update docs

docs/source/pipeline.rst

@@ -713,15 +713,15 @@ This section shows an example on how to do some post processing on the products
 
 ::
 
-	>>> def methodThatMeasuresSomething(pool,batch,settings,id,**kwargs):
+	>>> def methodThatMeasuresSomething(pool,batch,settings,node_id,**kwargs):
 		...
 
 where 
 
 - pool is a :py:class:`~lenstools.utils.MPIWhirlPool` instance that will take care of the parallelization of the code
 - batch is the simulation batch object, i.e. an instance of :py:class:`~lenstools.pipeline.SimulationBatch`
 - settings are the tunable settings of the code
-- id is the particular batch subset to process, for example "Om0.300_Ol0.700|512b240|ic1"
+- node_id is the particular batch subset to process, for example "Om0.300_Ol0.700|512b240|ic1"
 - kwargs are any other keyword arguments you may want to pass to the methodThatMeasuresSomething method
 
 lenstools will take care of distributing the methodThatMeasuresSomething calls on the computer cluster you are running on. Below is a working example of how to measure the 3D matter power spectrum out of the simulation boxes. 
@@ -747,39 +747,28 @@ Create a file "matter_power_spectrum.py"
 	from lenstools.utils import MPIWhirlPool
 
 	from lenstools.simulations.nbody import NbodySnapshot
-	from lenstools.simulations.gadget2 import Gadget2Snapshot
+	from lenstools.simulations.gadget2 import Gadget2SnapshotDE
+	from lenstools.simulation.logs import logdriver
 
 	from lenstools.pipeline.simulation import SimulationBatch
 
 	import numpy as np
 	import astropy.units as u
 
-	################################################
-	###########Loggers##############################
-	################################################
-
-	console = logging.StreamHandler(sys.stdout)
-	formatter = logging.Formatter("%(asctime)s:%(name)-12s:%(levelname)-4s: %(message)s",datefmt='%m-%d %H:%M')
-	console.setFormatter(formatter)
-
-	logdriver = logging.getLogger("lenstools.driver")
-	logdriver.addHandler(console)
-	logdriver.propagate = False
-
 	#Orchestra director of the execution
 	def powerSpectrumExecution():
 
 		script_to_execute = matterPowerSpectrum
 		settings_handler = PowerSpectrumSettings
-		kwargs = {"fmt":Gadget2Snapshot}
+		kwargs = {"fmt":Gadget2SnapshotDE}
 
 		return script_to_execute,settings_handler,kwargs
 
 	################################################################
 	################Snapshot power spectrum#########################
 	################################################################
 
-	def matterPowerSpectrum(pool,batch,settings,id,**kwargs):
+	def matterPowerSpectrum(pool,batch,settings,node_id,**kwargs):
 
 		assert "fmt" in kwargs.keys()
 		fmt = kwargs["fmt"]
@@ -791,7 +780,7 @@ Create a file "matter_power_spectrum.py"
 		assert isinstance(settings,PowerSpectrumSettings)
 
 		#Split the id into the model,collection and realization parts
-		cosmo_id,geometry_id = id.split("|")
+		cosmo_id,geometry_id = node_id.split("|")
 
 		#Get a handle on the simulation model
 		model = batch.getModel(cosmo_id)
@@ -824,6 +813,14 @@ Create a file "matter_power_spectrum.py"
 		#Construct the array of bin edges
 		k_egdes  = np.linspace(settings.kmin,settings.kmax,settings.num_k_bins+1).to(model.Mpc_over_h**-1)
 
+		#Placeholder for the density MPI communications
+		density_placeholder = np.empty((settings.fft_grid_size,)*3,dtype=np.float32)
+		if pool is not None:
+			pool.openWindow(density_placeholder)
+
+			if pool.is_master():
+				logdriver.debug("Opened density window of type {0}".format(pool._window_type))
+
 		#Cycle over snapshots
 		for n in range(settings.first_snapshot,settings.last_snapshot+1):
 
@@ -832,15 +829,15 @@ Create a file "matter_power_spectrum.py"
 
 			#Log to user
 			if (pool is None) or (pool.is_master()):
-				logdriver.info("Processing snapshot {0} of model {1}".format(n,id))
+				logdriver.info("Processing snapshot {0} of model {1}".format(n,node_id))
 				logdriver.info("Allocated memory for power spectrum Ensemble {0}".format(power_ensemble.shape))
 
 			for r,ic in enumerate(settings.nbody_realizations):
 
 				#Log to user
 				if (pool is None) or (pool.is_master()):
 					logdriver.info("Processing N-body realization {0}".format(ic))
-				
+			
 				#Instantiate the appropriate SimulationIC object
 				realization = collection.getRealization(ic)
 
@@ -851,7 +848,7 @@ Create a file "matter_power_spectrum.py"
 						sys.exit(1)
 
 				snap = fmt.open(realization.snapshotPath(n,sub=None),pool=pool)
-				k,power_ensemble[r],hits = snap.powerSpectrum(k_egdes,resolution=settings.fft_grid_size,return_num_modes=True)
+				k,power_ensemble[r],hits = snap.powerSpectrum(k_egdes,resolution=settings.fft_grid_size,return_num_modes=True,density_placeholder=density_placeholder)
 				snap.close()
 
 				#Safety barrier sync
@@ -871,7 +868,7 @@ Create a file "matter_power_spectrum.py"
 
 			#Save the ensemble
 			if (pool is None) or (pool.is_master()):
-				
+			
 				savename = os.path.join(collection.home_subdir,settings.ensemble_name,settings.ensemble_name+"_snap{0:03d}.npy".format(n))
 				logdriver.info("Saving power spectrum Ensemble ({0}) to {1}".format(power_ensemble.unit.to_string(),savename))
 				np.save(savename,power_ensemble.value)
@@ -881,8 +878,19 @@ Create a file "matter_power_spectrum.py"
 			if pool is not None:
 				pool.comm.Barrier()
 
+		###########
+		#Completed#
+		###########
+
+		#Close the RMA window
+		if pool is not None:
+			pool.comm.Barrier()
+			pool.closeWindow()
+		
+			if pool.is_master():
+				logdriver.debug("Closed density window of type {0}".format(pool._window_type))
+
 
-		#Completed
 		if pool is None or pool.is_master():
 			logdriver.info("DONE!!")
 
@@ -935,22 +943,22 @@ Create a file "matter_power_spectrum.py"
 			#Read in the nbody realizations that make up the ensemble
 			settings.nbody_realizations = list()
 			for r in options.get(section,"nbody_realizations").split(","): 
-				
+			
 				try:
 					l,h = r.split("-")
 					settings.nbody_realizations.extend(range(int(l),int(h)+1))
 				except ValueError:
 					settings.nbody_realizations.extend([int(r)])
-			
+		
 			settings.first_snapshot = options.getint(section,"first_snapshot")
 			settings.last_snapshot = options.getint(section,"last_snapshot")
-			
+		
 			settings.fft_grid_size = options.getint(section,"fft_grid_size")
 
 			settings.length_unit = getattr(u,options.get(section,"length_unit"))
 			settings.kmin = options.getfloat(section,"kmin") * settings.length_unit**-1
 			settings.kmax = options.getfloat(section,"kmax") * settings.length_unit**-1
-			
+		
 			settings.num_k_bins = options.getint(section,"num_k_bins")
 
 			#Return to user