Queen.pm 15.7 KB
Newer Older
Jessica Severin's avatar
Jessica Severin committed
1 2 3 4 5 6 7 8
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=pod 

=head1 NAME
9
  Bio::EnsEMBL::Hive::Queen
Jessica Severin's avatar
Jessica Severin committed
10 11

=head1 SYNOPSIS
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
  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,
27
  gets $worker->batch_size() jobs from the analysis_job table, does its
28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
  work, creates the next layer of analysis_job entries by interfacing to
  the DataflowRuleAdaptor to determine the analyses it needs to pass it's
  output data to and creates jobs on the next analysis's database.
  It repeats this cycle until it's lived it's lifetime or until there are no
  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
  or 'compute farm'.  It's job is to query Queens if they need any workers and to
  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
46 47

=head1 CONTACT
48 49
  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Jessica Severin's avatar
Jessica Severin committed
50 51

=head1 APPENDIX
52 53
  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
54 55 56 57 58 59 60

=cut

package Bio::EnsEMBL::Hive::Queen;

use strict;
use strict;
61
use POSIX;
Jessica Severin's avatar
Jessica Severin committed
62 63 64
use Bio::EnsEMBL::Hive::Worker;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Sys::Hostname;
65
use Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
Jessica Severin's avatar
Jessica Severin committed
66

67 68 69
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);

Jessica Severin's avatar
Jessica Severin committed
70 71 72
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);

#
73
# PUBLIC METHODS
Jessica Severin's avatar
Jessica Severin committed
74 75 76 77 78 79 80 81 82 83 84 85 86 87 88
#
################

=head2 create_new_worker

  Arg [1]    : $analysis_id
  Example    :
  Description:
  Returntype : Bio::EnsEMBL::Hive::Worker
  Exceptions :
  Caller     :

=cut

sub create_new_worker {
89 90
  my ($self, @args) = @_;

91 92
  my ($analysis_id, $beekeeper ,$pid) =
     rearrange([qw(analysis_id beekeeper process_id) ], @args);
Jessica Severin's avatar
Jessica Severin committed
93

94
  my $analStatsDBA = $self->db->get_AnalysisStatsAdaptor;
95
  return undef unless($analStatsDBA);
96

97 98
  return undef if($self->get_hive_current_load() >= 1.0);
  
99 100 101 102 103 104
  unless($analysis_id) {
    my ($anal_stats) = @{$analStatsDBA->fetch_by_needed_workers(1)};
    return undef unless($anal_stats);
    $analysis_id = $anal_stats->analysis_id;
    $analStatsDBA->decrement_needed_workers($analysis_id);
  }
105
  
106
  my $analysisStats = $analStatsDBA->fetch_by_analysis_id($analysis_id);
107 108 109 110 111 112 113 114 115 116
  return undef unless($analysisStats);
  $analysisStats->print_stats;
  
  if($analysisStats->status eq 'BLOCKED') {
    print("Analysis is BLOCKED, can't create workers\n");
    return undef;
  }
  if($analysisStats->status eq 'DONE') {
    print("Analysis is DONE, don't need to create workers\n");
    return undef;
Jessica Severin's avatar
Jessica Severin committed
117 118 119
  }

  my $host = hostname;
120
  $pid = getppid unless($pid);
121
  $beekeeper = '' unless($beekeeper);
Jessica Severin's avatar
Jessica Severin committed
122 123

  my $sql = "INSERT INTO hive SET born=now(), last_check_in=now()".
124
            ",process_id='$pid' ".
Jessica Severin's avatar
Jessica Severin committed
125
            ",analysis_id='$analysis_id' ".
126
            ",beekeeper='$beekeeper' ".
Jessica Severin's avatar
Jessica Severin committed
127 128 129 130 131 132 133 134 135 136
            ",host='$host'";

  my $sth = $self->prepare($sql);
  $sth->execute();
  my $hive_id = $sth->{'mysql_insertid'};
  $sth->finish;

  my $worker = $self->_fetch_by_hive_id($hive_id);
  $worker=undef unless($worker and $worker->analysis);

137
  if($worker and $analysisStats) {
138
    $analStatsDBA->update_status($analysis_id, 'WORKING');
139
    $worker->batch_size($analysisStats->batch_size);
Jessica Severin's avatar
Jessica Severin committed
140 141 142 143 144 145 146 147 148
  }
  return $worker;
}


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

  return unless($worker);
149 150 151 152

  # if called without a defined cause_of_death, assume catastrophic failure
  $worker->cause_of_death('FATALITY') unless(defined($worker->cause_of_death));
  
Jessica Severin's avatar
Jessica Severin committed
153 154 155 156 157 158 159 160
  my $sql = "UPDATE hive SET died=now(), last_check_in=now()";
  $sql .= " ,work_done='" . $worker->work_done . "'";
  $sql .= " ,cause_of_death='". $worker->cause_of_death ."'";
  $sql .= " WHERE hive_id='" . $worker->hive_id ."'";

  my $sth = $self->prepare($sql);
  $sth->execute();
  $sth->finish;
161 162

  if($worker->cause_of_death eq "NO_WORK") {
163
    $self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, "ALL_CLAIMED");
164 165 166
  }
  if($worker->cause_of_death eq "FATALITY") {
    #print("FATAL DEATH Arrrrgggghhhhhhhh (hive_id=",$worker->hive_id,")\n");
167
    $self->db->get_AnalysisJobAdaptor->reset_dead_jobs_for_worker($worker);
168
  }
Jessica Severin's avatar
Jessica Severin committed
169 170 171
}


172
sub worker_check_in {
Jessica Severin's avatar
Jessica Severin committed
173 174 175 176 177 178 179 180 181 182 183 184
  my ($self, $worker) = @_;

  return unless($worker);
  my $sql = "UPDATE hive SET last_check_in=now()";
  $sql .= " WHERE hive_id='" . $worker->hive_id ."'";

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


185 186 187 188 189 190 191 192 193 194
sub fetch_overdue_workers {
  my ($self,$overdue_secs) = @_;

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

  my $constraint = "h.cause_of_death='' ".
                   "AND (UNIX_TIMESTAMP()-UNIX_TIMESTAMP(h.last_check_in))>$overdue_secs";
  return $self->_generic_fetch($constraint);
}

Jessica Severin's avatar
Jessica Severin committed
195

196 197 198 199 200 201 202 203
sub update_analysis_stats {
  my $self = shift;

  my $sql = "SELECT analysis.analysis_id, status, count(*) ".
            "FROM analysis_job, analysis ".
            "WHERE analysis_job.analysis_id=analysis.analysis_id ".
            "GROUP BY analysis_job.analysis_id, status";

204
  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
205 206 207 208 209 210
  my $analysisStats = undef;

  my $sth = $self->prepare($sql);
  $sth->execute();
  while (my ($analysis_id, $status, $count)=$sth->fetchrow_array()) {
    unless(defined($analysisStats) and $analysisStats->analysis_id==$analysis_id) {
211
      $analysisStats->determine_status()->update() if($analysisStats);
212 213 214 215 216 217 218 219 220 221 222 223 224 225

      $analysisStats = $statsDBA->fetch_by_analysis_id($analysis_id);
      $analysisStats->total_job_count(0);
      $analysisStats->unclaimed_job_count(0);
      $analysisStats->done_job_count(0);
      $analysisStats->num_required_workers(0);
    }

    my $total = $analysisStats->total_job_count();
    $analysisStats->total_job_count($total + $count);
    
    if($status eq 'READY') {
      $analysisStats->unclaimed_job_count($count);
      my $numWorkers = $count/$analysisStats->batch_size;
226
      $numWorkers=1 if($numWorkers<1);
227
      if($analysisStats->hive_capacity>0 and $numWorkers > $analysisStats->hive_capacity) {
228 229 230 231 232 233
        $numWorkers=$analysisStats->hive_capacity;
      }
      $analysisStats->num_required_workers($numWorkers);
    }
    if($status eq 'DONE') { $analysisStats->done_job_count($count); }
  }
234 235 236 237 238 239 240 241 242 243
  $analysisStats->determine_status()->update() if($analysisStats);
  $sth->finish;

  $self->adjust_stats_for_living_workers();
}


sub adjust_stats_for_living_workers {
  my $self = shift;

244
  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
245 246 247 248 249 250
  
  my $sql = "SELECT analysis_id, count(*) FROM hive ".
            "WHERE cause_of_death='' GROUP BY analysis_id";
  my $sth = $self->prepare($sql);
  $sth->execute();
  while (my ($analysis_id, $liveCount)=$sth->fetchrow_array()) {
251

252 253 254 255 256 257 258 259 260 261 262 263 264
    my $analysis_stats = $statsDBA->fetch_by_analysis_id($analysis_id);

    if($analysis_stats->hive_capacity > 0) {
      my $numWorkers = $analysis_stats->num_required_workers;

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

      $analysis_stats->num_required_workers($numWorkers);
      $analysis_stats->update;
    }
  }
265 266 267 268
  $sth->finish;
}


269 270 271
sub get_hive_current_load {
  my $self = shift;
  my $sql = "SELECT sum(1/analysis_stats.hive_capacity) FROM hive, analysis_stats ".
272 273
            "WHERE hive.analysis_id=analysis_stats.analysis_id and cause_of_death ='' ".
            "AND analysis_stats.hive_capacity>0";
274 275 276 277 278 279 280 281 282 283
  my $sth = $self->prepare($sql);
  $sth->execute();
  (my $load)=$sth->fetchrow_array();
  $sth->finish;
  $load=0 unless($load);
  print("current hive load = $load\n");
  return $load;
}


284
sub get_num_needed_workers {
285 286
  my $self = shift;

287 288
  my $neededAnals = $self->db->get_AnalysisStatsAdaptor->fetch_by_needed_workers();
  return 0 unless($neededAnals);
289

290 291 292 293 294
  my $availableLoad = 1.0 - $self->get_hive_current_load();
  return 0 if($availableLoad <0.0);

  my $numWorkers = 0;
  foreach my $analysis_stats (@{$neededAnals}) {
295 296
    #$analysis_stats->print_stats();

297 298 299 300 301 302
    my $thisLoad = 0.0;
    if($analysis_stats->hive_capacity>0) {
      $thisLoad = $analysis_stats->num_required_workers * (1/$analysis_stats->hive_capacity);
    }

    if(($analysis_stats->hive_capacity<=0) or ($thisLoad < $availableLoad)) {
303 304 305 306 307
      $numWorkers += $analysis_stats->num_required_workers;
      $availableLoad -= $thisLoad;
      printf("  %d (%1.9f) ", $numWorkers, $availableLoad);
      $analysis_stats->print_stats();
    } else {
308
      my $workerCount = POSIX::ceil($availableLoad * $analysis_stats->hive_capacity                     );
309 310 311 312 313
      $numWorkers += $workerCount;
      $availableLoad -=  $workerCount * (1/$analysis_stats->hive_capacity);
      printf("  %d (%1.9f) use only %d ", $numWorkers, $availableLoad, $workerCount);
      $analysis_stats->print_stats();
      last;
314
    }
315
    last if($availableLoad <= 0.0);
316
  }
317

318
  printf("need $numWorkers workers (availLoad=%1.5f)\n", $availableLoad);
319
  return $numWorkers;
320 321 322
}


323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349
sub check_blocking_control_rules
{
  my $self = shift;

  my $analysisStatsList = $self->db->get_AnalysisStatsAdaptor->fetch_by_status('BLOCKED');
  foreach my $stats (@{$analysisStatsList}) {
    #print("BLOCKED analysis ");  $stats->print_stats;
    my $ctrlRules = $self->db->get_AnalysisCtrlRuleAdaptor->
                    fetch_by_ctrled_analysis_id($stats->analysis_id);
    my $allRulesDone = 1;                    
    foreach my $ctrlrule (@{$ctrlRules}) {
      #use this method because the condition_analysis objects can be
      #network distributed to a different database so use it's adaptor to get
      #the AnalysisStats object
      my $condStats = $ctrlrule->condition_analysis->stats;
      $allRulesDone = 0 unless($condStats->status eq 'DONE');
      #print("  "); $condStats->print_stats;
    }

    if($allRulesDone and @{$ctrlRules}) {
      #print("  UNBLOCK analysis : all conditions met\n");
      $stats->adaptor->update_status($stats->analysis_id, 'READY');
    }
    
  }
}

350 351 352 353 354
sub print_hive_status
{
  my $self = shift;

  my $allStats = $self->db->get_AnalysisStatsAdaptor->fetch_all();
355
 
356 357 358
  foreach my $analysis_stats (@{$allStats}) {
    $analysis_stats->print_stats;
  }
359 360 361 362 363 364 365 366 367 368 369 370

  print("HIVE LIVE WORKERS====\n");
  my $sql = "select logic_name, count(*) from hive, analysis ".
            "where hive.analysis_id=analysis.analysis_id and hive.cause_of_death='' ".
            "group by hive.analysis_id";
  my $sth = $self->prepare($sql);
  $sth->execute();
  while((my $logic_name, my $count)=$sth->fetchrow_array()) {
    printf("%20s : %d workers\n", $logic_name, $count);
  }
  print("=====================\n");
  $sth->finish;  
371
}
372

373 374


Jessica Severin's avatar
Jessica Severin committed
375 376 377 378 379 380 381 382 383
#
# INTERNAL METHODS
#
###################

=head2 _fetch_by_hive_id

  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
384
  Example    : $feat = $queen->fetch_by_dbID(1234);
Jessica Severin's avatar
Jessica Severin committed
385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::Hive::Worker
  Exceptions : thrown if $id is not defined
  Caller     : general

=cut

sub _fetch_by_hive_id{
  my ($self,$id) = @_;

  unless(defined $id) {
    $self->throw("fetch_by_dbID must have an id");
  }

  my @tabs = $self->_tables;

  my $constraint = "h.hive_id = $id";

  #return first element of _generic_fetch list
  my ($obj) = @{$self->_generic_fetch($constraint)};
  return $obj;
}

=head2 _generic_fetch

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  Example    : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch

=cut

sub _generic_fetch {
  my ($self, $constraint, $join) = @_;

  my @tables = $self->_tables;
  my $columns = join(', ', $self->_columns());

  if ($join) {
    foreach my $single_join (@{$join}) {
      my ($tablename, $condition, $extra_columns) = @{$single_join};
      if ($tablename && $condition) {
        push @tables, $tablename;

        if($constraint) {
          $constraint .= " AND $condition";
        } else {
          $constraint = " $condition";
        }
      }
      if ($extra_columns) {
        $columns .= ", " . join(', ', @{$extra_columns});
      }
    }
  }

  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql = "SELECT $columns FROM $tablenames";

  my $default_where = $self->_default_where_clause;
  my $final_clause = $self->_final_clause;

  #append a where clause if it was defined
  if($constraint) {
    $sql .= " WHERE $constraint ";
    if($default_where) {
      $sql .= " AND $default_where ";
    }
  } elsif($default_where) {
    $sql .= " WHERE $default_where ";
  }

  #append additional clauses which may have been defined
  $sql .= " $final_clause";

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

#  print STDERR $sql,"\n";

  return $self->_objs_from_sth($sth);
}

sub _tables {
  my $self = shift;

  return (['hive', 'h']);
}

sub _columns {
  my $self = shift;

  return qw (h.hive_id
             h.analysis_id
488
             h.beekeeper
Jessica Severin's avatar
Jessica Severin committed
489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511
             h.host
             h.process_id
             h.work_done
             h.born
             h.last_check_in
             h.died
             h.cause_of_death
            );
}

sub _objs_from_sth {
  my ($self, $sth) = @_;

  my %column;
  $sth->bind_columns( \( @column{ @{$sth->{NAME_lc} } } ));

  my @workers = ();

  while ($sth->fetch()) {
    my $worker = new Bio::EnsEMBL::Hive::Worker;
    $worker->init;

    $worker->hive_id($column{'hive_id'});
512
    $worker->beekeeper($column{'beekeeper'});
Jessica Severin's avatar
Jessica Severin committed
513 514 515 516 517 518 519
    $worker->host($column{'host'});
    $worker->process_id($column{'process_id'});
    $worker->work_done($column{'work_done'});
    $worker->born($column{'born'});
    $worker->last_check_in($column{'last_check_in'});
    $worker->died($column{'died'});
    $worker->cause_of_death($column{'cause_of_death'});
520
    $worker->queen($self);
Jessica Severin's avatar
Jessica Severin committed
521 522
    $worker->db($self->db);

523 524
    if($column{'analysis_id'} and $self->db->get_AnalysisAdaptor) {
      $worker->analysis($self->db->get_AnalysisAdaptor->fetch_by_dbID($column{'analysis_id'}));
Jessica Severin's avatar
Jessica Severin committed
525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545
    }

    push @workers, $worker;
  }
  $sth->finish;

  return \@workers
}

sub _default_where_clause {
  my $self = shift;
  return '';
}

sub _final_clause {
  my $self = shift;
  return '';
}


1;