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:



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# 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



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# 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:



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# File 'lib/ood_core/job/adapters/pbspro.rb', line 414

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 



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# File 'lib/ood_core/job/adapters/pbspro.rb', line 421

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:



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# File 'lib/ood_core/job/adapters/pbspro.rb', line 390

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:



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# File 'lib/ood_core/job/adapters/pbspro.rb', line 350

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:



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# File 'lib/ood_core/job/adapters/pbspro.rb', line 305

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:



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# File 'lib/ood_core/job/adapters/pbspro.rb', line 318

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

#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:



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# File 'lib/ood_core/job/adapters/pbspro.rb', line 402

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:



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# File 'lib/ood_core/job/adapters/pbspro.rb', line 381

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:



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# 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?

  # 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