This is probably a trivial question, but how do I parallelize the following loop in python?
# setup output lists
output1 = list()
output2 = list()
output3 = list()
for j in range(0, 10):
# calc individual parameter value
parameter = j * offset
# call the calculation
out1, out2, out3 = calc_stuff(parameter = parameter)
# put results into correct output list
output1.append(out1)
output2.append(out2)
output3.append(out3)
I know how to start single threads in Python but I don't know how to "collect" the results.
Multiple processes would be fine too - whatever is easiest for this case. I'm using currently Linux but the code should run on Windows and Mac as-well.
What's the easiest way to parallelize this code?
Using multiple threads on CPython won't give you better performance for pure-Python code due to the global interpreter lock (GIL). I suggest using the multiprocessing module instead:
pool = multiprocessing.Pool(4)
out1, out2, out3 = zip(*pool.map(calc_stuff, range(0, 10 * offset, offset)))
Note that this won't work in the interactive interpreter.
To avoid the usual FUD around the GIL: There wouldn't be any advantage to using threads for this example anyway. You want to use processes here, not threads, because they avoid a whole bunch of problems.
from joblib import Parallel, delayed
def process(i):
return i * i
results = Parallel(n_jobs=2)(delayed(process)(i) for i in range(10))
print(results) # prints [0, 1, 4, 9, 16, 25, 36, 49, 64, 81]
The above works beautifully on my machine (Ubuntu, package joblib was pre-installed, but can be installed via pip install joblib).
Taken from https://blog.dominodatalab.com/simple-parallelization/
Edit on Mar 31, 2021: On joblib, multiprocessing, threading and asyncio
joblib in the above code uses import multiprocessing under the hood (and thus multiple processes, which is typically the best way to run CPU work across cores - because of the GIL)
You can let joblib use multiple threads instead of multiple processes, but this (or using import threading directly) is only beneficial if the threads spend considerable time on I/O (e.g. read/write to disk, send an HTTP request). For I/O work, the GIL does not block the execution of another thread
Since Python 3.7, as an alternative to threading, you can parallelise work with asyncio, but the same advice applies like for import threading (though in contrast to latter, only 1 thread will be used; on the plus side, asyncio has a lot of nice features which are helpful for async programming)
Using multiple processes incurs overhead. Think about it: Typically, each process needs to initialise/load everything you need to run your calculation. You need to check yourself if the above code snippet improves your wall time. Here is another one, for which I confirmed that joblib produces better results:
import time
from joblib import Parallel, delayed
def countdown(n):
while n>0:
n -= 1
return n
t = time.time()
for _ in range(20):
print(countdown(10**7), end=" ")
print(time.time() - t)
# takes ~10.5 seconds on medium sized Macbook Pro
t = time.time()
results = Parallel(n_jobs=2)(delayed(countdown)(10**7) for _ in range(20))
print(results)
print(time.time() - t)
# takes ~6.3 seconds on medium sized Macbook Pro
To parallelize a simple for loop, joblib brings a lot of value to raw use of multiprocessing. Not only the short syntax, but also things like transparent bunching of iterations when they are very fast (to remove the overhead) or capturing of the traceback of the child process, to have better error reporting.
Disclaimer: I am the original author of joblib.
This IS the easiest way to do it!
You can use asyncio. (Documentation can be found here). It is used as a foundation for multiple Python asynchronous frameworks that provide high-performance network and web-servers, database connection libraries, distributed task queues, etc. Plus it has both high-level and low-level APIs to accomodate any kind of problem.
import asyncio
def background(f):
def wrapped(*args, **kwargs):
return asyncio.get_event_loop().run_in_executor(None, f, *args, **kwargs)
return wrapped
#background
def your_function(argument):
#code
Now this function will be run in parallel whenever called without putting main program into wait state. You can use it to parallelize for loop as well. When called for a for loop, though loop is sequential but every iteration runs in parallel to the main program as soon as interpreter gets there.
1. Firing loop in parallel to main thread without any waiting
#background
def your_function(argument):
time.sleep(5)
print('function finished for '+str(argument))
for i in range(10):
your_function(i)
print('loop finished')
This produces following output:
loop finished
function finished for 4
function finished for 8
function finished for 0
function finished for 3
function finished for 6
function finished for 2
function finished for 5
function finished for 7
function finished for 9
function finished for 1
Update: May 2022
Although this answers the original question, there are ways where we can wait for loops to finish as requested by upvoted comments. So adding them here as well. Keys to implementations are: asyncio.gather() & run_until_complete(). Consider the following functions:
import asyncio
import time
def background(f):
def wrapped(*args, **kwargs):
return asyncio.get_event_loop().run_in_executor(None, f, *args, **kwargs)
return wrapped
#background
def your_function(argument, other_argument): # Added another argument
time.sleep(5)
print(f"function finished for {argument=} and {other_argument=}")
def code_to_run_before():
print('This runs Before Loop!')
def code_to_run_after():
print('This runs After Loop!')
2. Run in parallel but wait for finish
code_to_run_before() # Anything you want to run before, run here!
loop = asyncio.get_event_loop() # Have a new event loop
looper = asyncio.gather(*[your_function(i, 1) for i in range(1, 5)]) # Run the loop
results = loop.run_until_complete(looper) # Wait until finish
code_to_run_after() # Anything you want to run after, run here!
This produces following output:
This runs Before Loop!
function finished for argument=2 and other_argument=1
function finished for argument=3 and other_argument=1
function finished for argument=1 and other_argument=1
function finished for argument=4 and other_argument=1
This runs After Loop!
3. Run multiple loops in parallel and wait for finish
code_to_run_before() # Anything you want to run before, run here!
loop = asyncio.get_event_loop() # Have a new event loop
group1 = asyncio.gather(*[your_function(i, 1) for i in range(1, 2)]) # Run all the loops you want
group2 = asyncio.gather(*[your_function(i, 2) for i in range(3, 5)]) # Run all the loops you want
group3 = asyncio.gather(*[your_function(i, 3) for i in range(6, 9)]) # Run all the loops you want
all_groups = asyncio.gather(group1, group2, group3) # Gather them all
results = loop.run_until_complete(all_groups) # Wait until finish
code_to_run_after() # Anything you want to run after, run here!
This produces following output:
This runs Before Loop!
function finished for argument=3 and other_argument=2
function finished for argument=1 and other_argument=1
function finished for argument=6 and other_argument=3
function finished for argument=4 and other_argument=2
function finished for argument=7 and other_argument=3
function finished for argument=8 and other_argument=3
This runs After Loop!
4. Loops running sequentially but iterations of each loop running in parallel to one another
code_to_run_before() # Anything you want to run before, run here!
for loop_number in range(3):
loop = asyncio.get_event_loop() # Have a new event loop
looper = asyncio.gather(*[your_function(i, loop_number) for i in range(1, 5)]) # Run the loop
results = loop.run_until_complete(looper) # Wait until finish
print(f"finished for {loop_number=}")
code_to_run_after() # Anything you want to run after, run here!
This produces following output:
This runs Before Loop!
function finished for argument=3 and other_argument=0
function finished for argument=4 and other_argument=0
function finished for argument=1 and other_argument=0
function finished for argument=2 and other_argument=0
finished for loop_number=0
function finished for argument=4 and other_argument=1
function finished for argument=3 and other_argument=1
function finished for argument=2 and other_argument=1
function finished for argument=1 and other_argument=1
finished for loop_number=1
function finished for argument=1 and other_argument=2
function finished for argument=4 and other_argument=2
function finished for argument=3 and other_argument=2
function finished for argument=2 and other_argument=2
finished for loop_number=2
This runs After Loop!
Update: June 2022
This in its current form may not run on some versions of jupyter notebook. Reason being jupyter notebook utilizing event loop. To make it work on such jupyter versions, nest_asyncio (which would nest the event loop as evident from the name) is the way to go. Just import and apply it at the top of the cell as:
import nest_asyncio
nest_asyncio.apply()
And all the functionality discussed above should be accessible in a notebook environment as well.
What's the easiest way to parallelize this code?
Use a PoolExecutor from concurrent.futures. Compare the original code with this, side by side. First, the most concise way to approach this is with executor.map:
...
with ProcessPoolExecutor() as executor:
for out1, out2, out3 in executor.map(calc_stuff, parameters):
...
or broken down by submitting each call individually:
...
with ThreadPoolExecutor() as executor:
futures = []
for parameter in parameters:
futures.append(executor.submit(calc_stuff, parameter))
for future in futures:
out1, out2, out3 = future.result() # this will block
...
Leaving the context signals the executor to free up resources
You can use threads or processes and use the exact same interface.
A working example
Here is working example code, that will demonstrate the value of :
Put this in a file - futuretest.py:
from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor
from time import time
from http.client import HTTPSConnection
def processor_intensive(arg):
def fib(n): # recursive, processor intensive calculation (avoid n > 36)
return fib(n-1) + fib(n-2) if n > 1 else n
start = time()
result = fib(arg)
return time() - start, result
def io_bound(arg):
start = time()
con = HTTPSConnection(arg)
con.request('GET', '/')
result = con.getresponse().getcode()
return time() - start, result
def manager(PoolExecutor, calc_stuff):
if calc_stuff is io_bound:
inputs = ('python.org', 'stackoverflow.com', 'stackexchange.com',
'noaa.gov', 'parler.com', 'aaronhall.dev')
else:
inputs = range(25, 32)
timings, results = list(), list()
start = time()
with PoolExecutor() as executor:
for timing, result in executor.map(calc_stuff, inputs):
# put results into correct output list:
timings.append(timing), results.append(result)
finish = time()
print(f'{calc_stuff.__name__}, {PoolExecutor.__name__}')
print(f'wall time to execute: {finish-start}')
print(f'total of timings for each call: {sum(timings)}')
print(f'time saved by parallelizing: {sum(timings) - (finish-start)}')
print(dict(zip(inputs, results)), end = '\n\n')
def main():
for computation in (processor_intensive, io_bound):
for pool_executor in (ProcessPoolExecutor, ThreadPoolExecutor):
manager(pool_executor, calc_stuff=computation)
if __name__ == '__main__':
main()
And here's the output for one run of python -m futuretest:
processor_intensive, ProcessPoolExecutor
wall time to execute: 0.7326343059539795
total of timings for each call: 1.8033506870269775
time saved by parallelizing: 1.070716381072998
{25: 75025, 26: 121393, 27: 196418, 28: 317811, 29: 514229, 30: 832040, 31: 1346269}
processor_intensive, ThreadPoolExecutor
wall time to execute: 1.190223217010498
total of timings for each call: 3.3561410903930664
time saved by parallelizing: 2.1659178733825684
{25: 75025, 26: 121393, 27: 196418, 28: 317811, 29: 514229, 30: 832040, 31: 1346269}
io_bound, ProcessPoolExecutor
wall time to execute: 0.533886194229126
total of timings for each call: 1.2977914810180664
time saved by parallelizing: 0.7639052867889404
{'python.org': 301, 'stackoverflow.com': 200, 'stackexchange.com': 200, 'noaa.gov': 301, 'parler.com': 200, 'aaronhall.dev': 200}
io_bound, ThreadPoolExecutor
wall time to execute: 0.38941240310668945
total of timings for each call: 1.6049387454986572
time saved by parallelizing: 1.2155263423919678
{'python.org': 301, 'stackoverflow.com': 200, 'stackexchange.com': 200, 'noaa.gov': 301, 'parler.com': 200, 'aaronhall.dev': 200}
Processor-intensive analysis
When performing processor intensive calculations in Python, expect the ProcessPoolExecutor to be more performant than the ThreadPoolExecutor.
Due to the Global Interpreter Lock (a.k.a. the GIL), threads cannot use multiple processors, so expect the time for each calculation and the wall time (elapsed real time) to be greater.
IO-bound analysis
On the other hand, when performing IO bound operations, expect ThreadPoolExecutor to be more performant than ProcessPoolExecutor.
Python's threads are real, OS, threads. They can be put to sleep by the operating system and reawakened when their information arrives.
Final thoughts
I suspect that multiprocessing will be slower on Windows, since Windows doesn't support forking so each new process has to take time to launch.
You can nest multiple threads inside multiple processes, but it's recommended to not use multiple threads to spin off multiple processes.
If faced with a heavy processing problem in Python, you can trivially scale with additional processes - but not so much with threading.
There are a number of advantages to using Ray:
You can parallelize over multiple machines in addition to multiple cores (with the same code).
Efficient handling of numerical data through shared memory (and zero-copy serialization).
High task throughput with distributed scheduling.
Fault tolerance.
In your case, you could start Ray and define a remote function
import ray
ray.init()
#ray.remote(num_return_vals=3)
def calc_stuff(parameter=None):
# Do something.
return 1, 2, 3
and then invoke it in parallel
output1, output2, output3 = [], [], []
# Launch the tasks.
for j in range(10):
id1, id2, id3 = calc_stuff.remote(parameter=j)
output1.append(id1)
output2.append(id2)
output3.append(id3)
# Block until the results have finished and get the results.
output1 = ray.get(output1)
output2 = ray.get(output2)
output3 = ray.get(output3)
To run the same example on a cluster, the only line that would change would be the call to ray.init(). The relevant documentation can be found here.
Note that I'm helping to develop Ray.
I found joblib is very useful with me. Please see following example:
from joblib import Parallel, delayed
def yourfunction(k):
s=3.14*k*k
print "Area of a circle with a radius ", k, " is:", s
element_run = Parallel(n_jobs=-1)(delayed(yourfunction)(k) for k in range(1,10))
n_jobs=-1: use all available cores
Dask futures; I'm surprised no one has mentioned it yet . . .
from dask.distributed import Client
client = Client(n_workers=8) # In this example I have 8 cores and processes (can also use threads if desired)
def my_function(i):
output = <code to execute in the for loop here>
return output
futures = []
for i in <whatever you want to loop across here>:
future = client.submit(my_function, i)
futures.append(future)
results = client.gather(futures)
client.close()
why dont you use threads, and one mutex to protect one global list?
import os
import re
import time
import sys
import thread
from threading import Thread
class thread_it(Thread):
def __init__ (self,param):
Thread.__init__(self)
self.param = param
def run(self):
mutex.acquire()
output.append(calc_stuff(self.param))
mutex.release()
threads = []
output = []
mutex = thread.allocate_lock()
for j in range(0, 10):
current = thread_it(j * offset)
threads.append(current)
current.start()
for t in threads:
t.join()
#here you have output list filled with data
keep in mind, you will be as fast as your slowest thread
thanks #iuryxavier
from multiprocessing import Pool
from multiprocessing import cpu_count
def add_1(x):
return x + 1
if __name__ == "__main__":
pool = Pool(cpu_count())
results = pool.map(add_1, range(10**12))
pool.close() # 'TERM'
pool.join() # 'KILL'
The concurrent wrappers by the tqdm library are a nice way to parallelize longer-running code. tqdm provides feedback on the current progress and remaining time through a smart progress meter, which I find very useful for long computations.
Loops can be rewritten to run as concurrent threads through a simple call to thread_map, or as concurrent multi-processes through a simple call to process_map:
from tqdm.contrib.concurrent import thread_map, process_map
def calc_stuff(num, multiplier):
import time
time.sleep(1)
return num, num * multiplier
if __name__ == "__main__":
# let's parallelize this for loop:
# results = [calc_stuff(i, 2) for i in range(64)]
loop_idx = range(64)
multiplier = [2] * len(loop_idx)
# either with threading:
results_threading = thread_map(calc_stuff, loop_idx, multiplier)
# or with multi-processing:
results_processes = process_map(calc_stuff, loop_idx, multiplier)
Let's say we have an async function
async def work_async(self, student_name: str, code: str, loop):
"""
Some async function
"""
# Do some async procesing
That needs to be run on a large array. Some attributes are being passed to the program and some are used from property of dictionary element in the array.
async def process_students(self, student_name: str, loop):
market = sys.argv[2]
subjects = [...] #Some large array
batchsize = 5
for i in range(0, len(subjects), batchsize):
batch = subjects[i:i+batchsize]
await asyncio.gather(*(self.work_async(student_name,
sub['Code'],
loop)
for sub in batch))
This could be useful when implementing multiprocessing and parallel/ distributed computing in Python.
YouTube tutorial on using techila package
Techila is a distributed computing middleware, which integrates directly with Python using the techila package. The peach function in the package can be useful in parallelizing loop structures. (Following code snippet is from the Techila Community Forums)
techila.peach(funcname = 'theheavyalgorithm', # Function that will be called on the compute nodes/ Workers
files = 'theheavyalgorithm.py', # Python-file that will be sourced on Workers
jobs = jobcount # Number of Jobs in the Project
)
Have a look at this;
http://docs.python.org/library/queue.html
This might not be the right way to do it, but I'd do something like;
Actual code;
from multiprocessing import Process, JoinableQueue as Queue
class CustomWorker(Process):
def __init__(self,workQueue, out1,out2,out3):
Process.__init__(self)
self.input=workQueue
self.out1=out1
self.out2=out2
self.out3=out3
def run(self):
while True:
try:
value = self.input.get()
#value modifier
temp1,temp2,temp3 = self.calc_stuff(value)
self.out1.put(temp1)
self.out2.put(temp2)
self.out3.put(temp3)
self.input.task_done()
except Queue.Empty:
return
#Catch things better here
def calc_stuff(self,param):
out1 = param * 2
out2 = param * 4
out3 = param * 8
return out1,out2,out3
def Main():
inputQueue = Queue()
for i in range(10):
inputQueue.put(i)
out1 = Queue()
out2 = Queue()
out3 = Queue()
processes = []
for x in range(2):
p = CustomWorker(inputQueue,out1,out2,out3)
p.daemon = True
p.start()
processes.append(p)
inputQueue.join()
while(not out1.empty()):
print out1.get()
print out2.get()
print out3.get()
if __name__ == '__main__':
Main()
Hope that helps.
very simple example of parallel processing is
from multiprocessing import Process
output1 = list()
output2 = list()
output3 = list()
def yourfunction():
for j in range(0, 10):
# calc individual parameter value
parameter = j * offset
# call the calculation
out1, out2, out3 = calc_stuff(parameter=parameter)
# put results into correct output list
output1.append(out1)
output2.append(out2)
output3.append(out3)
if __name__ == '__main__':
p = Process(target=pa.yourfunction, args=('bob',))
p.start()
p.join()
I'm working on a project that needs to run two different CPU-intensive functions. Hence using a multiproccessing approach seems to be the way to go. The challenge that I'm facing is that one function has a slower runtime than the other one. For the sake of argument lets say that execute has a runtime of .1 seconds while update takes a full second to run. The goal is that while update is running execute will have calculated an output value 10 times. Once update has finished it needs to pass a set of parameters to execute which can then continue generating an output with the new set of parameters. After sometime update needs to run again and once more generate a new set of parameters.
Furthermore both functions will require a different set of input variables.
The image link below should hopefully visualize my conundrum a bit better.
function runtime visualisation
From what I've gathered (https://zetcode.com/python/multiprocessing/) using an asymetric mapping approach might be the way to go, but it doesn't really seem to work. Any help is greatly appreciated.
Pseudo Code
from multiprocessing import Pool
from datetime import datetime
import time
import numpy as np
class MyClass():
def __init__(self, inital_parameter_1, inital_parameter_2):
self.parameter_1 = inital_parameter_1
self.parameter_2 = inital_parameter_2
def execute(self, input_1, input_2, time_in):
print('starting execute function for time:' + str(time_in))
time.sleep(0.1) # wait for 100 milliseconds
# generate some output
output = (self.parameter_1 * input_1) + (self.parameter_2 + input_2)
print('exiting execute function')
return output
def update(self, update_input_1, update_input_2, time_in):
print('starting update function for time:' + str(time_in))
time.sleep(1) # wait for 1 second
# generate parameters
self.parameter_1 += update_input_1
self.parameter_2 += update_input_2
print('exiting update function')
def smap(f):
return f()
if __name__ == "__main__":
update_input_1 = 3
update_input_2 = 4
input_1 = 0
input_2 = 1
# initialize class
my_class = MyClass(1, 2)
# total runtime (arbitrary)
runtime = int(10e6)
# update_time (arbitrary)
update_time = np.array([10, 10e2, 15e4, 20e5])
for current_time in range(runtime):
# if time equals update time run both functions simultanously until update is complete
if any(update_time == current_time):
with Pool() as pool:
res = pool.map_async(my_class.smap, [my_class.execute(input_1, input_2, current_time),
my_class.update(update_input_1, update_input_2, current_time)])
# otherwise run only execute
else:
output = my_class.execute(input_1, input_2,current_time)
# increment input
input_1 += 1
input_2 += 2
I confess to not being able to fully following your code vis-a-vis your description. But I see some issues:
Method update is not returning any value other than None, which is implicitly returned due to the lack of a return statement.
Your with Pool() ...: block will call terminate upon block exit, which is immediately after your call to pool.map_async, which is non-blocking. But you have no provision to wait for the completion of this submitted task (terminate will most likely kill the running task before it completes).
What you are passing to the map_async function is the worker function name and an iterable. But you are invoking method calls to execute and update from the current main process and using their return values as elements of the iterable and these return values are definitely not functions suitable for passing to smap. So there is no multiprocessing being done and this is just plain wrong.
You are also creating and destroying process pools over and over again. Much better to create the process pool just once.
I would therefore recommend the following changes at the very least. But note that this code potentially generates tasks much faster than they can be completed and you could have millions of tasks queued up to run given your current runtime value, which could be quite a strain on system resources such as memory. So I've inserted some code that ensures that the rate of submitting tasks is throttled so that the number of incomplete submitted tasks is never more than three times the number of CPU cores available.
# we won't need heavy-duty numpy for what we are doing:
#import numpy as np
from multiprocessing import cpu_count
from threading import Lock
... # etc.
if __name__ == "__main__":
update_input_1 = 3
update_input_2 = 4
input_1 = 0
input_2 = 1
# initialize class
my_class = MyClass(1, 2)
# total runtime (arbitrary)
runtime = int(10e6)
# update_time (arbitrary)
# we don't need overhead of numpy (remove import of numpy):
#update_time = np.array([10, 10e2, 15e4, 20e5])
update_time = [10, 10e2, 15e4, 20e5]
tasks_submitted = 0
lock = Lock()
execute_output = []
def execute_result(result):
global tasks_submitted
with lock:
tasks_submitted -= 1
# result is the return value from method execute
# do something with it, e.g. execute_output.append(result)
pass
update_output = []
def update_result(result):
global tasks_submitted
with lock:
tasks_submitted -= 1
# result is the return value from method update
# do something with it, e.g. update_output.append(result)
pass
n_processors = cpu_count()
with Pool() as pool:
for current_time in range(runtime):
# if time equals update time run both functions simultanously until update is complete
#if any(update_time == current_time):
if current_time in update_time:
# run both update and execute:
pool.apply_async(my_class.update, args=(update_input_1, update_input_2, current_time), callback=update_result)
with lock:
tasks_submitted += 1
pool.apply_async(my_class.execute, args=(input_1, input_2, current_time), callback=execute_result)
with lock:
tasks_submitted += 1
# increment input
input_1 += 1
input_2 += 2
while tasks_submitted > n_processors * 3:
time.sleep(.05)
# Ensure all tasks have completed:
pool.close()
pool.join()
assert(tasks_submitted == 0)