Class: QueueManager

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

Direct Known Subclasses

BashManager, SlurmManager

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(exec_folder, options, commands, persist_variables) ⇒ QueueManager

Returns a new instance of QueueManager.



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# File 'lib/autoflow/queue_manager.rb', line 5

def initialize(exec_folder, options, commands, persist_variables)
	@exec_folder = exec_folder
	@commands = commands
	@persist_variables = persist_variables
	@verbose = options[:verbose]
	@show_submit = options[:show_submit_command]
	@job_identifier = options[:identifier]
	@files = {}
	@remote = options[:remote]
	@ssh = options[:ssh]
	@write_sh = options[:write_sh]
	@external_dependencies = options[:external_dependencies]
	@active_jobs = []
	@extended_logging = options[:extended_logging]
end

Class Method Details

.available? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/autoflow/queue_manager.rb', line 322

def self.available?
	return FALSE
end

.descendants ⇒ Object

SELECT AND PREPARE MANAGER



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# File 'lib/autoflow/queue_manager.rb', line 25

def self.descendants
	ObjectSpace.each_object(Class).select { |klass| klass < self }
end

.priority ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 326

def self.priority
	return -1
end

.select_manager(options) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 42

def self.select_manager(options)
	queue_manager = nil
	priority = 0
	descendants.each do |descendant|
		if descendant.available?(options) && priority <= descendant.priority
			queue_manager = descendant
			priority = descendant.priority
		end
	end
	return queue_manager
end

.select_queue_manager(exec_folder, options, jobs, persist_variables) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 29

def self.select_queue_manager(exec_folder, options, jobs, persist_variables)
	path_managers = File.join(File.dirname(__FILE__),'queue_managers')
	Dir.glob(path_managers+'/*').each do |manager|
		require manager
	end
	if options[:batch]
		queue_manager = BashManager
	else
		queue_manager = select_manager(options)
	end
	return queue_manager.new(exec_folder, options, jobs, persist_variables)
end

.system_call(cmd, path = nil, remote = FALSE, ssh = nil) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 259

def self.system_call(cmd, path = nil, remote = FALSE, ssh = nil)
	cmd = "cd #{path}; " + cmd if !path.nil?
	if remote
		call = ssh.exec!(cmd)
	else
		call = %x[#{cmd}] 
	end
	return call
end

Instance Method Details

#asign_queue_id(ar_jobs, id) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 286

def asign_queue_id(ar_jobs, id)
	ar_jobs.each do |id_job, job|
		job.queue_id=id
	end
end

#close_file(file_name, permissions = nil) ⇒ Object

SSH



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# File 'lib/autoflow/queue_manager.rb', line 224

def close_file(file_name, permissions = nil) #SSH
	path, content = @files.delete(file_name)
	file_path = File.join(path, file_name)
	if @remote
		@ssh.exec!("echo '#{content}' > #{file_path}")
		@ssh.exec!("chmod #{permissions} #{file_path}") if !permissions.nil?
	else
		local_file = File.open(file_path,'w')
		local_file.chmod(permissions) if !permissions.nil?
		local_file.print content
		local_file.close
	end
end

#create_file(file_name, path) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 216

def create_file(file_name, path) 
	@files[file_name] = [path, '']
end

#create_folder(folder_name) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 208

def create_folder(folder_name)
	if @remote
		@ssh.exec!("if ! [ -d  #{folder_name} ]; then mkdir -p #{folder_name}; fi")
	else
		Dir.mkdir(folder_name) if !File.exists?(folder_name)
	end
end

#exec ⇒ Object

EXECUTING WORKFLOW WITH MANAGER



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# File 'lib/autoflow/queue_manager.rb', line 58

def exec
	create_folder(@exec_folder)
	make_environment_file if !@persist_variables.empty?
	create_file('versions', @exec_folder)
	write_file('versions',"autoflow\t#{Autoflow::VERSION}")
	close_file('versions')
	create_file('index_execution', @exec_folder)
	launch_all_jobs
	close_file('index_execution')
end

#get_all_deps(ar_dependencies) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 300

def get_all_deps(ar_dependencies)
	final_dep = []
	final_dep.concat(get_queue_system_dependencies(ar_dependencies)) if !ar_dependencies.empty?
	final_dep.concat(@external_dependencies)
	return final_dep
end

#get_dependencies(job, id = nil) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 279

def get_dependencies(job, id = nil)
	ar_dependencies = []
	ar_dependencies += job.dependencies
	ar_dependencies.delete(id) if !id.nil? #Delete autodependency
	return ar_dependencies
end

#get_queue_system_dependencies(ar_dependencies) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 292

def get_queue_system_dependencies(ar_dependencies)
	queue_system_ids=[]
	ar_dependencies.each do |dependency|
		queue_system_ids << @commands[dependency].queue_id
	end
	return queue_system_ids
end

#get_queue_system_id(shell_output) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 318

def get_queue_system_id(shell_output)

end

#get_relations_and_folders ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 89

def get_relations_and_folders
	relations = {}
	@commands.each do |name, job|
		relations[name] = [job.attrib[:exec_folder], job.dependencies]
	end
	return relations
end

#init_log ⇒ Object

TODO adapt to remote execution



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# File 'lib/autoflow/queue_manager.rb', line 69

def init_log #TODO adapt to remote execution
	log_path = [@exec_folder, '.wf_log'].join('/') #Join must assume linux systems so File.join canot be used for windows hosts
	log = parse_log(log_path) #TODO modify to folder
	job_relations_with_folders = get_relations_and_folders
	if @write_sh
		create_file('wf.json', @exec_folder)
		write_file('wf.json', job_relations_with_folders.to_json)
		close_file('wf.json')
	end
 		@active_jobs.each do |task|
 			query = log[task]
 			if query.nil?
			log[task] = {'set' => [Time.now.to_i]}
 			else
			log[task]['set'] << Time.now.to_i
 			end
	end
	write_log(log, log_path, job_relations_with_folders)
end

#launch2queue_system(job, id, buffered_jobs) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 154

def launch2queue_system(job, id, buffered_jobs)
	sh_name = job.name+'.sh'
	if @write_sh
		# Write sh file
		#--------------------------------
		create_file(sh_name, job.attrib[:exec_folder])
		write_file(sh_name, '#!/usr/bin/env bash')
		write_file(sh_name, '##JOB_GROUP_ID='+@job_identifier)
		write_header(id, job, sh_name)
	end

	#Get dependencies
	#------------------------------------
	ar_dependencies = get_dependencies(job, id)
	buffered_jobs.each do |id_buff_job, buff_job|
		ar_dependencies += get_dependencies(buff_job, id_buff_job)
		if @write_sh
			write_job(buff_job, sh_name)
			buff_job.attrib[:exec_folder] = job.attrib[:exec_folder]
		end
	end
	ar_dependencies.uniq!

	if @write_sh
		#Write sh body
		#--------------------------------
		write_file(sh_name, 'hostname')
		log_file_path = [@exec_folder, '.wf_log', File.basename(job.attrib[:exec_folder])].join('/')
		write_file(sh_name, "flow_logger -e #{log_file_path} -s #{job.name}")
		write_file(sh_name, "source #{File.join(@exec_folder, 'env_file')}") if !@persist_variables.empty?
		write_job(job, sh_name)
		write_file(sh_name, "flow_logger -e #{log_file_path} -f #{job.name}")
		write_file(sh_name, "echo 'General time'")
		write_file(sh_name, "times")
		close_file(sh_name, 0755)
	end

	#Submit node
	#-----------------------------------
	if !@verbose
		queue_id = submit_job(job, ar_dependencies)
		job.queue_id = queue_id # Returns id of running tag on queue system 
		asign_queue_id(buffered_jobs, queue_id)
	end
end

#launch_all_jobs ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 97

def launch_all_jobs
	buffered_jobs = []
	sorted_jobs = sort_jobs_by_dependencies
	sorted_jobs.each do |name, job|
		@active_jobs << job.name if !job.attrib[:done]
	end
	init_log
	sorted_jobs.each do |name, job|
		write_file('index_execution', "#{name}\t#{job.attrib[:exec_folder]}") 
		if job.attrib[:done]
			next
		else
			rm_done_dependencies(job)
		end	
		buffered_jobs = launch_job_in_folder(job, name, buffered_jobs)
	end
end

#launch_job_in_folder(job, id, buffered_jobs) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 142

def launch_job_in_folder(job, id, buffered_jobs)
	create_folder(job.attrib[:exec_folder])
	if !job.attrib[:buffer]  # Launch with queue_system the job and all buffered jobs
		launch2queue_system(job, id, buffered_jobs)
		buffered_jobs = []#Clean buffer
	else # Buffer job
		buffered_jobs << [id, job]
	end
	return buffered_jobs	
end

#make_environment_file ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 200

def make_environment_file
	create_file('env_file', @exec_folder)
	@persist_variables.each do |var, value|
		write_file('env_file', "export #{var}=#{value}")
	end
	close_file('env_file')
end

#read_file(file_path) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 238

def read_file(file_path)
	content = nil
	if @remote
		res = @ssh.exec!("[ ! -f #{file_path} ] && echo 'Autoflow:File Not Found' || cat #{file_path}")
		content = res if !content.include?('Autoflow:File Not Found')
	else
		content = File.open(file_path).read if File.exists?(file_path)
	end
	return content
end

#rm_done_dependencies(job) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 132

def rm_done_dependencies(job)
	remove=[]
	job.dependencies.each do |dependency|			
		remove << dependency if @commands[dependency].attrib[:done]
	end
	remove.each do |rm|
		job.dependencies.delete(rm)
	end
end

#sort_jobs_by_dependencies ⇒ Object

We need job ids from queue system so we ask for each job and we give the previous queue system ids as dependencies if necessary



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# File 'lib/autoflow/queue_manager.rb', line 115

def sort_jobs_by_dependencies # We need job ids from queue system so we ask for each job and we give the previous queue system ids as dependencies if necessary
	ar_jobs = @commands.to_a
	sorted_jobs = []
	jobs_without_dep = ar_jobs.select{|job| job.last.dependencies.empty?}
	sorted_jobs.concat(jobs_without_dep)
	while ar_jobs.length != sorted_jobs.length
		ids = sorted_jobs.map{|job| job.first}
		ar_jobs.each do |job|
			if !sorted_jobs.include?(job) 
				deps = job.last.dependencies - ids
				sorted_jobs << job if deps.empty?
			end
		end
	end
	return sorted_jobs
end

#submit_job(job, ar_dependencies) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 314

def submit_job(job, ar_dependencies)

end

#system_call(cmd, path = nil) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 249

def system_call(cmd, path = nil)
	cmd = "cd #{path}; " + cmd if !path.nil?
	if @remote
		call = @ssh.exec!(cmd)
	else
		call = %x[#{cmd}] 
	end
	return call
end

#write_file(file_name, content) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 220

def write_file(file_name, content)
	@files[file_name].last << content+"\n"
end

#write_header(id, node, sh) ⇒ Object

QUEUE DEPENDANT METHODS



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# File 'lib/autoflow/queue_manager.rb', line 310

def write_header(id, node, sh)

end

#write_job(job, sh_name) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 269

def write_job(job, sh_name)	
	write_file(sh_name, job.initialization) if !job.initialization.nil?
	if @extended_logging
		log_command = '/usr/bin/time -o process_data -v '
	else
		log_command = 'time '
	end
	write_file(sh_name, log_command + job.parameters)
end