Module: CodeRunner::Juropa

Defined in:
lib/coderunner/system_modules/juropa.rb

Overview

System module for Juropa and HPC-FF

Instance Method Summary collapse

Instance Method Details

#batch_script ⇒ Object 



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

def batch_script
  nodes, ppn = @nprocs.split(/x/)
  ppn ||= 8
  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)
"#!/bin/bash -x \n#MSUB -l nodes=\#{nodes}:ppn=\#{ppn} \n#MSUB -N \#{executable_name}.\#{job_identifier}\n\#{@wall_mins ? \"#MSUB -l walltime=\#{sprintf(\"%02d:%02d:%02d\", hours, mins, secs)}\" : \"\"}\n\n### start of jobscript \ncd $PBS_O_WORKDIR \necho \"workdir: $PBS_O_WORKDIR\" \nNSLOTS=\#{nodes.to_i * ppn.to_i} \necho \"running on $NSLOTS cpus ...\" \n\n"

#MSUB -e #{Dir.pwd}/#{error_file} 
#      if keyword omitted : default is submitting directory  
#MSUB -o #{Dir.pwd}/#{output_file}
#       if keyword omitted : default is submitting directory 
end

#batch_script_file ⇒ Object 



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

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

#cancel_job ⇒ Object 



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# File 'lib/coderunner/system_modules/juropa.rb', line 80

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
    `canceljob #{@job_no}`
  end
end

#error_file ⇒ Object 



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# File 'lib/coderunner/system_modules/juropa.rb', line 89

def error_file
  #For backwards compatibility
  return "#{executable_name}.sh.e" if kind_of? CodeRunner::Run and [:Completed, :Failed].include? @status
  return "#{executable_name}.#{job_identifier}.e#@job_no"
end

#execute ⇒ Object 



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# File 'lib/coderunner/system_modules/juropa.rb', line 25

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"}
    jn = %x[msub #{batch_script_file}].scan(/(\d+)\s*\Z/).flatten
    if jn[0]
       return jn[0].to_i
     else
       return nil
     end
  end
end

#get_run_status(job_no, current_status) ⇒ Object 



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# File 'lib/coderunner/system_modules/juropa.rb', line 100

def get_run_status(job_no, current_status)
  if ENV['CODE_RUNNER_LAUNCHER']
    return :Unknown
  end
  line = current_status.split(/\n/).grep(Regexp.new(job_no.to_s))[0]
  unless line
    return :Unknown
  else 
    if line =~ /\sQ\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

#output_file ⇒ Object 



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# File 'lib/coderunner/system_modules/juropa.rb', line 95

def output_file
  return "#{executable_name}.sh.o" if kind_of? CodeRunner::Run and [:Completed, :Failed].include? @status
  return "#{executable_name}.#{job_identifier}.o#@job_no"
end

#queue_status ⇒ Object 



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# File 'lib/coderunner/system_modules/juropa.rb', line 7

def queue_status
  if prefix = ENV['CODE_RUNNER_LAUNCHER']
    %x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status.txt]  +
    %x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status2.txt] 
  else
    %x[qstat | grep $USER]
  end
end

#run_command ⇒ Object 



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# File 'lib/coderunner/system_modules/juropa.rb', line 16

def run_command
#   "msub #{batch_script_file}"
  if ENV['CODE_RUNNER_LAUNCHER']
    return %[mpiexec -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
  else
    "mpiexec -np $NSLOTS #{executable_location}/#{executable_name} #{parameter_string}"
  end
end