Class: WorkflowManager::LocalComputer

Inherits:
Cluster
  • Object
show all
Defined in:
lib/workflow_manager/cluster.rb

Instance Attribute Summary

Attributes inherited from Cluster

#log_dir, #name, #options

Instance Method Summary collapse

Methods inherited from Cluster

#generate_new_job_script, #initialize

Constructor Details

This class inherits a constructor from WorkflowManager::Cluster

Instance Method Details

#copy_commands(org_dir, dest_parent_dir) ⇒ Object 



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# File 'lib/workflow_manager/cluster.rb', line 70

def copy_commands(org_dir, dest_parent_dir)
  commands = []
  commands << "mkdir -p #{dest_parent_dir}"
  commands << "cp -r #{org_dir} #{dest_parent_dir}"
  commands
end

#delete_command(target) ⇒ Object 



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# File 'lib/workflow_manager/cluster.rb', line 79

def delete_command(target)
  command = "rm -rf #{target}"
end

#job_ends?(log_file) ⇒ Boolean 



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# File 'lib/workflow_manager/cluster.rb', line 65

def job_ends?(log_file)
  command = "tail -n 20 #{log_file}|grep '__SCRIPT END__'"
  result = `#{command}`
  result.to_s.empty? ? false : true
end

#job_running?(pid) ⇒ Boolean 



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# File 'lib/workflow_manager/cluster.rb', line 50

def job_running?(pid)
  command = "ps aux"
  result = IO.popen(command) do |io|
    flag = false
    while line=io.gets
      x = line.split
      if x[1].to_i == pid.to_i
        flag = true
        break
      end
    end
    flag
  end
  result
end

#kill_command(job_id) ⇒ Object 



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# File 'lib/workflow_manager/cluster.rb', line 76

def kill_command(job_id)
  command = "kill #{job_id}"
end

#submit_job(script_file, script_content, option = '') ⇒ Object 



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# File 'lib/workflow_manager/cluster.rb', line 38

def submit_job(script_file, script_content, option='')
  if script_name = File.basename(script_file) and script_name =~ /\.sh$/
    new_job_script = generate_new_job_script(script_name, script_content)
    new_job_script_base = File.basename(new_job_script)
    log_file = File.join(@log_dir, new_job_script_base + "_o.log")
    err_file = File.join(@log_dir, new_job_script_base + "_e.log")
    command = "bash #{new_job_script} 1> #{log_file} 2> #{err_file}"
    pid = spawn(command)
    Process.detach(pid)
    [pid.to_s, log_file, command]
  end
end