Class: OodCore::Job::Adapters::Slurm

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

Overview

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

Defined Under Namespace

Classes: Batch

Constant Summary collapse

UNIT_FACTORS = 
{
  'K' =>                 1_024, 
  'M' =>             1_048_576, 
  'G' =>         1_073_741_824, 
  'T' =>     1_099_511_627_776, 
  'P' => 1_125_899_906_842_624
}
STATE_MAP =

Mapping of state codes for Slurm

{
  'BF' => :completed,  # BOOT_FAIL
  'CA' => :completed,  # CANCELLED
  'CD' => :completed,  # COMPLETED
  'CF' => :queued,     # CONFIGURING
  'CG' => :running,    # COMPLETING
  'F'  => :completed,  # FAILED
  'NF' => :completed,  # NODE_FAIL
  'PD' => :queued,     # PENDING
  'PR' => :suspended,  # PREEMPTED
  'RV' => :completed,  # REVOKED
  'R'  => :running,    # RUNNING
  'SE' => :completed,  # SPECIAL_EXIT
  'ST' => :running,    # STOPPED
  'S'  => :suspended,  # SUSPENDED
  'TO' => :completed,  # TIMEOUT
  'OOM' => :completed, # OUT_OF_MEMORY

  'BOOT_FAIL'     => :completed,
  'CANCELLED'     => :completed,
  'COMPLETED'     => :completed,
  'DEADLINE'      => :completed,
  'FAILED'        => :completed,
  'NODE_FAIL'     => :completed,
  'OUT_OF_MEMORY' => :completed,
  'PENDING'       => :queued,
  'PREEMPTED'     => :completed,
  'RUNNING'       => :running,
  'REQUEUED'      => :queued,
  'REVOKED'       => :completed,
  'SUSPENDED'     => :suspended,
  'TIMEOUT'       => :completed,
}

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from OodCore::Job::Adapter

#info_all_each, #info_where_owner_each, #job_name_illegal_chars, #sanitize_job_name, #supports_job_arrays?

Constructor Details

#initialize(opts = {}) ⇒ Slurm

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 Slurm.

Parameters:

  • opts (#to_h) (defaults to: {}) —

    the options defining this adapter

Options Hash (opts):

  • :slurm (Batch) —

    The Slurm batch object

See Also:



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# File 'lib/ood_core/job/adapters/slurm.rb', line 616

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

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

Class Method Details

.gpus_from_gres(gres) ⇒ Integer

Get integer representing the number of gpus used by a node or job, calculated from gres string

Returns:

  • (Integer) —

    the number of gpus in gres



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

def self.gpus_from_gres(gres)
  gres.to_s.scan(/gpu[s:]*[\w()-]*[=:]?(\d+)(?:[(,]|$)/).flatten.map(&:to_i).sum
end

.memory_from_tres(tres) ⇒ Integer

Get integer representing memory in bytes, computed from tres-alloc string

Returns:

  • (Integer) —

    the number of bytes of allocated memory



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# File 'lib/ood_core/job/adapters/slurm.rb', line 63

def self.memory_from_tres(tres)
  match = tres.to_s.match(/(?:^|,)mem=(\w+)(?:,|$)/)
  return unless match

  match_str = match[1]
  memory = UNIT_FACTORS[match_str[-1]].to_i * match_str.to_i 
  memory unless memory == 0
end

Instance Method Details

#accounts ⇒ Array<String>

Retrieve the accounts available to use for the current user.

Returns:

  • (Array<String>) —

    the accounts available to the user.



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# File 'lib/ood_core/job/adapters/slurm.rb', line 712

def accounts
  @slurm.accounts
end

#cluster_info ⇒ Hash

Retrieve info about active and total cpus, gpus, and nodes

Returns:

  • (Hash) —

    information about cluster usage



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# File 'lib/ood_core/job/adapters/slurm.rb', line 705

def cluster_info
  @slurm.get_cluster_info
end

#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/slurm.rb', line 866

def delete(id)
  @slurm.delete_job(id.to_s)
rescue Batch::Error => e
  # assume successful job deletion if can't find job id
  raise JobAdapterError, e.message unless /Invalid job id specified/ =~ e.message
end

#directive_prefix ⇒ Object 



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# File 'lib/ood_core/job/adapters/slurm.rb', line 873

def directive_prefix
  '#SBATCH'
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/slurm.rb', line 842

def hold(id)
  @slurm.hold_job(id.to_s)
rescue Batch::Error => e
  # assume successful job hold if can't find job id
  raise JobAdapterError, e.message unless /Invalid job id specified/ =~ 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/slurm.rb', line 772

def info(id)
  id = id.to_s
  info_ary = @slurm.get_jobs(id: id).map do |v|
    parse_job_info(v)
  end

  # If no job was found we assume that it has completed
  info_ary.empty? ? Info.new(id: id, status: :completed) : handle_job_array(info_ary, id)
rescue Batch::Error => e
  # set completed status if can't find job id
  if /Invalid job id specified/ =~ 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/slurm.rb', line 720

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

#info_historic(opts: {}) ⇒ Array<Info>

Retrieve historic info for all completed jobs from the resource manager.

Known options: job_ids [Array<#to_s>] optional list of job ids to filter the results. states [Array<#to_s>] optional list of job state codes. Selects jobs based on their state during the time period given. from [#to_s] optional date string to filter jobs in any state after the specified time. If states are provided, filter jobs in these states after this period to [#to_s] optional date string to filter jobs in any state before the specified time. If states are provided, filter jobs in these states before this period. show_steps [#Boolean] optional boolean to filter job steps from the results.

Returns:

  • (Array<Info>) —

    information describing submitted jobs

See Also:



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# File 'lib/ood_core/job/adapters/slurm.rb', line 742

def info_historic(opts: {})
  job_ids    = opts.fetch(:job_ids, [])
  states     = opts.fetch(:states, [])
  from       = opts.fetch(:from, nil)
  to         = opts.fetch(:to, nil)
  show_steps = opts.fetch(:show_steps, false)
  @slurm.sacct_info(job_ids, states, from, to, show_steps).map do |v|
    Info.new(
      id: v[:job_id],
      status: get_state(v[:state]),
      job_name: v[:job_name],
      job_owner: v[:user],
      procs: v[:alloc_cpus],
      queue_name: v[:partition],
      wallclock_time: duration_in_seconds(v[:elapsed]),
      wallclock_limit: duration_in_seconds(v[:time_limit]),
      cpu_time: duration_in_seconds(v[:total_cpu]),
      submission_time: parse_time(v[:submit_time]),
      dispatch_time: parse_time(v[:start_time]),
      native: v,
      gpus: self.class.gpus_from_gres(v[:gres])
    )
  end
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/slurm.rb', line 797

def info_where_owner(owner, attrs: nil)
  owner = Array.wrap(owner).map(&:to_s).join(',')
  @slurm.get_jobs(owner: owner).map do |v|
    parse_job_info(v)
  end
rescue Batch::Error => e
  raise JobAdapterError, e.message
end

#nodes ⇒ Object 



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# File 'lib/ood_core/job/adapters/slurm.rb', line 881

def nodes
  @slurm.nodes
end

#queues ⇒ Object 



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# File 'lib/ood_core/job/adapters/slurm.rb', line 877

def queues
  @slurm.queues
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/slurm.rb', line 854

def release(id)
  @slurm.release_job(id.to_s)
rescue Batch::Error => e
  # assume successful job release if can't find job id
  raise JobAdapterError, e.message unless /Invalid job id specified/ =~ 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/slurm.rb', line 811

def status(id)
  id = id.to_s
  jobs = @slurm.get_jobs(
    id: id,
    attrs: [:job_id, :array_job_task_id, :state_compact]
  )
  # A job id can return multiple jobs if it corresponds to a job array
  # id, so we need to find the job that corresponds to the given job id
  # (if we can't find it, we assume it has completed)
  #
  # Match against the job id or the formatted job & task id "1234_0"
  if job = jobs.detect { |j| j[:job_id] == id || j[:array_job_task_id] == id }
    Status.new(state: get_state(job[:state_compact]))
  else
    # set completed status if can't find job id
    Status.new(state: :completed)
  end
rescue Batch::Error => e
  # set completed status if can't find job id
  if /Invalid job id specified/ =~ e.message
    Status.new(state: :completed)
  else
    raise JobAdapterError, e.message
  end
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/slurm.rb', line 637

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 sbatch options
  args = []
  # ignore args, don't know how to do this for slurm
  args.concat ["-H"] if script.submit_as_hold
  args.concat (script.rerunnable ? ["--requeue"] : ["--no-requeue"]) unless script.rerunnable.nil?
  args.concat ["-D", script.workdir.to_s] unless script.workdir.nil?
  args.concat ["--mail-user", script.email.join(",")] unless script.email.nil?
  if script.email_on_started && script.email_on_terminated
    args.concat ["--mail-type", "ALL"]
  elsif script.email_on_started
    args.concat ["--mail-type", "BEGIN"]
  elsif script.email_on_terminated
    args.concat ["--mail-type", "END"]
  elsif script.email_on_started == false && script.email_on_terminated == false
    args.concat ["--mail-type", "NONE"]
  end
  args.concat ["-J", script.job_name] unless script.job_name.nil?
  args.concat ["-i", script.input_path] unless script.input_path.nil?
  args.concat ["-o", script.output_path] unless script.output_path.nil?
  args.concat ["-e", script.error_path] unless script.error_path.nil?
  args.concat ["--reservation", script.reservation_id] unless script.reservation_id.nil?
  args.concat ["-p", script.queue_name] unless script.queue_name.nil?
  args.concat ["--priority", script.priority] unless script.priority.nil?
  args.concat ["--begin", script.start_time.localtime.strftime("%C%y-%m-%dT%H:%M:%S")] unless script.start_time.nil?
  args.concat ["-A", script.accounting_id] unless script.accounting_id.nil?
  args.concat ["-t", seconds_to_duration(script.wall_time)] unless script.wall_time.nil?
  args.concat ['-a', script.job_array_request] unless script.job_array_request.nil?
  args.concat ['--qos', script.qos] unless script.qos.nil?
  args.concat ['--gpus-per-node', script.gpus_per_node] unless script.gpus_per_node.nil?
  args.concat ['-n', script.cores] unless script.cores.nil?
  # ignore nodes, don't know how to do this for slurm

  # 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 ["-d", depend.join(",")]               unless depend.empty?

  # Set environment variables
  env = script.job_environment || {}
  args.concat ["--export", export_arg(env, script.copy_environment?)]

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

  # Set content
  content = if script.shell_path.nil?
              script.content
            else
              "#!#{script.shell_path}\n#{script.content}"
            end

  # Submit job
  @slurm.submit_string(content, args: args, env: env)
rescue Batch::Error => e
  raise JobAdapterError, e.message
end