Skip to main content

The magic of mmap

Big data is sometimes described as data whose size is larger than your available RAM. I think that this is a good criterion because once the size of your data (or the size of any results of computing on your data) start to approach your RAM size you have to start worrying about how you are going to manage memory. If you leave it up to your OS you are going to be writing and reading to disk in somewhat unpredictable ways and depending on the software you use, your program might just quit with no warning or with a courtesy 'Out of memory' message. The fun challenge of "Big Data" is, of course, how to keep doing computations regardless of the size of your data and not have your computer quit on you. Some calculations can be done in a blocked fashion but some calculations require you to access different parts of the data all at once.

Python's mmap module is an excellent way to let someone else do the dirty work of handling data files that are comparable or larger than available memory.

import mmap
import numpy


@profile
def load_data():
  fin = open('../Data/human_chrom_11.smalla', 'r+b')
  x = fin.read()
  y = x[numpy.random.randint(0,len(x))]
  print y

@profile
def map_data():
  fin = open('../Data/human_chrom_11.smalla', 'r+b')
  x = mmap.mmap(fin.fileno(), 0)
  y = x[numpy.random.randint(0,len(x))]
  print y

load_data()
map_data()

Here the .smalla data files are simply somewhat large files that can be loaded into memory (which we do for illustration purposes) but which we'd rather not. Running this code with memory_profiler

python -m memory_profiler test.py

tells us:

Filename: test.py

Line #    Mem usage    Increment   Line Contents
================================================
     5   16.922 MiB    0.000 MiB   @profile
     6                             def load_data():
     7   16.926 MiB    0.004 MiB     fin = open('../Data/human_chrom_11.smalla', 'r+b')
     8  145.680 MiB  128.754 MiB     x = fin.read()
     9  145.691 MiB    0.012 MiB     y = x[numpy.random.randint(0,len(x))]
    10  145.691 MiB    0.000 MiB     print y


Filename: test.py

Line #    Mem usage    Increment   Line Contents
================================================
    12   16.941 MiB    0.000 MiB   @profile
    13                             def map_data():
    14   16.941 MiB    0.000 MiB     fin = open('../Data/human_chrom_11.smalla', 'r+b')
    15   16.945 MiB    0.004 MiB     x = mmap.mmap(fin.fileno(), 0)
    16   16.953 MiB    0.008 MiB     y = x[numpy.random.randint(0,len(x))]
    17   16.953 MiB    0.000 MiB     print y

As we can see from the 'increment' column, when we map the data we hardly use any memory at all compared to the 128 MB that we heat up when we load the data into memory at once.

We should keep in mind that we have traded off space for time here. Even with a SSD operating on data from disk is going to take much longer than operating on data that is all in memory, but at least we are able to do it.


Now, if you want both fast access and operability with limited RAM, you need a much larger bag of tricks which I don't have and which often heavily depends on tricks you can do with your particular data.



Comments

Popular posts from this blog

Flowing text in inkscape (Poster making)

You can flow text into arbitrary shapes in inkscape. (From a hint here).

You simply create a text box, type your text into it, create a frame with some drawing tool, select both the text box and the frame (click and shift) and then go to text->flow into frame.

UPDATE:

The omnipresent anonymous asked:
Trying to enter sentence so that text forms the number three...any ideas?
The solution:
Type '3' using the text toolConvert to path using object->pathSize as necessaryRemove fillUngroupType in actual text in new text boxSelect the text and the '3' pathFlow the text

Drawing circles using matplotlib

Use the pylab.Circle command

import pylab #Imports matplotlib and a host of other useful modules cir1 = pylab.Circle((0,0), radius=0.75, fc='y') #Creates a patch that looks like a circle (fc= face color) cir2 = pylab.Circle((.5,.5), radius=0.25, alpha =.2, fc='b') #Repeat (alpha=.2 means make it very translucent) ax = pylab.axes(aspect=1) #Creates empty axes (aspect=1 means scale things so that circles look like circles) ax.add_patch(cir1) #Grab the current axes, add the patch to it ax.add_patch(cir2) #Repeat pylab.show()

Pandas panel = collection of tables/data frames aligned by index and column

Pandas panel provides a nice way to collect related data frames together while maintaining correspondence between the index and column values:


import pandas as pd, pylab #Full dimensions of a slice of our panel index = ['1','2','3','4'] #major_index columns = ['a','b','c'] #minor_index df = pd.DataFrame(pylab.randn(4,3),columns=columns,index=index) #A full slice of the panel df2 = pd.DataFrame(pylab.randn(3,2),columns=['a','c'],index=['1','3','4']) #A partial slice df3 = pd.DataFrame(pylab.randn(2,2),columns=['a','b'],index=['2','4']) #Another partial slice df4 = pd.DataFrame(pylab.randn(2,2),columns=['d','e'],index=['5','6']) #Partial slice with a new column and index pn = pd.Panel({'A': df}) pn['B'] = df2 pn['C'] = df3 pn['D'] = df4 for key in pn.items: print pn[key] -> output …