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