Class: OodCore::Job::Adapters::Sge::Helper

Inherits:
Object
  • Object
show all
Defined in:
lib/ood_core/job/adapters/sge/helper.rb

Overview

Utility helper class for the SGE adapter to parse input and generate submission arguements.

Instance Method Summary collapse

Instance Method Details

#batch_submit_args(script, after: [], afterok: [], afternotok: [], afterany: []) ⇒ Object

Convert script and job dependencies to qsub argument vector



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# File 'lib/ood_core/job/adapters/sge/helper.rb', line 18

def batch_submit_args(script, after: [], afterok: [], afternotok: [], afterany: [])
  raise_error_on_unsupported_args(script, after: after, afterok: afterok, afternotok: afternotok, afterany: afterany)

  args = []
  args.concat ['-h'] if script.submit_as_hold
  args.concat ['-r', 'yes'] if script.rerunnable
  script.job_environment.each_pair {|k, v| args.concat ['-v', "#{k.to_s}=#{v.to_s}"]} unless script.job_environment.nil?
  args.concat ["-V"] if script.copy_environment?

  if script.workdir
    args.concat ['-wd', script.workdir]
  elsif ! script_contains_wd_directive?(script.content)
    args.concat ['-cwd']
  end

  on_event_email = []
  on_event_email << 'b' if script.email_on_started  # beginning
  on_event_email << 'ea' if script.email_on_terminated  # end, aborted

  args.concat ['-M', script.email.first, '-m', on_event_email.join] if script.email && ! on_event_email.empty?

  afterok  = Array(afterok).map(&:to_s)
  args.concat ['-hold_jid_ad', afterok.join(',')] unless afterok.empty?

  # ignoring email_on_started
  args.concat ['-N', script.job_name] unless script.job_name.nil?
  args.concat ['-e', script.error_path] unless script.error_path.nil?
  args.concat ['-o', script.output_path] unless script.output_path.nil?
  args.concat ['-ar', 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.strftime('%C%y%m%d%H%M.%S')] unless script.start_time.nil?
  args.concat ['-l', "h_rt=" + seconds_to_duration(script.wall_time)] unless script.wall_time.nil?
  args.concat ['-P', script.accounting_id] unless script.accounting_id.nil?
  args.concat ['-t', script.job_array_request] unless script.job_array_request.nil?
  args.concat Array.wrap(script.native) if script.native

  args
end

#parse_job_id_from_qsub(qsub_output) ⇒ Object

Extract the job id from qsub’s output e.g. Your job 1043 (“job_16”) has been submitted

Parameters:

  • qsub_output (#to_s) 


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# File 'lib/ood_core/job/adapters/sge/helper.rb', line 103

def parse_job_id_from_qsub(qsub_output)
  /Your job(?:-array)? (?<job_id>[0-9]+)/.match(qsub_output)[:job_id]
end

#raise_error_on_unsupported_args(script, after:, afterok:, afternotok:, afterany:) ⇒ Object

Raise exceptions when adapter is asked to perform an action that SGE does not support

Raises:

  • (Error) —

    when an incompatible action is requested



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# File 'lib/ood_core/job/adapters/sge/helper.rb', line 92

def raise_error_on_unsupported_args(script, after:, afterok:, afternotok:, afterany:)
  # SGE job dependencies only supports one kind of event: completion
  raise OodCore::Job::Adapters::Sge::Error.new('SGE does not support job dependencies on after start') if after && ! after.empty?
  raise OodCore::Job::Adapters::Sge::Error.new('SGE does not support job dependencies on after not ok') if afternotok && ! afternotok.empty?
  raise OodCore::Job::Adapters::Sge::Error.new('SGE does not support job dependencies on after any') if afterany && ! afterany.empty?
end

#script_contains_wd_directive?(content) ⇒ bool

Examples:

#$-wd /home/ood/ondemand  # should match
#$  -wd /home/ood/ondemand  # should match
#$  -cwd /home/ood/ondemand  # should match
#$ -j yes -wd /home/ood/ondemand  # should match
#$ -j yes -o this-wd /home/ood/ondemand  # should NOT match
  #$ -t 1-10:5 -wd /home/ood/ondemand  # should NOT match

Parameters:

  • content —

    The script content

Returns:

  • (bool) 


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# File 'lib/ood_core/job/adapters/sge/helper.rb', line 72

def script_contains_wd_directive?(content)
  content.slice(
    # Only search within the script's first 1024 characters in case the user is
    # putting lots of non-line delimited data into their scripts.
    0, 1024
  ).split(
    "\n"
  ).any? {
    |line|
    # String must start with #$
    # Match may be:
    #   Immediate -c?wd
    #   Eventual space or tab followed by -c?wd
    # String may end with multiple characters
    /^#\$(?:-c?wd|.*[ \t]+-c?wd).*$/ =~ line
  }
end

#seconds_to_duration(time) ⇒ String

Convert seconds to duration

Parameters:

  • time (#to_i)

Returns:

  • (String) —

    an SGE qsub compatible wallclock limit



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# File 'lib/ood_core/job/adapters/sge/helper.rb', line 11

def seconds_to_duration(time)
  time = time.to_i
  "%02d:%02d:%02d" % [time/3600, time/60%60, time%60]
end