bug fix: mandatory partitioning while training

pipeline.py

@@ -61,27 +61,23 @@ class Components :
 		logger = factory.instance(type='mongo.MongoWriter',args={'dbname':'aou','doc':args['context']})
 		log_folder = args['logs'] if 'logs' in args else 'logs'
 		_args = {"batch_size":10000,"logs":log_folder,"context":args['context'],"max_epochs":150,"column":args['columns'],"id":"person_id","logger":logger}
+		
 		_args['max_epochs'] = 150 if 'max_epochs' not in args else int(args['max_epochs'])
 		_args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1 
 		_args['gpu'] = args['gpu'] if 'gpu' in args else 0
 
-		MAX_ROWS = args['max_rows'] 	if 'max_rows' in args else 0
+		# MAX_ROWS = args['max_rows'] 	if 'max_rows' in args else 0
-		PART_SIZE = args['part_size'] 	if 'part_size' in args else 0
+		PART_SIZE = int(args['part_size']) if 'part_size' in args else 8
 		
-		if df.shape[0] > MAX_ROWS and 'partition' not in args:
+		if 'partition' not in args:
 			lbound = 0
-			bounds = list(pd.cut( np.arange(df.shape[0]+1),PART_SIZE).categories)
+			# bounds = list(pd.cut( np.arange(df.shape[0]+1),PART_SIZE).categories)
 			# bounds = Components.split(df,MAX_ROWS,PART_SIZE)
-			
+			columns = args['columns']
+			df = np.array_split(df[columns].values,PART_SIZE)
 			qwriter = factory.instance(type='queue.QueueWriter',args={'queue':'aou.io'})
-			
+			part_index  = 0			
-			for b in bounds :
+			for _df in df:
-				part_index = bounds.index(b)
-				ubound = int(b.right)
-				
-					
-				_data =  df.iloc[lbound:ubound][args['columns']]
-				lbound = ubound
 				
 				# _args['logs'] = os.sep.join([log_folder,str(part_index)])
 				_args['partition'] = str(part_index)
@@ -92,14 +88,20 @@ class Components :
 				#	- where to get the data
 				#	- and athe arguments to use (partition #,columns,gpu,epochs)
 				#
-				info = {"rows":_data.shape[0],"cols":_data.shape[1], "partition":part_index,"logs":_args['logs']}
+
-				p = {"args":_args,"data":_data.to_dict(orient="records"),"info":info}
+				_df = pd.DataFrame(_df,columns=columns)
+				# print (columns)
+				
+				info = {"rows":_df.shape[0],"cols":_df.shape[1], "partition":part_index,"logs":_args['logs'],"num_gpu":2,"part_size":PART_SIZE}
+				p = {"args":_args,"data":_df.to_dict(orient="records"),"info":info}
+				part_index += 1
 				qwriter.write(p)
 				#
 				# @TODO:
 				#	- Notify that information was just posted to the queue
-				info['max_rows'] 	= MAX_ROWS
+				#	In case we want slow-mode, we can store the partitions in mongodb and process (Yes|No)?
-				info['part_size'] 	= PART_SIZE
+				#
+				
 				logger.write({"module":"train","action":"setup-partition","input":info})
 			
 			pass
@@ -137,37 +139,18 @@ class Components :
 		_args['num_gpu'] = int(args['num_gpu']) if 'num_gpu' in args else 1 
 		os.environ['CUDA_VISIBLE_DEVICES'] = str(args['gpu']) if 'gpu' in args else '0'
 		_args['no_value']= args['no_value']
-		MAX_ROWS = args['max_rows']  	if 'max_rows' in args else 0
+		# MAX_ROWS = args['max_rows']  	if 'max_rows' in args else 0
-		PART_SIZE = args['part_size'] 	if 'part_size' in args else 0
+		PART_SIZE = int(args['part_size']) if 'part_size' in args else 8
 		
 		# credentials = service_account.Credentials.from_service_account_file('/home/steve/dev/aou/accounts/curation-prod.json')
 		# _args['data'] = pd.read_gbq(SQL,credentials=credentials,dialect='standard').dropna()
 		reader = args['reader']
 		df = reader()
-		bounds = Components.split(df,MAX_ROWS,PART_SIZE)
+		# bounds = Components.split(df,MAX_ROWS,PART_SIZE)
 		if partition != '' and os.path.exists(log_folder):
-			bounds = Components.split(df,MAX_ROWS,PART_SIZE)
+			columns = args['columns']
-			# bounds = list(pd.cut( np.arange(df.shape[0]+1),PART_SIZE).categories)
+			df = np.array_split(df[columns].values,PART_SIZE)
-			lbound = int(bounds[int(partition)].left)
+			df = pd.DataFrame(df[ int (partition) ],columns = columns)
-			ubound = int(bounds[int(partition)].right)
-			df = df.iloc[lbound:ubound]
-		else:
-			#
-			# We have an implicit partition here
-			# bounds = Components.split(df,MAX_ROWS,PART_SIZE)
-			logger.write({"module":"generate","action":"virtual-parititions","input":{"rows":df.shape[0],"max_rows":MAX_ROWS,"part_size":PART_SIZE}})
-			for item in bounds :
-
-				lbound = int(item.left)
-				ubound = int(item.right)
-				args['reader'] = lambda: df[lbound:ubound]
-				args['partition'] = bounds.index(item)
-				
-				self.generate(args)
-			return ;
-		if not os.path.exists(log_folder) :
-			log_folder = log_folder.replace(partition,'')
-			_args['logs'] = log_folder
 
 		_args['data'] = df
 			# _args['data'] = reader()
@@ -189,7 +172,7 @@ class Components :
 			_args['data'][name] = _dc[name]
 			info = {"module":"generate","action":"io","input":{"rows":_dc[name].shape[0],"name":name}}
 			if partition != '' :
-				info['partition'] = partition
+				info['partition'] = int(partition)
 			logger.write(info)
 			# filename = os.sep.join([log_folder,'output',name+'.csv'])
 			# data_comp[[name]].to_csv(filename,index=False)
@@ -218,7 +201,7 @@ class Components :
 		
 		info = {"full":{"path":_fname,"rows":_args['data'].shape[0]},"compare":{"name":_pname,"rows":data_comp.shape[0]} }
 		if partition :
-			info ['partition'] = partition
+			info ['partition'] = int(partition)
 		logger.write({"module":"generate","action":"write","info":info} )
 	@staticmethod
 	def callback(channel,method,header,stream):
@@ -229,8 +212,12 @@ class Components :
 		logger.write({'module':'process','action':'read-partition','input':info['info']})
 		df = pd.DataFrame(info['data'])
 		args = info['args']
-		MAX_GPUS = 8
+		if args['num_gpu'] > 1 :
-		args['gpu'] = int(info['info']['partition']) if info['info']['partition'] < MAX_GPUS else np.random.choice(np.arange(MAX_GPUS),1).astype(int).tolist()[0]
+			args['gpu'] = int(info['info']['partition']) if info['info']['partition'] == 0 else info['info']['partition'] + 2
+			args['num_gpu'] = 2
+		else:
+			args['gpu'] 	= 0
+			args['num_gpu'] = 1
 		# if int(args['num_gpu']) > 1 and args['gpu'] > 0:
 		# 	args['gpu'] = args['gpu'] + args['num_gpu'] if args['gpu'] + args['num_gpu'] < 8 else args['gpu'] #-- 8 max gpus
 		args['reader'] = lambda: df
@@ -296,7 +283,7 @@ if __name__ == '__main__' :
 		SYS_ARGS = dict(args)	#-- things get lost in context
 		if 'read' in SYS_ARGS :
 			QUEUE_TYPE = 'queue.QueueReader'
-			pointer = lambda qreader: qreader.read(1)
+			pointer = lambda qreader: qreader.read()
 		else:
 			QUEUE_TYPE = 'queue.QueueListener'
 			pointer = lambda qlistener: qlistener.listen()

setup.py

@@ -4,7 +4,7 @@ import sys
 
 def read(fname):
     return open(os.path.join(os.path.dirname(__file__), fname)).read() 
-args = {"name":"data-maker","version":"1.1.8","author":"Vanderbilt University Medical Center","author_email":"steve.l.nyemba@vanderbilt.edu","license":"MIT",
+args = {"name":"data-maker","version":"1.1.9","author":"Vanderbilt University Medical Center","author_email":"steve.l.nyemba@vanderbilt.edu","license":"MIT",
         "packages":find_packages(),"keywords":["healthcare","data","transport","protocol"]}
 args["install_requires"] = ['data-transport@git+https://dev.the-phi.com/git/steve/data-transport.git','tensorflow==1.15','pandas','pandas-gbq','pymongo']
 args['url'] = 'https://hiplab.mc.vanderbilt.edu/git/aou/data-maker.git'