submit_old

#!/usr/bin/env ruby

require 'optparse'
require 'shellwords'

options = {}

OptionParser.new do |option_parser|
  option_parser.set_banner <<-BANNER
A Ruby script to automate the generation and submission of qsub scripts

Usage:
  submit [-k] [-j NAME] [-n N] [-p P] [-w HH:MM:SS] working_directory executable
  submit -h/--help

  BANNER

  option_parser.version = 1
  option_parser.release = 9
  option_parser.set_summary_indent("  ")

  options[:keep_script] = false
  option_parser.on('-k', '--keep-script', 'Retain the generated qsub script (default is to discard it)') do
    options[:keep_script] = true
  end

  options[:job_name] = 'pbs_job'
  option_parser.on('-j', '--job-name NAME', "Identify job as NAME in the PBS job queue (default: #{options[:job_name]})") do |name|
    options[:job_name] = name
  end

  options[:nodes] = 1
  option_parser.on('-n', '--nodes N', Integer, "Use N nodes (default: #{options[:nodes]})") do |n|
    options[:nodes] = n
  end

  options[:ppn] = 4
  option_parser.on('-p', '--processors P', Integer, "Use P processors per node (default: #{options[:ppn]})") do |ppn|
    options[:ppn] = ppn
  end

  options[:walltime] = '20:00'
  option_parser.on('-w', '--walltime MAXRUNTIME', "Run for at most this long [[HH:]MM:]SS (default: #{options[:walltime]})") do |walltime_string|
    seconds, minutes, hours = walltime_string.split(':').reverse.map { |string| string.to_i.abs }
    [minutes, seconds].compact.map! { |int| [59, int].min }
    options[:walltime] = [hours, minutes, seconds].compact.map { |int| int.to_s.rjust(2, '0') }.join(':')
  end

  option_parser.on_tail('-h', '--help', 'Show this help content') do
    puts option_parser
    exit
  end

  option_parser.on_tail('-v', '--version', 'Show version information') do
    puts OptionParser::Version.join('.')
    exit
  end
end.parse!

fail ArgumentError, "wrong number of arguments (#{ARGV.length} for 2)" if ARGV.length != 2
working_directory = Dir.new(ARGV[0])
executable = File.basename(ARGV[1], '.*').gsub(/\s/, '_')
submit_script = File.new("submit_#{executable}.sh", 'w')
original_working_directory = Dir.pwd
Dir.chdir(working_directory.path)

submit_script.write(<<-BATCH)
#!/bin/bash

#PBS -q batch
#PBS -N #{options[:job_name]}
#PBS -r n
#PBS -k oe
#PBS -l nodes=#{options[:nodes]}:ppn=#{options[:ppn]},walltime=#{options[:walltime]}

echo PBS working directory: $PBS_O_WORKDIR
echo Running host: "$(hostname)"
echo Current time: "$(date)"
echo Working directory before cd: "$(pwd)"
cd #{Dir.pwd.shellescape}
echo Working directory after cd: "$(pwd)"
mpiexec -hostfile $PBS_NODEFILE -np #{options[:nodes] * options[:ppn]} #{executable} > #{executable}_output.txt
BATCH

Dir.chdir original_working_directory
submit_script.close
puts `qsub #{submit_script.path}`
File.delete(submit_script.path) unless options[:keep_script]