Python:如何将巨大的文本文件读取到内存中 [英] Python: How to read huge text file into memory

问题描述

我在具有1GB RAM的Mac Mini上使用Python 2.6.我想阅读一个巨大的文本文件

I'm using Python 2.6 on a Mac Mini with 1GB RAM. I want to read in a huge text file

$ ls -l links.csv; file links.csv; tail links.csv 
-rw-r--r--  1 user  user  469904280 30 Nov 22:42 links.csv
links.csv: ASCII text, with CRLF line terminators
4757187,59883
4757187,99822
4757187,66546
4757187,638452
4757187,4627959
4757187,312826
4757187,6143
4757187,6141
4757187,3081726
4757187,58197

因此，文件中的每一行都由两个逗号分隔的整数值组成的元组. 我想阅读整个文件，并根据第二列对其进行排序.我知道，我可以进行排序而无需将整个文件读入内存.但是我认为对于500MB的文件，由于我有1GB的可用空间，因此仍然应该可以在内存中进行处理.

So each line in the file consists of a tuple of two comma separated integer values. I want to read in the whole file and sort it according to the second column. I know, that I could do the sorting without reading the whole file into memory. But I thought for a file of 500MB I should still be able to do it in memory since I have 1GB available.

但是，当我尝试读取文件时，Python似乎分配了比磁盘上的文件所需更多的内存.因此，即使具有1GB的RAM，我也无法将500MB的文件读入内存. 我用于读取文件和打印一些有关内存消耗信息的Python代码是:

However when I try to read in the file, Python seems to allocate a lot more memory than is needed by the file on disk. So even with 1GB of RAM I'm not able to read in the 500MB file into memory. My Python code for reading the file and printing some information about the memory consumption is:

#!/usr/bin/python
# -*- coding: utf-8 -*-

import sys

infile=open("links.csv", "r")

edges=[]
count=0
#count the total number of lines in the file
for line in infile:
 count=count+1

total=count
print "Total number of lines: ",total

infile.seek(0)
count=0
for line in infile:
 edge=tuple(map(int,line.strip().split(",")))
 edges.append(edge)
 count=count+1
 # for every million lines print memory consumption
 if count%1000000==0:
  print "Position: ", edge
  print "Read ",float(count)/float(total)*100,"%."
  mem=sys.getsizeof(edges)
  for edge in edges:
   mem=mem+sys.getsizeof(edge)
   for node in edge:
    mem=mem+sys.getsizeof(node) 

  print "Memory (Bytes): ", mem 

我得到的输出是:

Total number of lines:  30609720
Position:  (9745, 2994)
Read  3.26693612356 %.
Memory (Bytes):  64348736
Position:  (38857, 103574)
Read  6.53387224712 %.
Memory (Bytes):  128816320
Position:  (83609, 63498)
Read  9.80080837067 %.
Memory (Bytes):  192553000
Position:  (139692, 1078610)
Read  13.0677444942 %.
Memory (Bytes):  257873392
Position:  (205067, 153705)
Read  16.3346806178 %.
Memory (Bytes):  320107588
Position:  (283371, 253064)
Read  19.6016167413 %.
Memory (Bytes):  385448716
Position:  (354601, 377328)
Read  22.8685528649 %.
Memory (Bytes):  448629828
Position:  (441109, 3024112)
Read  26.1354889885 %.
Memory (Bytes):  512208580

仅读取500MB文件的25％之后，Python消耗了500MB.因此，将文件内容存储为int元组列表似乎并不是很有效的内存使用. 有没有更好的方法可以做到，以便我可以将500MB的文件读入1GB的内存中?

Already after reading only 25% of the 500MB file, Python consumes 500MB. So it seem that storing the content of the file as a list of tuples of ints is not very memory efficient. Is there a better way to do it, so that I can read in my 500MB file into my 1GB of memory?

推荐答案

有一个用于对大于RAM的文件进行排序的方法

There is a recipe for sorting files larger than RAM on this page, though you'd have to adapt it for your case involving CSV-format data. There are also links to additional resources there.

的确，磁盘上的文件并不大于RAM"，但是内存中的表示形式很容易变得比"可用RAM "大得多.一方面，您自己的程序无法获得全部1GB(操作系统开销等).另外，即使您以最紧凑的形式将其存储为纯Python(两个整数列表，假设使用32位计算机等)，对于这30M对整数，您仍将使用934MB.

True, the file on disk is not "larger than RAM", but the in-memory representation can easily become much larger than available RAM. For one thing, your own program doesn't get the entire 1GB (OS overhead etc). For another, even if you stored this in the most compact form for pure Python (two lists of integers, assuming 32-bit machine etc), you'd be using 934MB for those 30M pairs of integers.

使用numpy，您也可以完成这项工作，仅使用大约250MB.加载这种方式并不是特别快，因为您必须计算行数并预分配数组，但是考虑到它在内存中，它可能是最快的实际排序:

Using numpy you can also do the job, using only about 250MB. It isn't particular fast to load this way, as you have to count the lines and pre-allocate the array, but it may be the fastest actual sort given that it's in-memory:

import time
import numpy as np
import csv

start = time.time()
def elapsed():
    return time.time() - start

# count data rows, to preallocate array
f = open('links.csv', 'rb')
def count(f):
    while 1:
        block = f.read(65536)
        if not block:
             break
        yield block.count(',')

linecount = sum(count(f))
print '\n%.3fs: file has %s rows' % (elapsed(), linecount)

# pre-allocate array and load data into array
m = np.zeros(linecount, dtype=[('a', np.uint32), ('b', np.uint32)])
f.seek(0)
f = csv.reader(open('links.csv', 'rb'))
for i, row in enumerate(f):
    m[i] = int(row[0]), int(row[1])

print '%.3fs: loaded' % elapsed()
# sort in-place
m.sort(order='b')

print '%.3fs: sorted' % elapsed()

在我的计算机上输出的示例文件类似于您显示的内容:

Output on my machine with a sample file similar to what you showed:

6.139s: file has 33253213 lines
238.130s: read into memory
517.669s: sorted

numpy中的默认值为 Quicksort . ndarray.sort()例程(可在适当位置进行排序)也可以使用关键字参数kind="mergesort"或kind="heapsort"，但似乎这两个参数均不能在

The default in numpy is Quicksort. The ndarray.sort() routine (which sorts in-place) can also take keyword argument kind="mergesort" or kind="heapsort" but it appears neither of these is capable of sorting on a Record Array which, incidentally, I used as the only way I could see to sort the columns together as opposed to the default which would sort them independently (totally messing up your data).

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