Class: Comana::ComputationManager

Inherits:
Object
  • Object
show all
Defined in:
lib/comana/computationmanager.rb

Overview

This class provides a framework of scientific computation. Users have to redefine some methods in subclasses for various computation.

Defined Under Namespace

Classes: AlreadyStartedError, AlreadySubmittedError, ExecuteError, InitializeError, NotImplementedError

Constant Summary collapse

QSUB_SCRIPT_NAME = 
'qsub.sh'
QSUB_LOG_NAME = 
'qsub.log'

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(dir) ⇒ ComputationManager

You can redefine in subclass to modify from default values.



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# File 'lib/comana/computationmanager.rb', line 20

def initialize(dir)
  @dir = dir # redefine in subclass. 
  @lockdir    = "lock_comana"
  @alive_time = 3600
end

Instance Attribute Details

#dir ⇒ Object (readonly)

Returns the value of attribute dir.



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# File 'lib/comana/computationmanager.rb', line 17

def dir
  @dir
end

Class Method Details

.effective_queue(queues, jobs, hosts, benchmarks) ⇒ Object

jobs < hosts のキューがあれば(空きホストがあれば)、その中で bench が最小のもの なければ、self.guess_end_time の値が最小のもの。



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# File 'lib/comana/computationmanager.rb', line 115

def self.effective_queue(queues, jobs, hosts, benchmarks)
  candidates = queues.select do |q|
    jobs[q] < hosts[q] 
  end
  if candidates.empty?
    result = queues.min_by{|q| self.guess_end_time(jobs[q], hosts[q], benchmarks[q]) }
  else
    result = candidates.min_by {|q| benchmarks[q]}
  end
  result
end

.execute(args) ⇒ Object 



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# File 'lib/comana/computationmanager.rb', line 26

def self.execute(args)
  targets = args
  targets = [ENV['PWD']] if targets.empty?

  targets.each do |dir|
    print "#{dir}..."
    begin
      calc_dir = self.new(dir)
    rescue => exc
      puts "Not #{self}: #{dir}"
      next
    end

    begin
      calc_dir.start
    rescue self::AlreadyStartedError
      puts "Already started: #{dir}"
      next
    end
  end
end

.guess_end_time(num_jobs, num_hosts, benchmark) ⇒ Object

新しく1個ジョブを追加した場合の終了見込み時間 ジョブの終了時刻がランダムであり、ジョブの実行時間は等しいと仮定して算出。 空きホストがあれば benchmark 通りの見込み。 空きホストがなければ、ホストがあくまでの見込み時間を加算。



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# File 'lib/comana/computationmanager.rb', line 131

def self.guess_end_time(num_jobs , num_hosts, benchmark)
  if num_jobs < num_hosts
    unit = 1.0 #unit 
  else
    unit = (num_jobs.to_f + 1.0) / (num_hosts.to_f)
  end
  result = unit * benchmark
  result
end

.qsub(args, options) ⇒ Object 



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# File 'lib/comana/computationmanager.rb', line 48

def self.qsub(args, options)
  if options[:auto] || options[:load_group]
    # OK
  elsif !(options[:q_name] && options[:pe_name] && options[:ppn] && options[:command])
    puts "Lack of required options."
    puts "Need (--auto) or (--load-group) or (--q-name && --pe-name && --ppn && --command )"
    puts "E.g., OK: #{File.basename($0)} --auto"
    puts "      OK: #{File.basename($0)} --load-group=cluster_name"
    puts "      OK: #{File.basename($0)} --q-name=a --pe-name=b --ppn=1 --command=c"
    puts "      NG: #{File.basename($0)} --q-name=a --pe-name=b --ppn=1"
    puts "Exit."
    exit
  end

  tgts = args
  tgts = [ENV['PWD']] if tgts.empty?

  tgts.each do |dir|
    cs = Comana::ClusterSetting.load_file
    if options[:load_group]
      q_name = options[:load_group]
    elsif options[:auto]
      queues = Comana::GridEngine.queues
      jobs = {}
      hosts = {}
      benchmarks = {}
      queues.each do |q|
        jobs[q] = Comana::GridEngine.queue_jobs(q).size
        hosts[q] = Comana::GridEngine.queue_alive_nums[q]
        benchmarks[q] = Comana::ClusterSetting.load_file.settings_queue(q)['benchmark']
      end
      q_name =  self.effective_queue(queues, jobs, hosts, benchmarks)
    end

    if options[:load_group] || options[:auto]
      gs = cs.settings_queue(q_name)
      q_name          ||= gs['queue']
      pe_name         ||= gs['pe']
      ppn             ||= gs['ppn']
      ld_library_path ||= gs['ld_library_path']
    end

    q_name          = options[:q_name]          if options[:q_name]
    pe_name         = options[:pe_name]         if options[:pe_name]
    ppn             = options[:ppn]             if options[:ppn]
    ld_library_path = options[:ld_library_path] if options[:ld_library_path]
    command = options[:command] || "#{`which #{__FILE__}`.chomp} execute"

    begin
      calc_dir = self.new(dir)
      calc_dir.queue_submit(
        q_name:           q_name,
        pe_name:          pe_name,
        ppn:              ppn,
        ld_library_path:  ld_library_path,
        command:          command
      )
    rescue self::InitializeError
      puts "Not #{self} : #{dir}"
    rescue Comana::ComputationManager::AlreadySubmittedError
      puts "Already started: #{dir}"
    end
  end
end

Instance Method Details

#execute ⇒ Object Also known as: start

Execute calculation. If log of ComputationManager exist, raise ComputationManager::AlreadyStartedError, because the calculation has been done by other process already. This method is aliased to ‘start’.



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# File 'lib/comana/computationmanager.rb', line 157

def execute
  begin
    Dir.mkdir "#{@dir}/#{@lockdir}"
  rescue Errno::EEXIST
    raise AlreadyStartedError, "Exist #{@dir}/#{@lockdir}"
  end

  while true
    calculate
    break if finished?
    prepare_next
  end
end

#latest_modified_time ⇒ Object

Return latest modified time of files in calc dir recursively. require “find”



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# File 'lib/comana/computationmanager.rb', line 174

def latest_modified_time
  tmp = Dir.glob("#{@dir}/**/*").max_by do |file|
    File.mtime(file)
  end
  File.mtime(tmp)
end

#queue_submit(q_name:, pe_name:, ppn:, ld_library_path:, command:, submit: true) ⇒ Object 



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# File 'lib/comana/computationmanager.rb', line 181

def queue_submit(q_name:, pe_name:, ppn:, ld_library_path: , command:, submit: true)

  qsub_path = "#{@dir}/#{QSUB_SCRIPT_NAME}"
  if FileTest.exist? qsub_path
    raise AlreadySubmittedError,
      "Already exist #{qsub_path}."
  end
  File.open(qsub_path, "w") do |io|
    Comana::GridEngine.write_qsub_script(
      q_name:          q_name,
      pe_name:         pe_name,
      ppn:             ppn,
      ld_library_path: ld_library_path,
      command:         command,
      io:              io
    )
  end
  cur_dir = Dir.pwd
  Dir.chdir @dir
  print   "Submitting #{qsub_path}..."
  system("qsub #{QSUB_SCRIPT_NAME} > #{QSUB_LOG_NAME}") if submit
  puts   "Done."
  Dir.chdir cur_dir
end

#state ⇒ Object

Return a symbol which indicate state of calculation.

:yet           not started
:started       started, but not ended, including short time from last output
:terminated    started, but long time no output
:finished      started, normal ended and not need next calculation



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# File 'lib/comana/computationmanager.rb', line 146

def state
  return :finished   if finished?
  return :yet        unless started?
  return :terminated if (Time.now - latest_modified_time > @alive_time)
  return :started    
end