Class: WorkflowManager::FGCZCluster

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

Direct Known Subclasses

FGCZCourseCluster

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 121

def copy_commands(org_dir, dest_parent_dir)
  commands = ["g-req -w copy #{org_dir} #{dest_parent_dir}"]
end

#delete_command(target) ⇒ Object 



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# File 'lib/workflow_manager/cluster.rb', line 127

def delete_command(target)
  command = "g-req remove #{target}"
end

#job_ends?(log_file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/workflow_manager/cluster.rb', line 109

def job_ends?(log_file)
  log_flag = false
  IO.popen("tail -n 10 #{log_file}") do |io|
    while line=io.gets
      if line =~ /__SCRIPT END__/
        log_flag = true
        break
      end
    end
  end
  log_flag
end

#job_running?(job_id) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/workflow_manager/cluster.rb', line 97

def job_running?(job_id)
 qstat_flag = false
  IO.popen('qstat -u "*"') do |io|
    while line=io.gets
      if line =~ /#{job_id}/
        qstat_flag = true
        break
      end
    end
  end
  qstat_flag
end

#kill_command(job_id) ⇒ Object 



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# File 'lib/workflow_manager/cluster.rb', line 124

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

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



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# File 'lib/workflow_manager/cluster.rb', line 85

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 = "g-sub -o #{log_file} -e #{err_file} #{option} #{new_job_script}"
    job_id = `#{command}`
    job_id = job_id.match(/Your job (\d+) \(/)[1]
    [job_id, log_file, command]
  end
end