CODEWITHSUNDEEP
pythonfortran
Pradeep Kumar Jha
Pradeep Kumar Jha

Reputation: 877

Huge difference between python and fortran difference for a small program

I am reading a file containing single precision data with 512**3 data points. Based on a threshold, I assign each point a flag of 1 or 0. I wrote two programs doing the same thing, one in fortran, the other in python. But the one in fortran takes like 0.1 sec while the one in python takes minutes. Is it normal? Or can you please point out the problem with my python program:

fortran.f

  program vorticity_tracking

  implicit none

  integer, parameter :: length = 512**3
  integer, parameter :: threshold = 1320.0

  character(255) :: filen
  real, dimension(length) :: stored_data
  integer, dimension(length) :: flag
  integer index

  filen = "vor.dat"

  print *, "Reading the file ", trim(filen)
  open(10, file=trim(filen),form="unformatted",
 &     access="direct", recl = length*4)
  read (10, rec=1) stored_data
  close(10)

  do index = 1, length
     if (stored_data(index).ge.threshold) then
        flag(index) = 1
     else
        flag(index) = 0
     end if
  end do

  stop
  end program

Python file:

#!/usr/bin/env python

import struct
import numpy as np

f_type = 'float32'
length = 512**3
threshold = 1320.0
file = 'vor_00000_455.float'

f = open(file,'rb')
data = np.fromfile(f, dtype=f_type, count=-1)
f.close()

flag = []

for index in range(length):
    if (data[index] >= threshold):
        flag.append(1)
    else:
        flag.append(0)

********* Edit ******

Thanks for your comments. I am not sure then how to do this in fortran. I tried the following but this is still as slow. 

 flag = np.ndarray(length, dtype=np.bool)    
 for index in range(length):
     if (data[index] >= threshold):
         flag[index] = 1
     else:
         flag[index] = 0

Can anyone please show me?

Upvotes: 0

Views: 1796

Answers (3)

David Schwartz
David Schwartz

Reputation: 182789

Your two programs are totally different. Your Python code repeatedly changes the size of a structure. Your Fortran code does not. You're not comparing two languages, you're comparing two algorithms and one of them is obviously inferior.

Upvotes: 6

dlangenk
dlangenk

Reputation: 350

In general Python is an interpreted language while Fortran is a compiled one. Therefore you have some overhead in Python. But it shouldn't take that long.

One thing that can be improved in the python version is to replace the for loop by an index operation.

#create flag filled with zeros with same shape as data
flag=numpy.zeros(data.shape)
#get bool array stating where data>=threshold
barray=data>=threshold
#everywhere where barray==True put a 1 in flag
flag[barray]=1

shorter version:

#create flag filled with zeros with same shape as data
flag=numpy.zeros(data.shape)
#combine the two operations without temporary barray
flag[data>=threshold]=1

Upvotes: 3

Alexander Mihailov
Alexander Mihailov

Reputation: 1152

Try this for python:

flag = data > threshhold

It will give you an array of flags as you want.

Upvotes: 1

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