Issue with Python garbage collector?
https://stackoverflow.com/questions/12452017
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I have a simple program which reads a large file containing few million rows, parses each row (numpy array) and converts into an array of doubles (python array) and later writes into an hdf5 file. I repeat this loop for multiple days. After reading each file, i delete all the objects and call garbage collector. When I run the program, First day is parsed without any error but on the second day i get MemoryError. I monitored the memory usage of my program, during first day of parsing, memory usage is around 1.5 GB. When the first day parsing is finished, memory usage goes down to 50 MB. Now when 2nd day starts and i try to read the lines from the file I get MemoryError. Following is the output of the program.
source file extracted at C:\rfadump\au\2012.08.07.txt
parsing started
current time: 2012-09-16 22:40:16.829000
500000 lines parsed
1000000 lines parsed
1500000 lines parsed
2000000 lines parsed
2500000 lines parsed
3000000 lines parsed
3500000 lines parsed
4000000 lines parsed
4500000 lines parsed
5000000 lines parsed
parsing done.
end time is 2012-09-16 23:34:19.931000
total time elapsed 0:54:03.102000
repacking file
done
> s:\users\aaj\projects\pythonhf\rfadumptohdf.py(132)generateFiles()
-> while single_date <= self.end_date:
(Pdb) c
*** 2012-08-08 ***
source file extracted at C:\rfadump\au\2012.08.08.txt
cought an exception while generating file for day 2012-08-08.
Traceback (most recent call last):
File "rfaDumpToHDF.py", line 175, in generateFile
lines = self.rawfile.read().split('|\n')
MemoryError
I am very sure that windows system task manager shows the memory usage as 50 MB for this process. It looks like the garbage collector or memory manager for Python is not calculating the free memory correcly. There should be lot of free memory but it thinks there is not enough.
Any idea?
EDIT
Adding my code here
I will put parts of my code. I am new to python, please pardon my python coding style.
module 1
def generateFile(self, current_date):
try:
print "*** %s ***" % current_date.strftime("%Y-%m-%d")
weekday=current_date.weekday()
if weekday >= 5:
print "skipping weekend"
return
self.taqdb = taqDB(self.index, self.offset)
cache_filename = os.path.join(self.cache_dir,current_date.strftime("%Y.%m.%d.h5"))
outputFile = config.hdf5.filePath(self.index, date=current_date)
print "cache file: ", cache_filename
print "output file: ", outputFile
tempdir = "C:\\rfadump\\"+self.region+"\\"
input_filename = tempdir + filename
print "source file extracted at %s " % input_filename
## universe
reader = rfaTextToTAQ.rfaTextToTAQ(self.tickobj) ## PARSER
count = 0
self.rawfile = open(input_filename, 'r')
lines = self.rawfile.read().split('|\n')
total_lines = len(lines)
self.rawfile.close()
del self.rawfile
print "parsing started"
start_time = dt.datetime.now()
print "current time: %s" % start_time
#while(len(lines) > 0):
while(count < total_lines):
#line = lines.pop(0) ## This slows down processing
result = reader.parseline(lines[count]+"|")
count += 1
if(count % 500000 == 0):
print "%d lines parsed" %(count)
if(result == None):
continue
ric, timestamp, quotes, trades, levelsUpdated, tradeupdate = result
if(len(levelsUpdated) == 0 and tradeupdate == False):
continue
self.taqdb.insert(result)
## write to hdf5 TODO
writer = h5Writer.h5Writer(cache_filename, self.tickobj)
writer.write(self.taqdb.groups)
writer.close()
del lines
del self.taqdb, self.tickobj
##########################################################
print "parsing done."
end_time = dt.datetime.now()
print "end time is %s" % end_time
print "total time elapsed %s" % (end_time - start_time)
defragger = hdf.HDF5Defragmenter()
defragger.Defrag(cache_filename,outputFile)
del defragger
print "done"
gc.collect(2)
except:
print "cought an exception while generating file for day %s." % current_date.strftime("%Y-%m-%d")
tb = traceback.format_exc()
print tb
module 2 - taqdb - to store parsed data in an array
class taqDB:
def __init__(self, index, offset):
self.index = index
self.tickcfg = config.hdf5.getTickConfig(index)
self.offset = offset
self.groups = {}
def getGroup(self,ric):
if (self.groups.has_key(ric) == False):
self.groups[ric] = {}
return self.groups[ric]
def getOrderbookArray(self, ric, group):
datasetname = orderBookName
prodtype = self.tickcfg.getProdType(ric)
if(prodtype == ProdType.INDEX):
return
orderbookArrayShape = self.tickcfg.getOrderBookArrayShape(prodtype)
if(group.has_key(datasetname) == False):
group[datasetname] = array.array("d")
orderbookArray = self.tickcfg.getOrderBookArray(prodtype)
return orderbookArray
else:
orderbookArray = group[datasetname]
if(len(orderbookArray) == 0):
return self.tickcfg.getOrderBookArray(prodtype)
lastOrderbook = orderbookArray[-orderbookArrayShape[1]:]
return np.array([lastOrderbook])
def addToDataset(self, group, datasetname, timestamp, arr):
if(group.has_key(datasetname) == False):
group[datasetname] = array.array("d")
arr[0,0]=timestamp
a1 = group[datasetname]
a1.extend(arr[0])
def addToOrderBook(self, group, timestamp, arr):
self.addToDataset(self, group, orderBookName, timestamp, arr)
def insert(self, data):
ric, timestamp, quotes, trades, levelsUpdated, tradeupdate = data
delta = dt.timedelta(hours=timestamp.hour,minutes=timestamp.minute, seconds=timestamp.second, microseconds=(timestamp.microsecond/1000))
timestamp = float(str(delta.seconds)+'.'+str(delta.microseconds)) + self.offset
## write to array
group = self.getGroup(ric)
orderbookUpdate = False
orderbookArray = self.getOrderbookArray(ric, group)
nonzero = quotes.nonzero()
orderbookArray[nonzero] = quotes[nonzero]
if(np.any(nonzero)):
self.addToDataset(group, orderBookName, timestamp, orderbookArray)
if(tradeupdate == True):
self.addToDataset(group, tradeName, timestamp, trades)
Module 3- Parser
class rfaTextToTAQ:
"""RFA Raw dump file reader. Readers single line (record) and returns an array or array of fid value pairs."""
def __init__(self,tickconfig):
self.tickconfig = tickconfig
self.token = ''
self.state = ReadState.SEQ_NUM
self.fvstate = fvstate.FID
self.quotes = np.array([]) # read from tickconfig
self.trades = np.array([]) # read from tickconfig
self.prodtype = ProdType.STOCK
self.allquotes = {}
self.alltrades = {}
self.acvol = 0
self.levelsUpdated = []
self.quoteUpdate = False
self.tradeUpdate = False
self.depth = 0
def updateLevel(self, index):
if(self.levelsUpdated.__contains__(index) == False):
self.levelsUpdated.append(index)
def updateQuote(self, fidindex, field):
self.value = float(self.value)
if(self.depth == 1):
index = fidindex[0]+(len(self.tickconfig.stkQuotes)*(self.depth - 1))
self.quotes[index[0]][fidindex[1][0]] = self.value
self.updateLevel(index[0])
else:
self.quotes[fidindex] = self.value
self.updateLevel(fidindex[0][0])
self.quoteUpdate = True
def updateTrade(self, fidindex, field):
#self.value = float(self.value)
if(self.tickconfig.tradeUpdate(self.depth) == False):
return
newacvol = float(self.value)
if(field == acvol):
if(self.value > self.acvol):
tradesize = newacvol - self.acvol
self.acvol = newacvol
self.trades[fidindex] = tradesize
if(self.trades.__contains__(0) == False):
self.tradeUpdate = True
else:
self.trades[fidindex] = self.value
if(not (self.trades[0,1]==0 or self.trades[0,2]==0)):
self.tradeUpdate = True
def updateResult(self):
field = ''
valid, field = field_dict.FIDToField(int(self.fid), field)
if(valid == False):
return
if(self.value == '0'):
return
if(self.prodtype == ProdType.STOCK):
fidindex = np.where(self.tickconfig.stkQuotes == field)
if(len(fidindex[0]) == 0):
fidindex = np.where(self.tickconfig.stkTrades == field)
if(len(fidindex[0]) == 0):
return
else:
self.updateTrade(fidindex, field)
else:
self.updateQuote(fidindex, field)
else:
fidindex = np.where(self.tickconfig.futQuotes == field)
if(len(fidindex[0]) == 0):
fidindex = np.where(self.tickconfig.futTrades == field)
if(len(fidindex[0]) == 0):
return
else:
self.updateTrade(fidindex, field)
else:
self.updateQuote(fidindex, field)
def getOrderBookTrade(self):
if (self.allquotes.has_key(self.ric) == False):
acvol = 0
self.allquotes[self.ric] = self.tickconfig.getOrderBookArray(self.prodtype)
trades = self.tickconfig.getTradesArray()
self.alltrades[self.ric] = [trades, acvol]
return self.allquotes[self.ric], self.alltrades[self.ric]
def parseline(self, line):
self.tradeUpdate = False
self.levelsUpdated = []
pos = 0
length = len(line)
self.state = ReadState.SEQ_NUM
self.fvstate = fvstate.FID
self.token = ''
ch = ''
while(pos < length):
prevChar = ch
ch = line[pos]
pos += 1
#SEQ_NUM
if(self.state == ReadState.SEQ_NUM):
if(ch != ','):
self.token += ch
else:
self.seq_num = int(self.token)
self.state = ReadState.TIMESTAMP
self.token = ''
# TIMESTAMP
elif(self.state == ReadState.TIMESTAMP):
if(ch == ' '):
self.token = ''
elif(ch != ','):
self.token += ch
else:
if(len(self.token) != 12):
print "Invalid timestamp format. %s. skipping line.\n", self.token
self.state = ReadState.SKIPLINE
else:
self.timestamp = datetime.strptime(self.token,'%H:%M:%S.%f')
self.state = ReadState.RIC
self.token = ''
# RIC
elif(self.state == ReadState.RIC):
if(ch != ','):
self.token += ch
else:
self.ric = self.token
self.token = ''
self.ric, self.depth = self.tickconfig.replaceRic(self.ric)
self.prodtype = self.tickconfig.getProdType(self.ric)
if(self.tickconfig.subscribed(self.ric)):
self.state = ReadState.UPDATE_TYPE
self.quotes, trades = self.getOrderBookTrade()
self.trades = trades[0]
self.acvol = trades[1]
else:
self.state = ReadState.SKIPLINE
# UPDATE_TYPE
elif(self.state == ReadState.UPDATE_TYPE):
if(ch != '|'):
self.token += ch
else:
self.update_type = self.token
self.token = ''
self.state = ReadState.FVPAIRS
#SKIPLINE
elif(self.state == ReadState.SKIPLINE):
return None
# FV PAIRS
elif(self.state == ReadState.FVPAIRS):
# FID
if(self.fvstate == fvstate.FID):
if(ch != ','):
if(ch.isdigit() == False):
self.token = self.value+ch
self.fvstate = fvstate.FIDVALUE
self.state = ReadState.FVPAIRS
else:
self.token += ch
else:
self.fid = self.token
self.token = ''
self.fvstate = fvstate.FIDVALUE
self.state = ReadState.FVPAIRS
# FIDVALUE
elif(self.fvstate == fvstate.FIDVALUE):
if(ch != '|'):
self.token += ch
else:
self.value = self.token
self.token = ''
self.state = ReadState.FVPAIRS
self.fvstate = fvstate.FID
# TODO set value
self.updateResult()
return self.ric, self.timestamp, self.quotes, self.trades, self.levelsUpdated, self.tradeUpdate
Thanks.
解决方案
The only reliable way to free memory is to terminate the process.
So, if your main program spawns a worker process to do most of the work (the stuff that is done in one day) then when that worker process completes, the memory used will be freed:
import multiprocessing as mp
def work(date):
# Do most of the memory-intensive work here
...
while single_date <= self.end_date:
proc = mp.Process(target = work, args = (single_date,))
proc.start()
proc.join()
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