Queen.pm 32.4 KB
Newer Older
Jessica Severin's avatar
Jessica Severin committed
1 2 3 4 5 6
#
# You may distribute this module under the same terms as perl itself

=pod 

=head1 NAME
7

8
  Bio::EnsEMBL::Hive::Queen
Jessica Severin's avatar
Jessica Severin committed
9 10

=head1 SYNOPSIS
11

12
  The Queen of the Hive based job control system
Jessica Severin's avatar
Jessica Severin committed
13 14

=head1 DESCRIPTION
15

16 17 18 19 20 21 22 23 24 25 26 27
  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,
28
  gets $worker->batch_size() jobs from the analysis_job table, does its
29
  work, creates the next layer of analysis_job entries by interfacing to
30 31 32
  the DataflowRuleAdaptor to determine the analyses it needs to pass its
  output data to and creates jobs on the next analysis database.
  It repeats this cycle until it has lived its lifetime or until there are no
33 34 35 36 37 38 39 40 41 42
  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
43
  or 'compute farm'.  Its job is to query Queens if they need any workers and to
44 45 46
  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.
Jessica Severin's avatar
Jessica Severin committed
47 48

=head1 CONTACT
49

50
  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Jessica Severin's avatar
Jessica Severin committed
51 52

=head1 APPENDIX
53

54 55
  The rest of the documentation details each of the object methods. 
  Internal methods are usually preceded with a _
Jessica Severin's avatar
Jessica Severin committed
56 57 58

=cut

59

Jessica Severin's avatar
Jessica Severin committed
60 61 62
package Bio::EnsEMBL::Hive::Queen;

use strict;
63
use POSIX;
64 65 66
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;

Jessica Severin's avatar
Jessica Severin committed
67 68 69
use Bio::EnsEMBL::Hive::Worker;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Sys::Hostname;
70
use Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
Jessica Severin's avatar
Jessica Severin committed
71

72

Jessica Severin's avatar
Jessica Severin committed
73 74
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);

75
############################
Jessica Severin's avatar
Jessica Severin committed
76
#
77
# PUBLIC API for Workers
Jessica Severin's avatar
Jessica Severin committed
78
#
79
############################
Jessica Severin's avatar
Jessica Severin committed
80 81 82

=head2 create_new_worker

83
  Arg [1]    : $analysis_id (optional)
Jessica Severin's avatar
Jessica Severin committed
84
  Example    :
85 86 87 88 89 90
  Description: If analysis_id is specified it will try to create a worker based
               on that analysis.  If not specified the queen will analyze the hive
               and pick the analysis that has the most amount of work to be done.
               It creates an entry in the hive table, and returns a Worker object 
               based on that insert.  This guarantees that each worker registered
               in this queens hive is properly registered.
Jessica Severin's avatar
Jessica Severin committed
91 92 93 94 95 96 97
  Returntype : Bio::EnsEMBL::Hive::Worker
  Exceptions :
  Caller     :

=cut

sub create_new_worker {
98 99
  my ($self, @args) = @_;

Leo Gordon's avatar
Leo Gordon committed
100 101
  my ($rc_id, $analysis_id, $beekeeper ,$pid, $job, $no_write) =
     rearrange([qw(rc_id analysis_id beekeeper process_id job no_write) ], @args);
Jessica Severin's avatar
Jessica Severin committed
102

103
  my $analStatsDBA = $self->db->get_AnalysisStatsAdaptor;
104
  return undef unless($analStatsDBA);
105

106
  $analysis_id = $job->analysis_id if(defined($job));
107
  
108 109 110
  my $analysisStats;
  if($analysis_id) {
    $analysisStats = $analStatsDBA->fetch_by_analysis_id($analysis_id);
111
    $self->safe_synchronize_AnalysisStats($analysisStats);
112
    #return undef unless(($analysisStats->status ne 'BLOCKED') and ($analysisStats->num_required_workers > 0));
113
  } else {
Leo Gordon's avatar
Leo Gordon committed
114
    $analysisStats = $self->_pick_best_analysis_for_new_worker($rc_id);
115
  }
116
  return undef unless($analysisStats);
117

118 119
  unless($job) {
    #go into autonomous mode
120
    return undef if($self->get_hive_current_load() >= 1.1);
121
    
122 123
    $analStatsDBA->decrease_needed_workers($analysisStats->analysis_id);
    $analStatsDBA->increase_running_workers($analysisStats->analysis_id);
124 125 126 127 128 129 130 131 132 133
    $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;
    }
134
  }
135
  
Jessica Severin's avatar
Jessica Severin committed
136
  my $host = hostname;
137
  $pid = $$ unless($pid);
138
  $beekeeper = '' unless($beekeeper);
Jessica Severin's avatar
Jessica Severin committed
139

140 141 142
  my $sql = q{INSERT INTO hive 
              (born, last_check_in, process_id, analysis_id, beekeeper, host)
              VALUES (NOW(), NOW(), ?,?,?,?)};
Jessica Severin's avatar
Jessica Severin committed
143 144

  my $sth = $self->prepare($sql);
145
  $sth->execute($pid, $analysisStats->analysis_id, $beekeeper, $host);
Leo Gordon's avatar
Leo Gordon committed
146
  my $worker_id = $sth->{'mysql_insertid'};
Jessica Severin's avatar
Jessica Severin committed
147 148
  $sth->finish;

Leo Gordon's avatar
Leo Gordon committed
149
  my $worker = $self->fetch_by_worker_id($worker_id);
Jessica Severin's avatar
Jessica Severin committed
150 151
  $worker=undef unless($worker and $worker->analysis);

152
  if($worker and $analysisStats) {
153
    $analysisStats->update_status('WORKING');
Jessica Severin's avatar
Jessica Severin committed
154
  }
155 156 157 158
  
  $worker->_specific_job($job) if(defined($job));
  $worker->execute_writes(0) if($no_write);
  
Jessica Severin's avatar
Jessica Severin committed
159 160 161 162 163 164 165
  return $worker;
}

sub register_worker_death {
  my ($self, $worker) = @_;

  return unless($worker);
Leo Gordon's avatar
Leo Gordon committed
166

Leo Gordon's avatar
bugfix  
Leo Gordon committed
167 168 169
  my $cod = $worker->cause_of_death();

  unless ($cod eq 'HIVE_OVERLOAD') {
170 171 172 173
    ## HIVE_OVERLOAD occurs after a successful update of the analysis_stats teble. (c.f. Worker.pm)
    $worker->analysis->stats->adaptor->decrease_running_workers($worker->analysis->stats->analysis_id);
  }

Jessica Severin's avatar
Jessica Severin committed
174
  my $sql = "UPDATE hive SET died=now(), last_check_in=now()";
175
  $sql .= " ,status='DEAD'";
Jessica Severin's avatar
Jessica Severin committed
176
  $sql .= " ,work_done='" . $worker->work_done . "'";
Leo Gordon's avatar
bugfix  
Leo Gordon committed
177
  $sql .= " ,cause_of_death='$cod'";
Leo Gordon's avatar
Leo Gordon committed
178
  $sql .= " WHERE worker_id='" . $worker->worker_id ."'";
Jessica Severin's avatar
Jessica Severin committed
179

Leo Gordon's avatar
bugfix  
Leo Gordon committed
180
  $self->dbc->do( $sql );
181

Leo Gordon's avatar
bugfix  
Leo Gordon committed
182
  if($cod eq 'NO_WORK') {
183
    $self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, 'ALL_CLAIMED');
184
  }
Leo Gordon's avatar
bugfix  
Leo Gordon committed
185 186 187 188
  if($cod eq 'FATALITY'
  or $cod eq 'MEMLIMIT'
  or $cod eq 'RUNLIMIT'
  or $cod eq 'KILLED_BY_USER') {
Leo Gordon's avatar
Leo Gordon committed
189
    $self->db->get_AnalysisJobAdaptor->release_undone_jobs_from_worker($worker);
190
  }
191
  
192
  # re-sync the analysis_stats when a worker dies as part of dynamic sync system
193
  if($self->safe_synchronize_AnalysisStats($worker->analysis->stats)->status ne 'DONE') {
194 195
    # since I'm dying I should make sure there is someone to take my place after I'm gone ...
    # above synch still sees me as a 'living worker' so I need to compensate for that
196
    $self->db->get_AnalysisStatsAdaptor->increase_needed_workers($worker->analysis->dbID);
197 198
  }

Jessica Severin's avatar
Jessica Severin committed
199 200
}

Leo Gordon's avatar
Leo Gordon committed
201 202 203
sub check_for_dead_workers {
    my ($self, $meadow, $check_buried_in_haste) = @_;

204
    my $worker_status_hash    = $meadow->status_of_all_our_workers();
Leo Gordon's avatar
Leo Gordon committed
205 206 207 208 209
    my %worker_status_summary = ();
    my $queen_worker_list     = $self->fetch_overdue_workers(0);

    print "====== Live workers according to    Queen:".scalar(@$queen_worker_list).", Meadow:".scalar(keys %$worker_status_hash)."\n";

210 211
    my %gc_wpid_to_worker = ();

Leo Gordon's avatar
Leo Gordon committed
212 213 214 215 216 217 218 219
    foreach my $worker (@$queen_worker_list) {
        next unless($meadow->responsible_for_worker($worker));

        my $worker_pid = $worker->process_id();
        if(my $status = $worker_status_hash->{$worker_pid}) { # can be RUN|PEND|xSUSP
            $worker_status_summary{$status}++;
        } else {
            $worker_status_summary{'AWOL'}++;
220

221
            $gc_wpid_to_worker{$worker_pid} = $worker;
Leo Gordon's avatar
Leo Gordon committed
222 223 224 225
        }
    }
    print "\t".join(', ', map { "$_:$worker_status_summary{$_}" } keys %worker_status_summary)."\n\n";

226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242
    if(my $total_lost = scalar(keys %gc_wpid_to_worker)) {
        warn "GarbageCollector: Discovered $total_lost lost workers\n";

        my $wpid_to_cod = {};
        if(UNIVERSAL::can($meadow, 'find_out_causes')) {
            $wpid_to_cod = $meadow->find_out_causes( keys %gc_wpid_to_worker );
            my $lost_with_known_cod = scalar(keys %$wpid_to_cod);
            warn "GarbageCollector: Found why $lost_with_known_cod of them died\n";
        }

        warn "GarbageCollector: Releasing the jobs\n";
        while(my ($worker_pid, $worker) = each %gc_wpid_to_worker) {
            $worker->cause_of_death( $wpid_to_cod->{$worker_pid} || 'FATALITY');
            $self->register_worker_death($worker);
        }
    }

Leo Gordon's avatar
Leo Gordon committed
243 244 245 246 247 248 249 250
    if($check_buried_in_haste) {
        print "====== Checking for workers buried in haste... ";
        my $buried_in_haste_list = $self->fetch_dead_workers_with_jobs();
        if(my $bih_number = scalar(@$buried_in_haste_list)) {
            print "$bih_number, reclaiming jobs.\n\n";
            if($bih_number) {
                my $job_adaptor = $self->db->get_AnalysisJobAdaptor();
                foreach my $worker (@$buried_in_haste_list) {
Leo Gordon's avatar
Leo Gordon committed
251
                    $job_adaptor->release_undone_jobs_from_worker($worker);
Leo Gordon's avatar
Leo Gordon committed
252 253 254 255 256 257 258
                }
            }
        } else {
            print "none\n";
        }
    }
}
Jessica Severin's avatar
Jessica Severin committed
259

260
sub worker_check_in {
Jessica Severin's avatar
Jessica Severin committed
261 262 263 264
  my ($self, $worker) = @_;

  return unless($worker);
  my $sql = "UPDATE hive SET last_check_in=now()";
265
  $sql .= " ,work_done='" . $worker->work_done . "'";
Leo Gordon's avatar
Leo Gordon committed
266
  $sql .= " WHERE worker_id='" . $worker->worker_id ."'";
Jessica Severin's avatar
Jessica Severin committed
267 268 269 270

  my $sth = $self->prepare($sql);
  $sth->execute();
  $sth->finish;
271
  
272
  $self->safe_synchronize_AnalysisStats($worker->analysis->stats);
Jessica Severin's avatar
Jessica Severin committed
273 274 275
}


276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301
=head2 worker_grab_jobs

  Arg [1]           : Bio::EnsEMBL::Hive::Worker object $worker
  Example: 
    my $jobs  = $queen->worker_grab_jobs();
  Description: 
    For the specified worker, it will search available jobs, 
    and using the workers requested batch_size, claim/fetch that
    number of jobs, and then return them.
  Returntype : 
    reference to array of Bio::EnsEMBL::Hive::AnalysisJob objects
  Exceptions :
  Caller     :

=cut

sub worker_grab_jobs {
  my $self            = shift;
  my $worker          = shift;
  
  my $jobDBA = $self->db->get_AnalysisJobAdaptor;
  my $claim = $jobDBA->claim_jobs_for_worker($worker);
  my $jobs = $jobDBA->fetch_by_claim_analysis($claim, $worker->analysis->dbID);
  return $jobs;
}

302
=head2 reset_and_fetch_job_by_dbID
303 304 305

  Arg [1]: int $analysis_job_id
  Example: 
306
    my $job = $queen->reset_and_fetch_job_by_dbID($analysis_job_id);
307 308
  Description: 
    For the specified analysis_job_id it will fetch just that job, 
309 310 311
    reset it completely as if it has never run, and return it.  
    Specifying a specific job bypasses the safety checks, 
    thus multiple workers could be running the 
312 313
    same job simultaneously (use only for debugging).
  Returntype : 
314
    Bio::EnsEMBL::Hive::AnalysisJob object
315
  Exceptions :
316
  Caller     : beekeepers, runWorker.pl scripts
317 318 319

=cut

320 321
sub reset_and_fetch_job_by_dbID {
  my $self = shift;
322
  my $analysis_job_id = shift;
323
  
324
  my $jobDBA = $self->db->get_AnalysisJobAdaptor;
325 326 327 328 329
  $jobDBA->reset_job_by_dbID($analysis_job_id); 

  my $job = $jobDBA->fetch_by_dbID($analysis_job_id); 
  my $stats = $self->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id($job->analysis_id);
  $self->synchronize_AnalysisStats($stats);
330
  
331 332 333 334 335 336 337 338 339 340
  return $job;
}


sub worker_reclaim_job {
  my $self   = shift;
  my $worker = shift;
  my $job    = shift;

  return undef unless($job and $worker);
Leo Gordon's avatar
Leo Gordon committed
341
  $job->worker_id($worker->worker_id);
342
  $self->db->get_AnalysisJobAdaptor->reclaim_job($job);
343 344 345 346 347 348 349 350 351 352
  return $job;
}


######################################
#
# Public API interface for beekeeper
#
######################################

353 354 355
    # Note: asking for Queen->fetch_overdue_workers(0) essentially means
    #       "fetch all workers known to the Queen not to be officially dead"
    #
356 357 358 359 360 361 362 363 364 365
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);
}

366 367
sub fetch_failed_workers {
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
368

369 370 371 372
  my $constraint = "h.cause_of_death='FATALITY' ";
  return $self->_generic_fetch($constraint);
}

Leo Gordon's avatar
Leo Gordon committed
373 374 375
sub fetch_dead_workers_with_jobs {
  my $self = shift;

Leo Gordon's avatar
Leo Gordon committed
376
  # select h.worker_id from hive h, analysis_job WHERE h.worker_id=analysis_job.worker_id AND h.cause_of_death!='' AND analysis_job.status not in ('DONE', 'READY','FAILED') group by h.worker_id
Leo Gordon's avatar
Leo Gordon committed
377

Leo Gordon's avatar
bugfix  
Leo Gordon committed
378
  my $constraint = "h.cause_of_death!='' ";
Leo Gordon's avatar
Leo Gordon committed
379
  my $join = [[['analysis_job', 'j'], " h.worker_id=j.worker_id AND j.status NOT IN ('DONE', 'READY', 'FAILED') GROUP BY h.worker_id"]];
Leo Gordon's avatar
Leo Gordon committed
380 381
  return $self->_generic_fetch($constraint, $join);
}
Jessica Severin's avatar
Jessica Severin committed
382

383 384
=head2 synchronize_hive

Leo Gordon's avatar
Leo Gordon committed
385
  Arg [1]    : $filter_analysis (optional)
386 387 388 389 390 391 392 393 394 395 396
  Example    : $queen->synchronize_hive();
  Description: Runs through all analyses in the system and synchronizes
              the analysis_stats summary with the states in the analysis_job 
              and hive tables.  Then follows by checking all the blocking rules
              and blocks/unblocks analyses as needed.
  Exceptions : none
  Caller     : general

=cut

sub synchronize_hive {
Leo Gordon's avatar
Leo Gordon committed
397
  my $self          = shift;
Leo Gordon's avatar
Leo Gordon committed
398
  my $filter_analysis = shift; # optional parameter
399

400
  my $start_time = time();
401

Leo Gordon's avatar
Leo Gordon committed
402
  my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
403

Leo Gordon's avatar
Leo Gordon committed
404
  print STDERR "\nSynchronizing the hive (".scalar(@$list_of_analyses)." analyses this time):\n";
Leo Gordon's avatar
Leo Gordon committed
405 406
  foreach my $analysis (@$list_of_analyses) {
    $self->synchronize_AnalysisStats($analysis->stats);
Leo Gordon's avatar
Leo Gordon committed
407
    print STDERR '.';
408
  }
Leo Gordon's avatar
Leo Gordon committed
409
  print STDERR "\n";
Leo Gordon's avatar
Leo Gordon committed
410

Leo Gordon's avatar
Leo Gordon committed
411
  print STDERR "Checking blocking control rules:\n";
Leo Gordon's avatar
Leo Gordon committed
412
  foreach my $analysis (@$list_of_analyses) {
413
    $self->check_blocking_control_rules_for_AnalysisStats($analysis->stats);
Leo Gordon's avatar
Leo Gordon committed
414
    print STDERR '.';
415
  }
Leo Gordon's avatar
Leo Gordon committed
416
  print STDERR "\n";
Leo Gordon's avatar
Leo Gordon committed
417

Leo Gordon's avatar
Leo Gordon committed
418
  print STDERR ''.((time() - $start_time))." seconds to synchronize_hive\n\n";
419
}
420

421

422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443
=head2 safe_synchronize_AnalysisStats

  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
  Description: Prewrapper around synchronize_AnalysisStats that does
               checks and grabs sync_lock before proceeding with sync.
               Used by distributed worker sync system to avoid contention.
  Exceptions : none
  Caller     : general

=cut

sub safe_synchronize_AnalysisStats {
  my $self = shift;
  my $stats = shift;

  return $stats unless($stats);
  return $stats unless($stats->analysis_id);
  return $stats if($stats->status eq 'SYNCHING');
  return $stats if($stats->status eq 'DONE');
  return $stats if($stats->sync_lock);
  return $stats if(($stats->status eq 'WORKING') and
444
                   ($stats->seconds_since_last_update < 3*60));
445 446 447 448

  # OK try to claim the sync_lock
  my $sql = "UPDATE analysis_stats SET status='SYNCHING', sync_lock=1 ".
            "WHERE sync_lock=0 and analysis_id=" . $stats->analysis_id;
449
  #print("$sql\n");
450 451
  my $row_count = $self->dbc->do($sql);  
  return $stats unless($row_count == 1);
452
  #printf("got sync_lock on analysis_stats(%d)\n", $stats->analysis_id);
453 454 455
  
  #OK have the lock, go and do the sync
  $self->synchronize_AnalysisStats($stats);
456

457 458 459 460
  return $stats;
}


461
=head2 synchronize_AnalysisStats
462

463 464 465 466 467 468 469 470
  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
  Description: Queries the analysis_job and hive tables to get summary counts
               and rebuilds the AnalysisStats object.  Then updates the
               analysis_stats table with the new summary info
  Returntype : newly synced Bio::EnsEMBL::Hive::AnalysisStats object
  Exceptions : none
  Caller     : general
471

472
=cut
473

474
sub synchronize_AnalysisStats {
475
  my $self = shift;
476
  my $analysisStats = shift;
477

478
  return $analysisStats unless($analysisStats);
479
  return $analysisStats unless($analysisStats->analysis_id);
480
  
481
  $analysisStats->refresh(); ## Need to get the new hive_capacity for dynamic analyses
482 483 484 485 486 487
  $analysisStats->total_job_count(0);
  $analysisStats->unclaimed_job_count(0);
  $analysisStats->done_job_count(0);
  $analysisStats->failed_job_count(0);
  $analysisStats->num_required_workers(0);

488 489
  my $sql = "SELECT status, count(*), semaphore_count FROM analysis_job ".
            "WHERE analysis_id=? GROUP BY status, semaphore_count";
490 491 492
  my $sth = $self->prepare($sql);
  $sth->execute($analysisStats->analysis_id);

493 494
  my $hive_capacity = $analysisStats->hive_capacity;

495
  while (my ($status, $count, $semaphore_count)=$sth->fetchrow_array()) {
496
# print STDERR "$status - $count\n";
497 498 499 500

    my $total = $analysisStats->total_job_count();
    $analysisStats->total_job_count($total + $count);

501
    if(($status eq 'READY') and ($semaphore_count<=0)) {
502
      $analysisStats->unclaimed_job_count($count);
503 504 505 506 507 508 509 510 511
      my $numWorkers;
      if($analysisStats->batch_size > 0) {
        $numWorkers = POSIX::ceil($count / $analysisStats->batch_size);
      } else {
        my $job_msec = $analysisStats->avg_msec_per_job;
        $job_msec = 100 if($job_msec>0 and $job_msec<100);
        $numWorkers = POSIX::ceil(($count * $job_msec) / (3*60*1000)); 
        # guess num needed workers by total jobs / (num jobs a worker could do in 3 minutes)
      }
512
      $numWorkers=$count if($numWorkers==0);
513 514 515 516 517
      if($analysisStats->hive_capacity>0 and $numWorkers > $analysisStats->hive_capacity) {
        $numWorkers=$analysisStats->hive_capacity;
      }
      $analysisStats->num_required_workers($numWorkers);
    }
518 519
    if ($status eq 'DONE') { $analysisStats->done_job_count($count); }
    if ($status eq 'FAILED') { $analysisStats->failed_job_count($count); }
520 521
  }
  $sth->finish;
522

523
  $self->check_blocking_control_rules_for_AnalysisStats($analysisStats);
524

525 526 527
  if($analysisStats->status ne 'BLOCKED') {
    $analysisStats->determine_status();
  }
528

529 530 531 532
  #
  # adjust_stats_for_living_workers
  #
  
533
  if($analysisStats->hive_capacity > 0) {
534
    my $liveCount = $analysisStats->get_running_worker_count();
535 536 537 538 539 540 541 542

    my $numWorkers = $analysisStats->num_required_workers;

    my $capacityAdjust = ($numWorkers + $liveCount) - $analysisStats->hive_capacity;
    $numWorkers -= $capacityAdjust if($capacityAdjust > 0);
    $numWorkers=0 if($numWorkers<0);

    $analysisStats->num_required_workers($numWorkers);
543
  }
544

545
  $analysisStats->update;  #update and release sync_lock
546

547
  return $analysisStats;
548
}
549 550


551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573
sub check_blocking_control_rules_for_AnalysisStats
{
  my $self = shift;
  my $stats = shift;
  
  return unless($stats);

  #print("check ctrl on analysis ");  $stats->print_stats;
  my $ctrlRules = $self->db->get_AnalysisCtrlRuleAdaptor->
                  fetch_by_ctrled_analysis_id($stats->analysis_id);
  my $allRulesDone = 1;
  if(scalar @$ctrlRules > 0) {
    #print("HAS blocking_ctrl_rules to check\n");
    foreach my $ctrlrule (@{$ctrlRules}) {
      #use this method because the condition_analysis objects can be
      #network distributed to a different database so use it's adaptor to get
      #the AnalysisStats object
      #$ctrlrule->print_rule;
      my $condAnalysis = $ctrlrule->condition_analysis;
      my $condStats = $condAnalysis->stats if($condAnalysis);
      $allRulesDone = 0 unless($condStats and $condStats->status eq 'DONE');
      #print("  "); $condStats->print_stats;
    }
574

575 576 577
    if($allRulesDone) {
      if($stats->status eq 'BLOCKED') {
        #print("  UNBLOCK analysis : all conditions met\n");
578
        $stats->update_status('LOADING'); #trigger sync
579 580 581 582
      }
    } else {
      #print("  RE-BLOCK analysis : some conditions failed\n");
      $stats->update_status('BLOCKED');
583 584
    }
  }
585 586 587
}


Leo Gordon's avatar
Leo Gordon committed
588 589
sub get_num_failed_analyses {
  my ($self, $analysis) = @_;
590 591

  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
Leo Gordon's avatar
Leo Gordon committed
592
  my $failed_analyses = $statsDBA->fetch_by_statuses(['FAILED']);
593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614
  if ($analysis) {
    foreach my $this_failed_analysis (@$failed_analyses) {
      if ($this_failed_analysis->analysis_id == $analysis->dbID) {
        print "#########################################################\n",
            " Too many jobs failed for analysis ".$analysis->logic_name.". FAIL!!\n",
            "#########################################################\n\n";
        return 1;
      }
    }
    return 0;
  }

  if (@$failed_analyses) {
    print "##################################################\n",
        " Too many failed jobs. FAIL!!\n",
        "##################################################\n";
  }

  return scalar(@$failed_analyses);
}


615 616
sub get_hive_current_load {
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
617
  my $sql = "SELECT sum(1/analysis_stats.hive_capacity) FROM hive, analysis_stats ".
618 619
            "WHERE hive.analysis_id=analysis_stats.analysis_id and cause_of_death ='' ".
            "AND analysis_stats.hive_capacity>0";
620 621 622 623 624
  my $sth = $self->prepare($sql);
  $sth->execute();
  (my $load)=$sth->fetchrow_array();
  $sth->finish;
  $load=0 unless($load);
Leo Gordon's avatar
Leo Gordon committed
625
  print("current hive load = $load\n");
626 627 628 629
  return $load;
}


630 631 632 633 634 635 636 637
sub get_num_running_workers {
  my $self = shift;
  my $sql = "SELECT count(*) FROM hive WHERE cause_of_death =''";
  my $sth = $self->prepare($sql);
  $sth->execute();
  (my $runningCount)=$sth->fetchrow_array();
  $sth->finish;
  $runningCount=0 unless($runningCount);
Leo Gordon's avatar
Leo Gordon committed
638
  print("current hive num_running_workers = $runningCount\n");
639 640 641
  return $runningCount;
}

642 643 644
sub enter_status {
  my ($self, $worker, $status) = @_;

Leo Gordon's avatar
Leo Gordon committed
645
  $self->dbc->do("UPDATE hive SET status = '$status' WHERE worker_id = ".$worker->worker_id);
646 647
}

648 649
=head2 get_num_needed_workers

650
  Arg[1]     : Bio::EnsEMBL::Analysis object (optional)
651 652 653 654
  Example    : $count = $queen->get_num_needed_workers();
  Description: Runs through the analyses in the system which are waiting
               for workers to be created for them.  Calculates the maximum
               number of workers needed to fill the current needs of the system
655
               If Arg[1] is defined, does it only for the given analysis.
656
  Exceptions : none
657
  Caller     : beekeepers and other external processes
658 659 660

=cut

661
sub get_num_needed_workers {
Leo Gordon's avatar
Leo Gordon committed
662
  my ($self, $filter_analysis) = @_;
663

664
  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
Leo Gordon's avatar
Leo Gordon committed
665 666 667
  my $clearly_needed_analyses     = $statsDBA->fetch_by_needed_workers(undef,$self->{maximise_concurrency});
  my $potentially_needed_analyses = $statsDBA->fetch_by_statuses(['LOADING', 'BLOCKED']);
  my @all_analyses = (@$clearly_needed_analyses, @$potentially_needed_analyses);
668

Leo Gordon's avatar
Leo Gordon committed
669
  return 0 unless(@all_analyses);
670

Leo Gordon's avatar
Leo Gordon committed
671
  my $available_load = 1.0 - $self->get_hive_current_load();
672

Leo Gordon's avatar
Leo Gordon committed
673
  return 0 if($available_load <=0.0);
674

Leo Gordon's avatar
Leo Gordon committed
675 676
  my $total_workers = 0;
  my %rc2workers = ();
677

678 679
# FIXME: I have a feeling sometimes this method returns an incorrect value. Please doublecheck.

Leo Gordon's avatar
Leo Gordon committed
680 681
  foreach my $analysis_stats (@all_analyses) {
    next if (defined $filter_analysis && $filter_analysis->dbID != $analysis_stats->analysis_id);
682

Leo Gordon's avatar
Leo Gordon committed
683
        #digging deeper under the surface so need to sync
684 685 686 687 688 689 690
    if(($analysis_stats->status eq 'LOADING') or ($analysis_stats->status eq 'BLOCKED')) {
      $self->synchronize_AnalysisStats($analysis_stats);
    }

    next if($analysis_stats->status eq 'BLOCKED');
    next if($analysis_stats->num_required_workers == 0);

Leo Gordon's avatar
Leo Gordon committed
691
    my $workers_this_analysis = $analysis_stats->num_required_workers;
692

Leo Gordon's avatar
Leo Gordon committed
693 694 695 696 697 698 699 700
    if($analysis_stats->hive_capacity > 0) {   # if there is a limit, use it for cut-off
        my $limit_workers_this_analysis = int($available_load * $analysis_stats->hive_capacity);

        if($workers_this_analysis > $limit_workers_this_analysis) {
            $workers_this_analysis = $limit_workers_this_analysis;
        }

        $available_load -= 1.0*$workers_this_analysis/$analysis_stats->hive_capacity;
701
    }
Leo Gordon's avatar
Leo Gordon committed
702 703 704 705 706 707
    $total_workers += $workers_this_analysis;
    $rc2workers{$analysis_stats->rc_id} += $workers_this_analysis;
    $analysis_stats->print_stats();
    printf("  (%1.3f remaining-hive-load) use %3d workers of analysis_id=%d\n", $available_load, $workers_this_analysis, $analysis_stats->analysis_id);

    last if($available_load <= 0.0);
708
  }
709

Leo Gordon's avatar
Leo Gordon committed
710 711 712 713
  printf("need a total of $total_workers workers (availLoad=%1.5f)\n", $available_load);
  return ($total_workers, \%rc2workers);
}

Leo Gordon's avatar
Leo Gordon committed
714
sub get_needed_workers_resync_if_necessary {
Leo Gordon's avatar
Leo Gordon committed
715 716 717 718 719 720 721 722 723 724 725 726 727 728 729
    my ($self, $meadow, $analysis) = @_;

    my $load                     = $self->get_hive_current_load();
    my $running_count            = $self->get_num_running_workers();
    my ($needed_count, $rc_hash) = $self->get_num_needed_workers($analysis);

    if($load==0 and $needed_count==0 and $running_count==0) {
        print "*** nothing is running and nothing to do (according to analysis_stats) => perform a hard resync\n" ;

        $self->synchronize_hive($analysis);
        $self->check_for_dead_workers($meadow, 1);

        ($needed_count, $rc_hash) = $self->get_num_needed_workers($analysis);
    }

Leo Gordon's avatar
Leo Gordon committed
730
    return ($needed_count, $rc_hash);
731 732
}

Leo Gordon's avatar
Leo Gordon committed
733
sub get_remaining_jobs_show_hive_progress {
734
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
735
  my $sql = "SELECT sum(done_job_count), sum(failed_job_count), sum(total_job_count), ".
736 737
            "sum(unclaimed_job_count * analysis_stats.avg_msec_per_job)/1000/60/60 ".
            "FROM analysis_stats";
738 739
  my $sth = $self->prepare($sql);
  $sth->execute();
740
  my ($done, $failed, $total, $cpuhrs) = $sth->fetchrow_array();
741
  $sth->finish;
742 743 744 745 746 747 748

  $done   ||= 0;
  $failed ||= 0;
  $total  ||= 0;
  my $completed = $total
    ? ((100.0 * ($done+$failed))/$total)
    : 0.0;
749 750 751
  my $remaining = $total - $done - $failed;
  printf("hive %1.3f%% complete (< %1.3f CPU_hrs) (%d todo + %d done + %d failed = %d total)\n", 
          $completed, $cpuhrs, $remaining, $done, $failed, $total);
Leo Gordon's avatar
Leo Gordon committed
752
  return $remaining;
753 754
}

755 756 757 758 759 760 761 762
## Can't see where this method is used.
#
#sub print_hive_status {
#    my ($self, $filter_analysis) = @_;
#
#    $self->print_analysis_status($filter_analysis);
#    $self->print_running_worker_status;
#}
763 764


Leo Gordon's avatar
Leo Gordon committed
765
sub print_analysis_status {
Leo Gordon's avatar
Leo Gordon committed
766
    my ($self, $filter_analysis) = @_;
767

Leo Gordon's avatar
Leo Gordon committed
768
    my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
769 770 771
    foreach my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {
        $analysis->stats->print_stats($self->{'verbose_stats'});
    }
772 773 774
}


Leo Gordon's avatar
Leo Gordon committed
775
sub print_running_worker_status {
776
  my $self = shift;
777

Leo Gordon's avatar
Leo Gordon committed
778
  print "====== Live workers according to Queen:\n";
779 780 781
  my $sql = "select logic_name, count(*) from hive, analysis ".
            "where hive.analysis_id=analysis.analysis_id and hive.cause_of_death='' ".
            "group by hive.analysis_id";
Leo Gordon's avatar
Leo Gordon committed
782 783

  my $total = 0;
784 785 786 787
  my $sth = $self->prepare($sql);
  $sth->execute();
  while((my $logic_name, my $count)=$sth->fetchrow_array()) {
    printf("%20s : %d workers\n", $logic_name, $count);
788
    $total += $count;
789
  }
790
  printf("  %d total workers\n", $total);
Leo Gordon's avatar
Leo Gordon committed
791
  print "===========================\n";
792
  $sth->finish;
793
}
794

795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823
=head2 monitor

  Arg[1]     : --none--
  Example    : $queen->monitor();
  Description: Monitors current throughput and store the result in the monitor
               table
  Exceptions : none
  Caller     : beekeepers and other external processes

=cut

sub monitor
{
  my $self = shift;
  my $sql = qq{
      INSERT INTO monitor
      SELECT
          now(),
          count(*),
          sum(work_done/TIME_TO_SEC(TIMEDIFF(now(),born))),
          sum(work_done/TIME_TO_SEC(TIMEDIFF(now(),born)))/count(*),
          group_concat(DISTINCT logic_name)
      FROM hive left join analysis USING (analysis_id)
      WHERE cause_of_death = ""};
      
  my $sth = $self->prepare($sql);
  $sth->execute();
}

Leo Gordon's avatar
Leo Gordon committed
824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841
=head2 register_all_workers_dead

  Example    : $queen->register_all_workers_dead();
  Description: Registers all workers dead
  Exceptions : none
  Caller     : beekeepers and other external processes

=cut

sub register_all_workers_dead {
    my $self = shift;

    my $overdueWorkers = $self->fetch_overdue_workers(0);
    foreach my $worker (@{$overdueWorkers}) {
        $self->register_worker_death($worker);
    }
}

842

Jessica Severin's avatar
Jessica Severin committed
843 844 845 846 847
#
# INTERNAL METHODS
#
###################

848
sub _pick_best_analysis_for_new_worker {
Leo Gordon's avatar
Leo Gordon committed
849 850
  my $self  = shift;
  my $rc_id = shift;    # this parameter will need to percolate very deep
851 852 853 854

  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
  return undef unless($statsDBA);

Leo Gordon's avatar
Leo Gordon committed
855
  my ($stats) = @{$statsDBA->fetch_by_needed_workers(1,$self->{maximise_concurrency}, $rc_id)};
856 857 858 859 860
  if($stats) {
    #synchronize and double check that it can be run
    $self->safe_synchronize_AnalysisStats($stats);
    return $stats if(($stats->status ne 'BLOCKED') and ($stats->num_required_workers > 0));
  }
861 862

  # ok so no analyses 'need' workers.
863 864 865
  if ($self->get_num_failed_analyses()) {
    return undef;
  }
866 867 868 869
  # see if anything needs an update, in case there are
  # hidden jobs that haven't made it into the summary stats

  print("QUEEN: no obvious needed workers, need to dig deeper\n");
Leo Gordon's avatar
Leo Gordon committed
870
  my $stats_list = $statsDBA->fetch_by_statuses(['LOADING', 'BLOCKED']);
871
  foreach $stats (@$stats_list) {
872
    $self->safe_synchronize_AnalysisStats($stats);
873

Leo Gordon's avatar
Leo Gordon committed
874
    return $stats if(($stats->status ne 'BLOCKED') and ($stats->num_required_workers > 0) and (!defined($rc_id) or ($stats->rc_id == $rc_id)));
875 876
  }

Leo Gordon's avatar
Leo Gordon committed
877
  ($stats) = @{$statsDBA->fetch_by_needed_workers(1,$self->{maximise_concurrency}, $rc_id)};
878 879 880 881 882 883
  return $stats if($stats);

  return undef;
}


Leo Gordon's avatar
Leo Gordon committed
884
=head2 fetch_by_worker_id
Jessica Severin's avatar
Jessica Severin committed
885 886 887

  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
888
  Example    : $feat = $queen->fetch_by_dbID(1234);
Jessica Severin's avatar
Jessica Severin committed
889 890 891 892 893 894 895 896
  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

Leo Gordon's avatar
Leo Gordon committed
897
sub fetch_by_worker_id {
Jessica Severin's avatar
Jessica Severin committed
898 899 900
  my ($self,$id) = @_;

  unless(defined $id) {
901
    throw("fetch_by_dbID must have an id");
Jessica Severin's avatar
Jessica Severin committed
902 903 904 905
  }

  my @tabs = $self->_tables;

Leo Gordon's avatar
Leo Gordon committed
906
  my $constraint = "h.worker_id = $id";
Jessica Severin's avatar
Jessica Severin committed
907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989

  #return first element of _generic_fetch list
  my ($obj) = @