Class: Batch

Inherits:
Object
  • Object
show all
Defined in:
lib/autoflow/batch.rb

Constant Summary collapse

@@all_batch = 
{}
@@jobs_names = 
[]
@@batch_iterator_relations = 
{}
@@nested_iteration_relations = 
{}
@@general_computation_attrib = 
{
  :cpu => nil, 
  :mem => nil, 
  :time => nil,
  :node => nil,
  :multinode => nil,
  :ntask => nil,
  :additional_job_options => nil
}

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(tag, init, main_command, id, exec_folder) ⇒ Batch

Returns a new instance of Batch.



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# File 'lib/autoflow/batch.rb', line 23

def initialize(tag, init, main_command, id, exec_folder)
  @regex_deps = nil
  replace_regexp(tag, init, main_command)
  @name = nil
  @id = id
  @iterator = [nil] 
  @parent = nil
  @dependencies = [] # [batch_name, dependency_type, keyword2replace]

    # nil => There isn't dependecies, 

    # 'simple' => One job needs a previous job, 

    # '1to1' => A job in a batch needs another job in other batch, 

    # '*to1' => A job need a previous full batch of jobs

    # 'local' => A simple job needs one job of a batch

  @initialization = init
  @main_command = main_command
  @attrib = {
    :done => false,
    :folder => true,
    :buffer => false,
    :exec_folder => exec_folder,
    :cpu_asign => nil # number, list or mono

  }.merge(@@general_computation_attrib)
  get_name_and_iterators_and_modifiers(tag)
  set_execution_attrib
  set_cpu
  @jobs = []
  @@all_batch[@name] = self
end

Instance Attribute Details

#attrib ⇒ Object

Returns the value of attribute attrib.



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# File 'lib/autoflow/batch.rb', line 2

def attrib
  @attrib
end

#dependencies ⇒ Object

Returns the value of attribute dependencies.



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# File 'lib/autoflow/batch.rb', line 2

def dependencies
  @dependencies
end

#id ⇒ Object

Returns the value of attribute id.



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# File 'lib/autoflow/batch.rb', line 2

def id
  @id
end

#init ⇒ Object

Returns the value of attribute init.



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# File 'lib/autoflow/batch.rb', line 2

def init
  @init
end

#iterator ⇒ Object

Returns the value of attribute iterator.



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# File 'lib/autoflow/batch.rb', line 2

def iterator
  @iterator
end

#jobs ⇒ Object

Returns the value of attribute jobs.



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# File 'lib/autoflow/batch.rb', line 2

def jobs
  @jobs
end

#main_command ⇒ Object

Returns the value of attribute main_command.



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# File 'lib/autoflow/batch.rb', line 2

def main_command
  @main_command
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/autoflow/batch.rb', line 2

def name
  @name
end

#parent ⇒ Object

Returns the value of attribute parent.



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# File 'lib/autoflow/batch.rb', line 2

def parent
  @parent
end

Class Method Details

.set_general_attrib(attrib_hash) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 18

def self.set_general_attrib(attrib_hash)
  @@general_computation_attrib = attrib_hash
end

Instance Method Details

#add_nested_iteration_relation(tmp_j, new_job) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 296

def add_nested_iteration_relation(tmp_j, new_job)
  query = @@nested_iteration_relations[tmp_j.name]
  if query.nil?
    @@nested_iteration_relations[tmp_j.name] = [new_job.name]
  else
    query << new_job.name
  end
end

#asign_child_batch ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 113

def asign_child_batch
  batches = []
  if @main_command.class.to_s == 'Array'
    @main_command.each do |id|
      batch = get_batch(id)
      batch.parent = @name
      batches << batch
    end
    @main_command = batches
  end
end

#check_dependencies(tmp_j, iter, jobs) ⇒ Object

tmp_j => job to set dependencies in iteration iter => sufix of current iteration jobs => array of jobs which has the job dependency



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# File 'lib/autoflow/batch.rb', line 354

def check_dependencies(tmp_j, iter, jobs)
  jobs_names = jobs.map{|job| job.name}
  deps = {}
  tmp_j.dependencies.each_with_index do |dep, i|   
    deps[dep] = i if jobs_names.include?(dep)
  end
  deps.each do |name, index|
    dep = name+'_'+iter
    tmp_j.initialization.gsub!(name+')', dep+')')
    tmp_j.parameters.gsub!(name+')', dep+')')
    tmp_j.dependencies[index] = dep 
  end
end

#check_dependencies_with_DinVar(command, dinamic_variables) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 459

def check_dependencies_with_DinVar(command, dinamic_variables)
  dep = []
  dinamic_variables.each do |var, name|
    dep << [name, 'DinVar'] if command.include?(var)
  end
  return dep
end

#check_execution_modifiers(name, iter_type = false) ⇒ Object

The last paremeter iused to indicate tha name is a iterator not an orignal node name



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# File 'lib/autoflow/batch.rb', line 159

def check_execution_modifiers(name, iter_type = false) #The last paremeter iused to indicate tha name is a iterator not an orignal node name

  done = false
  folder = true
  buffer = false
  done = true if name.include?('%')
  folder = false if name.include?('!')
  buffer = true if name.include?('&')
  if !iter_type
    name.gsub!(/&|\!|\%|\)/,'')# Delete function characters

  else
    name.gsub!(/&|\!|\%/,'')# Delete function characters

  end
  return name, done, folder, buffer
end

#check_regex_dependencies ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 305

def check_regex_dependencies
  if @regex_deps == 'tag'
    new_job_names = []
    @iterator.each do |iter|
      new_names = find_job_names(iter.gsub(')', ''))
      new_job_names.concat(new_names) 
    end
    @iterator = new_job_names.map{|nj| nj + ')'} if !new_job_names.empty?
  elsif @regex_deps == 'command'
    [@initialization, @main_command].each do |command|
      patterns = command.scan(/([^\s)]+)\)([^\s]*)/)
      if !patterns.empty?
        patterns.each do |putative_job, sufix|
          job_names = find_job_names(putative_job)
          if !job_names.empty?
            new_string = job_names.map{|jn| "#{jn})#{sufix}"}.join(' ')
            old_string = "#{putative_job})#{sufix}"
            command.gsub!(old_string, new_string)
          end
        end
      end
    end
  end
end

#collect_dinamic_variables(command) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 443

def collect_dinamic_variables(command)
  dinamic_variables = []
  if !command.nil? && command.include?('env_manager')
    command =~ /env_manager "([^"]+)/
    command =~ /env_manager '([^']+)/ if $1.nil?
    if !$1.nil?
      $1.split(';').each do |variable|
        name, value = variable.split('=')
        name.gsub!(' ', '') #Remove spaces

        dinamic_variables << [name, @name]
      end
    end
  end
  return dinamic_variables
end

#delete_jobs(jobs2delete, job_array) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 242

def delete_jobs(jobs2delete, job_array)
  jobs2delete.uniq!
  jobs2delete.sort{|s1, s2| s2 <=> s1}.each do |index|
    job_array.delete_at(index)
  end
  return job_array
end

#duplicate_job(tmp_j, sufix_name = '') ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 232

def duplicate_job(tmp_j, sufix_name = '')
  new_job = tmp_j.clone
  new_job.name = tmp_j.name+'_'+sufix_name
  new_job.attrib = tmp_j.attrib.clone
  new_job.dependencies = tmp_j.dependencies.clone
  new_job.initialization = tmp_j.initialization.clone
  new_job.parameters = tmp_j.parameters.clone
  return new_job
end

#find_job_names(name) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 330

def find_job_names(name)
  final_names = []
  intermediary_names = @@nested_iteration_relations[name]
  if !intermediary_names.nil?
    while !intermediary_names.empty?
      final_names = intermediary_names
      i_names = []
      intermediary_names.each do |i_n|
        query = @@nested_iteration_relations[i_n]
        i_names.concat(query) if !query.nil?
      end
      if !i_names.empty?
        intermediary_names = i_names
      else 
        break
      end
    end
  end
  return final_names
end

#get_batch(id) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 125

def get_batch(id)
  selected_batch = nil
  @@all_batch.each do |name, batch|
    if batch.id == id
      selected_batch = batch  
      break
    end
  end
  return selected_batch
end

#get_dependencies_by_regexp(batch_pattern, iterator_pattern) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 85

def get_dependencies_by_regexp(batch_pattern, iterator_pattern)
  selected_batches = @@all_batch.keys.select{|cmd_name| cmd_name =~ /#{batch_pattern}/}
  job_names = []
  selected_batches.each do |batch_name|
    iterators = @@all_batch[batch_name].iterator
    iterators = iterators.map{|it| it.gsub(/&|\!|\%|\)/,'')} if !iterators.first.nil?
    if iterator_pattern != '-'
      next if iterators.first.nil?
      iterators = iterators.select{|iter| iter =~ /#{iterator_pattern}/} 
    end
    if !iterators.empty?
      if iterators.first.nil? 
        job_names << batch_name
      else
        iterators.each do |iter|
          job_names << batch_name+iter
        end
      end
    end
  end
  return job_names
end

#get_jobs ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 250

def get_jobs
  jobs = []
  #@@batch_iterator_relations[@name] = @iterator #??????

  if @main_command.class.to_s == 'Array' # There are nested batchs

    temp_jobs = []
    @main_command.each do |batch|
      temp_jobs.concat(batch.get_jobs)
    end
    jobs2delete = []
    @iterator.each_with_index do |iter, i|
      temp_jobs.each_with_index do |tmp_j, tmp_i|
        new_job = duplicate_job(tmp_j, iter)
        check_dependencies(new_job, iter, temp_jobs)
        parse_iter(iter, @name, new_job)
        add_nested_iteration_relation(tmp_j, new_job)
        @@jobs_names << new_job.name
        jobs << new_job
        @jobs << new_job
        jobs2delete << tmp_i
      end
    end
    temp_jobs = delete_jobs(jobs2delete, temp_jobs) #Remove temporal jobs

  else
    check_regex_dependencies
    @iterator.each_with_index do |iter, num|
      job_attrib = @attrib.dup
      if !iter.nil?
        iter, done, job_attrib[:folder], job_attrib[:buffer] = check_execution_modifiers(iter, true)
        job_attrib[:done] = done if !@attrib[:done] # To keep attrib priority in batch on job

      end
      name = "#{@name}#{iter}"
      job_dependencies = []
      batch_deps = @dependencies.length
      initialization = replace_dependencies(@initialization, job_dependencies, iter, num)
      parameters = replace_dependencies(@main_command, job_dependencies, iter, num)
      @dependencies.pop(@dependencies.length - batch_deps) # Clean temporal dependencies by regexp

      job = Program.new(name, initialization, parameters, job_dependencies, job_attrib)
      job.batch = @name
      @@jobs_names << job.name
      jobs << job
      @jobs << job 
    end
  end
  return jobs
end

#get_jobs_by_batch_name(batch_name) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 536

def get_jobs_by_batch_name(batch_name)
  jobs = @jobs.select{|j| j.batch == batch_name}
  return jobs
end

#get_name_and_iterators_and_modifiers(tag) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 136

def get_name_and_iterators_and_modifiers(tag)
  tag =~ /(^.+)\[([^\]]+)\]\)/ # iterative node

  name = $1
  if $1.nil? # Non iterative node (simple node)

    tag =~ /(^.+)\)/
    name = $1
  end
  @name , @attrib[:done], @attrib[:folder], @attrib[:buffer] = check_execution_modifiers(name)
  if !$2.nil?
    @iterator = []
    #$2.split(';').map{|iter| iter.gsub(')','')}.each do |interval|

    $2.split(';').each do |interval|
      if interval.include?('-')
        limits = interval.split('-')
        @iterator.concat((limits.first..limits.last).to_a.map{|n| n.to_s})
      else
        @iterator << interval
      end
    end
  end
  @@batch_iterator_relations[@name] = @iterator
end

#get_root(batch_name) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 530

def get_root(batch_name)
  root_batch = @@all_batch[batch_name]
  root_batch = root_batch.get_root(root_batch.parent) if !root_batch.nil? && !root_batch.parent.nil?
  return root_batch
end

#get_string_position(substr, string) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 419

def get_string_position(substr, string)
  start = string.index(substr)
  ending = start + substr.length - 1
  range = [start, ending]
  return range
end

#handle_dependencies(dinamic_variables) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 378

def handle_dependencies(dinamic_variables)
  [@initialization, @main_command].each do |instructions|
    if instructions.class.to_s == 'String'
      #scan_dependencies(instructions) # NOT NECESSARY? REMOVED BY COLLISION CON REGEX SYSTEM. THE DINAMYC VARIABLES ARE NO USED

      dinamic_variables.concat(collect_dinamic_variables(instructions))
      @dependencies.concat(check_dependencies_with_DinVar(instructions, dinamic_variables))
    end
  end
  return dinamic_variables
end

#has_jobs? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/autoflow/batch.rb', line 108

def has_jobs?
  res = !@jobs.empty?
  return res
end

#parse_iter(iter, name, job) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 368

def parse_iter(iter, name, job)
  job.parameters = set_iter(name, iter, job.parameters)
  job.initialization = set_iter(name, iter, job.initialization)
end

#replace_dependencies(command, job_dependencies, iter, num) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 467

def replace_dependencies(command, job_dependencies, iter, num)
  if !command.nil?
    command = command.gsub('(*)', "#{iter}") if command.class.to_s == 'String'
    scan_dependencies(command)
    @dependencies.each do |batch_name, dep_type, dep_keyword2replace, dep_info|
      if dep_type == 'simple'
        if @@all_batch[batch_name].parent.nil?
          new_string = batch_name + ')'
        end
        job_dependencies << batch_name          
      elsif dep_type == '1to1'
        if @@all_batch[batch_name].parent.nil? || !@parent.nil?
          dep_name = "#{batch_name}#{@@batch_iterator_relations[batch_name][num]}"
        else
          root_batch = get_root(batch_name)
          selected_jobs = root_batch.get_jobs_by_batch_name(batch_name)
          dep_name = selected_jobs[num].name
        end
        job_dependencies << dep_name
        new_string = dep_name + ')' 
      elsif dep_type == '*to1'
        if @@all_batch[batch_name].parent.nil? || !@parent.nil?
          new_string = @@batch_iterator_relations[batch_name].map{|iter|
            dep_name =  batch_name + iter
            job_dependencies << dep_name
            "#{dep_name})#{dep_info}"
          }.join(' ')
        else
          root_batch = get_root(batch_name)
          selected_jobs = root_batch.get_jobs_by_batch_name(batch_name)
          new_string = selected_jobs.map{|j|
            job_dependencies << j.name
            "#{j.name + ')'}#{dep_info}"
          }.join(' ')
        end
        dep_keyword2replace = "#{dep_keyword2replace}#{dep_info}"
      elsif dep_type == 'local'
        if @@all_batch[batch_name].parent.nil? || !@parent.nil?
          #@@batch_iterator_relations.each do |key,val|

          #  puts "#{key}\t#{val.inspect}"

          #end

          if @@batch_iterator_relations[batch_name].map{|iter| iter.gsub(')','')}.include?(dep_info) #This avoids cross dependencies by similar names, map used for regexp deps

            dep_name = batch_name + dep_info
            job_dependencies << dep_name
            new_string = dep_name + ')'
          end
        else
          dep_name = dep_keyword2replace.gsub(')','') #This avoids cross dependencies by similar names

          #if !@@jobs_names.include?(dep_name)

          job_dependencies << dep_name
          new_string = dep_name + ')'
          #end

        end
      elsif dep_type == 'DinVar'
        job_dependencies << batch_name if batch_name != @name # This condition avoids autodependencies

      end
      job_dependencies.uniq!
      command = command.gsub(dep_keyword2replace, new_string) if dep_type != 'DinVar' && !dep_keyword2replace.nil? && !new_string.nil?
    end
  end
  return command
end

#replace_regexp(tag, init, main_command) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 52

def replace_regexp(tag, init, main_command)
  scan_JobRegExp_tag(tag) if tag.include?('JobRegExp:') 
  [init, main_command].each do |intructions|
    if intructions.class.to_s == 'String'
      while intructions.include?('!JobRegExp:')
        scan_JobRegExp(intructions)
      end
    end
  end
  #puts main_command.inspect

end

#scan_cpu(command) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 218

def scan_cpu(command)
  if command.include?('[cpu]')
    command.gsub!('[cpu]', @attrib[:cpu].to_s)
    @attrib[:cpu_asign] = 'number'
  elsif command.include?('[lcpu]')
    command.gsub!('[lcpu]', 'workers')
    @attrib[:cpu_asign] = 'list'
  elsif @attrib[:cpu_asign].nil?
    @attrib[:cpu_asign] = 'mono'
  end        
  return command
end

#scan_dependencies(command) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 389

def scan_dependencies(command)
  if !command.nil?# When command is the initialize, sometimes can be undefined

    matched_regions = []
    batches = []
    @@all_batch.each do |k , val| #sorting is used to match last jobs first, and avoid small matches of first nodes

      batches << [k , val]
    end
    batches.reverse.each do |name, batch| 
      if command.include?(name+')') && !string_overlap(matched_regions, name+')', command)
        @dependencies << [name, 'simple', name+')']
      end
      if command.include?("!#{name}*!") && !string_overlap(matched_regions, "!#{name}*!", command)
        @dependencies << [name, '1to1', "!#{name}*!"]
      end
      if command.include?("!#{name}!") && !string_overlap(matched_regions, "!#{name}!", command)
        #command =~ /!#{name}!([^ \n]+)/

        command.scan(/!#{name}!([^ \n]+)/).each do |string_match|
          @dependencies << [name, '*to1', "!#{name}!", string_match.first]
        end
      end
      local_dependencies = command.scan(/#{name}([^\( \n]+)\)/)
      local_dependencies.each do |local_dependency|
        if !string_overlap(matched_regions, "#{name}#{local_dependency.first}"+')', command)
          @dependencies << [name, 'local', "#{name}#{local_dependency.first}"+')', local_dependency.first] 
        end
      end
    end
  end
end

#scan_JobRegExp(command) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 64

def scan_JobRegExp(command)
  data = /!JobRegExp:([^ \n]+):([^ \n]+)!([^ \n]+)/.match(command) # *to1 with regexp

  #data[0] => reference string (command), data[1] => batch_pattern, data[2] => iterator_pattern, data[3] => adyacent string to regexp as regexp/file_name

  job_names = get_dependencies_by_regexp(data[1], data[2])
  @regex_deps = 'command' if job_names.length > 0
  new_string = job_names.map{|jn| jn + ')' + data[3] }.join(' ')
  command.gsub!(data[0], new_string)
  #puts command.inspect

end

#scan_JobRegExp_tag(tag) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 74

def scan_JobRegExp_tag(tag)
  data = /JobRegExp:([^ \n]+):([^;\] \n]+)/.match(tag) # 1to1 with regexp

  #data[0] => reference string (command), data[1] => batch_pattern, data[2] => iterator_pattern

  job_names = get_dependencies_by_regexp(data[1], data[2])
  if job_names.length > 0
    @regex_deps = 'tag' 
  end
  new_string = job_names.map{|jn| jn + ')'}.join(';')
  tag.gsub!(data[0], new_string)
end

#scan_resources(command) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 179

def scan_resources(command)
  resources_line = nil
  command.each_line do |line|
    if line.include?('resources:')
      line = line.chomp
      resources_line = line
      fields = line.split(' ')
      fields.each_with_index do |field, index|
        if field == '-c'
          @attrib[:cpu] = fields[index+1].to_i
        elsif field == '-m'
          @attrib[:mem] = fields[index+1]
        elsif field == '-n'
          @attrib[:node] = fields[index+1]
        elsif field == '-t'
          @attrib[:time] = fields[index+1]
        elsif field == '-u'
          @attrib[:multinode] = fields[index+1].to_i
        elsif field == '-A'
          @attrib[:additional_job_options] = fields[index+1].split(':')
        end 
      end
      if fields.include?('-s')
        @attrib[:ntask] = true
      else
        @attrib[:ntask] = false
      end
    end
  end
  command.gsub!(resources_line, '') if !resources_line.nil?
  return command
end

#set_cpu ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 212

def set_cpu
  @initialization = scan_cpu(@initialization) if !@initialization.nil?
  @main_command = scan_cpu(@main_command) if @main_command.class.to_s == 'String'
  @attrib[:cpu] = 1 if @attrib[:cpu_asign] == 'mono'
end

#set_execution_attrib ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 174

def set_execution_attrib
  @initialization = scan_resources(@initialization) if !@initialization.nil?
  @main_command = scan_resources(@main_command) if @main_command.class.to_s == 'String'
end

#set_iter(name, iter, string) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 373

def set_iter(name, iter, string)
  string = string.gsub(name+'(+)', iter)
  return string
end

#string_overlap(matched_regions, substr, string) ⇒ Object 



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# File 'lib/autoflow/batch.rb', line 426

def string_overlap(matched_regions, substr, string)
  match = false
  range = get_string_position(substr, string)
  if !range.empty?
    matched_regions.each do |start, ending|
      if (range.first >= start && range.first <= ending) || 
        (range.last >= start && range.last <= ending) ||
        (range.first <= start && range.last >= ending)
        match = true
        break
      end
    end
    matched_regions << range 
  end
  return match
end