Class: TORQUE::Qsub

Inherits:
Object
  • Object
show all
Defined in:
lib/torque_rm/qsub.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}, &block) ⇒ Qsub

Returns a new instance of Qsub.



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# File 'lib/torque_rm/qsub.rb', line 80

def initialize(opts={}, &block)
  @id = nil # configure when the job is submitted
@a =opts[:a] || opts[:date_time]
@A = opts[:A] || opts[:account]
@b = opts[:b]
@c = validate_checkpoint(opts[:c] || opts[:checkpoint])
@C = opts[:C] || opts[:directive_prefix]
@d = opts[:d] || opts[:working_directory] # PBS_O_INITDIR
@D = opts[:D] || opts[:root_directory] # PBS_O_ROOTDIR
@e = opts[:e] || opts[:stderr] # [hostname:]path_name
@f = opts[:f] || opts[:fault_tolerant] # boolean
@h = opts[:h] || opts[:user_hold] # boolean
@I = opts[:I] || opts[:interactive]
@j = opts[:j] || opts[:join_stdout_stderr]  		
@k = validate_keep(opts) # check manual because I'm not going to implement this now.
@l = opts[:l]
@nodes = opts[:nodes]
@walltime = opts[:walltime]
@gres = opts[:gres]
@ppn = opts[:ppn]
@procs = opts[:procs]
@m = validate_mail_options(opts)
@M = opts[:M] || opts[:email]
@N = opts[:N] || opts[:name]
@o = opts[:o] || opts[:stdout] # [hostname:]path_name
@p = validate_priority(opts) # between -1024, +1023
@P = opts[:P] || opts[:root_as_user]
@q = opts[:q] || opts[:queue]
@r = opts[:r] || opts[:rerunnable] # y|n
@S = opts[:S] || opts[:shell]
@t = opts[:t] || opts[:array_request]
@u = opts[:u] || opts[:user_list]
@v = opts[:v] || opts[:variable_list]
@V = opts[:V] || opts[:exports] #this is just a boolean 
@W = opts[:W] || opts[:additional_attributes] # to DEVELOP, chaining jobs together.
@X = opts[:X] || opts[:X_forwardning] # boolean
@z = opts[:z] || opts[:no_jobid]
@script = opts[:script]
  if block_given?
    if block.arity == 1
      yield self
    end
  end

end

Instance Attribute Details

#a ⇒ Object Also known as: when

Returns the value of attribute a.



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# File 'lib/torque_rm/qsub.rb', line 18

def a
  @a
end

#A ⇒ Object Also known as: account

Returns the value of attribute A.



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# File 'lib/torque_rm/qsub.rb', line 18

def A
  @A
end

#b ⇒ Object

Returns the value of attribute b.



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# File 'lib/torque_rm/qsub.rb', line 18

def b
  @b
end

#c ⇒ Object Also known as: checkpoint

Returns the value of attribute c.



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# File 'lib/torque_rm/qsub.rb', line 18

def c
  @c
end

#C ⇒ Object

Returns the value of attribute C.



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# File 'lib/torque_rm/qsub.rb', line 18

def C
  @C
end

#d ⇒ Object Also known as: wd, working_directory

Returns the value of attribute d.



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# File 'lib/torque_rm/qsub.rb', line 18

def d
  @d
end

#D ⇒ Object Also known as: root_directory

Returns the value of attribute D.



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# File 'lib/torque_rm/qsub.rb', line 18

def D
  @D
end

#e ⇒ Object Also known as: stderr

Returns the value of attribute e.



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# File 'lib/torque_rm/qsub.rb', line 18

def e
  @e
end

#f ⇒ Object

Returns the value of attribute f.



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# File 'lib/torque_rm/qsub.rb', line 18

def f
  @f
end

#gres ⇒ Object

Returns the value of attribute gres.



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# File 'lib/torque_rm/qsub.rb', line 20

def gres
  @gres
end

#h ⇒ Object

Returns the value of attribute h.



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# File 'lib/torque_rm/qsub.rb', line 18

def h
  @h
end

#I ⇒ Object

Returns the value of attribute I.



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# File 'lib/torque_rm/qsub.rb', line 18

def I
  @I
end

#id ⇒ Object

Returns the value of attribute id.



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# File 'lib/torque_rm/qsub.rb', line 21

def id
  @id
end

#j ⇒ Object

Returns the value of attribute j.



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# File 'lib/torque_rm/qsub.rb', line 18

def j
  @j
end

#k ⇒ Object

Returns the value of attribute k.



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# File 'lib/torque_rm/qsub.rb', line 18

def k
  @k
end

#l ⇒ Object

config



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# File 'lib/torque_rm/qsub.rb', line 137

def l
  @l
end

#m ⇒ Object

Returns the value of attribute m.



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# File 'lib/torque_rm/qsub.rb', line 19

def m
  @m
end

#M ⇒ Object Also known as: email

Returns the value of attribute M.



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# File 'lib/torque_rm/qsub.rb', line 19

def M
  @M
end

#N ⇒ Object Also known as: name

def script(*args)

if args.size == 1
  @script =  args[0]
else
  @script
end

end



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# File 'lib/torque_rm/qsub.rb', line 32

def N
  if @N.nil?
    @N = SecureRandom.urlsafe_base64(20)
  else
    @N
  end
end

#nodes ⇒ Object 



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# File 'lib/torque_rm/qsub.rb', line 146

def nodes
	str_nodes = if @nodes
		           @nodes
	            elsif ppn
		           "nodes=1"
	            end

	if ppn
		str_nodes << ':' << "ppn=#{ppn}"
	elsif procs
		str_nodes << '+' << "procs=#{procs}"
	end
			
end

#o ⇒ Object Also known as: stdout

Returns the value of attribute o.



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# File 'lib/torque_rm/qsub.rb', line 19

def o
  @o
end

#P ⇒ Object Also known as: run_as_user

Returns the value of attribute P.



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# File 'lib/torque_rm/qsub.rb', line 19

def P
  @P
end

#p ⇒ Object

Returns the value of attribute p.



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# File 'lib/torque_rm/qsub.rb', line 19

def p
  @p
end

#ppn ⇒ Object Also known as: cpus

Returns the value of attribute ppn.



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# File 'lib/torque_rm/qsub.rb', line 20

def ppn
  @ppn
end

#procs ⇒ Object

Returns the value of attribute procs.



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# File 'lib/torque_rm/qsub.rb', line 20

def procs
  @procs
end

#q ⇒ Object Also known as: queue

Returns the value of attribute q.



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# File 'lib/torque_rm/qsub.rb', line 19

def q
  @q
end

#r ⇒ Object Also known as: rerunnable

Returns the value of attribute r.



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# File 'lib/torque_rm/qsub.rb', line 19

def r
  @r
end

#S ⇒ Object Also known as: shell

Returns the value of attribute S.



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# File 'lib/torque_rm/qsub.rb', line 19

def S
  @S
end

#script ⇒ Object

Returns the value of attribute script.



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# File 'lib/torque_rm/qsub.rb', line 19

def script
  @script
end

#t ⇒ Object

Returns the value of attribute t.



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# File 'lib/torque_rm/qsub.rb', line 19

def t
  @t
end

#u ⇒ Object Also known as: user_list

Returns the value of attribute u.



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# File 'lib/torque_rm/qsub.rb', line 19

def u
  @u
end

#v ⇒ Object Also known as: variable_list

Returns the value of attribute v.



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# File 'lib/torque_rm/qsub.rb', line 19

def v
  @v
end

#V ⇒ Object Also known as: exports

Returns the value of attribute V.



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# File 'lib/torque_rm/qsub.rb', line 19

def V
  @V
end

#W ⇒ Object

Returns the value of attribute W.



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# File 'lib/torque_rm/qsub.rb', line 19

def W
  @W
end

#walltime ⇒ Object

Returns the value of attribute walltime.



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# File 'lib/torque_rm/qsub.rb', line 20

def walltime
  @walltime
end

#X ⇒ Object Also known as: additional_attributes

Returns the value of attribute X.



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# File 'lib/torque_rm/qsub.rb', line 19

def X
  @X
end

#z ⇒ Object

Returns the value of attribute z.



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# File 'lib/torque_rm/qsub.rb', line 19

def z
  @z
end

Instance Method Details

#config(&block) ⇒ Object

initialize



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# File 'lib/torque_rm/qsub.rb', line 126

def config(&block)
   if block_given?
     if block.arity == 1
       yield self
     else
       instance_eval &block
       self
     end
   end
end

#rm ⇒ Object

delete this job from the queue



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# File 'lib/torque_rm/qsub.rb', line 196

def rm
  if id.nil? 
    warn("No job submitted")
  else
    TORQUE::Qdel.rm(id)
  end
end

#stat ⇒ Object

get the stats for this job



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# File 'lib/torque_rm/qsub.rb', line 185

def stat
  if id.nil? 
    warn("No job submitted")
  else
    @qstat = @qstat || TORQUE::Qstat.new
    @qstat.query(job_id: id)
  end
end

#submit(opts = {dry: false}) ⇒ Object

Create a qsub job on the remote server and then submits it return the job_id from qsub and set it as a job variable. :dry => true will only transfer the file to the destination server and will not submit the job to the scheduler

the job object will not have an id associated.



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# File 'lib/torque_rm/qsub.rb', line 179

def submit(opts={dry: false})
  TORQUE.server.file_upload StringIO.new(to_s), script_absolute_filename
  @id = TORQUE.server.qsub(script_absolute_filename).first unless opts[:dry] == true
end

#to_s ⇒ Object 



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# File 'lib/torque_rm/qsub.rb', line 162

def to_s
 pbs_script = ""
 [:a, :A,:b,:c,:C,:d,:D,:e,:f,:h,:I,:j,:k,:l,:m,:M,:N,:o,:p,:P,:q,:r,:S,:t,:u,:v,:V,:W,:X,:z].each do |option|
 	value = send(option)
 	pbs_script << "#PBS -#{option} #{value}\n" unless value.nil?
 end
 pbs_script << "#{script}" unless script.nil?
 if script.nil?
 	warn("You are converting this qsub job into a script without a real code.")
 end
 pbs_script
end