module MiGA::Cli::Action::Init::DaemonHelper

Helper module with daemon configuration functions for MiGA::Cli::Action::Init

Public Instance Methods

configure_bash_daemon(v) click to toggle source
# File lib/miga/cli/action/init/daemon_helper.rb, line 34
def configure_bash_daemon(v)
  v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '2').to_i
  v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '6').to_i
  v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
  v[:nodelist] = nil # <- To enable non-default with default SSH
  cli.puts 'Setting up internal daemon defaults.'
  cli.puts 'If you don\t understand this just leave default values:'
  v[:cmd] = cli.ask_user(
    "How should I launch tasks?\n"          "  {{variables}}: script, vars, cpus, log, task_name, miga\n ",
    "{{vars}} {{miga}} run -r '{{script}}' -l '{{log}}' -e"
  )
  v[:var] = cli.ask_user(
    "How should I pass variables?\n"          "  {{variables}}: key, value\n ",
    "{{key}}={{value}}"
  )
  v[:varsep]  = cli.ask_user('What should I use to separate variables?', ' ')
  v[:alive]   = cli.ask_user(
    "How can I know that a process is still alive?\n"          "  Output should be 1 for running and 0 for non-running\n"          "  {{variables}}: pid\n ",
    "ps -p '{{pid}}' | tail -n +2 | wc -l"
  )
  v[:kill] = cli.ask_user(
    "How should I terminate tasks?\n"          "  {{variables}}: pid\n ",
    "kill -9 '{{pid}}'"
  )
  v
end
configure_daemon() click to toggle source
# File lib/miga/cli/action/init/daemon_helper.rb, line 6
def configure_daemon
  cli.puts 'Default daemon configuration:'
  daemon_f = File.expand_path('.miga_daemon.json', ENV['MIGA_HOME'])
  unless File.exist?(daemon_f) and cli.ask_user(
    'A template daemon already exists, do you want to preserve it?',
    'yes', %w(yes no)
  ) == 'yes'
    v = { created: Time.now.to_s, updated: Time.now.to_s }
    v[:type] = cli.ask_user(
      'Please select the type of daemon you want to setup',
      cli[:dtype], %w(bash ssh qsub msub slurm)
    )
    case v[:type]
    when 'bash'
      v = configure_bash_daemon(v)
    when 'ssh'
      v = configure_ssh_daemon(v)
    when 'slurm'
      v = configure_slurm_daemon(v)
    else # [qm]sub
      v = configure_qsub_msub_daemon(v)
    end
    v[:format_version] = 1
    File.open(daemon_f, 'w') { |fh| fh.puts JSON.pretty_generate(v) }
  end
  cli.puts ''
end
configure_qsub_msub_daemon(v) click to toggle source
# File lib/miga/cli/action/init/daemon_helper.rb, line 138
def configure_qsub_msub_daemon(v)
  flavor      = v[:type] == 'msub' ? 'msub' :
                cli.ask_user('Select qsub flavor', 'torque', %w[torque sge])
  queue       = cli.ask_user('What queue should I use?', nil, nil, true)
  v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
  v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
  v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
  v[:nodelist] = nil # <- To enable non-default with default SSH
  cli.puts 'Setting up internal daemon defaults.'
  cli.puts 'If you don\t understand this just leave default values:'
  if flavor == 'sge'
    v[:cmd] = cli.ask_user(
      "How should I launch tasks?\n"            "  {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
      "#{v[:type]} -q '#{queue}' -v '{{vars}}' -pe openmp {{cpus}} "            "-j y -o '{{log}}' -N '{{task_name_simple}}' -l h_vmem=9g "            "-l h_rt=12:00:00 '{{script}}' | grep . "            "| perl -pe 's/^Your job (\\S+) .*/$1/'"
    )
  else
    v[:cmd] = cli.ask_user(
      "How should I launch tasks?\n"            "  {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
      "#{v[:type]} -q '#{queue}' -v '{{vars}}' -l nodes=1:ppn={{cpus}} "            "-j oe -o '{{log}}' -N '{{task_name}}' -l mem=9g "            "-l walltime=12:00:00 '{{script}}' | grep ."
    )
  end
  v[:var] = cli.ask_user(
    "How should I pass variables?\n"          "  {{variables}}: key, value\n ",
    "{{key}}={{value}}"
  )
  v[:varsep] = cli.ask_user(
    'What should I use to separate variables?', ','
  )
  if v[:type] == 'qsub'
    if flavor == 'sge'
      v[:alive] = cli.ask_user(
        "How can I know that a process is still alive?\n"              "  Output should be 1 for running and 0 for non-running\n"              "  {{variables}}: pid\n ",
        "qstat -j '{{pid}}' -s pr 2>/dev/null | head -n 1 | wc -l "              "| awk '{print $1}'"
      )
    else
      v[:alive] = cli.ask_user(
        "How can I know that a process is still alive?\n"              "  Output should be 1 for running and 0 for non-running\n"              "  {{variables}}: pid\n ",
        "qstat -f '{{pid}}' | grep ' job_state =' | perl -pe 's/.*= //' "              "| grep '[^C]' | tail -n 1 | wc -l | awk '{print $1}'"
      )
    end
    v[:kill] = cli.ask_user(
      "How should I terminate tasks?\n"            "  {{variables}}: pid\n ",
      "qdel '{{pid}}'"
    )
  else # msub
    v[:alive] = cli.ask_user(
      "How can I know that a process is still alive?\n"            "  Output should be 1 for running and 0 for non-running\n"            "  {{variables}}: pid\n ",
      "checkjob '{{pid}}'|grep '^State:' | perl -pe 's/.*: //' "            "| grep 'Deferred\\|Hold\\|Idle\\|Starting\\|Running\\|Blocked'"            "| tail -n 1 | wc -l | awk '{print $1}'"
    )
    v[:kill] = cli.ask_user(
      "How should I terminate tasks?\n"            "  {{variables}}: pid\n ",
      "canceljob '{{pid}}'"
    )
  end
  v
end
configure_slurm_daemon(v) click to toggle source
# File lib/miga/cli/action/init/daemon_helper.rb, line 99
def configure_slurm_daemon(v)
  queue       = cli.ask_user('What queue should I use?', nil, nil, true)
  v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
  v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
  v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
  v[:nodelist] = nil # <- To enable non-default with default SSH
  cli.puts 'Setting up internal daemon defaults'
  cli.puts 'If you don\t understand this just leave default values:'
  v[:cmd] = cli.ask_user(
    "How should I launch tasks?\n"          "  {{variables}}: script, vars, cpus, log, task_name, miga\n ",
    "{{vars}} sbatch --partition='#{queue}' --export=ALL "          "--nodes=1 --ntasks-per-node={{cpus}} --output='{{log}}' "          "--job-name='{{task_name}}' --mem=9G --time=12:00:00 {{script}} "          "| perl -pe 's/.* //'"
  )
  v[:var] = cli.ask_user(
    "How should I pass variables?\n"          "  {{variables}}: key, value\n ",
    "{{key}}={{value}}"
  )
  v[:varsep] = cli.ask_user(
    'What should I use to separate variables?', ' '
  )
  v[:alive] = cli.ask_user(
    "How can I know that a process is still alive?\n"          "  Output should be 1 for running and 0 for non-running\n"          "  {{variables}}: pid\n ",
    "squeue -h -o %t -j '{{pid}}' | grep '^PD\\|R\\|CF\\|CG$' "          "| tail -n 1 | wc -l"
  )
  v[:kill] = cli.ask_user(
    "How should I terminate tasks?\n"          "  {{variables}}: pid\n ",
    "scancel '{{pid}}'"
  )
  v
end
configure_ssh_daemon(v) click to toggle source
# File lib/miga/cli/action/init/daemon_helper.rb, line 66
def configure_ssh_daemon(v)
  v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '3').to_i
  v[:nodelist] = cli.ask_user(
    'What environmental variable points to node list?', '$MIGA_NODELIST'
  )
  v[:ppn] = cli.ask_user('How many CPUs can I use per job?', '2').to_i
  cli.puts 'Setting up internal daemon defaults.'
  cli.puts 'If you don\t understand this just leave default values:'
  v[:cmd] = cli.ask_user(
    "How should I launch tasks?\n"          "  {{variables}}: script, vars, cpus, log, task_name, miga, host\n ",
    "{{vars}} {{miga}} run -r '{{script}}' -l '{{log}}' -R {{host}} -e"
  )
  v[:var] = cli.ask_user(
    "How should I pass variables?\n"          "  {{variables}}: key, value\n ",
    "{{key}}={{value}}"
  )
  v[:varsep]  = cli.ask_user('What should I use to separate variables?', ' ')
  v[:alive]   = cli.ask_user(
    "How can I know that a process is still alive?\n"          "  Output should be 1 for running and 0 for non-running\n"          "  {{variables}}: pid\n ",
    "ps -p '{{pid}}' | tail -n +2 | wc -l"
  )
  v[:kill] = cli.ask_user(
    "How should I terminate tasks?\n"          "  {{variables}}: pid\n ",
    "kill -9 '{{pid}}'"
  )
  v
end