Tuesday, November 9, 2010

Parallelizing & Multiprocessing Commands Using Python

My computer has multiple processor cores. That means I could speed up scripts by running some of their tasks in parallel. I have written up a simple Python script that uses the Multiprocessing library to take a list of jobs (each is a unix command string) and then executes them on a specified number of independent processes. These processes are created only once and act as a pool of "workers" which undertake a job, submit the result of the computation, and then undertake another job (if available in the job queue). The script ends when there are no more jobs in the job queue.
This approach is useful when (1) You have a multi-processor/multicore CPU. (2) Your tasks are CPU intensive. (3) You are reasonably sure that the jobs are not internally parallelized to take advantage of multiple CPUs. In my case, I had two directories full of numerically-named image (.ppm) files whose PSNR's had to be compared using the pnmpsnr utility. Computing PSNR is a computationally intensive task. Running the comparisons serially (single process) was significantly slower than adopting a multiprocess approach.
The code below should get you started on parallelizing your computationally intensive script. You can download the script from here.

#! /usr/bin/env python
# Sachin Agarwal, Google, Twitter: sachinkagarwal, Web: http://sites.google.com/site/sachinkagarwal/ 
# November 2010
# Using Python to execute a bunch of job strings on multiple processors and print out the results of the jobs in the order they were listed in the job list (e.g. serially).
# Partly adapted from http://jeetworks.org/node/81

#These are needed by the multiprocessing scheduler
from multiprocessing import Queue
import multiprocessing
import commands
import sys

#These are specific to my jobs requirement
import os
import re
def RunCommand (fullCmd):
        return commands.getoutput(fullCmd)
        return "Error executing command %s" %(fullCmd)

class Worker(multiprocessing.Process):
    def __init__(self,
        # base class initialization
        self.work_queue = work_queue
        self.result_queue = result_queue
        self.kill_received = False
    def run(self):
        while (not (self.kill_received)) and (self.work_queue.empty()==False):
                job = self.work_queue.get_nowait()

            (jobid,runCmd) = job
            rtnVal = (jobid,RunCommand(runCmd))

def execute(jobs, num_processes=2):
    # load up work queue
    work_queue = multiprocessing.Queue()
    for job in jobs:
    # create a queue to pass to workers to store the results
    result_queue = multiprocessing.Queue()
    # spawn workers
    worker = []
    for i in range(num_processes):
        worker.append(Worker(work_queue, result_queue))
    # collect the results from the queue
    results = []
    while len(results) < len(jobs): #Beware - if a job hangs, then the whole program will hang
        result = result_queue.get()
    results.sort() # The tuples in result are sorted according to the first element - the jobid
    return (results) 

if __name__ == "__main__":
    import time #Code to measure time
    starttime = time.time() #Code to measure time
    jobs = [] #List of jobs strings to execute
    jobid = 0#Ordering of results in the results list returned

    #Code to generate my job strings. Generate your own, or load joblist into the jobs[] list from a text file
    lagFactor = 5
    ppmDir1 = sys.argv[1]
    ppmDir2 = sys.argv[2]
    decNumRe = re.compile(u"((\d+)\.(\d+))")
    ctr = 0
    for root, dirs, files in os.walk(ppmDir1):
        numFiles = len(files)
        fNameLen = len(files[0].split('.')[0])
        for fName in files:
            for offset in range(0,lagFactor):
                fNumber = int(fName.split('.')[0])
                targetFile =  '%0*d' % (fNameLen, max(fNumber-offset,1))
                targetPath = ppmDir2+'/'+targetFile+'.ppm'
                origPath = ppmDir1+'/'+fName
                fullCmd = "pnmpsnr "+origPath+' '+targetPath  #Linux command to execute
                jobs.append((jobid,fullCmd)) # Append to joblist
                jobid = jobid+1

    # run
    numProcesses = 2
    if len(sys.argv) == 3:
        numProcesses = int(sys.argv[1])
    results = execute(jobs,numProcesses) #job list and number of worker processes
    #Code to print out results as needed by me. Change this to suit your own need
    # dump results
    ctr = 0
    for r in results:
        (jobid, cmdop) = r  
        if jobid % lagFactor == 0:
            print jobid/lagFactor,
        print '\t',
            print cmdop.split()[10],
            print "Err",
        ctr = ctr+1

    print "Time taken = %f" %(time.time()-starttime) #Code to measure time

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