Module: CodeRunner::Slurm

Included in:
Helios
Defined in:
lib/coderunner/system_modules/slurm.rb

Overview

A module to let CodeRunner run using the SLURM queue system, used on certain HPC systems.

Instance Method Summary collapse

Instance Method Details

#batch_script ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 50

def batch_script

	nodes, ppn = @nprocs.split(/x/)
	eputs "Warning: Underuse of nodes (#{ppn} cores per node instead of #{max_ppn})" if ppn.to_i < max_ppn 
	raise "Error: cores per node cannot excede #{max_ppn}" if ppn.to_i > max_ppn
#		raise "Error: project (i.e. budget) not specified" unless @project
	ppn ||= max_ppn
	raise "Please specify wall minutes" unless @wall_mins
	if @wall_mins
		ep @wall_mins
		hours = (@wall_mins / 60).floor
		mins = @wall_mins.to_i % 60
		secs = ((@wall_mins - @wall_mins.to_i) * 60).to_i
	end
	eputs "Allotted wall time is " + sprintf("%02d:%02d:%02d", hours, mins, secs)
	nprocstot = nodes.to_i * ppn.to_i
<<EOF
#!/bin/bash
#SBATCH -J #{executable_name}.#{job_identifier} # jobname
#SBATCH -N #{nodes.to_i}        # number of nodes
#SBATCH -n #{nprocstot}         # number of tasks
#SBATCH -o #{executable_name}.#{job_identifier}.o%j              # strout filename (%j is jobid)
#SBATCH -e #{executable_name}.#{job_identifier}.e%j               # stderr filename (%j is jobid)
#{@project ? "#SBATCH -A #@project # project to charge" : ""}
#{@wall_mins ? "#SBATCH -t #{sprintf("%02d:%02d:%02d", hours, mins, secs)} # walltime" : ""}

#{code_run_environment}
echo "Submitting #{nodes}x#{ppn} job on #{CodeRunner::SYS} for project #@project..."



EOF

end

#batch_script_file ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 42

def batch_script_file
	"#{executable_name}.#{job_identifier}.sh"
end

#cancel_job ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 85

def cancel_job
	if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false)
		 fname = ENV['HOME'] + "/.coderunner_to_launch_#{prefix}/#{$$}.stop"
		 File.open(fname, 'w'){|file| file.puts "\n"}
	else
		`scancel #{@job_no}`
	end
end

#error_file ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 94

def error_file
	return "#{executable_name}.#{job_identifier}.e#@job_no"
end

#execute ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 26

def execute
	if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false)
		launch_id = "#{Time.now.to_i}#{$$}"
		fname = ENV['HOME'] + "/.coderunner_to_launch_#{prefix}/#{launch_id}"
		File.open(fname + '.start', 'w'){|file| file.puts "cd #{Dir.pwd};#{run_command}"}
		sleep 1 until FileTest.exist? fname + '.pid'
		pid = File.read(fname + '.pid').to_i
		FileUtils.rm fname + '.pid'
		return pid
	else
		File.open(batch_script_file, 'w'){|file| file.puts batch_script + run_command + "\n"}
		pid = %x[sbatch #{batch_script_file}].to_i
		return nil
	end
end

#get_run_status(job_no, current_status) ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 102

def get_run_status(job_no, current_status)
	if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false)
		return :Unknown
	end
	line = current_status.split(/\n/).grep(Regexp.new(job_no.to_s))[0]
	unless line
		return :Unknown
	else 
		if line =~ /\sPD\s/
			return :Queueing
		elsif line =~ /\sR\s/
			return :Running
		elsif line =~ /\sC\s/
			return :Unknown
		else
			ep 'line', line
			raise 'Could not get run status'
		end
	end
end

#max_ppn ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 46

def max_ppn
	raise "Please define max_ppn for your system"
end

#output_file ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 98

def output_file
	return "#{executable_name}.#{job_identifier}.o#@job_no"
end

#queue_status ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 6

def queue_status
	if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false)
		%x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status.txt]  +
		%x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status2.txt] 
	else
		%x[squeue | grep #{ENV['USER'][0..7]}]
	end
end

#run_command ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 15

def run_command
# 		"qsub #{batch_script_file}"
	if (ENV['CODE_RUNNER_LAUNCHER'].size > 0 rescue false)
		return %[mpiexec -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
	else
		nodes, ppn = @nprocs.split(/x/)
		nprocstot = nodes.to_i * ppn.to_i
		"mpirun -np #{nprocstot}  #{executable_location}/#{executable_name} #{parameter_string}"
	end
end