Sunday, August 30, 2015

Simple Way of Python's subprocess.Popen with a Timeout Option

subprocess module in Python provides us a variety of methods to start a process from a Python script. We may use these methods to run an external commands / programs, collect their output and manage them. An example use of it might be as following:

from subprocess import Popen, PIPE 
p = Popen(['ls', '-l'], stdout=PIPE, stderr=PIPE)
stdout, stderr = p.communicate()
print stdout, stderr

These lines can be used to run ls -l command in Terminal and collect the output (standard output and standard error) in stdout and stderr variables using communicate method defined in the process.

However, if the ls command never ends, we will never get any output because the external program just hangs. This happens sometimes with some programs e.g. trying to generate 3D molecule from 2D MOL file using Open Babel when the MOL file is not correctly formed. As the Open Babel just tries to generate 3D and doesn't check if the MOL file is okay, we never get an output from that run. So the program and our script hang.

Python has many different options to solve this problem like using multiprocessing or threading module, signal module etc. But here I'll describe a very simple method that worked for me fine. This is tested in Linux environment with Python version 2.7.

from time import sleep
from subprocess import Popen, PIPE 
def popen_timeout(command, timeout):
    p = Popen(command, stdout=PIPE, stderr=PIPE)
    for t in xrange(timeout):
        if p.poll() is not None:
            return p.communicate()
    return False 
print popen_timeout(['python',
                    '/home/gungor/Desktop/'], 25)

import time 
for i in xrange(10):
    print "Gungor", i

Example run 1 where the external program doesn't exceed the timeout threshold

gungor@gungors-mint ~/Desktop $ python
('Gungor 0\nGungor 1\nGungor 2\nGungor 3\nGungor 4\nGungor 5\nGungor 6\nGungor 7\nGungor 8\nGungor 9\n', '')

In this example, I ran with 25 seconds timeout on an external program ( which runs for 20 seconds and outputs lines of strings to the standard output which are collected with communicate method by

Example run 2 where the external program would take longer than the timeout threshold

gungor@gungors-mint ~/Desktop $ python

The just returns False. Because the external program was still running when the timeout has been achieved and it has been killed afterwards.

You can use this method to control the execution of the external programs in Python.

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