Module: CodeRunner::Moab

Includes:
Launcher
Included in:
Archer, Dirac, Edison, Franklin, Hector, Hopper, Iridis, Loki
Defined in:
lib/coderunner/system_modules/moab.rb

Instance Method Summary collapse

Methods included from Launcher

#cancel_job_launcher, #error_file_launcher, #execute_launcher, #launcher_prefix, #output_file_launcher, #queue_status_launcher, #use_launcher

Instance Method Details

#batch_script ⇒ Object 



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

def batch_script
  ppn_checks
  hours, mins, secs = hours_minutes_seconds
"#!/bin/bash --login \n#PBS -N \#{executable_name}.\#{job_identifier}\n#PBS -l mppwidth=\#{nprocstot}\n#PBS -l mppnppn=\#{ppn}\n#PBS -l walltime=\#{sprintf(\"%02d:%02d:%02d\", hours, mins, secs)}\n\#{@project ? \"#PBS -A \#@project\" : \"\"}\n\#{@queue ? \"#PBS -q \#@queue\" : \"\"}\n\n### start of jobscript \ncd $PBS_O_WORKDIR \necho \"workdir: $PBS_O_WORKDIR\" \n\#{code_run_environment}\n\necho \"Submitting \#{nodes}x\#{ppn} job on \#{CodeRunner::SYS} for project \#@project...\"\n"
end

#batch_script_file ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 61

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

#cancel_job ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 106

def cancel_job
  use_launcher ? cancel_job_launcher : `qdel #{@job_no}`
end

#error_file ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 110

def error_file
  use_launcher ? error_file_launcher :
    "#{executable_name}.#{job_identifier}.e#@job_no"
end

#execute ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 52

def execute
  if use_launcher
     return execute_launcher
  else
    File.open(batch_script_file, 'w'){|file| file.puts batch_script + run_command + "\n"}
    _pid = %x[qsub #{batch_script_file}].to_i
  end
end

#get_run_status(job_no, current_status) ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 120

def get_run_status(job_no, current_status)
  if use_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 =~ /\sH\s/
      return :Queueing
    elsif line =~ /\sC\s/
      @running=false
      return :Unknown
    else
      ep 'line', line
      raise 'Could not get run status'
    end
  end
end

#hours_minutes_seconds ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 69

def hours_minutes_seconds
  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
  else
    raise "Please specify wall mins using the W flag"
  end
  eputs "Allotted wall time is " + sprintf("%02d:%02d:%02d", hours, mins, secs)
  return [hours, mins, secs]
end

#max_ppn ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 65

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

#mpi_prog ⇒ Object 



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

def mpi_prog
  "aprun -n #{nprocstot} -N #{ppn}"
end

#nodes ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 29

def nodes
  nodes, _ppn = @nprocs.split(/:/)[0].split(/x/)
  nodes.to_i
end

#nprocstot ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 37

def nprocstot
  
    #nodes, ppn = @nprocs.split(/x/)
    _nprocstot = nodes.to_i * ppn.to_i
end

#output_file ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 115

def output_file
  use_launcher ? output_file_launcher :
    "#{executable_name}.#{job_identifier}.o#@job_no"
end

#ppn ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 33

def ppn
    _nodes, ppn = @nprocs.split(/:/)[0].split(/x/)
    ppn.to_i
end

#ppn_checks ⇒ Object 



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# File 'lib/coderunner/system_modules/moab.rb', line 81

def ppn_checks
  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
end

#queue_status ⇒ Object

Kernel.change_environment_with_shell_script(conf) end



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# File 'lib/coderunner/system_modules/moab.rb', line 17

def queue_status
  if use_launcher
     queue_status_launcher
  else
    %x[qstat | grep $USER]
  end
end

#run_command ⇒ Object 



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

def run_command
#     "qsub #{batch_script_file}"
  if use_launcher
    return %[#{code_run_environment}
      #{mpi_prog} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
  else
    "#{mpi_prog}  #{executable_location}/#{executable_name} #{parameter_string}"
  end
end