Queen.pm 30.1 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
use Clone 'clone';
65
66
67
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;

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

72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');


sub default_table_name {
    return 'worker';
}


sub default_insertion_method {
    return 'INSERT';
}


sub object_class {
    return 'Bio::EnsEMBL::Hive::Worker';
}
88

Jessica Severin's avatar
Jessica Severin committed
89

90
############################
Jessica Severin's avatar
Jessica Severin committed
91
#
92
# PUBLIC API
Jessica Severin's avatar
Jessica Severin committed
93
#
94
############################
Jessica Severin's avatar
Jessica Severin committed
95

96

Jessica Severin's avatar
Jessica Severin committed
97
98
=head2 create_new_worker

99
100
101
102
  Description: Creates an entry in the worker table,
               populates some non-storable attributes
               and returns a Worker object based on that insert.
               This guarantees that each worker registered in this Queen's hive is properly registered.
Jessica Severin's avatar
Jessica Severin committed
103
  Returntype : Bio::EnsEMBL::Hive::Worker
104
  Caller     : runWorker.pl
Jessica Severin's avatar
Jessica Severin committed
105
106
107
108

=cut

sub create_new_worker {
109
    my ($self, @args) = @_;
110

111
112
113
114
115
116
    my ($meadow_type, $meadow_name, $process_id, $exec_host, $resource_class_id, $resource_class_name,
        $no_write, $debug, $worker_log_dir, $hive_log_dir, $job_limit, $life_span, $no_cleanup, $retry_throwing_jobs, $compile_module_once) =

    rearrange([qw(meadow_type meadow_name process_id exec_host resource_class_id resource_class_name
                no_write debug worker_log_dir hive_log_dir job_limit life_span no_cleanup retry_throwing_jobs compile_module_once) ], @args);

117
    if( defined($resource_class_name) ) {
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
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
        my $rc = $self->db->get_ResourceClassAdaptor->fetch_by_name($resource_class_name)
            or die "resource_class with name='$resource_class_name' could not be fetched from the database";

        $resource_class_id = $rc->dbID;
    }

    my $sql = q{INSERT INTO worker (born, last_check_in, meadow_type, meadow_name, host, process_id, resource_class_id)
              VALUES (CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, ?, ?, ?, ?, ?)};

    my $sth = $self->prepare($sql);
    $sth->execute($meadow_type, $meadow_name, $exec_host, $process_id, $resource_class_id);
    my $worker_id = $self->dbc->db_handle->last_insert_id(undef, undef, 'worker', 'worker_id')
        or die "Could not create a new worker";
    $sth->finish;

    if($hive_log_dir or $worker_log_dir) {
        my $dir_revhash = dir_revhash($worker_id);
        $worker_log_dir ||= $hive_log_dir .'/'. ($dir_revhash ? "$dir_revhash/" : '') .'worker_id_'.$worker_id;

            # Note: the following die-message will not reach the log files for circular reason!
        system("mkdir -p $worker_log_dir") && die "Could not create '$worker_log_dir' because: $!";

        my $sth_add_log = $self->prepare( "UPDATE worker SET log_dir=? WHERE worker_id=?" );
        $sth_add_log->execute($worker_log_dir, $worker_id);
        $sth_add_log->finish;
    }

    my $worker = $self->fetch_by_dbID($worker_id)
        or die "Could not fetch worker with dbID=$worker_id";

    $worker->init;

    if($job_limit) {
      $worker->job_limit($job_limit);
      $worker->life_span(0);
    }

    $worker->life_span($life_span * 60)                 if($life_span);

    $worker->execute_writes(0)                          if($no_write);

    $worker->perform_cleanup(0)                         if($no_cleanup);

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

    $worker->retry_throwing_jobs($retry_throwing_jobs)  if(defined $retry_throwing_jobs);

    $worker->compile_module_once($compile_module_once)  if(defined $compile_module_once);

    return $worker;
}


=head2 specialize_new_worker
172

173
174
  Description: If analysis_id or logic_name is specified it will try to specialize the Worker into this analysis.
               If not specified the Queen will analyze the hive and pick the most suitable analysis.
175
  Caller     : Bio::EnsEMBL::Hive::Worker
176
177
178
179
180
181
182
183

=cut

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

    my ($analysis_id, $logic_name, $job_id, $force) =
        rearrange([qw(analysis_id logic_name job_id force) ], @args);
184

185
186
    if( scalar( grep {defined($_)} ($analysis_id, $logic_name, $job_id) ) > 1) {
        die "At most one of the options {-analysis_id, -logic_name, -job_id} can be set to pre-specialize a Worker";
Leo Gordon's avatar
Leo Gordon committed
187
188
    }

189
    my ($analysis, $stats, $special_batch);
190
    my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor;
Jessica Severin's avatar
Jessica Severin committed
191

192
    if($job_id or $analysis_id or $logic_name) {    # probably pre-specialized from command-line
193

194
        if($job_id) {
195
196
197
            print "resetting and fetching job for job_id '$job_id'\n";

            my $job_adaptor = $self->db->get_AnalysisJobAdaptor;
198

199
200
201
202
203
204
205
206
207
            my $job = $job_adaptor->fetch_by_dbID( $job_id )
                or die "Could not fetch job with dbID='$job_id'";
            my $job_status = $job->status();

            if($job_status =~/(CLAIMED|PRE_CLEANUP|FETCH_INPUT|RUN|WRITE_OUTPUT|POST_CLEANUP)/ ) {
                die "Job with dbID='$job_id' is already in progress, cannot run";   # FIXME: try GC first, then complain
            } elsif($job_status =~/(DONE|SEMAPHORED)/ and !$force) {
                die "Job with dbID='$job_id' is $job_status, please use -force 1 to override";
            }
208

209
210
211
212
213
214
215
216
            if(($job_status eq 'DONE') and $job->semaphored_job_id) {
                warn "Increasing the semaphore count of the dependent job";
                $job_adaptor->increase_semaphore_count_for_jobid( $job->semaphored_job_id );
            }

            my $worker_id = $worker->dbID;
            if($job = $job_adaptor->reset_or_grab_job_by_dbID($job_id, $worker_id)) {
                $special_batch = [ $job ];
217
218
                $analysis_id = $job->analysis_id;
            } else {
219
                die "Could not claim job with dbID='$job_id' for worker with dbID='$worker_id'";
220
            }
221
222
223
224
225
226
227
228
229
230
231
232
233
        }

        if($logic_name) {
            $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name)
                or die "analysis with name='$logic_name' could not be fetched from the database";

            $analysis_id = $analysis->dbID;

        } elsif($analysis_id) {
            $analysis = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id)
                or die "analysis with dbID='$analysis_id' could not be fetched from the database";
        }

234
235
236
        if( $worker->resource_class_id
        and $worker->resource_class_id != $analysis->resource_class_id) {
                die "resource_class of analysis ".$analysis->logic_name." is incompatible with this Worker's resource_class";
237
238
        }

239
240
241
        $stats = $analysis_stats_adaptor->fetch_by_analysis_id($analysis_id);
        $self->safe_synchronize_AnalysisStats($stats);

242
        unless($special_batch or $force) {    # do we really need to run this analysis?
243
            if($self->get_hive_current_load() >= 1.1) {
244
                $worker->cause_of_death('HIVE_OVERLOAD');
245
                die "Hive is overloaded, can't specialize a worker";
246
247
            }
            if($stats->status eq 'BLOCKED') {
248
                die "Analysis is BLOCKED, can't specialize a worker";
249
250
            }
            if($stats->num_required_workers <= 0) {
251
                die "Analysis requires 0 workers at the moment";
252
253
            }
            if($stats->status eq 'DONE') {
254
                die "Analysis is DONE, and doesn't require workers";
255
256
            }
        }
257

258
    } else {    # probably scheduled by beekeeper.pl
259

260
        $stats = $self->suggest_analysis_to_specialize_by_rc_id_meadow_type($worker->resource_class_id, $worker->meadow_type)
261
            or die "Queen failed to pick an analysis for the worker";
262

263
        print "Queen picked analysis with dbID=".$stats->analysis_id." for the worker\n";
264
265

        $analysis_id = $stats->analysis_id;
266
    }
267

268
        # now set it in the $worker:
Jessica Severin's avatar
Jessica Severin committed
269

270
    $worker->analysis_id( $analysis_id );
Jessica Severin's avatar
Jessica Severin committed
271

272
273
274
275
    my $sth_update_analysis_id = $self->prepare( "UPDATE worker SET analysis_id=? WHERE worker_id=?" );
    $sth_update_analysis_id->execute($worker->analysis_id, $worker->dbID);
    $sth_update_analysis_id->finish;

276
277
    if($special_batch) {
        $worker->special_batch( $special_batch );
278
    } else {    # count it as autonomous worker sharing the load of that analysis:
279
280
281

        $stats->update_status('WORKING');

282
        $analysis_stats_adaptor->decrease_required_workers($worker->analysis_id);
283
284
285
286
287
288
289
290
291
    }

        # 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() ) {
292
        $analysis_stats_adaptor->increase_running_workers($worker->analysis_id);
293
    }
Jessica Severin's avatar
Jessica Severin committed
294
295
}

296

Jessica Severin's avatar
Jessica Severin committed
297
sub register_worker_death {
298
    my ($self, $worker) = @_;
299

300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
    return unless($worker);

    my $cod = $worker->cause_of_death() || 'UNKNOWN';    # make sure we do not attempt to insert a void

    my $sql = qq{UPDATE worker SET died=CURRENT_TIMESTAMP
                    ,last_check_in=CURRENT_TIMESTAMP
                    ,status='DEAD'
                    ,work_done='}. $worker->work_done . qq{'
                    ,cause_of_death='$cod'
                WHERE worker_id='}. $worker->dbID . qq{'};
    $self->dbc->do( $sql );

    if(my $analysis_id = $worker->analysis_id) {
        my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor;

        unless( $self->db->hive_use_triggers() ) {
            $analysis_stats_adaptor->decrease_running_workers($worker->analysis_id);
        }

        if($cod eq 'NO_WORK') {
            $analysis_stats_adaptor->update_status($worker->analysis_id, 'ALL_CLAIMED');
        } elsif($cod eq 'UNKNOWN'
            or $cod eq 'MEMLIMIT'
            or $cod eq 'RUNLIMIT'
324
            or $cod eq 'KILLED_BY_USER'
325
            or $cod eq 'SEE_MSG'
326
            or $cod eq 'CONTAMINATED') {
327
328
329
330
331
332
333
334
335
336
                $self->db->get_AnalysisJobAdaptor->release_undone_jobs_from_worker($worker);
        }

            # re-sync the analysis_stats when a worker dies as part of dynamic sync system
        if($self->safe_synchronize_AnalysisStats($worker->analysis->stats)->status ne 'DONE') {
            # 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
            $analysis_stats_adaptor->increase_required_workers($worker->analysis_id);
        }
    }
Jessica Severin's avatar
Jessica Severin committed
337
338
}

339

340
sub check_for_dead_workers {    # scans the whole Valley for lost Workers (but ignores unreachagle ones)
341
    my ($self, $valley, $check_buried_in_haste) = @_;
Leo Gordon's avatar
Leo Gordon committed
342

343
    warn "GarbageCollector:\tChecking for lost Workers...\n";
344

345
346
347
348
    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
349

350
    warn "GarbageCollector:\t[Queen:] we have ".scalar(@$queen_worker_list)." Workers alive.\n";
351

Leo Gordon's avatar
Leo Gordon committed
352
353
    foreach my $worker (@$queen_worker_list) {

354
355
356
        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
357
        } else {
358
            $worker_status_counts{$meadow_type}{'UNREACHABLE'}++;
359

360
            next;   # Worker is unreachable from this Valley
Leo Gordon's avatar
Leo Gordon committed
361
362
        }

363
364
365
366
367
        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'}++;
368

369
            $mt_and_pid_to_lost_worker{$meadow_type}{$process_id} = $worker;
370
        }
371
372
373
374
375
376
    }

        # 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";
    }
377

378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
    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) {
395
                $worker->cause_of_death( $wpid_to_cod->{$process_id} || 'UNKNOWN');
396
397
                $self->register_worker_death($worker);
            }
398
399
400
        }
    }

401
        # the following bit is completely Meadow-agnostic and only restores database integrity:
Leo Gordon's avatar
Leo Gordon committed
402
    if($check_buried_in_haste) {
403
        warn "GarbageCollector:\tChecking for Workers buried in haste...\n";
404
        my $buried_in_haste_list = $self->fetch_all_dead_workers_with_jobs();
Leo Gordon's avatar
Leo Gordon committed
405
        if(my $bih_number = scalar(@$buried_in_haste_list)) {
406
            warn "GarbageCollector:\tfound $bih_number jobs, reclaiming.\n\n";
Leo Gordon's avatar
Leo Gordon committed
407
408
409
            if($bih_number) {
                my $job_adaptor = $self->db->get_AnalysisJobAdaptor();
                foreach my $worker (@$buried_in_haste_list) {
Leo Gordon's avatar
Leo Gordon committed
410
                    $job_adaptor->release_undone_jobs_from_worker($worker);
Leo Gordon's avatar
Leo Gordon committed
411
412
413
                }
            }
        } else {
414
            warn "GarbageCollector:\tfound none\n";
Leo Gordon's avatar
Leo Gordon committed
415
416
417
        }
    }
}
Jessica Severin's avatar
Jessica Severin committed
418
419


420
421
422
    # 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
423

424
    $self->dbc->do("UPDATE worker SET last_check_in=CURRENT_TIMESTAMP, status='".$worker->status."', work_done='".$worker->work_done."' WHERE worker_id='".$worker->dbID."'");
Jessica Severin's avatar
Jessica Severin committed
425
426
427
}


428
=head2 reset_job_by_dbID_and_sync
429

430
  Arg [1]: int $job_id
431
  Example: 
432
    my $job = $queen->reset_job_by_dbID_and_sync($job_id);
433
  Description: 
434
    For the specified job_id it will fetch just that job, 
435
436
437
    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 
438
    same job simultaneously (use only for debugging).
439
  Returntype : none
440
  Exceptions :
441
  Caller     : beekeeper.pl
442
443
444

=cut

445
446
sub reset_job_by_dbID_and_sync {
    my ($self, $job_id) = @_;
447

448
    my $job_adaptor = $self->db->get_AnalysisJobAdaptor;
449
    my $job = $job_adaptor->reset_or_grab_job_by_dbID($job_id); 
450
451
452

    my $stats = $self->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id($job->analysis_id);
    $self->synchronize_AnalysisStats($stats);
453
454
455
}


456
457
458
459
460
461
######################################
#
# Public API interface for beekeeper
#
######################################

462

463
464
465
    # Note: asking for Queen->fetch_overdue_workers(0) essentially means
    #       "fetch all workers known to the Queen not to be officially dead"
    #
466
sub fetch_overdue_workers {
467
    my ($self,$overdue_secs) = @_;
468

469
    $overdue_secs = 3600 unless(defined($overdue_secs));
470

471
    my $constraint = "status!='DEAD' AND ".
472
                    ( ($self->dbc->driver eq 'sqlite')
473
474
475
                        ? "(strftime('%s','now')-strftime('%s',last_check_in))>$overdue_secs"
                        : "(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(last_check_in))>$overdue_secs");
    return $self->fetch_all( $constraint );
476
477
}

478
479
480

sub fetch_all_dead_workers_with_jobs {
    my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
481

482
    return $self->fetch_all( "JOIN job j USING(worker_id) WHERE worker.status='DEAD' AND j.status NOT IN ('DONE', 'READY', 'FAILED', 'PASSED_ON') GROUP BY worker_id" );
Leo Gordon's avatar
Leo Gordon committed
483
}
Jessica Severin's avatar
Jessica Severin committed
484

485

486
487
=head2 synchronize_hive

Leo Gordon's avatar
Leo Gordon committed
488
  Arg [1]    : $filter_analysis (optional)
489
490
  Example    : $queen->synchronize_hive();
  Description: Runs through all analyses in the system and synchronizes
491
492
              the analysis_stats summary with the states in the job 
              and worker tables.  Then follows by checking all the blocking rules
493
494
495
496
497
498
499
              and blocks/unblocks analyses as needed.
  Exceptions : none
  Caller     : general

=cut

sub synchronize_hive {
Leo Gordon's avatar
Leo Gordon committed
500
  my $self          = shift;
Leo Gordon's avatar
Leo Gordon committed
501
  my $filter_analysis = shift; # optional parameter
502

503
  my $start_time = time();
504

Leo Gordon's avatar
Leo Gordon committed
505
  my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
506

Leo Gordon's avatar
Leo Gordon committed
507
  print STDERR "\nSynchronizing the hive (".scalar(@$list_of_analyses)." analyses this time):\n";
Leo Gordon's avatar
Leo Gordon committed
508
509
  foreach my $analysis (@$list_of_analyses) {
    $self->synchronize_AnalysisStats($analysis->stats);
510
    print STDERR ( ($analysis->stats()->status eq 'BLOCKED') ? 'x' : 'o');
511
  }
Leo Gordon's avatar
Leo Gordon committed
512
  print STDERR "\n";
Leo Gordon's avatar
Leo Gordon committed
513

Leo Gordon's avatar
Leo Gordon committed
514
  print STDERR ''.((time() - $start_time))." seconds to synchronize_hive\n\n";
515
}
516

517

518
519
520
=head2 safe_synchronize_AnalysisStats

  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
521
  Example    : $self->safe_synchronize_AnalysisStats($stats);
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
  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->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
539
                   ($stats->seconds_since_last_update < 3*60));
540
541
542
543

  # 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=" . $stats->analysis_id;
544
  #print("$sql\n");
545
  my $row_count = $self->dbc->do($sql);  
546
  return $stats unless($row_count == 1);        # return the un-updated status if locked
547
  #printf("got sync_lock on analysis_stats(%d)\n", $stats->analysis_id);
548
  
549
      # since we managed to obtain the lock, let's go and perform the sync:
550
  $self->synchronize_AnalysisStats($stats);
551

552
553
554
555
  return $stats;
}


556
=head2 synchronize_AnalysisStats
557

558
559
  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
560
  Description: Queries the job and worker tables to get summary counts
561
562
563
564
565
               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
566

567
=cut
568

569
sub synchronize_AnalysisStats {
570
  my $self = shift;
571
  my $analysisStats = shift;
572

573
  return $analysisStats unless($analysisStats);
574
  return $analysisStats unless($analysisStats->analysis_id);
575

576
  $analysisStats->refresh(); ## Need to get the new hive_capacity for dynamic analyses
577
578
  my $hive_capacity = $analysisStats->hive_capacity;

579
580
  if($self->db->hive_use_triggers()) {

581
582
            my $job_count = $analysisStats->ready_job_count();
            my $required_workers = $hive_capacity && POSIX::ceil( $job_count / $analysisStats->get_or_estimate_batch_size() );
583

584
585
                # adjust_stats_for_living_workers:
            if($hive_capacity > 0) {
586
                my $unfulfilled_capacity = $hive_capacity - $analysisStats->num_running_workers();
587

588
589
                if($unfulfilled_capacity < $required_workers ) {
                    $required_workers = (0 < $unfulfilled_capacity) ? $unfulfilled_capacity : 0;
590
591
592
593
594
595
                }
            }
            $analysisStats->num_required_workers( $required_workers );

  } else {
      $analysisStats->total_job_count(0);
596
597
      $analysisStats->semaphored_job_count(0);
      $analysisStats->ready_job_count(0);
598
599
600
      $analysisStats->done_job_count(0);
      $analysisStats->failed_job_count(0);
      $analysisStats->num_required_workers(0);
601

602
            # ask for analysis_id to force MySQL to use existing index on (analysis_id, status)
603
      my $sql = "SELECT analysis_id, status, count(*) FROM job WHERE analysis_id=? GROUP BY analysis_id, status";
604
605
      my $sth = $self->prepare($sql);
      $sth->execute($analysisStats->analysis_id);
606

607
608
609
      my $done_here       = 0;
      my $done_elsewhere  = 0;
      my $total_job_count = 0;
610
      while (my ($dummy_analysis_id, $status, $job_count)=$sth->fetchrow_array()) {
611
    # print STDERR "$status: $job_count\n";
612

613
        $total_job_count += $job_count;
614

615
        if($status eq 'READY') {
616
            $analysisStats->ready_job_count($job_count);
617

618
            my $required_workers = $hive_capacity && POSIX::ceil( $job_count / $analysisStats->get_or_estimate_batch_size() );
619
620
621

                # adjust_stats_for_living_workers:
            if($hive_capacity > 0) {
622
                my $unfulfilled_capacity = $hive_capacity - $self->count_running_workers( $analysisStats->analysis_id() );
623

624
625
                if($unfulfilled_capacity < $required_workers ) {
                    $required_workers = (0 < $unfulfilled_capacity) ? $unfulfilled_capacity : 0;
626
                }
627
            }
628
629
            $analysisStats->num_required_workers( $required_workers );

630
631
        } elsif($status eq 'SEMAPHORED') {
            $analysisStats->semaphored_job_count($job_count);
632
        } elsif($status eq 'DONE') {
633
            $done_here = $job_count;
634
        } elsif($status eq 'PASSED_ON') {
635
636
637
            $done_elsewhere = $job_count;
        } elsif ($status eq 'FAILED') {
            $analysisStats->failed_job_count($job_count);
638
        }
639
      } # /while
640
      $sth->finish;
641

642
643
      $analysisStats->total_job_count( $total_job_count );
      $analysisStats->done_job_count( $done_here + $done_elsewhere );
644
  } # /unless $self->{'_hive_use_triggers'}
645

646
  $analysisStats->check_blocking_control_rules();
647

648
649
650
  if($analysisStats->status ne 'BLOCKED') {
    $analysisStats->determine_status();
  }
651

652
  # $analysisStats->sync_lock(0); ## do we perhaps need it here?
653
  $analysisStats->update;  #update and release sync_lock
654

655
  return $analysisStats;
656
}
657
658


659
660
661
662
663
664
665
666
667
668
669
670
671
672
=head2 get_num_failed_analyses

  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object (optional)
  Example    : if( $self->get_num_failed_analyses( $my_analysis )) { do_something; }
  Example    : my $num_failed_analyses = $self->get_num_failed_analyses();
  Description: Reports all failed analyses and returns
                either the number of total failed (if no $filter_analysis was provided)
                or 1/0, depending on whether $filter_analysis failed or not.
  Returntype : int
  Exceptions : none
  Caller     : general

=cut

Leo Gordon's avatar
Leo Gordon committed
673
sub get_num_failed_analyses {
674
    my ($self, $filter_analysis) = @_;
675

676
677
678
679
680
681
682
683
684
685
686
687
    my $failed_analyses = $self->db->get_AnalysisAdaptor->fetch_all_failed_analyses();

    my $filter_analysis_failed = 0;

    foreach my $failed_analysis (@$failed_analyses) {
        print "\t##########################################################\n";
        print "\t# Too many jobs in analysis '".$failed_analysis->logic_name."' FAILED #\n";
        print "\t##########################################################\n\n";
        if($filter_analysis and ($filter_analysis->dbID == $failed_analysis)) {
            $filter_analysis_failed = 1;
        }
    }
688

689
    return $filter_analysis ? $filter_analysis_failed : scalar(@$failed_analyses);
690
691
692
}


693
sub get_hive_current_load {
694
695
696
    my $self = shift;
    my $sql = qq{
        SELECT sum(1/hive_capacity)
697
698
699
700
        FROM worker w
        JOIN analysis_stats USING(analysis_id)
        WHERE w.status!='DEAD'
        AND hive_capacity>0
701
702
703
704
705
706
    };
    my $sth = $self->prepare($sql);
    $sth->execute();
    my ($load)=$sth->fetchrow_array();
    $sth->finish;
    return ($load || 0);
707
708
709
}


710
711
712
sub count_running_workers {
    my ($self, $analysis_id) = @_;

713
714
715
716
717
    my $sql = qq{
            SELECT count(*)
            FROM worker
            WHERE status!='DEAD'
        } . ($analysis_id ? " AND analysis_id='$analysis_id'" : '');
718
719
720
721
722
723
724

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

    return $running_workers_count || 0;
725
726
}

727

Leo Gordon's avatar
Leo Gordon committed
728
sub get_remaining_jobs_show_hive_progress {
729
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
730
  my $sql = "SELECT sum(done_job_count), sum(failed_job_count), sum(total_job_count), ".
731
            "sum(ready_job_count * analysis_stats.avg_msec_per_job)/1000/60/60 ".
732
            "FROM analysis_stats";
733
734
  my $sth = $self->prepare($sql);
  $sth->execute();
735
  my ($done, $failed, $total, $cpuhrs) = $sth->fetchrow_array();
736
  $sth->finish;
737
738
739
740
741
742
743

  $done   ||= 0;
  $failed ||= 0;
  $total  ||= 0;
  my $completed = $total
    ? ((100.0 * ($done+$failed))/$total)
    : 0.0;
744
745
746
  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
747
  return $remaining;
748
749
}

750

Leo Gordon's avatar
Leo Gordon committed
751
sub print_analysis_status {
Leo Gordon's avatar
Leo Gordon committed
752
    my ($self, $filter_analysis) = @_;
753

Leo Gordon's avatar
Leo Gordon committed
754
    my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
755
    foreach my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {
756
        $analysis->stats->print_stats();
Leo Gordon's avatar
Leo Gordon committed
757
    }
758
759
760
}


Leo Gordon's avatar
Leo Gordon committed
761
sub print_running_worker_counts {
762
    my $self = shift;
763

764
765
766
767
768
769
770
    my $sql = qq{
        SELECT logic_name, count(*)
        FROM worker w
        JOIN analysis_base USING(analysis_id)
        WHERE w.status!='DEAD'
        GROUP BY analysis_id
    };
Leo Gordon's avatar
Leo Gordon committed
771

772
773
774
775
776
777
778
779
780
781
782
    my $total_workers = 0;
    my $sth = $self->prepare($sql);
    $sth->execute();

    print "\n===== Stats of live Workers according to the Queen: ======\n";
    while((my $logic_name, my $worker_count)=$sth->fetchrow_array()) {
        printf("%30s : %d workers\n", $logic_name, $worker_count);
        $total_workers += $worker_count;
    }
    $sth->finish;
    printf("%30s : %d workers\n\n", '======= TOTAL =======', $total_workers);
783
}
784

785

786
787
788
789
790
791
792
793
794
795
796
=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
797
sub monitor {
798
799
800
801
  my $self = shift;
  my $sql = qq{
      INSERT INTO monitor
      SELECT
802
          CURRENT_TIMESTAMP,
803
          count(*),
Leo Gordon's avatar
Leo Gordon committed
804
805
806
807
808
809
  }. ( ($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{
810
          group_concat(DISTINCT logic_name)
811
812
813
      FROM worker w
      LEFT JOIN analysis_base USING (analysis_id)
      WHERE w.status!='DEAD'
814
  };
815
816
817
818
819
      
  my $sth = $self->prepare($sql);
  $sth->execute();
}

820

Leo Gordon's avatar
Leo Gordon committed
821
822
823
824
825
826
827
828
829
830
831
832
833
834
=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}) {
835
        $worker->cause_of_death( 'UNKNOWN' );  # well, maybe we could have investigated further...
Leo Gordon's avatar
Leo Gordon committed
836
837
838
839
        $self->register_worker_death($worker);
    }
}

840

841
sub suggest_analysis_to_specialize_by_rc_id_meadow_type {
842
    my $self                = shift;
843
    my $rc_id               = shift;
844
    my $meadow_type         = shift;
845

846
    my @suitable_analyses = @{ $self->db->get_AnalysisStatsAdaptor->fetch_all_by_suitability_rc_id_meadow_type( $rc_id, $meadow_type ) };
847

848
    foreach my $stats (@suitable_analyses) {
849

850
            #synchronize and double check that it can be run:
851
        $self->safe_synchronize_AnalysisStats($stats);
852
        return $stats if( ($stats->status ne 'BLOCKED') and ($stats->status ne 'SYNCHING') and ($stats->num_required_workers > 0) );
853
    }
854

855
    return undef;
856
857
858
}


Jessica Severin's avatar
Jessica Severin committed
859
1;