@ -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
PART_SIZE = args [ ' part_size ' ] if ' part_size ' in args else 0
# MAX_ROWS = args['max_rows'] if 'max_rows' in args else
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 ' } )
for b in bounds :
part_index = bounds . index ( b )
ubound = int ( b . right )
_data = df . iloc [ lbound : ubound ] [ args [ ' columns ' ] ]
lbound = ubound
part_index = 0
for _df in df :
# _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
info [ ' part_size ' ] = PART_SIZE
# In case we want slow-mode, we can store the partitions in mongodb and process (Yes|No)?
#
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
PART_SIZE = args [ ' part_size ' ] if ' part_size ' in args else 0
# MAX_ROWS = args['max_rows'] if 'max_rows' in args else
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 )
# bounds = list(pd.cut( np.arange(df.shape[0]+1),PART_SIZE).categories)
lbound = int ( bounds [ int ( partition ) ] . left )
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
columns = args [ ' columns ' ]
df = np . array_split ( df [ columns ] . values , PART_SIZE )
df = pd . DataFrame ( df [ int ( partition ) ] , columns = columns )
_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
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 ]
if args [ ' num_gpu ' ] > 1 :
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 ( )
