Queen.pm 13.7 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 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
  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,
  gets $runnable->batch_size() jobs from the analysis_job table, does its
  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 61 62 63

=cut

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

use strict;
use strict;
use Bio::EnsEMBL::Hive::Worker;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Sys::Hostname;
64
use Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
Jessica Severin's avatar
Jessica Severin committed
65 66 67 68

our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);

#
69
# PUBLIC METHODS
Jessica Severin's avatar
Jessica Severin committed
70 71 72 73 74 75 76 77 78 79 80 81 82 83 84
#
################

=head2 create_new_worker

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

=cut

sub create_new_worker {
85 86 87
  my $self        = shift;
  my $analysis_id = shift;
  my $beekeeper   = shift;
Jessica Severin's avatar
Jessica Severin committed
88

89
  my $analStatsDBA = $self->db->get_AnalysisStatsAdaptor;
90 91
  return undef unless($analStatsDBA);
  
92
  my $analysisStats = $analStatsDBA->fetch_by_analysis_id($analysis_id);
93 94 95 96 97 98 99 100 101 102
  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
103 104 105 106
  }

  my $host = hostname;
  my $ppid = getppid;
107
  $beekeeper = '' unless($beekeeper);
Jessica Severin's avatar
Jessica Severin committed
108 109 110 111

  my $sql = "INSERT INTO hive SET born=now(), last_check_in=now()".
            ",process_id='$ppid' ".
            ",analysis_id='$analysis_id' ".
112
            ",beekeeper='$beekeeper' ".
Jessica Severin's avatar
Jessica Severin committed
113 114 115 116 117 118 119 120 121 122
            ",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);

123
  if($worker and $analysisStats) {
124
    $analStatsDBA->update_status($analysis_id, 'WORKING');
Jessica Severin's avatar
Jessica Severin committed
125 126 127 128 129 130 131 132 133
  }
  return $worker;
}


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

  return unless($worker);
134 135 136 137

  # 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
138 139 140 141 142 143 144 145
  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;
146 147

  if($worker->cause_of_death eq "NO_WORK") {
148
    $self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, "ALL_CLAIMED");
149 150 151
  }
  if($worker->cause_of_death eq "FATALITY") {
    #print("FATAL DEATH Arrrrgggghhhhhhhh (hive_id=",$worker->hive_id,")\n");
152
    $self->db->get_AnalysisJobAdaptor->reset_dead_jobs_for_worker($worker);
153
  }
Jessica Severin's avatar
Jessica Severin committed
154 155 156
}


157
sub worker_check_in {
Jessica Severin's avatar
Jessica Severin committed
158 159 160 161 162 163 164 165 166 167 168 169
  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;
}


170 171 172 173 174 175 176 177 178 179
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
180

181 182 183 184 185 186 187 188
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";

189
  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
190 191 192 193 194 195
  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) {
196
      $analysisStats->determine_status()->update() if($analysisStats);
197 198 199 200 201 202 203 204 205 206 207 208 209 210

      $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;
211
      $numWorkers=1 if($numWorkers<1);
212
      if($analysisStats->hive_capacity>0 and $numWorkers > $analysisStats->hive_capacity) {
213 214 215 216 217 218
        $numWorkers=$analysisStats->hive_capacity;
      }
      $analysisStats->num_required_workers($numWorkers);
    }
    if($status eq 'DONE') { $analysisStats->done_job_count($count); }
  }
219 220 221 222 223 224 225 226 227 228
  $analysisStats->determine_status()->update() if($analysisStats);
  $sth->finish;

  $self->adjust_stats_for_living_workers();
}


sub adjust_stats_for_living_workers {
  my $self = shift;

229
  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
230 231 232 233 234 235
  
  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()) {
236

237 238 239 240 241 242 243 244 245 246 247 248 249
    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;
    }
  }
250 251 252 253
  $sth->finish;
}


254 255 256
sub next_clutch {
  my $self = shift;

257
  my $clutches = $self->db->get_AnalysisStatsAdaptor->fetch_by_needed_workers();
258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279
  return (0, 0) unless($clutches);

  my $smallestClutch = undef;
  
  # keep simple : return the clutch with the smallest number of workers first
  #print("\nCheck for CLUTCH!!\n");
  foreach my $analysis_stats (@{$clutches}) {
    #$analysis_stats->print_stats();

    $smallestClutch = $analysis_stats unless($smallestClutch);
    if($analysis_stats->num_required_workers < $smallestClutch->num_required_workers) {
      $smallestClutch = $analysis_stats;
    }
  }
  
  if($smallestClutch) {
    return ($smallestClutch->analysis_id, $smallestClutch->num_required_workers);
  }
  return (0,0);
}


280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306
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');
    }
    
  }
}

307 308 309 310 311 312 313 314 315 316
sub print_hive_status
{
  my $self = shift;

  my $allStats = $self->db->get_AnalysisStatsAdaptor->fetch_all();

  foreach my $analysis_stats (@{$allStats}) {
    $analysis_stats->print_stats;
  }
}
317

318 319


Jessica Severin's avatar
Jessica Severin committed
320 321 322 323 324 325 326 327 328
#
# INTERNAL METHODS
#
###################

=head2 _fetch_by_hive_id

  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
329
  Example    : $feat = $queen->fetch_by_dbID(1234);
Jessica Severin's avatar
Jessica Severin committed
330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432
  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
433
             h.beekeeper
Jessica Severin's avatar
Jessica Severin committed
434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456
             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'});
457
    $worker->beekeeper($column{'beekeeper'});
Jessica Severin's avatar
Jessica Severin committed
458 459 460 461 462 463 464
    $worker->host($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'});
465
    $worker->queen($self);
Jessica Severin's avatar
Jessica Severin committed
466 467
    $worker->db($self->db);

468 469
    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
470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490
    }

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

  return \@workers
}

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

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


1;