Queen.pm 38.2 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,
Leo Gordon's avatar
Leo Gordon committed
101
        $rc_id, $rc_name, $analysis_id, $logic_name, $job_id, $input_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
Leo Gordon's avatar
Leo Gordon committed
105
        rc_id rc_name analysis_id logic_name job_id input_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

Leo Gordon's avatar
Leo Gordon committed
108
109
110
111
112
113
114
115
116
117
118
    if($rc_name) {
        if($rc_id) {
            die "You should either define -rc_id or -rc_name, but not both\n";
        }
        if(my $rc = $self->db->get_ResourceClassAdaptor->fetch_by_name($rc_name)) {
            $rc_id = $rc->dbID;
        } else {
            die "rc_name '$rc_name' could not be fetched from the database\n";
        }
    }

119
120
121
122
123
124
125
126
127
128
    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
129

130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
    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 {
155
156
157
158
159
            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)) {
160
161
162
163
164
165
                $analysis_id = $job->analysis_id;
            } else {
                die "job_id '$job_id' could not be fetched from the database\n";
            }
        }
    }
166

167
  
168
  my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor or return undef;
169
170
  my $analysisStats;
  if($analysis_id) {
171
    $analysisStats = $analysis_stats_adaptor->fetch_by_analysis_id($analysis_id);
172
    $self->safe_synchronize_AnalysisStats($analysisStats);
173
    #return undef unless(($analysisStats->status ne 'BLOCKED') and ($analysisStats->num_required_workers > 0));
174
  } else {
175
176
177
178
179
    if( $analysisStats = $self->_pick_best_analysis_for_new_worker($rc_id) ) {
        print "Scheduler picked analysis_id=".$analysisStats->analysis_id()." for the worker\n";
    } else {
        print "Scheduler failed to pick analysis_id for the worker\n";
    }
180
  }
181
  return undef unless($analysisStats);
182

183
184
  unless($job) {
    #go into autonomous mode
185
186
187
188
189

    if($self->get_hive_current_load() >= 1.1) {
        print "Hive is overloaded, can't create a worker\n";
        return;
    }
190
    if($analysisStats->status eq 'BLOCKED') {
191
192
      print "Analysis is BLOCKED, can't create workers\n";
      return;
193
194
    }
    if($analysisStats->status eq 'DONE') {
195
196
      print "Analysis is DONE, don't need to create workers\n";
      return;
197
    }
198

199
200
    $analysis_stats_adaptor->decrease_required_workers($analysisStats->analysis_id);

201
    $analysisStats->print_stats;
202
  }
203
  
204
205
206
207
208
209
210
211
212
213
    # 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);
  }

214
  my $sql = q{INSERT INTO worker 
215
216
              (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
217
218

  my $sth = $self->prepare($sql);
219
  $sth->execute($meadow_type, $meadow_name, $process_id, $exec_host, $analysisStats->analysis_id);
Leo Gordon's avatar
Leo Gordon committed
220
  my $worker_id = $self->dbc->db_handle->last_insert_id(undef, undef, 'worker', 'worker_id');
Jessica Severin's avatar
Jessica Severin committed
221
222
  $sth->finish;

223
  my $worker = $self->fetch_by_dbID($worker_id);
Jessica Severin's avatar
Jessica Severin committed
224
225
  $worker=undef unless($worker and $worker->analysis);

226
227
  $worker->init;

228
  if($worker and $analysisStats) {
229
    $analysisStats->update_status('WORKING');
Jessica Severin's avatar
Jessica Severin committed
230
  }
231
  
232
  $worker->_specific_job($job) if($job);
233
  $worker->execute_writes(0) if($no_write);
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258

    $worker->debug($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);
    }
259
260
261
    if(defined $compile_module_once) {
        $worker->compile_module_once($compile_module_once);
    }
262

263
    return $worker;
Jessica Severin's avatar
Jessica Severin committed
264
265
}

266

Jessica Severin's avatar
Jessica Severin committed
267
268
269
270
sub register_worker_death {
  my ($self, $worker) = @_;

  return unless($worker);
Leo Gordon's avatar
Leo Gordon committed
271

Leo Gordon's avatar
bugfix  
Leo Gordon committed
272
273
  my $cod = $worker->cause_of_death();

274
  my $sql = "UPDATE worker SET died=CURRENT_TIMESTAMP, last_check_in=CURRENT_TIMESTAMP";
275
  $sql .= " ,status='DEAD'";
Jessica Severin's avatar
Jessica Severin committed
276
  $sql .= " ,work_done='" . $worker->work_done . "'";
Leo Gordon's avatar
bugfix  
Leo Gordon committed
277
  $sql .= " ,cause_of_death='$cod'";
278
  $sql .= " WHERE worker_id='" . $worker->dbID ."'";
Jessica Severin's avatar
Jessica Severin committed
279

Leo Gordon's avatar
bugfix  
Leo Gordon committed
280
  $self->dbc->do( $sql );
281

282
283
284
285
  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
286
  if($cod eq 'NO_WORK') {
287
    $self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, 'ALL_CLAIMED');
288
  }
Leo Gordon's avatar
bugfix  
Leo Gordon committed
289
290
291
292
  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
293
    $self->db->get_AnalysisJobAdaptor->release_undone_jobs_from_worker($worker);
294
  }
295
  
296
  # re-sync the analysis_stats when a worker dies as part of dynamic sync system
297
  if($self->safe_synchronize_AnalysisStats($worker->analysis->stats)->status ne 'DONE') {
298
299
    # 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
300
    $self->db->get_AnalysisStatsAdaptor->increase_required_workers($worker->analysis->dbID);
301
302
  }

Jessica Severin's avatar
Jessica Severin committed
303
304
}

305
sub check_for_dead_workers {    # scans the whole Valley for lost Workers (but ignores unreachagle ones)
306
    my ($self, $valley, $check_buried_in_haste) = @_;
Leo Gordon's avatar
Leo Gordon committed
307

308
    warn "GarbageCollector:\tChecking for lost Workers...\n";
309

310
311
312
313
    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
314

315
    warn "GarbageCollector:\t[Queen:] we have ".scalar(@$queen_worker_list)." Workers alive.\n";
316

Leo Gordon's avatar
Leo Gordon committed
317
318
    foreach my $worker (@$queen_worker_list) {

319
320
321
        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
322
        } else {
323
            $worker_status_counts{$meadow_type}{'UNREACHABLE'}++;
324

325
            next;   # Worker is unreachable from this Valley
Leo Gordon's avatar
Leo Gordon committed
326
327
        }

328
329
330
331
332
        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'}++;
333

334
            $mt_and_pid_to_lost_worker{$meadow_type}{$process_id} = $worker;
335
        }
336
337
338
339
340
341
    }

        # 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";
    }
342

343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
    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);
            }
363
364
365
        }
    }

366
        # the following bit is completely Meadow-agnostic and only restores database integrity:
Leo Gordon's avatar
Leo Gordon committed
367
    if($check_buried_in_haste) {
368
        warn "GarbageCollector:\tChecking for Workers buried in haste...\n";
369
        my $buried_in_haste_list = $self->fetch_all_dead_workers_with_jobs();
Leo Gordon's avatar
Leo Gordon committed
370
        if(my $bih_number = scalar(@$buried_in_haste_list)) {
371
            warn "GarbageCollector:\tfound $bih_number jobs, reclaiming.\n\n";
Leo Gordon's avatar
Leo Gordon committed
372
373
374
            if($bih_number) {
                my $job_adaptor = $self->db->get_AnalysisJobAdaptor();
                foreach my $worker (@$buried_in_haste_list) {
Leo Gordon's avatar
Leo Gordon committed
375
                    $job_adaptor->release_undone_jobs_from_worker($worker);
Leo Gordon's avatar
Leo Gordon committed
376
377
378
                }
            }
        } else {
379
            warn "GarbageCollector:\tfound none\n";
Leo Gordon's avatar
Leo Gordon committed
380
381
382
        }
    }
}
Jessica Severin's avatar
Jessica Severin committed
383
384


385
386
387
    # 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
388

389
    $self->dbc->do("UPDATE worker SET last_check_in=CURRENT_TIMESTAMP, status='".$worker->status."', work_done='".$worker->work_done."' WHERE worker_id='".$worker->dbID."'");
Jessica Severin's avatar
Jessica Severin committed
390
391
392
}


393
=head2 reset_job_by_dbID_and_sync
394

395
  Arg [1]: int $job_id
396
  Example: 
397
    my $job = $queen->reset_job_by_dbID_and_sync($job_id);
398
  Description: 
399
    For the specified job_id it will fetch just that job, 
400
401
402
    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 
403
    same job simultaneously (use only for debugging).
404
  Returntype : none
405
  Exceptions :
406
  Caller     : beekeeper.pl
407
408
409

=cut

410
411
sub reset_job_by_dbID_and_sync {
    my ($self, $job_id) = @_;
412

413
414
415
416
417
418
    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);
419
420
421
}


422
423
424
425
426
427
######################################
#
# Public API interface for beekeeper
#
######################################

428
429
430
    # Note: asking for Queen->fetch_overdue_workers(0) essentially means
    #       "fetch all workers known to the Queen not to be officially dead"
    #
431
432
433
434
435
sub fetch_overdue_workers {
  my ($self,$overdue_secs) = @_;

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

436
437
438
439
  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");
440
441
442
  return $self->_generic_fetch($constraint);
}

443
444
sub fetch_failed_workers {
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
445

446
  my $constraint = "w.cause_of_death='FATALITY' ";
447
448
449
  return $self->_generic_fetch($constraint);
}

450
sub fetch_all_dead_workers_with_jobs {
Leo Gordon's avatar
Leo Gordon committed
451
452
  my $self = shift;

453
  # 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
454

455
456
  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
457
458
  return $self->_generic_fetch($constraint, $join);
}
Jessica Severin's avatar
Jessica Severin committed
459

460
461
=head2 synchronize_hive

Leo Gordon's avatar
Leo Gordon committed
462
  Arg [1]    : $filter_analysis (optional)
463
464
  Example    : $queen->synchronize_hive();
  Description: Runs through all analyses in the system and synchronizes
465
466
              the analysis_stats summary with the states in the job 
              and worker tables.  Then follows by checking all the blocking rules
467
468
469
470
471
472
473
              and blocks/unblocks analyses as needed.
  Exceptions : none
  Caller     : general

=cut

sub synchronize_hive {
Leo Gordon's avatar
Leo Gordon committed
474
  my $self          = shift;
Leo Gordon's avatar
Leo Gordon committed
475
  my $filter_analysis = shift; # optional parameter
476

477
  my $start_time = time();
478

Leo Gordon's avatar
Leo Gordon committed
479
  my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
480

Leo Gordon's avatar
Leo Gordon committed
481
  print STDERR "\nSynchronizing the hive (".scalar(@$list_of_analyses)." analyses this time):\n";
Leo Gordon's avatar
Leo Gordon committed
482
483
  foreach my $analysis (@$list_of_analyses) {
    $self->synchronize_AnalysisStats($analysis->stats);
484
    print STDERR ( ($analysis->stats()->status eq 'BLOCKED') ? 'x' : 'o');
485
  }
Leo Gordon's avatar
Leo Gordon committed
486
  print STDERR "\n";
Leo Gordon's avatar
Leo Gordon committed
487

488
489
490
491
492
493
#  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
494

Leo Gordon's avatar
Leo Gordon committed
495
  print STDERR ''.((time() - $start_time))." seconds to synchronize_hive\n\n";
496
}
497

498

499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
=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
521
                   ($stats->seconds_since_last_update < 3*60));
522
523
524
525

  # 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=" . $stats->analysis_id;
526
  #print("$sql\n");
527
  my $row_count = $self->dbc->do($sql);  
528
  return $stats unless($row_count == 1);        # return the un-updated status if locked
529
  #printf("got sync_lock on analysis_stats(%d)\n", $stats->analysis_id);
530
  
531
      # since we managed to obtain the lock, let's go and perform the sync:
532
  $self->synchronize_AnalysisStats($stats);
533

534
535
536
537
  return $stats;
}


538
=head2 synchronize_AnalysisStats
539

540
541
  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
542
  Description: Queries the job and worker tables to get summary counts
543
544
545
546
547
               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
548

549
=cut
550

551
sub synchronize_AnalysisStats {
552
  my $self = shift;
553
  my $analysisStats = shift;
554

555
  return $analysisStats unless($analysisStats);
556
  return $analysisStats unless($analysisStats->analysis_id);
557

558
  $analysisStats->refresh(); ## Need to get the new hive_capacity for dynamic analyses
559
560
  my $hive_capacity = $analysisStats->hive_capacity;

561
562
563
564
  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() );
565

566
567
                # adjust_stats_for_living_workers:
            if($hive_capacity > 0) {
568
                my $unfulfilled_capacity = $hive_capacity - $analysisStats->num_running_workers();
569

570
571
                if($unfulfilled_capacity < $required_workers ) {
                    $required_workers = (0 < $unfulfilled_capacity) ? $unfulfilled_capacity : 0;
572
573
574
575
576
577
578
579
580
581
                }
            }
            $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);
582

583
      my $sql = "SELECT status, semaphore_count, count(*) FROM job ".
584
585
586
                "WHERE analysis_id=? GROUP BY status, semaphore_count";
      my $sth = $self->prepare($sql);
      $sth->execute($analysisStats->analysis_id);
587
588


589
590
591
592
      my $done_here       = 0;
      my $done_elsewhere  = 0;
      my $total_job_count = 0;
      while (my ($status, $semaphore_count, $job_count)=$sth->fetchrow_array()) {
593
    # print STDERR "$status: $job_count\n";
594

595
        $total_job_count += $job_count;
596
597
598
599
600
601
602
603

        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) {
604
                my $unfulfilled_capacity = $hive_capacity - $self->count_running_workers( $analysisStats->analysis_id() );
605

606
607
                if($unfulfilled_capacity < $required_workers ) {
                    $required_workers = (0 < $unfulfilled_capacity) ? $unfulfilled_capacity : 0;
608
                }
609
            }
610
611
            $analysisStats->num_required_workers( $required_workers );

612
        } elsif($status eq 'DONE') {
613
            $done_here = $job_count;
614
        } elsif($status eq 'PASSED_ON') {
615
616
617
            $done_elsewhere = $job_count;
        } elsif ($status eq 'FAILED') {
            $analysisStats->failed_job_count($job_count);
618
        }
619
      } # /while
620
      $sth->finish;
621

622
623
      $analysisStats->total_job_count( $total_job_count );
      $analysisStats->done_job_count( $done_here + $done_elsewhere );
624
  } # /unless $self->{'_hive_use_triggers'}
625

626
  $analysisStats->check_blocking_control_rules();
627

628
629
630
  if($analysisStats->status ne 'BLOCKED') {
    $analysisStats->determine_status();
  }
631

632
  # $analysisStats->sync_lock(0); ## do we perhaps need it here?
633
  $analysisStats->update;  #update and release sync_lock
634

635
  return $analysisStats;
636
}
637
638


Leo Gordon's avatar
Leo Gordon committed
639
640
sub get_num_failed_analyses {
  my ($self, $analysis) = @_;
641
642

  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
Leo Gordon's avatar
Leo Gordon committed
643
  my $failed_analyses = $statsDBA->fetch_by_statuses(['FAILED']);
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
  if ($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);
}


666
667
sub get_hive_current_load {
  my $self = shift;
668
669
670
  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";
671
672
673
674
675
  my $sth = $self->prepare($sql);
  $sth->execute();
  (my $load)=$sth->fetchrow_array();
  $sth->finish;
  $load=0 unless($load);
676
#  print("current hive load = $load\n");
677
678
679
680
  return $load;
}


681
682
683
684
685
686
687
688
689
690
691
692
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;
693
694
}

695

696
=head2 schedule_workers
697

698
  Arg[1]     : Bio::EnsEMBL::Hive::Analysis object (optional)
699
  Example    : $count = $queen->schedule_workers();
700
701
702
  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
703
               If Arg[1] is defined, does it only for the given analysis.
704
  Exceptions : none
705
  Caller     : beekeepers and other external processes
706
707
708

=cut

709
710
sub schedule_workers {
  my ($self, $filter_analysis, $orig_pending_by_rc_id, $available_submit_limit) = @_;
711

712
  my $statsDBA                      = $self->db->get_AnalysisStatsAdaptor;
713
  my $clearly_needed_analyses       = $statsDBA->fetch_by_needed_workers();
714
715
  my $potentially_needed_analyses   = $statsDBA->fetch_by_statuses(['LOADING', 'BLOCKED', 'ALL_CLAIMED']);
  my @all_analyses                  = (@$clearly_needed_analyses, @$potentially_needed_analyses);
716

717
  return {} unless(@all_analyses);
718

719
720
721
722
  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();
723

724

Leo Gordon's avatar
Leo Gordon committed
725
  foreach my $analysis_stats (@all_analyses) {
726
727
    last if ($available_load <= 0.0);
    last if (defined($available_submit_limit) and !$available_submit_limit);
Leo Gordon's avatar
Leo Gordon committed
728
    next if (defined $filter_analysis && $filter_analysis->dbID != $analysis_stats->analysis_id);
729

Leo Gordon's avatar
Leo Gordon committed
730
        #digging deeper under the surface so need to sync
731
    if(($analysis_stats->status eq 'LOADING') or ($analysis_stats->status eq 'BLOCKED') or ($analysis_stats->status eq 'ALL_CLAIMED')) {
732
733
734
735
736
737
      $self->synchronize_AnalysisStats($analysis_stats);
    }

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

738
        # 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
739
    my $workers_this_analysis = $analysis_stats->num_required_workers;
740

741
742
743
744
745
746
    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
747

748
749
750
751
752
    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
753
754
        }

755
        $available_load -= 1.0*$workers_this_analysis/$hive_capacity;
756
    }
Leo Gordon's avatar
Leo Gordon committed
757

758
    my $curr_rc_id = $analysis_stats->resource_class_id;
759
760
761
    if($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;

762
        print "Scheduler detected $pending_this_analysis pending workers with rc_id=$curr_rc_id\n";
763
764
765
766
        $workers_this_analysis              -= $pending_this_analysis;
        $pending_by_rc_id{ $curr_rc_id }    -= $pending_this_analysis;
    }

767
768
    next unless($workers_this_analysis);    # do not autovivify the hash by a zero

769
770
771
    $total_workers_to_run += $workers_this_analysis;
    $workers_to_run_by_rc_id{ $curr_rc_id } += $workers_this_analysis;
    $analysis_stats->print_stats();
772
    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);
773
  }
774

775
  printf("Scheduler suggests adding a total of %d workers [%1.5f hive_load remaining]\n", $total_workers_to_run, $available_load);
776
  return \%workers_to_run_by_rc_id;
Leo Gordon's avatar
Leo Gordon committed
777
778
}

779

780
sub schedule_workers_resync_if_necessary {
781
782
783
    my ($self, $valley, $analysis) = @_;

    my $meadow              = $valley->get_current_meadow();
Leo Gordon's avatar
Leo Gordon committed
784

785
786
787
    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
788

789
790
791
792
    my $available_submit_limit = ($submit_limit and $meadow_limit)
                                    ? (($submit_limit<$meadow_limit) ? $submit_limit : $meadow_limit)
                                    : (defined($submit_limit) ? $submit_limit : $meadow_limit);

793
    my $workers_to_run_by_rc_id = $self->schedule_workers($analysis, $pending_by_rc_id, $available_submit_limit);
794

795
    unless( keys %$workers_to_run_by_rc_id or $self->get_hive_current_load() or $self->count_running_workers() ) {
796
        print "\nScheduler: nothing is running and nothing to do (according to analysis_stats) => executing garbage collection and sync\n" ;
Leo Gordon's avatar
Leo Gordon committed
797

798
        $self->check_for_dead_workers($valley, 1);
799
        $self->synchronize_hive($analysis);
Leo Gordon's avatar
Leo Gordon committed
800

801
        $workers_to_run_by_rc_id = $self->schedule_workers($analysis, $pending_by_rc_id, $available_submit_limit);
Leo Gordon's avatar
Leo Gordon committed
802
803
    }

804
    return $workers_to_run_by_rc_id;
805
806
}

807

Leo Gordon's avatar
Leo Gordon committed
808
sub get_remaining_jobs_show_hive_progress {
809
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
810
  my $sql = "SELECT sum(done_job_count), sum(failed_job_count), sum(total_job_count), ".
811
812
            "sum(unclaimed_job_count * analysis_stats.avg_msec_per_job)/1000/60/60 ".
            "FROM analysis_stats";
813
814
  my $sth = $self->prepare($sql);
  $sth->execute();
815
  my ($done, $failed, $total, $cpuhrs) = $sth->fetchrow_array();
816
  $sth->finish;
817
818
819
820
821
822
823

  $done   ||= 0;
  $failed ||= 0;
  $total  ||= 0;
  my $completed = $total
    ? ((100.0 * ($done+$failed))/$total)
    : 0.0;
824
825
826
  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
827
  return $remaining;
828
829
}

830

Leo Gordon's avatar
Leo Gordon committed
831
sub print_analysis_status {
Leo Gordon's avatar
Leo Gordon committed
832
    my ($self, $filter_analysis) = @_;
833

Leo Gordon's avatar
Leo Gordon committed
834
    my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
835
836
837
    foreach my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {
        $analysis->stats->print_stats($self->{'verbose_stats'});
    }
838
839
840
}


Leo Gordon's avatar
Leo Gordon committed
841
sub print_running_worker_counts {
842
  my $self = shift;
843

Leo Gordon's avatar
Leo Gordon committed
844
  print "\n===== Stats of live Workers according to the Queen: ======\n";
845
846
847
848
849
850
  my $sql = qq{ SELECT logic_name, count(*)
                FROM worker
                JOIN analysis_base USING(analysis_id)
                WHERE worker.cause_of_death=''
                GROUP BY worker.analysis_id
  };
Leo Gordon's avatar
Leo Gordon committed
851

852
  my $total_workers = 0;
853
854
  my $sth = $self->prepare($sql);
  $sth->execute();
855
  while((my $logic_name, my $worker_count)=$sth->fetchrow_array()) {
Leo Gordon's avatar
Leo Gordon committed
856
    printf("%30s : %d workers\n", $logic_name, $worker_count);
857
    $total_workers += $worker_count;
858
  }
859
  $sth->finish;
Leo Gordon's avatar
Leo Gordon committed
860
  printf("%30s : %d workers\n\n", '======= TOTAL =======', $total_workers);
861
}
862

863
864
865
866
867
868
869
870
871
872
873
=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
874
sub monitor {
875
876
877
878
  my $self = shift;
  my $sql = qq{
      INSERT INTO monitor
      SELECT
879
          CURRENT_TIMESTAMP,
880
          count(*),