Class: BashManager

Inherits:
QueueManager show all
Defined in:
lib/autoflow/queue_managers/bash_manager.rb

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from QueueManager

#asign_queue_id, #close_file, #create_file, #create_folder, descendants, #exec, #get_all_deps, #get_dependencies, #get_queue_system_dependencies, #get_relations_and_folders, #init_log, #launch2queue_system, #launch_job_in_folder, #make_environment_file, #read_file, #rm_done_dependencies, select_manager, select_queue_manager, #sort_jobs_by_dependencies, #system_call, system_call, #write_file, #write_job

Constructor Details

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

Returns a new instance of BashManager.



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# File 'lib/autoflow/queue_managers/bash_manager.rb', line 4

def initialize(exec_folder, options, commands, persist_variables)
	super
	@queued = []
	@count = 0
	@pids = {}
	@path2execution_script = File.join(@exec_folder, 'execution.sh') 
	create_file('execution.sh', @exec_folder)
	write_file('execution.sh', '#! /usr/bin/env bash')
end

Class Method Details

.available?(options) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/autoflow/queue_managers/bash_manager.rb', line 44

def self.available?(options)
	return true
end

.priority ⇒ Object 



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# File 'lib/autoflow/queue_managers/bash_manager.rb', line 48

def self.priority
	return 0 
end

Instance Method Details

#get_queue_system_id(shell_output) ⇒ Object 



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# File 'lib/autoflow/queue_managers/bash_manager.rb', line 40

def get_queue_system_id(shell_output)
	return nil
end

#launch_all_jobs ⇒ Object 



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# File 'lib/autoflow/queue_managers/bash_manager.rb', line 14

def launch_all_jobs
	super
	close_file('execution.sh', 0755)
	system_call("#{@path2execution_script} > #{File.join(File.dirname(@path2execution_script),'output')} & ", @exec_folder)
end

#submit_job(job, ar_dependencies) ⇒ Object 



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# File 'lib/autoflow/queue_managers/bash_manager.rb', line 24

def submit_job(job, ar_dependencies)
	write_file('execution.sh','')
	if !ar_dependencies.empty? 
		ar_dependencies.each do |dep|
			cmd = "wait \"$pid#{@pids[dep]}\"\nif [ $? -ne 0 ]\nthen \n\techo \"#{job.name} failed\"\n\texit\nfi"
			write_file('execution.sh', cmd) 
		end
	end
	write_file('execution.sh', "cd #{job.attrib[:exec_folder]}")
	write_file('execution.sh', "./#{job.name}.sh &> task_log & pid#{@count}=$!")
	@pids[job.name] = @count
	@count += 1
	@queued << job.name # For dependencies purposes
	return nil
end

#write_header(id, node, sh) ⇒ Object 



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# File 'lib/autoflow/queue_managers/bash_manager.rb', line 20

def write_header(id, node, sh)
	#@queued << id # For dependencies purposes
end