Python垃圾收集器有问题吗？

Question

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.

Answer 1

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()