Queen.pm 37.8 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
29
  gets $analysis->stats->batch_size jobs from the job table, does its work,
  creates the next layer of 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;

67
use Bio::EnsEMBL::Hive::Utils 'destringify';  # import 'destringify()'
68
use Bio::EnsEMBL::Hive::AnalysisJob;
Jessica Severin's avatar
Jessica Severin committed
69
use Bio::EnsEMBL::Hive::Worker;
70
use Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
Jessica Severin's avatar
Jessica Severin committed
71

Leo Gordon's avatar
Leo Gordon committed
72
use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
73

Jessica Severin's avatar
Jessica Severin committed
74

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
  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.
88
               It creates an entry in the worker table, and returns a Worker object 
89
90
               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) = @_;

100
  my (  $meadow_type, $meadow_name, $process_id, $exec_host,
101
        $rc_id, $logic_name, $analysis_id, $input_id, $job_id,
102
        $no_write, $debug, $worker_output_dir, $hive_output_dir, $job_limit, $life_span, $no_cleanup, $retry_throwing_jobs, $compile_module_once) =
103

104
 rearrange([qw(meadow_type meadow_name process_id exec_host
105
        rc_id logic_name analysis_id input_id job_id
106
        no_write debug worker_output_dir hive_output_dir job_limit life_span no_cleanup retry_throwing_jobs compile_module_once) ], @args);
107
108
109
110
111
112
113
114
115
116
117

    if($logic_name) {
        if($analysis_id) {
            die "You should either define -analysis_id or -logic_name, but not both\n";
        }
        if(my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name)) {
            $analysis_id = $analysis->dbID;
        } else {
            die "logic_name '$logic_name' could not be fetched from the database\n";
        }
    }
Jessica Severin's avatar
Jessica Severin committed
118

119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
    my $job;

    if($input_id) {
        if($job_id) {
            die "You should either define -input_id or -job_id, but not both\n";

        } elsif($analysis_id) {
            $job = Bio::EnsEMBL::Hive::AnalysisJob->new(
                -INPUT_ID       => $input_id,
                -ANALYSIS_ID    => $analysis_id,
                -DBID           => -1,
            );
            print "creating a job outside the database\n";
            $job->print_job;
            $debug=1 unless(defined($debug));
            $hive_output_dir='' unless(defined($hive_output_dir)); # make it defined but empty/false
        } else {
            die "For creating a job outside the database either -analysis_id or -logic_name must also be defined\n";
        }
    }

    if($job_id) {
        if($analysis_id) {
            die "When you specify -job_id, please omit both -logic_name and -analysis_id to avoid confusion\n";
        } else {
144
145
146
147
148
            print "resetting and fetching job for job_id '$job_id'\n";

            my $job_adaptor = $self->db->get_AnalysisJobAdaptor;
            $job_adaptor->reset_job_by_dbID($job_id); 
            if($job = $job_adaptor->fetch_by_dbID($job_id)) {
149
150
151
152
153
154
                $analysis_id = $job->analysis_id;
            } else {
                die "job_id '$job_id' could not be fetched from the database\n";
            }
        }
    }
155

156
  
157
  my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor or return undef;
158
159
  my $analysisStats;
  if($analysis_id) {
160
    $analysisStats = $analysis_stats_adaptor->fetch_by_analysis_id($analysis_id);
161
    $self->safe_synchronize_AnalysisStats($analysisStats);
162
    #return undef unless(($analysisStats->status ne 'BLOCKED') and ($analysisStats->num_required_workers > 0));
163
  } else {
164
165
166
167
168
    if( $analysisStats = $self->_pick_best_analysis_for_new_worker($rc_id) ) {
        print "Scheduler picked analysis_id=".$analysisStats->analysis_id()." for the worker\n";
    } else {
        print "Scheduler failed to pick analysis_id for the worker\n";
    }
169
  }
170
  return undef unless($analysisStats);
171

172
173
  unless($job) {
    #go into autonomous mode
174
175
176
177
178

    if($self->get_hive_current_load() >= 1.1) {
        print "Hive is overloaded, can't create a worker\n";
        return;
    }
179
    if($analysisStats->status eq 'BLOCKED') {
180
181
      print "Analysis is BLOCKED, can't create workers\n";
      return;
182
183
    }
    if($analysisStats->status eq 'DONE') {
184
185
      print "Analysis is DONE, don't need to create workers\n";
      return;
186
    }
187

188
189
    $analysis_stats_adaptor->decrease_required_workers($analysisStats->analysis_id);

190
    $analysisStats->print_stats;
191
  }
192
  
193
194
195
196
197
198
199
200
201
202
    # The following increment used to be done only when no specific task was given to the worker,
    # thereby excluding such "special task" workers from being counted in num_running_workers.
    #
    # However this may be tricky to emulate by triggers that know nothing about "special tasks",
    # so I am (temporarily?) simplifying the accounting algorithm.
    #
  unless( $self->db->hive_use_triggers() ) {
        $analysis_stats_adaptor->increase_running_workers($analysisStats->analysis_id);
  }

203
  my $sql = q{INSERT INTO worker 
204
205
              (born, last_check_in, meadow_type, meadow_name, process_id, host, analysis_id)
              VALUES (CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, ?,?,?,?,?)};
Jessica Severin's avatar
Jessica Severin committed
206
207

  my $sth = $self->prepare($sql);
208
  $sth->execute($meadow_type, $meadow_name, $process_id, $exec_host, $analysisStats->analysis_id);
Leo Gordon's avatar
Leo Gordon committed
209
  my $worker_id = $self->dbc->db_handle->last_insert_id(undef, undef, 'worker', 'worker_id');
Jessica Severin's avatar
Jessica Severin committed
210
211
  $sth->finish;

212
  my $worker = $self->fetch_by_dbID($worker_id);
Jessica Severin's avatar
Jessica Severin committed
213
214
  $worker=undef unless($worker and $worker->analysis);

215
  if($worker and $analysisStats) {
216
    $analysisStats->update_status('WORKING');
Jessica Severin's avatar
Jessica Severin committed
217
  }
218
  
219
  $worker->_specific_job($job) if($job);
220
  $worker->execute_writes(0) if($no_write);
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245

    $worker->debug($debug) if($debug);
    $worker->worker_output_dir($worker_output_dir) if(defined($worker_output_dir));

    unless(defined($hive_output_dir)) {
        my $arrRef = $self->db->get_MetaContainer->list_value_by_key( 'hive_output_dir' );
        if( @$arrRef ) {
            $hive_output_dir = destringify($arrRef->[0]);
        } 
    }
    $worker->hive_output_dir($hive_output_dir);

    if($job_limit) {
      $worker->job_limit($job_limit);
      $worker->life_span(0);
    }
    if($life_span) {
      $worker->life_span($life_span * 60);
    }
    if($no_cleanup) { 
      $worker->perform_cleanup(0); 
    }
    if(defined $retry_throwing_jobs) {
        $worker->retry_throwing_jobs($retry_throwing_jobs);
    }
246
247
248
    if(defined $compile_module_once) {
        $worker->compile_module_once($compile_module_once);
    }
249

250
    return $worker;
Jessica Severin's avatar
Jessica Severin committed
251
252
}

253

Jessica Severin's avatar
Jessica Severin committed
254
255
256
257
sub register_worker_death {
  my ($self, $worker) = @_;

  return unless($worker);
Leo Gordon's avatar
Leo Gordon committed
258

Leo Gordon's avatar
bugfix    
Leo Gordon committed
259
260
  my $cod = $worker->cause_of_death();

261
  my $sql = "UPDATE worker SET died=CURRENT_TIMESTAMP, last_check_in=CURRENT_TIMESTAMP";
262
  $sql .= " ,status='DEAD'";
Jessica Severin's avatar
Jessica Severin committed
263
  $sql .= " ,work_done='" . $worker->work_done . "'";
Leo Gordon's avatar
bugfix    
Leo Gordon committed
264
  $sql .= " ,cause_of_death='$cod'";
265
  $sql .= " WHERE worker_id='" . $worker->dbID ."'";
Jessica Severin's avatar
Jessica Severin committed
266

Leo Gordon's avatar
bugfix    
Leo Gordon committed
267
  $self->dbc->do( $sql );
268

269
270
271
272
  unless( $self->db->hive_use_triggers() ) {
      $worker->analysis->stats->adaptor->decrease_running_workers($worker->analysis->stats->analysis_id);
  }

Leo Gordon's avatar
bugfix    
Leo Gordon committed
273
  if($cod eq 'NO_WORK') {
274
    $self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, 'ALL_CLAIMED');
275
  }
Leo Gordon's avatar
bugfix    
Leo Gordon committed
276
277
278
279
  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
280
    $self->db->get_AnalysisJobAdaptor->release_undone_jobs_from_worker($worker);
281
  }
282
  
283
  # re-sync the analysis_stats when a worker dies as part of dynamic sync system
284
  if($self->safe_synchronize_AnalysisStats($worker->analysis->stats)->status ne 'DONE') {
285
286
    # 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
287
    $self->db->get_AnalysisStatsAdaptor->increase_required_workers($worker->analysis->dbID);
288
289
  }

Jessica Severin's avatar
Jessica Severin committed
290
291
}

292
sub check_for_dead_workers {    # scans the whole Valley for lost Workers (but ignores unreachagle ones)
293
    my ($self, $valley, $check_buried_in_haste) = @_;
Leo Gordon's avatar
Leo Gordon committed
294

295
    warn "GarbageCollector:\tChecking for lost Workers...\n";
296

297
298
299
300
    my $queen_worker_list           = $self->fetch_overdue_workers(0);
    my %mt_and_pid_to_worker_status = ();
    my %worker_status_counts        = ();
    my %mt_and_pid_to_lost_worker   = ();
Leo Gordon's avatar
Leo Gordon committed
301

302
    warn "GarbageCollector:\t[Queen:] we have ".scalar(@$queen_worker_list)." Workers alive.\n";
303

Leo Gordon's avatar
Leo Gordon committed
304
305
    foreach my $worker (@$queen_worker_list) {

306
307
308
        my $meadow_type = $worker->meadow_type;
        if(my $meadow = $valley->find_available_meadow_responsible_for_worker($worker)) {
            $mt_and_pid_to_worker_status{$meadow_type} ||= $meadow->status_of_all_our_workers;
Leo Gordon's avatar
Leo Gordon committed
309
        } else {
310
            $worker_status_counts{$meadow_type}{'UNREACHABLE'}++;
311

312
            next;   # Worker is unreachable from this Valley
Leo Gordon's avatar
Leo Gordon committed
313
314
        }

315
316
317
318
319
        my $process_id = $worker->process_id;
        if(my $status = $mt_and_pid_to_worker_status{$meadow_type}{$process_id}) { # can be RUN|PEND|xSUSP
            $worker_status_counts{$meadow_type}{$status}++;
        } else {
            $worker_status_counts{$meadow_type}{'LOST'}++;
320

321
            $mt_and_pid_to_lost_worker{$meadow_type}{$process_id} = $worker;
322
        }
323
324
325
326
327
328
    }

        # just a quick summary report:
    foreach my $meadow_type (keys %worker_status_counts) {
        warn "GarbageCollector:\t[$meadow_type Meadow:]\t".join(', ', map { "$_:$worker_status_counts{$meadow_type}{$_}" } keys %{$worker_status_counts{$meadow_type}})."\n\n";
    }
329

330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
    while(my ($meadow_type, $pid_to_lost_worker) = each %mt_and_pid_to_lost_worker) {
        my $this_meadow = $valley->available_meadow_hash->{$meadow_type};

        if(my $lost_this_meadow = scalar(keys %$pid_to_lost_worker) ) {
            warn "GarbageCollector:\tDiscovered $lost_this_meadow lost $meadow_type Workers\n";

            my $wpid_to_cod = {};
            if($this_meadow->can('find_out_causes')) {
                $wpid_to_cod = $this_meadow->find_out_causes( keys %$pid_to_lost_worker );
                my $lost_with_known_cod = scalar(keys %$wpid_to_cod);
                warn "GarbageCollector:\tFound why $lost_with_known_cod of $meadow_type Workers died\n";
            } else {
                warn "GarbageCollector:\t$meadow_type meadow does not support post-mortem examination\n";
            }

            warn "GarbageCollector:\tReleasing the jobs\n";
            while(my ($process_id, $worker) = each %$pid_to_lost_worker) {
                $worker->cause_of_death( $wpid_to_cod->{$process_id} || 'FATALITY');
                $self->register_worker_death($worker);
            }
350
351
352
        }
    }

353
        # the following bit is completely Meadow-agnostic and only restores database integrity:
Leo Gordon's avatar
Leo Gordon committed
354
    if($check_buried_in_haste) {
355
        warn "GarbageCollector:\tChecking for Workers buried in haste...\n";
356
        my $buried_in_haste_list = $self->fetch_all_dead_workers_with_jobs();
Leo Gordon's avatar
Leo Gordon committed
357
        if(my $bih_number = scalar(@$buried_in_haste_list)) {
358
            warn "GarbageCollector:\tfound $bih_number jobs, reclaiming.\n\n";
Leo Gordon's avatar
Leo Gordon committed
359
360
361
            if($bih_number) {
                my $job_adaptor = $self->db->get_AnalysisJobAdaptor();
                foreach my $worker (@$buried_in_haste_list) {
Leo Gordon's avatar
Leo Gordon committed
362
                    $job_adaptor->release_undone_jobs_from_worker($worker);
Leo Gordon's avatar
Leo Gordon committed
363
364
365
                }
            }
        } else {
366
            warn "GarbageCollector:\tfound none\n";
Leo Gordon's avatar
Leo Gordon committed
367
368
369
        }
    }
}
Jessica Severin's avatar
Jessica Severin committed
370
371


372
373
374
    # a new version that both checks in and updates the status
sub check_in_worker {
    my ($self, $worker) = @_;
Jessica Severin's avatar
Jessica Severin committed
375

376
    $self->dbc->do("UPDATE worker SET last_check_in=CURRENT_TIMESTAMP, status='".$worker->status."', work_done='".$worker->work_done."' WHERE worker_id='".$worker->dbID."'");
Jessica Severin's avatar
Jessica Severin committed
377
378
379
}


380
=head2 reset_job_by_dbID_and_sync
381

382
  Arg [1]: int $job_id
383
  Example: 
384
    my $job = $queen->reset_job_by_dbID_and_sync($job_id);
385
  Description: 
386
    For the specified job_id it will fetch just that job, 
387
388
389
    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 
390
    same job simultaneously (use only for debugging).
391
  Returntype : none
392
  Exceptions :
393
  Caller     : beekeeper.pl
394
395
396

=cut

397
398
sub reset_job_by_dbID_and_sync {
    my ($self, $job_id) = @_;
399

400
401
402
403
404
405
    my $job_adaptor = $self->db->get_AnalysisJobAdaptor;
    $job_adaptor->reset_job_by_dbID($job_id); 

    my $job = $job_adaptor->fetch_by_dbID($job_id); 
    my $stats = $self->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id($job->analysis_id);
    $self->synchronize_AnalysisStats($stats);
406
407
408
}


409
410
411
412
413
414
######################################
#
# Public API interface for beekeeper
#
######################################

415
416
417
    # Note: asking for Queen->fetch_overdue_workers(0) essentially means
    #       "fetch all workers known to the Queen not to be officially dead"
    #
418
419
420
421
422
sub fetch_overdue_workers {
  my ($self,$overdue_secs) = @_;

  $overdue_secs = 3600 unless(defined($overdue_secs));

423
424
425
426
  my $constraint = "w.cause_of_death='' AND ".
                    ( ($self->dbc->driver eq 'sqlite')
                        ? "(strftime('%s','now')-strftime('%s',w.last_check_in))>$overdue_secs"
                        : "(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(w.last_check_in))>$overdue_secs");
427
428
429
  return $self->_generic_fetch($constraint);
}

430
431
sub fetch_failed_workers {
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
432

433
  my $constraint = "w.cause_of_death='FATALITY' ";
434
435
436
  return $self->_generic_fetch($constraint);
}

437
sub fetch_all_dead_workers_with_jobs {
Leo Gordon's avatar
Leo Gordon committed
438
439
  my $self = shift;

440
  # SELECT w.* FROM worker h, job j WHERE w.worker_id=j.worker_id AND w.cause_of_death!='' AND j.status NOT IN ('DONE', 'READY','FAILED', 'PASSED_ON') GROUP BY w.worker_id
Leo Gordon's avatar
Leo Gordon committed
441

442
443
  my $constraint = "w.cause_of_death!='' ";
  my $join = [[['job', 'j'], " w.worker_id=j.worker_id AND j.status NOT IN ('DONE', 'READY', 'FAILED', 'PASSED_ON') GROUP BY w.worker_id"]];
Leo Gordon's avatar
Leo Gordon committed
444
445
  return $self->_generic_fetch($constraint, $join);
}
Jessica Severin's avatar
Jessica Severin committed
446

447
448
=head2 synchronize_hive

Leo Gordon's avatar
Leo Gordon committed
449
  Arg [1]    : $filter_analysis (optional)
450
451
  Example    : $queen->synchronize_hive();
  Description: Runs through all analyses in the system and synchronizes
452
453
              the analysis_stats summary with the states in the job 
              and worker tables.  Then follows by checking all the blocking rules
454
455
456
457
458
459
460
              and blocks/unblocks analyses as needed.
  Exceptions : none
  Caller     : general

=cut

sub synchronize_hive {
Leo Gordon's avatar
Leo Gordon committed
461
  my $self          = shift;
Leo Gordon's avatar
Leo Gordon committed
462
  my $filter_analysis = shift; # optional parameter
463

464
  my $start_time = time();
465

Leo Gordon's avatar
Leo Gordon committed
466
  my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
467

Leo Gordon's avatar
Leo Gordon committed
468
  print STDERR "\nSynchronizing the hive (".scalar(@$list_of_analyses)." analyses this time):\n";
Leo Gordon's avatar
Leo Gordon committed
469
470
  foreach my $analysis (@$list_of_analyses) {
    $self->synchronize_AnalysisStats($analysis->stats);
471
    print STDERR ( ($analysis->stats()->status eq 'BLOCKED') ? 'x' : 'o');
472
  }
Leo Gordon's avatar
Leo Gordon committed
473
  print STDERR "\n";
Leo Gordon's avatar
Leo Gordon committed
474

475
476
477
478
479
480
#  print STDERR "Checking blocking control rules:\n";
#  foreach my $analysis (@$list_of_analyses) {
#    my $open = $analysis->stats->check_blocking_control_rules();
#    print STDERR ($open ? 'o' : 'x');
#  }
#  print STDERR "\n";
Leo Gordon's avatar
Leo Gordon committed
481

Leo Gordon's avatar
Leo Gordon committed
482
  print STDERR ''.((time() - $start_time))." seconds to synchronize_hive\n\n";
483
}
484

485

486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
=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
508
                   ($stats->seconds_since_last_update < 3*60));
509
510
511
512

  # 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=" . $stats->analysis_id;
513
  #print("$sql\n");
514
  my $row_count = $self->dbc->do($sql);  
515
  return $stats unless($row_count == 1);        # return the un-updated status if locked
516
  #printf("got sync_lock on analysis_stats(%d)\n", $stats->analysis_id);
517
  
518
      # since we managed to obtain the lock, let's go and perform the sync:
519
  $self->synchronize_AnalysisStats($stats);
520

521
522
523
524
  return $stats;
}


525
=head2 synchronize_AnalysisStats
526

527
528
  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
529
  Description: Queries the job and worker tables to get summary counts
530
531
532
533
534
               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
535

536
=cut
537

538
sub synchronize_AnalysisStats {
539
  my $self = shift;
540
  my $analysisStats = shift;
541

542
  return $analysisStats unless($analysisStats);
543
  return $analysisStats unless($analysisStats->analysis_id);
544

545
  $analysisStats->refresh(); ## Need to get the new hive_capacity for dynamic analyses
546
547
  my $hive_capacity = $analysisStats->hive_capacity;

548
549
550
551
  if($self->db->hive_use_triggers()) {

            my $job_count = $analysisStats->unclaimed_job_count();
            my $required_workers = POSIX::ceil( $job_count / $analysisStats->get_or_estimate_batch_size() );
552

553
554
                # adjust_stats_for_living_workers:
            if($hive_capacity > 0) {
555
                my $unfulfilled_capacity = $hive_capacity - $analysisStats->num_running_workers();
556

557
558
                if($unfulfilled_capacity < $required_workers ) {
                    $required_workers = (0 < $unfulfilled_capacity) ? $unfulfilled_capacity : 0;
559
560
561
562
563
564
565
566
567
568
                }
            }
            $analysisStats->num_required_workers( $required_workers );

  } else {
      $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);
569

570
      my $sql = "SELECT status, semaphore_count, count(*) FROM job ".
571
572
573
                "WHERE analysis_id=? GROUP BY status, semaphore_count";
      my $sth = $self->prepare($sql);
      $sth->execute($analysisStats->analysis_id);
574
575


576
577
578
579
      my $done_here       = 0;
      my $done_elsewhere  = 0;
      my $total_job_count = 0;
      while (my ($status, $semaphore_count, $job_count)=$sth->fetchrow_array()) {
580
    # print STDERR "$status: $job_count\n";
581

582
        $total_job_count += $job_count;
583
584
585
586
587
588
589
590

        if(($status eq 'READY') and ($semaphore_count<=0)) {
            $analysisStats->unclaimed_job_count($job_count);

            my $required_workers = POSIX::ceil( $job_count / $analysisStats->get_or_estimate_batch_size() );

                # adjust_stats_for_living_workers:
            if($hive_capacity > 0) {
591
                my $unfulfilled_capacity = $hive_capacity - $self->count_running_workers( $analysisStats->analysis_id() );
592

593
594
                if($unfulfilled_capacity < $required_workers ) {
                    $required_workers = (0 < $unfulfilled_capacity) ? $unfulfilled_capacity : 0;
595
                }
596
            }
597
598
            $analysisStats->num_required_workers( $required_workers );

599
        } elsif($status eq 'DONE') {
600
            $done_here = $job_count;
601
        } elsif($status eq 'PASSED_ON') {
602
603
604
            $done_elsewhere = $job_count;
        } elsif ($status eq 'FAILED') {
            $analysisStats->failed_job_count($job_count);
605
        }
606
      } # /while
607
      $sth->finish;
608

609
610
      $analysisStats->total_job_count( $total_job_count );
      $analysisStats->done_job_count( $done_here + $done_elsewhere );
611
  } # /unless $self->{'_hive_use_triggers'}
612

613
  $analysisStats->check_blocking_control_rules();
614

615
616
617
  if($analysisStats->status ne 'BLOCKED') {
    $analysisStats->determine_status();
  }
618

619
  # $analysisStats->sync_lock(0); ## do we perhaps need it here?
620
  $analysisStats->update;  #update and release sync_lock
621

622
  return $analysisStats;
623
}
624
625


Leo Gordon's avatar
Leo Gordon committed
626
627
sub get_num_failed_analyses {
  my ($self, $analysis) = @_;
628
629

  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
Leo Gordon's avatar
Leo Gordon committed
630
  my $failed_analyses = $statsDBA->fetch_by_statuses(['FAILED']);
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
  if ($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);
}


653
654
sub get_hive_current_load {
  my $self = shift;
655
656
657
  my $sql = "SELECT sum(1/s.hive_capacity) FROM worker w, analysis_stats s ".
            "WHERE w.analysis_id=s.analysis_id and w.cause_of_death ='' ".
            "AND s.hive_capacity>0";
658
659
660
661
662
  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
663
  print("current hive load = $load\n");
664
665
666
667
  return $load;
}


668
669
670
671
672
673
674
675
676
677
678
679
sub count_running_workers {
    my ($self, $analysis_id) = @_;

    my $sql = "SELECT count(*) FROM worker WHERE cause_of_death =''"
        . ($analysis_id ? " AND analysis_id='$analysis_id'" : '');

    my $sth = $self->prepare($sql);
    $sth->execute();
    (my $running_workers_count)=$sth->fetchrow_array();
    $sth->finish();

    return $running_workers_count || 0;
680
681
}

682

683
=head2 schedule_workers
684

685
  Arg[1]     : Bio::EnsEMBL::Analysis object (optional)
686
  Example    : $count = $queen->schedule_workers();
687
688
689
  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
690
               If Arg[1] is defined, does it only for the given analysis.
691
  Exceptions : none
692
  Caller     : beekeepers and other external processes
693
694
695

=cut

696
697
sub schedule_workers {
  my ($self, $filter_analysis, $orig_pending_by_rc_id, $available_submit_limit) = @_;
698

699
700
701
702
  my $statsDBA                      = $self->db->get_AnalysisStatsAdaptor;
  my $clearly_needed_analyses       = $statsDBA->fetch_by_needed_workers(undef);
  my $potentially_needed_analyses   = $statsDBA->fetch_by_statuses(['LOADING', 'BLOCKED', 'ALL_CLAIMED']);
  my @all_analyses                  = (@$clearly_needed_analyses, @$potentially_needed_analyses);
703

704
  return {} unless(@all_analyses);
705

706
707
708
709
  my %pending_by_rc_id          = %{ $orig_pending_by_rc_id || {} };
  my $total_workers_to_run      = 0;
  my %workers_to_run_by_rc_id   = ();
  my $available_load            = 1.0 - $self->get_hive_current_load();
710

Leo Gordon's avatar
Leo Gordon committed
711
  foreach my $analysis_stats (@all_analyses) {
712
713
    last if ($available_load <= 0.0);
    last if (defined($available_submit_limit) and !$available_submit_limit);
Leo Gordon's avatar
Leo Gordon committed
714
    next if (defined $filter_analysis && $filter_analysis->dbID != $analysis_stats->analysis_id);
715

Leo Gordon's avatar
Leo Gordon committed
716
        #digging deeper under the surface so need to sync
717
    if(($analysis_stats->status eq 'LOADING') or ($analysis_stats->status eq 'BLOCKED') or ($analysis_stats->status eq 'ALL_CLAIMED')) {
718
719
720
721
722
723
      $self->synchronize_AnalysisStats($analysis_stats);
    }

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

724
        # FIXME: the following call *sometimes* returns a stale number greater than the number of workers actually needed for an analysis; -sync fixes it
Leo Gordon's avatar
Leo Gordon committed
725
    my $workers_this_analysis = $analysis_stats->num_required_workers;
726

727
728
729
730
731
732
    if(defined($available_submit_limit)) {                              # submit_limit total capping, if available
        if($workers_this_analysis > $available_submit_limit) {
            $workers_this_analysis = $available_submit_limit;
        }
        $available_submit_limit -= $workers_this_analysis;
    }
Leo Gordon's avatar
Leo Gordon committed
733

734
735
736
737
738
    if((my $hive_capacity = $analysis_stats->hive_capacity) > 0) {      # per-analysis hive_capacity capping, if available
        my $remaining_capacity_for_this_analysis = int($available_load * $hive_capacity);

        if($workers_this_analysis > $remaining_capacity_for_this_analysis) {
            $workers_this_analysis = $remaining_capacity_for_this_analysis;
Leo Gordon's avatar
Leo Gordon committed
739
740
        }

741
        $available_load -= 1.0*$workers_this_analysis/$hive_capacity;
742
    }
Leo Gordon's avatar
Leo Gordon committed
743

744
    my $curr_rc_id = $analysis_stats->resource_class_id;
745
746
747
748
749
750
751
    if($pending_by_rc_id{ $curr_rc_id }) {                              # per-rc_id capping by pending processes, if available
        my $pending_this_analysis = ($pending_by_rc_id{ $curr_rc_id } < $workers_this_analysis) ? $pending_by_rc_id{ $curr_rc_id } : $workers_this_analysis;

        $workers_this_analysis              -= $pending_this_analysis;
        $pending_by_rc_id{ $curr_rc_id }    -= $pending_this_analysis;
    }

752
753
    next unless($workers_this_analysis);    # do not autovivify the hash by a zero

754
755
756
    $total_workers_to_run += $workers_this_analysis;
    $workers_to_run_by_rc_id{ $curr_rc_id } += $workers_this_analysis;
    $analysis_stats->print_stats();
757
    printf("Scheduler suggests adding %d more workers of resource_class_id=%d for analysis_id=%d [%1.3f hive_load remaining]\n", $workers_this_analysis, $curr_rc_id, $analysis_stats->analysis_id, $available_load);
758
  }
759

760
  printf("Scheduler suggests adding a total of %d workers [%1.5f hive_load remaining]\n", $total_workers_to_run, $available_load);
761
  return \%workers_to_run_by_rc_id;
Leo Gordon's avatar
Leo Gordon committed
762
763
}

764

765
sub schedule_workers_resync_if_necessary {
766
767
768
    my ($self, $valley, $analysis) = @_;

    my $meadow              = $valley->get_current_meadow();
Leo Gordon's avatar
Leo Gordon committed
769

770
771
772
    my $pending_by_rc_id    = ($meadow->can('count_pending_workers_by_rc_id') and $meadow->config_get('PendingAdjust')) ? $meadow->count_pending_workers_by_rc_id() : {};
    my $submit_limit        = $meadow->config_get('SubmitWorkersMax');
    my $meadow_limit        = ($meadow->can('count_running_workers') and defined($meadow->config_get('TotalRunningWorkersMax'))) ? $meadow->config_get('TotalRunningWorkersMax') - $meadow->count_running_workers : undef;
Leo Gordon's avatar
Leo Gordon committed
773

774
775
776
777
    my $available_submit_limit = ($submit_limit and $meadow_limit)
                                    ? (($submit_limit<$meadow_limit) ? $submit_limit : $meadow_limit)
                                    : (defined($submit_limit) ? $submit_limit : $meadow_limit);

778
    my $workers_to_run_by_rc_id = $self->schedule_workers($analysis, $pending_by_rc_id, $available_submit_limit);
779

780
    unless( keys %$workers_to_run_by_rc_id or $self->get_hive_current_load() or $self->count_running_workers() ) {
Leo Gordon's avatar
Leo Gordon committed
781
782
        print "*** nothing is running and nothing to do (according to analysis_stats) => perform a hard resync\n" ;

783
        $self->check_for_dead_workers($valley, 1);
784
        $self->synchronize_hive($analysis);
Leo Gordon's avatar
Leo Gordon committed
785

786
        $workers_to_run_by_rc_id = $self->schedule_workers($analysis, $pending_by_rc_id, $available_submit_limit);
Leo Gordon's avatar
Leo Gordon committed
787
788
    }

789
    return $workers_to_run_by_rc_id;
790
791
}

792

Leo Gordon's avatar
Leo Gordon committed
793
sub get_remaining_jobs_show_hive_progress {
794
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
795
  my $sql = "SELECT sum(done_job_count), sum(failed_job_count), sum(total_job_count), ".
796
797
            "sum(unclaimed_job_count * analysis_stats.avg_msec_per_job)/1000/60/60 ".
            "FROM analysis_stats";
798
799
  my $sth = $self->prepare($sql);
  $sth->execute();
800
  my ($done, $failed, $total, $cpuhrs) = $sth->fetchrow_array();
801
  $sth->finish;
802
803
804
805
806
807
808

  $done   ||= 0;
  $failed ||= 0;
  $total  ||= 0;
  my $completed = $total
    ? ((100.0 * ($done+$failed))/$total)
    : 0.0;
809
810
811
  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
812
  return $remaining;
813
814
}

815

Leo Gordon's avatar
Leo Gordon committed
816
sub print_analysis_status {
Leo Gordon's avatar
Leo Gordon committed
817
    my ($self, $filter_analysis) = @_;
818

Leo Gordon's avatar
Leo Gordon committed
819
    my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
820
821
822
    foreach my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {
        $analysis->stats->print_stats($self->{'verbose_stats'});
    }
823
824
825
}


Leo Gordon's avatar
Leo Gordon committed
826
sub print_running_worker_counts {
827
  my $self = shift;
828

Leo Gordon's avatar
Leo Gordon committed
829
  print "\n===== Stats of live Workers according to the Queen: ======\n";
830
831
832
  my $sql = "SELECT logic_name, count(*) FROM worker, analysis ".
            "WHERE worker.analysis_id=analysis.analysis_id AND worker.cause_of_death='' ".
            "GROUP BY worker.analysis_id";
Leo Gordon's avatar
Leo Gordon committed
833

834
  my $total_workers = 0;
835
836
  my $sth = $self->prepare($sql);
  $sth->execute();
837
  while((my $logic_name, my $worker_count)=$sth->fetchrow_array()) {
Leo Gordon's avatar
Leo Gordon committed
838
    printf("%30s : %d workers\n", $logic_name, $worker_count);
839
    $total_workers += $worker_count;
840
  }
841
  $sth->finish;
Leo Gordon's avatar
Leo Gordon committed
842
  printf("%30s : %d workers\n\n", '======= TOTAL =======', $total_workers);
843
}
844

845
846
847
848
849
850
851
852
853
854
855
=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

Leo Gordon's avatar
Leo Gordon committed
856
sub monitor {
857
858
859
860
  my $self = shift;
  my $sql = qq{
      INSERT INTO monitor
      SELECT
861
          CURRENT_TIMESTAMP,
862
          count(*),
Leo Gordon's avatar
Leo Gordon committed
863
864
865
866
867
868
  }. ( ($self->dbc->driver eq 'sqlite')
        ? qq{ sum(work_done/(strftime('%s','now')-strftime('%s',born))),
              sum(work_done/(strftime('%s','now')-strftime('%s',born)))/count(*), }
        : qq{ sum(work_done/(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(born))),
              sum(work_done/(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(born)))/count(*), }
  ). qq{
869
          group_concat(DISTINCT logic_name)
870
      FROM worker left join analysis USING (analysis_id)
871
872
      WHERE cause_of_death = ''
  };
873
874
875
876
877
      
  my $sth = $self->prepare($sql);
  $sth->execute();
}

Leo Gordon's avatar
Leo Gordon committed
878
879
880
881
882
883
884
885
886
887
888
889
890
891
=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}) {
892
        $worker->cause_of_death( 'FATALITY' );  # well, maybe we could have investigated further...
Leo Gordon's avatar
Leo Gordon committed
893
894
895
896
        $self->register_worker_death($worker);
    }
}

897

Jessica Severin's avatar
Jessica Severin committed
898
899
900
901
902
#
# INTERNAL METHODS
#
###################

903
sub _pick_best_analysis_for_new_worker {
Leo Gordon's avatar
Leo Gordon committed
904
905
  my $self  = shift;
  my $rc_id = shift;    # this parameter will need to percolate very deep
906
907
908
909

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

910
  my ($stats) = @{$statsDBA->fetch_by_needed_workers(1, $rc_id)};
911
912
913
  if($stats) {
    #synchronize and double check that it can be run
    $self->safe_synchronize_AnalysisStats($stats);
914
    return $stats if(($stats->status ne 'BLOCKED') and ($stats->num_required_workers > 0) and (!defined($rc_id) or ($stats->resource_class_id == $rc_id)));
915
  }
916

917
  # ok so no analyses 'need' workers with the given $rc_id.
918
919
920
  if ($self->get_num_failed_analyses()) {
    return undef;
  }
921
922
923
924
  # 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");
925
  my $stats_list = $statsDBA->fetch_by_statuses(['LOADING', 'BLOCKED', 'ALL_CLAIMED']);
926
  foreach $stats (@$stats_list) {
927
    $self->safe_synchronize_AnalysisStats($stats);
928

929
    return $stats if(($stats->status ne 'BLOCKED') and ($stats->num_required_workers > 0) and (!defined($rc_id) or ($stats->resource_class_id == $rc_id)));
930
931
  }

932
    # does the following really ever help?
933
  ($stats) = @{$statsDBA->fetch_by_needed_workers(1, $rc_id)};
934
  return $stats;
935
936
937
}


938
=head2 fetch_by_dbID
Jessica Severin's avatar
Jessica Severin committed
939
940
941

  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
942
  Example    : $feat = $queen->fetch_by_dbID(1234);
Jessica Severin's avatar
Jessica Severin committed
943
944
945
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::Hive::Worker
946
  Exceptions : thrown if $worker_id is not defined
Jessica Severin's avatar
Jessica Severin committed
947
948
949
950
  Caller     : general

=cut