Class: OodCore::Job::Adapters::Torque

Inherits:
OodCore::Job::Adapter show all
Defined in:
lib/ood_core/job/adapters/torque.rb,
lib/ood_core/job/adapters/torque/batch.rb,
lib/ood_core/job/adapters/torque/attributes.rb

Overview

Utility class to maintain all the Torque attributes available.

Defined Under Namespace

Classes: Batch, FFI

Constant Summary collapse

STATE_MAP =

Mapping of state characters for PBS

{
  'Q' => :queued,
  'H' => :queued_held,
  'T' => :queued_held,    # transiting (being moved to new location)
  'W' => :queued_held,    # waiting (waiting for its execution time)
  'R' => :running,
  'S' => :suspended,
  'E' => :running,        # exiting, but still running
  'C' => :completed
}
ATTR =

Maintains a constant Hash of defined PBS attribute types Includes:

Attribute names used by user commands
Additional job and general attribute names
Additional queue attribute names
Additional server attribute names
Additional node attribute names

{
  # Attribute names used by user commands
  a:                 :Execution_Time,
  c:                 :Checkpoint,
  e:                 :Error_Path,
  f:                 :fault_tolerant,
  g:                 :group_list,
  h:                 :Hold_Types,
  j:                 :Join_Path,
  k:                 :Keep_Files,
  l:                 :Resource_List,
  m:                 :Mail_Points,
  o:                 :Output_Path,
  p:                 :Priority,
  q:                 :destination,
  r:                 :Rerunable,
  t:                 :job_array_request,
  array_id:          :job_array_id,
  u:                 :User_List,
  v:                 :Variable_List,
  A:                 :Account_Name,
  args:              :job_arguments,
  reservation_id:    :reservation_id,
  login_node_id:     :login_node_id,
  login_prop:        :login_property,
  external_nodes:    :external_nodes,
  multi_req_alps:    :multi_req_alps,
  M:                 :Mail_Users,
  N:                 :Job_Name,
  S:                 :Shell_Path_List,
  depend:            :depend,
  inter:             :interactive,
  stagein:           :stagein,
  stageout:          :stageout,
  jobtype:           :jobtype,
  submit_host:       :submit_host,
  init_work_dir:     :init_work_dir,

  # Additional job and general attribute names
  ctime:             :ctime,
  exechost:          :exec_host,
  execport:          :exec_port,
  mtime:             :mtime,
  qtime:             :qtime,
  session:           :session_id,
  euser:             :euser,
  egroup:            :egroup,
  hashname:          :hashname,
  hopcount:          :hop_count,
  security:          :security,
  sched_hint:        :sched_hint,
  substate:          :substate,
  name:              :Job_Name,
  owner:             :Job_Owner,
  used:              :resources_used,
  state:             :job_state,
  queue:             :queue,
  server:            :server,
  maxrun:            :max_running,
  maxreport:         :max_report,
  total:             :total_jobs,
  comment:           :comment,
  cookie:            :cookie,
  qrank:             :queue_rank,
  altid:             :alt_id,
  etime:             :etime,
  exitstat:          :exit_status,
  forwardx11:        :forward_x11,
  submit_args:       :submit_args,
  tokens:            :tokens,
  netcounter:        :net_counter,
  umask:             :umask,
  start_time:        :start_time,
  start_count:       :start_count,
  checkpoint_dir:    :checkpoint_dir,
  checkpoint_name:   :checkpoint_name,
  checkpoint_time:   :checkpoint_time,
  checkpoint_restart_status:  :checkpoint_restart_status,
  restart_name:      :restart_name,
  comp_time:         :comp_time,
  reported:          :reported,
  intcmd:            :inter_cmd,
  job_radix:         :job_radix,
  sister_list:       :sister_list,
  total_runtime:     :total_runtime,
  P:                 :proxy_user,
  node_exclusive:    :node_exclusive,
  exec_gpus:         :exec_gpus,
  exec_mics:         :exec_mics,
  J:                 :job_id,
  pagg:              :pagg_id,
  system_start_time: :system_start_time,
  gpu_flags:         :gpu_flags,

  # Additional queue attribute names

  # Additional server attribute names

  # Additional node attribute names
}

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 = {}) ⇒ Torque

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 Torque.

Parameters:

  • opts (#to_h) (defaults to: {}) —

    the options defining this adapter

Options Hash (opts):

See Also:



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# File 'lib/ood_core/job/adapters/torque.rb', line 57

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

  @pbs = o.fetch(:pbs) { raise ArgumentError, "No pbs object specified. Missing argument: pbs" }
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/torque.rb', line 291

def delete(id)
  @pbs.delete_job(id.to_s)
rescue Torque::FFI::UnkjobidError, Torque::FFI::BadstateError
  # assume successful job deletion if can't find job id
  # assume successful job deletion if job is exiting or completed
  nil
rescue Torque::Batch::Error => e
  raise JobAdapterError, e.message
end

#directive_prefix ⇒ Object 



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# File 'lib/ood_core/job/adapters/torque.rb', line 301

def directive_prefix
  '#QSUB'
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/torque.rb', line 263

def hold(id)
  @pbs.hold_job(id.to_s)
rescue Torque::FFI::UnkjobidError
  # assume successful job hold if can't find job id
  nil
rescue Torque::Batch::Error => e
  raise JobAdapterError, 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/torque.rb', line 218

def info(id)
  id = id.to_s
  result = @pbs.get_job(id)

  if result.keys.length == 1
    parse_job_info(*result.flatten)
  else
    parse_job_array(id, result)
  end
rescue Torque::FFI::UnkjobidError
  # set completed status if can't find job id
  Info.new(
    id: id,
    status: :completed
  )
rescue Torque::Batch::Error => e
  raise JobAdapterError, e.message
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/torque.rb', line 187

def info_all(attrs: nil)
  @pbs.get_jobs.map do |k, v|
    parse_job_info(k, v)
  end
rescue Torque::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/torque.rb', line 200

def info_where_owner(owner, attrs: nil)
  owner = Array.wrap(owner).map(&:to_s)
  @pbs.select_jobs(
    attribs: [
      { name: "User_List", value: owner.join(","), op: :eq }
    ]
  ).map do |k, v|
    parse_job_info(k, v)
  end
rescue Torque::Batch::Error => e
  raise JobAdapterError, e.message
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/torque.rb', line 277

def release(id)
  @pbs.release_job(id.to_s)
rescue Torque::FFI::UnkjobidError
  # assume successful job release if can't find job id
  nil
rescue Torque::Batch::Error => e
  raise JobAdapterError, 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/torque.rb', line 242

def status(id)
  id = id.to_s
  @pbs.get_job(id, filters: [:job_state]).values.map {
    |job_status| OodCore::Job::Status.new(
      state: STATE_MAP.fetch(
        job_status[:job_state], :undetermined
      )
    )
  }.max
rescue Torque::FFI::UnkjobidError
  # set completed status if can't find job id
  Status.new(state: :completed)
rescue Torque::Batch::Error => e
  raise JobAdapterError, e.message
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/torque.rb', line 77

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 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?

  # Set mailing options
  mail_points = ""
  mail_points += "b" if script.email_on_started
  mail_points += "e" if script.email_on_terminated

  # FIXME: Remove the Hash option once all Interactive Apps are
  # converted to Array format
  if script.native.is_a?(Hash)
    # Set headers
    headers = {}
    headers.merge!(job_arguments: script.args.join(' ')) unless script.args.nil?
    headers.merge!(Hold_Types: :u) if script.submit_as_hold
    headers.merge!(Rerunable: script.rerunnable ? 'y' : 'n') unless script.rerunnable.nil?
    headers.merge!(init_work_dir: script.workdir) unless script.workdir.nil?
    headers.merge!(Mail_Users: script.email.join(',')) unless script.email.nil?
    headers.merge!(Mail_Points: mail_points) unless mail_points.empty?
    headers.merge!(Job_Name: script.job_name) unless script.job_name.nil?
    headers.merge!(Shell_Path_List: script.shell_path) unless script.shell_path.nil?
    # ignore input_path (not defined in Torque)
    headers.merge!(Output_Path: script.output_path) unless script.output_path.nil?
    headers.merge!(Error_Path: script.error_path) unless script.error_path.nil?
    # If error_path is not specified we join stdout & stderr (as this
    # mimics what the other resource managers do)
    headers.merge!(Join_Path: 'oe') if script.error_path.nil?
    headers.merge!(reservation_id: script.reservation_id) unless script.reservation_id.nil?
    headers.merge!(Priority: script.priority) unless script.priority.nil?
    headers.merge!(Execution_Time: script.start_time.localtime.strftime("%C%y%m%d%H%M.%S")) unless script.start_time.nil?
    headers.merge!(Account_Name: script.accounting_id) unless script.accounting_id.nil?
    headers.merge!(depend: depend.join(','))       unless depend.empty?
    headers.merge!(job_array_request: script.job_array_request) unless script.job_array_request.nil?

    # Set resources
    resources = {}
    resources.merge!(walltime: seconds_to_duration(script.wall_time)) unless script.wall_time.nil?

    # Set environment variables
    envvars = script.job_environment || {}

    # Set native options
    if script.native
      headers.merge!   script.native.fetch(:headers, {})
      resources.merge! script.native.fetch(:resources, {})
      envvars.merge!   script.native.fetch(:envvars, {})
    end

    # Destructively change envvars to shellescape values
    envvars.transform_values! { |v| Shellwords.escape(v) }

    # Submit job
    @pbs.submit_string(script.content, queue: script.queue_name, headers: headers, resources: resources, envvars: envvars)
  else
    # Set qsub arguments
    args = []
    args.concat ["-F", script.args.join(" ")] unless script.args.nil?
    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?
    args.concat ["-m", mail_points] unless mail_points.empty?
    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 Torque)
    args.concat ["-o", script.output_path] unless script.output_path.nil?
    args.concat ["-e", script.error_path] unless script.error_path.nil?
    args.concat ["-W", "x=advres:#{script.reservation_id}"] unless script.reservation_id.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 ["-W", "depend=#{depend.join(",")}"] unless depend.empty?
    args.concat ["-l", "walltime=#{seconds_to_duration(script.wall_time)}"] unless script.wall_time.nil?
    args.concat ['-t', script.job_array_request] unless script.job_array_request.nil?
    args.concat ['-l', "qos=#{script.qos}"] unless script.qos.nil?
    args.concat ['-l', "gpus=#{script.gpus_per_node}"] unless script.gpus_per_node.nil?

    # Set environment variables
    env = script.job_environment.to_h
    args.concat ["-v", env.keys.join(",")] unless env.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?

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

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