = $self->fetch_overdue_workers(0);