Module: Marenostrum::SLURM

Defined in:
lib/rbbt/hpc.rb

Constant Summary collapse

TEMPLATE = 
<<-EOF


EOF

Class Method Summary collapse

Class Method Details

.done?(id, options = {}) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/hpc.rb', line 73

def self.done?(id, options = {})
  ! query(id, options).include? id
end

.gather(id, file = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc.rb', line 77

def self.gather(id, file = nil, options = {})
  key_file, user, workdir, output = options.values_at :key_file, :user, :workdir, :output

  TmpFile.with_file do |result|

    begin
      cmd = "scp -i #{key_file} #{ user }@#{ SERVER }:'#{workdir}/#{output}' '#{ result }' " 
      Log.debug cmd
      CMD.cmd(cmd)
      if file.nil?
        Open.read(result)
      else
        Misc.sensiblewrite(result, file)
      end
    rescue
      raise "Could not gather job: #{ id }: " << $!.message
    end
  end
end

.issue(cmd, name = nil, time = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc.rb', line 11

def self.issue(cmd, name = nil, time = nil, options = {})
  name = "rbbt-job-" << rand(10000).to_s if name.nil?
  time = "00:00:10" if time.nil?
  workdir = "rbbt-workdir/" << name

  new_options = Misc.add_defaults options, "job-name" => name, "workdir" => workdir,
    "output" => "log", 
    "error" => "log.err", 
    "ntasks" => "1", 
    "time" => time.to_s,
    "user" => ENV["USER"],
    "key_file" => File.join(ENV['HOME'], '.ssh/id_rsa.pub')

  options.merge!(new_options)
  IndiferentHash.setup(options)

  key_file, user = options.values_at :key_file, :user

  template = <<-EOF
#!/bin/bash
#{options.collect do |name,value|
  next if name == 'user'
  next if name == 'key_file'
name = "--" << name.to_s.sub(/^--/,'')
[name, '"' << value << '"'] * "="
  end.compact.collect{|str| "#SBATCH #{str}"} * "\n"
}
#{ cmd }
  EOF

  TmpFile.with_file do |slurm|
    res = nil
    begin
      Open.write(slurm, template)
      Log.medium("Issuing job:\n" + template)

      cmd = "ssh -i #{key_file} #{ user }@#{ SERVER } mkdir -p '#{ workdir }'; scp -i #{key_file} #{ slurm } #{ user }@#{ SERVER }:'#{ workdir }/#{ name }.slurm'; ssh -i #{key_file} #{ user }@#{ SERVER } sbatch #{ workdir }/#{ name }.slurm"
      Log.debug cmd
      res = CMD.cmd(cmd).read
    rescue
      raise "Could not issue job"
    end

    res.scan(/\d+/).first
  end
end

.query(id, options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc.rb', line 58

def self.query(id, options = {})
  key_file, user = options.values_at :key_file, :user

  res = nil
  begin
    cmd = "ssh -i #{key_file} #{ user }@#{ SERVER } squeue |grep '#{id}\\|JOBID'"
    Log.debug cmd
    res = CMD.cmd(cmd).read
  rescue
    raise "Could not query job: #{ id }" << $!.message
  end

  res
end

.run(cmd, name = nil, time = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc.rb', line 97

def self.run(cmd, name = nil, time = nil, options = {})
  sleep_time = Misc.process_options options, :sleep

  id = issue(cmd, name, time, options)

  if sleep_time.nil?
    times = [1,2,3,5,10,30]
  else
    times = Array ===  sleep_time ? sleep_time.dup : [sleep_time]
  end

  while not done?(id, options)
    Log.debug "Waiting on #{ id }"
    sleep_time = times.shift || sleep_time
    sleep sleep_time
  end

  gather(id, nil, options)
end