Class: OodCore::Job::Adapters::PBSPro

Inherits:
OodCore::Job::Adapter show all
Defined in:
lib/ood_core/job/adapters/pbspro.rb

Overview

An adapter object that describes the communication with a PBS Pro resource manager for job management.

Defined Under Namespace

Classes: Batch

Constant Summary collapse

STATE_MAP =

Mapping of state codes for PBSPro

{
  'Q' => :queued,
  'W' => :queued_held,    # job is waiting for its submitter-assigned start time to be reached
  'H' => :queued_held,
  'T' => :queued_held,    # job is being moved to a new location
  'M' => :completed,      # job was moved to another server
  'R' => :running,
  'S' => :suspended,
  'U' => :suspended,      # cycle-harvesting job is suspended due to keyboard activity
  'E' => :running,        # job is exiting after having run
  'F' => :completed,      # job is finished
  'X' => :completed,      # subjob has completed execution or has been deleted
  'B' => :running         # job array has at least one child running
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from OodCore::Job::Adapter

#accounts, #cluster_info, #info_all_each, #info_where_owner_each, #job_name_illegal_chars, #nodes, #queues, #sanitize_job_name, #supports_job_arrays?

Constructor Details

#initialize(opts = {}) ⇒ PBSPro

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Returns a new instance of PBSPro.

Parameters:

  • opts (#to_h) (defaults to: {}) —

    the options defining this adapter

Options Hash (opts):

  • :pbspro (Batch) —

    The PBS Pro batch object

  • :qstat_factor (#to_f) — default: 0.10 —

    The qstat deciding factor

See Also:



219
220
221
222
223
224
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 219

def initialize(opts = {})
  o = opts.to_h.compact.symbolize_keys

  @pbspro = o.fetch(:pbspro) { raise ArgumentError, "No pbspro object specified. Missing argument: pbspro" }
  @qstat_factor = o.fetch(:qstat_factor, 0.10).to_f
end

Instance Attribute Details

#qstat_factor ⇒ Float (readonly)

What percentage of jobs a user owns out of all jobs, used to decide whether we filter the owner's jobs from a `qstat` of all jobs or call `qstat` on each of the owner's individual jobs

Returns:

  • (Float) —

    ratio of owner's jobs to all jobs



212
213
214
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 212

def qstat_factor
  @qstat_factor
end

Instance Method Details

#delete(id) ⇒ void

This method returns an undefined value.

Delete the submitted job

Parameters:

  • id (#to_s) —

    the id of the job

Raises:

See Also:



415
416
417
418
419
420
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 415

def delete(id)
  @pbspro.delete_job(id.to_s)
rescue Batch::Error => e
  # assume successful job deletion if can't find job id
  raise JobAdapterError, e.message unless /Unknown Job Id/ =~ e.message || /Job has finished/ =~ e.message
end

#directive_prefix ⇒ Object 



422
423
424
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 422

def directive_prefix
  '#PBS'
end

#hold(id) ⇒ void

This method returns an undefined value.

Put the submitted job on hold

Parameters:

  • id (#to_s) —

    the id of the job

Raises:

See Also:



391
392
393
394
395
396
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 391

def hold(id)
  @pbspro.hold_job(id.to_s)
rescue Batch::Error => e
  # assume successful job hold if can't find job id
  raise JobAdapterError, e.message unless /Unknown Job Id/ =~ e.message || /Job has finished/ =~ e.message
end

#info(id) ⇒ Info

Retrieve job info from the resource manager

Parameters:

  • id (#to_s) —

    the id of the job

Returns:

  • (Info) —

    information describing submitted job

Raises:

See Also:



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
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 351

def info(id)
  id = id.to_s

  job_infos = @pbspro.get_jobs(id: id).map do |v|
    parse_job_info(v)
  end

  if job_infos.empty?
    Info.new(id: id, status: :completed)
  elsif job_infos.length == 1
    job_infos.first
  else
    process_job_array(id, job_infos)
  end
rescue Batch::Error => e
  # set completed status if can't find job id
  if /Unknown Job Id/ =~ e.message || /Job has finished/ =~ e.message
    Info.new(
      id: id,
      status: :completed
    )
  else
    raise JobAdapterError, e.message
  end
end

#info_all(attrs: nil) ⇒ Array<Info>

Retrieve info for all jobs from the resource manager

Returns:

  • (Array<Info>) —

    information describing submitted jobs

Raises:

See Also:



306
307
308
309
310
311
312
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 306

def info_all(attrs: nil)
  @pbspro.get_jobs.map do |v|
    parse_job_info(v)
  end
rescue Batch::Error => e
  raise JobAdapterError, e.message
end

#info_where_owner(owner, attrs: nil) ⇒ Array<Info>

Retrieve info for all jobs for a given owner or owners from the resource manager

Parameters:

  • owner (#to_s, Array<#to_s>) —

    the owner(s) of the jobs

Returns:

  • (Array<Info>) —

    information describing submitted jobs

Raises:



319
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
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 319

def info_where_owner(owner, attrs: nil)
  owner = Array.wrap(owner).map(&:to_s)

  usr_jobs = @pbspro.select_jobs(args: ["-u", owner.join(",")])
  all_jobs = @pbspro.select_jobs(args: ["-T"])

  # `qstat` all jobs if user has too many jobs, otherwise `qstat` each
  # individual job (default factor is 10%)
  if usr_jobs.size > (qstat_factor * all_jobs.size)
    super
  else
    begin
      user_job_infos = []
      usr_jobs.each do |id|
        job = info(id)
        user_job_infos << job

        job.tasks.each {|task| user_job_infos << job.build_child_info(task)}
      end

      user_job_infos
    rescue Batch::Error => e
      raise JobAdapterError, e.message
    end
  end
end

#ppn(script) ⇒ Object

place holder for when we support both nodes and cpus.



427
428
429
430
431
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 427

def ppn(script)
  return [] if script.cores.nil?

  ['-l', "ncpus=#{script.cpus}"]
end

#release(id) ⇒ void

This method returns an undefined value.

Release the job that is on hold

Parameters:

  • id (#to_s) —

    the id of the job

Raises:

See Also:



403
404
405
406
407
408
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 403

def release(id)
  @pbspro.release_job(id.to_s)
rescue Batch::Error => e
  # assume successful job release if can't find job id
  raise JobAdapterError, e.message unless /Unknown Job Id/ =~ e.message || /Job has finished/ =~ e.message
end

#status(id) ⇒ Status

Retrieve job status from resource manager

Parameters:

  • id (#to_s) —

    the id of the job

Returns:

Raises:

See Also:



382
383
384
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 382

def status(id)
  info(id.to_s).status
end

#submit(script, after: [], afterok: [], afternotok: [], afterany: []) ⇒ String

Submit a job with the attributes defined in the job template instance

Parameters:

  • script (Script) —

    script object that describes the script and attributes for the submitted job

  • after (#to_s, Array<#to_s>) (defaults to: []) —

    this job may be scheduled for execution at any point after dependent jobs have started execution

  • afterok (#to_s, Array<#to_s>) (defaults to: []) —

    this job may be scheduled for execution only after dependent jobs have terminated with no errors

  • afternotok (#to_s, Array<#to_s>) (defaults to: []) —

    this job may be scheduled for execution only after dependent jobs have terminated with errors

  • afterany (#to_s, Array<#to_s>) (defaults to: []) —

    this job may be scheduled for execution after dependent jobs have terminated

Returns:

  • (String) —

    the job id returned after successfully submitting a job

Raises:

See Also:



241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
 
# File 'lib/ood_core/job/adapters/pbspro.rb', line 241

def submit(script, after: [], afterok: [], afternotok: [], afterany: [])
  after      = Array(after).map(&:to_s)
  afterok    = Array(afterok).map(&:to_s)
  afternotok = Array(afternotok).map(&:to_s)
  afterany   = Array(afterany).map(&:to_s)

  # Set qsub options
  args = []
  # ignore args, can't use these if submitting from STDIN
  args.concat ["-h"] if script.submit_as_hold
  args.concat ["-r", script.rerunnable ? "y" : "n"] unless script.rerunnable.nil?
  args.concat ["-M", script.email.join(",")] unless script.email.nil?
  if script.email_on_started && script.email_on_terminated
    args.concat ["-m", "be"]
  elsif script.email_on_started
    args.concat ["-m", "b"]
  elsif script.email_on_terminated
    args.concat ["-m", "e"]
  end
  args.concat ["-N", script.job_name] unless script.job_name.nil?
  args.concat ["-S", script.shell_path] unless script.shell_path.nil?
  # ignore input_path (not defined in PBS Pro)
  args.concat ["-o", script.output_path] unless script.output_path.nil?
  args.concat ["-e", script.error_path] unless script.error_path.nil?
  # Reservations are actually just queues in PBS Pro
  args.concat ["-q", script.reservation_id] if !script.reservation_id.nil? && script.queue_name.nil?
  args.concat ["-q", script.queue_name] unless script.queue_name.nil?
  args.concat ["-p", script.priority] unless script.priority.nil?
  args.concat ["-a", script.start_time.localtime.strftime("%C%y%m%d%H%M.%S")] unless script.start_time.nil?
  args.concat ["-A", script.accounting_id] unless script.accounting_id.nil?
  args.concat ["-l", "walltime=#{seconds_to_duration(script.wall_time)}"] unless script.wall_time.nil?
  args.concat ppn(script)

  # Set dependencies
  depend = []
  depend << "after:#{after.join(":")}"           unless after.empty?
  depend << "afterok:#{afterok.join(":")}"       unless afterok.empty?
  depend << "afternotok:#{afternotok.join(":")}" unless afternotok.empty?
  depend << "afterany:#{afterany.join(":")}"     unless afterany.empty?
  args.concat ["-W", "depend=#{depend.join(",")}"]   unless depend.empty?

  # Set environment variables
  envvars = script.job_environment.to_h
  args.concat ["-v", envvars.map{|k,v| "#{k}=#{v}"}.join(",")] unless envvars.empty?
  args.concat ["-V"] if script.copy_environment?

  # If error_path is not specified we join stdout & stderr (as this
  # mimics what the other resource managers do)
  args.concat ["-j", "oe"] if script.error_path.nil?

  args.concat ["-J", script.job_array_request] unless script.job_array_request.nil?

  # Set native options
  args.concat script.native if script.native

  # Submit job
  @pbspro.submit_string(script.content, args: args, chdir: script.workdir)
rescue Batch::Error => e
  raise JobAdapterError, e.message
end