July 10, 2020

Parallel programming with python multiprocessing

Any modern language has features to work with concurrency and parallelism, python is no exception. In this short introduction I will show you how to use multiple cores for data processing with python.

Let's start with a short example of multiprocessing:

class Worker(Process):
    def run(self):
        pass

worker_list = [Worker() for idx in range(cpu_count)]
[worker.start() for worker in worker_list]
[worker.join() for worker in worker_list]

Yes, with less than 10 lines of code you can take advantage of all cores available in your computer. In a short breakdown what we have:

  • a class that inherit from multiprocessing.Process
  • a run() method override (the only thing required from the original abstraction)
  • a list of workers matching the number of cores in your machine.
  • a list of started workers
  • a list of finished workers joined back to the main process.

Let's move ahead and create something fancier. We are going to create a bunch of workers to do sequence alignment, each worker will consume one record from a queue, process it and pick another record. This will be repeated until the queue dry-off.

Let's start extending or Worker class, we need to include some logging (the print statements) a infinity loop that reads from a queue and our expensive computation logic:

REFERENCE = "GAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGCAG"

class Worker(Process):
    def __init__(self, name, queue):
        super().__init__()
        self.name = name
        self.queue = queue

    def run(self):
        print(f"Started {self.name}")
        count = 0
        while True:
            try:
                sequence = self.queue.get(timeout=5)
                self.compute(sequence)
                count += 1
            except Empty:
                break
        print(f"{self.name} done with {count} records")

    @staticmethod
    def compute(sequence):
        s1 = DNA(REFERENCE)
        s2 = DNA(sequence)
        global_pairwise_align_nucleotide(s1, s2, penalize_terminal_gaps=True)

We also need a function to populate our queue, for this short example it's going to create one thousand random sequences with 64 base pairs:

def load_record_into_queue(queue):
    for _ in range(1000):
        sequence = "".join(choice("ACTG") for _ in range(64))
        queue.put(sequence)

Next we need to glue everything together in the main:

if __name__ == "__main__":
    worker_list = []
    queue = Queue()
    for idx in range(cpu_count()):
        worker = Worker(f"worker-{idx}", queue)
        worker_list.append(worker)

    [worker.start() for worker in worker_list]
    load_record_into_queue(queue)
    [worker.join() for worker in worker_list]

One important thing to notice is that the load_record_into_queue is call after we start the workers, this is important! Since this function is running in the main process, if you call it before the workers start, it's going to block until everything is loaded in the queue, and if your function is actually populating the queue from a infinite stream of data your workers will never get the chance to start.

Multiprocessing vs Threads

It's hard to tell when you should be using multiprocessing or multithreading. In theory it's simple: if you code is cpu bounded, it will likely benefit from multiprocessing, if your code is i/o bounded you may be better with threads. Sadly real life is not so black and white as you may have a function that's 50/50. In general if you go with multiprocessing it's less likely that you will make a mistake. But you get other problems...

The number of process you can handle usually will be lower than the number of threads, as process are more expensive and will eat more RAM. Other problem is your ability to share data, while threads will get you more options it also gives you more opportunities to shoot yourself in the foot.

A few considerations about computation

Not all computation are made equally. If you create two functions for two different computations, and those functions eat 100% of a single core during the same amount of time, when you parallelize them, they will have different improvement over extra core additions.

Never expect that parallelism is going to give you linearity, usually the jump from one process to two process is where you get the biggest improvement (maybe even cutting the execution time by half), but the 3rd core is going to cut less, and so on... Most tools that implement some level of parallelism will have a plateau, at some point adding more cores will give the tool a negligible gain in speed.

That's it, the full version including all imports should look like this:

from _queue import Empty
from multiprocessing import Process, Queue, cpu_count
from random import choice
from skbio import DNA
from skbio.alignment import global_pairwise_align_nucleotide

REFERENCE = "GAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGCAG"


class Worker(Process):
    def __init__(self, name, queue):
        super().__init__()
        self.name = name
        self.queue = queue

    def run(self):
        print(f"Started {self.name}")
        count = 0
        while True:
            try:
                sequence = self.queue.get(timeout=5)
                self.compute(sequence)
                count += 1
            except Empty:
                break
        print(f"{self.name} done with {count} records")

    @staticmethod
    def compute(sequence):
        s1 = DNA(REFERENCE)
        s2 = DNA(sequence)
        global_pairwise_align_nucleotide(s1, s2, penalize_terminal_gaps=True)


def load_record_into_queue(queue):
    for _ in range(1000):
        sequence = "".join(choice("ACTG") for _ in range(64))
        queue.put(sequence)


if __name__ == "__main__":
    worker_list = []
    queue = Queue()
    for idx in range(cpu_count()):
        worker = Worker(f"worker-{idx}", queue)
        worker_list.append(worker)

    [worker.start() for worker in worker_list]
    load_record_into_queue(queue)
    [worker.join() for worker in worker_list]

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