Class: SlurmManager2

Inherits:
QueueManager show all
Defined in:
lib/autoflow/queue_managers/slurm2_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, #initialize, #launch2queue_system, #launch_all_jobs, #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

This class inherits a constructor from QueueManager

Class Method Details

.available?(options) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/autoflow/queue_managers/slurm2_manager.rb', line 52

def self.available?(options)
	available = false
	shell_output = system_call("type 'sbatch'", nil, options[:remote], options[:ssh])
	if !shell_output.empty?
		shell_output = system_call("sbatch --version", nil, options[:remote], options[:ssh])
		slurm_version = shell_output.split(' ').last.split('.').first.to_i # "slurm 17.11.4"
		available = true if slurm_version >= 20
	end
	return available
end

.priority ⇒ Object 



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# File 'lib/autoflow/queue_managers/slurm2_manager.rb', line 63

def self.priority
	return 100 
end

Instance Method Details

#get_queue_system_id(shell_output) ⇒ Object 



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# File 'lib/autoflow/queue_managers/slurm2_manager.rb', line 43

def get_queue_system_id(shell_output)
	queue_id = nil
	shell_output.chomp!
	shell_output =~ /Submitted batch job (\d+)/
	queue_id = $1
	raise("A queue id cannot be obtained. The queue manager has given this message:#{shell_output}") if queue_id.nil?
	return queue_id
end

#parse_additional_options(string, attribs) ⇒ Object

SLURM 20 or greater



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# File 'lib/autoflow/queue_managers/slurm2_manager.rb', line 4

def parse_additional_options(string, attribs)
	expresions = %w[%C %T %M %N ]
	values = [attribs[:cpu], attribs[:time], attribs[:mem], attribs[:node]]
	new_string = string.dup
	expresions.each_with_index do |exp, i|
		new_string.gsub!(exp, "#{values[i]}")
	end
	return new_string
end

#submit_job(job, ar_dependencies) ⇒ Object 



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# File 'lib/autoflow/queue_managers/slurm2_manager.rb', line 33

def submit_job(job, ar_dependencies)
	final_dep = get_all_deps(ar_dependencies)
	dependencies = nil
	dependencies='--dependency=afterok:'+final_dep.join(':') if !final_dep.empty?  
	cmd = "sbatch #{dependencies} #{job.name}.sh"
	STDOUT.puts cmd if @show_submit
	queue_id = get_queue_system_id(system_call(cmd, job.attrib[:exec_folder]))
	return queue_id
end

#write_header(id, job, sh_name) ⇒ Object 



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# File 'lib/autoflow/queue_managers/slurm2_manager.rb', line 14

def write_header(id, job, sh_name)
	if !job.attrib[:ntask]
		write_file(sh_name, "#SBATCH --cpus-per-task=#{job.attrib[:cpu]}")
	else
		write_file(sh_name, "#SBATCH --ntasks=#{job.attrib[:cpu]}")
		write_file(sh_name, "#SBATCH --nodes=#{job.attrib[:multinode]}") if job.attrib[:multinode] > 0
	end
	write_file(sh_name,	"#SBATCH --mem=#{job.attrib[:mem]}")
	write_file(sh_name, "#SBATCH --time=#{job.attrib[:time]}")
	write_file(sh_name,	"#SBATCH --constraint=#{job.attrib[:node]}") if !job.attrib[:node].nil?
	write_file(sh_name, '#SBATCH --error=job.%J.err')
	write_file(sh_name, '#SBATCH --output=job.%J.out')
	write_file(sh_name, "#SBATCH --#{job.attrib[:additional_job_options][0]}=#{parse_additional_options(job.attrib[:additional_job_options][1], job.attrib)}") if !job.attrib[:additional_job_options].nil?
	if job.attrib[:ntask]
		write_file(sh_name, 'srun hostname -s > workers') if job.attrib[:cpu_asign] == 'list'
	end
end