Module: CodeRunner::Slurm

Included in:
Helios, Stampede
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 53

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
"#!/bin/bash\n#SBATCH -J \#{executable_name}.\#{job_identifier} # jobname\n#SBATCH -N \#{nodes.to_i}        # number of nodes\n#SBATCH -n \#{nprocstot}         # number of tasks\n#SBATCH -o \#{executable_name}.\#{job_identifier}.o%j              # strout filename (%j is jobid)\n#SBATCH -e \#{executable_name}.\#{job_identifier}.e%j               # stderr filename (%j is jobid)\n\#{@project ? \"#SBATCH -A \#@project # project to charge\" : \"\"}\n\#{@queue ? \"#SBATCH -p \#@queue # submission queue\" : \"\"}\n\#{@wall_mins ? \"#SBATCH -t \#{sprintf(\"%02d:%02d:%02d\", hours, mins, secs)} # walltime\" : \"\"}\n\n\#{code_run_environment}\necho \"Submitting \#{nodes}x\#{ppn} job on \#{CodeRunner::SYS} for project \#@project...\"\n\n\n\n"

end

#batch_script_file ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 45

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 89

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 98

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 29

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 106

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 
    @running = true
    if line =~ /\sPD\s/
      return :Queueing
    elsif line =~ /\sR\s/
      return :Running
    elsif line =~ /\sC\s/
      @running = false
      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 49

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

#mpi_prog ⇒ Object 



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# File 'lib/coderunner/system_modules/slurm.rb', line 23

def mpi_prog
 nodes, ppn = @nprocs.split(/x/)
 nprocstot = nodes.to_i * ppn.to_i
  "mpirun -np #{nprocstot}"
end

#output_file ⇒ Object 



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

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
    "#@preamble #{mpi_prog}  #{executable_location}/#{executable_name} #{parameter_string}"
  end
end