I have searched the site but I am not sure precisely what terms would yield relevant answers, my apologies if this question is redundant.
I need to process a very very large matrix (14,000,000 * 250,000) and would like to exploit Python's multiprocessing module to speed things up. For each pair of columns in the matrix I need to apply a function which will then store the results in a proprietary class.
I will be implementing a double four loop which provides the necessary combinations of columns.
I do not want to load up a pool with 250,000 tasks as I fear the memory usage will be significant.Ideally, I would like to have one column then be tasked out amongst the pool I.e
Process 1 takes Column A and Column B and a function F takes A,B and G and then stores the result in Class G[A,B]
Process 2 takes Column A and Column C and proceeds similarly
The processes will never access the same element of G.
So I would like to pause the for loop every N tasks. The set/get methods of G will be overriden to perform some back end tasks.
What I do not understand is whether or not pausing the loop is necessary? I.e is Python smart enough to only take what it can work on? Or will it be populating a massive amount of tasks?
Lastly, I am unclear of how the results work. I just want them to be set in G and not return anything. I do not want to have to worry about about .get() etc. but from my understanding the pool method returns a result object. Can I just ignore this?
Is there a better way? Am I completly lost?
First off - you will want to create a multiprocessing pool class. You setup how many workers you want and then use map to start up tasks. I am sure you already know but here is the python multiprocessing docs.
You say that you don't want to return data because you don't need to but how are you planning on viewing results? Will each task write the data to disk? To pass data between your processes you will want to use something like the multiprocessing queue.
Here is example code from the link on how to use process and queue:
from multiprocessing import Process, Queue
def f(q):
q.put([42, None, 'hello'])
if __name__ == '__main__':
q = Queue()
p = Process(target=f, args=(q,))
p.start()
print q.get() # prints "[42, None, 'hello']"
p.join()
And this is an example of using the Pool:
from multiprocessing import Pool
def f(x):
return x*x
if __name__ == '__main__':
pool = Pool(processes=4) # start 4 worker processes
result = pool.apply_async(f, [10]) # evaluate "f(10)" asynchronously
print result.get(timeout=1) # prints "100" unless your computer is *very* slow
print pool.map(f, range(10)) # prints "[0, 1, 4,..., 81]"
Edit: #goncalopp makes a very important point that you may not want to do heavy numerical calculations in python due to how slow it is. Numpy is a great package for doing number crunching.
If you are heavily IO bound due to writing to disk on each process you should consider running something like 4*num_processors so that you always have something to do. You also should make sure you have a very fast disk :)
Related
I am trying to figure out how to perfom a multiprocessing task with an unusual formulation.
Basically, given two lists containing 10 matrices for each list, I have to check if applying an operation (that I'll call fn) gives the same results if the input is (A, B) or vice versa (B, A).
With a sequential approach, the solution is streightforward:
#Given
A = [matrix_a1, ... , matrix_a10]
B = [matrix_b1, ... , matrix_b10]
AB_BA= [fn(A[i], B[i])==fn(B[i], A[i]) for i in range(0, len(A)) ]
The next task is a bit strange because it requires setting strictly more than ten threads and applying multiprocessing. The restriction is that you can not assign all the single comparisons to ten different processes because the remaining processes will be unused. I do not know why the request seems to be using "process" and "thread" interchangeably.
This task seems a bit confusing because in multiprocessing, generally, you set the maximum number of workers, not the minimum.
I tried to use a solution that uses a ProcessPoolExecutor, as follows:
def equality(A, B,i):
res= fn(A[i], B[i]) == fn(B[i],A[i] )
return(res)
with concurrent.futures.ProcessPoolExecutor(max_workers=20) as executor:
idx=range(0, len(A))
results= executor.map(equality, A, B, idx)
for result in results:
print(result)
My problem is that I am not sure how to check resource usage. I have naively tried to monitor the CPU usage using the ubuntu system monitor as well as "top" from the command line.
In addition, this solution is the most efficient among those I tried, but there is not a direct specification to use at least 11 workers, so this solution seems not to stick with what was requested.
I also tried other solutions, such as using pool directly. This causes to evoke 10 python instances using top, but again, not more than 10. Here's what I tried:
def equality(A, B):
res=fn(A, B) == fn(B,A )
return(res)
with mp.Pool(20) as p:
print(p.starmap(equality, ((A[i], B[i]) for i in range(0, len(A)))))
Do you have any suggestions to address this request as well as monitor the resource usage to be sure it is working as expected?
Thank you very much for your help in advance.
I wish you had published the actual problem word for word, since your description is a bit unclear. But this is what I know (or think I know):
Unless the amount of CPU processing done by your worker function equality is great enough so that what is gained by running the function in parallel more than offsets the additional multiprocessing overhead you would not otherwise have if not using multiprocessing (i.e. starting processes, moving data from one address space to another, etc.), your multiprocessing code will run more slowly. Therefore, you should design your worker function to do the most work possible and to pass as little data as possible.
When you specify ...
results = executor.map(equality, A, B, idx)
... your equality function will be invoked once for each element of A, B and idx. So what is being passed is not the entire lists A and B but rather individual elements (e.g. matrix_a1 and matrix_b1). Therefore, there is no point in even passing an idx argument:
def equality(matrix_a, matrix_b):
"""
matrix_a and matrix_a are each single elements of
lists A and B respecticely.
"""
return fn(matrix_a) == fn(matrix_b)
def main():
from os import cpu_count
from concurrent.futures import ProcessPoolExecutor
A = [matrix_a1, ... , matrix_a10]
B = [matrix_b1, ... , matrix_b10]
# Do not create more processes then we have either
# CPU cores or the number of tasks that need to submit:
pool_size = min(cpu_count(), len(A))
with ProcessPoolExecutor(max_workers=pool_size) as executor:
AB_BA = list(executor.map(equality, A, B))
# This will be a list of 10 elements, each either `True` or `False`:
print(AB_BA)
# Required for Windows:
if __name__ == '__main__':
main()
So we will be submitting 10 tasks to a pool size of 10. Internally there is a "task queue" on which all the arguments being passed to equality exist:
matrix_a1, matrix_b1 # task 1
matrix_a2, matrix_b2 # task 2
...
matrix_a10, matrix_b10 # task 10
Any process in the pool that is idle will grap the next task in the queue to work on and the results will be returned in task submission order. But since equality is such a short-running function unless function fn is sufficiently complicated, there is the possibility that the pool process that grabs the first task can complete it and then grab the second task before some other pool process is dispatched by the operating system and can grab it. So there is no guarantee that all 10 tasks will be worked on in parallel by 10 pool processes even if function fn is sufficiently CPU-intensive. If you were to insert a call to time.sleep(.1) at the beginning of equality, that would give the other pool processes a chance to "wake up" and grab its own task from the task queue. But that would slow your program down even more since sleeping for this purposes is totally non-productive. But the point I am trying to make is that you cannot ensure that all pool processes will always be active concurrently.
Suppose I have the following in Python
# A loop
for i in range(10000):
Do Task A
# B loop
for i in range(10000):
Do Task B
How do I run these loops simultaneously in Python?
If you want concurrency, here's a very simple example:
from multiprocessing import Process
def loop_a():
while 1:
print("a")
def loop_b():
while 1:
print("b")
if __name__ == '__main__':
Process(target=loop_a).start()
Process(target=loop_b).start()
This is just the most basic example I could think of. Be sure to read http://docs.python.org/library/multiprocessing.html to understand what's happening.
If you want to send data back to the program, I'd recommend using a Queue (which in my experience is easiest to use).
You can use a thread instead if you don't mind the global interpreter lock. Processes are more expensive to instantiate but they offer true concurrency.
There are many possible options for what you wanted:
use loop
As many people have pointed out, this is the simplest way.
for i in xrange(10000):
# use xrange instead of range
taskA()
taskB()
Merits: easy to understand and use, no extra library needed.
Drawbacks: taskB must be done after taskA, or otherwise. They can't be running simultaneously.
multiprocess
Another thought would be: run two processes at the same time, python provides multiprocess library, the following is a simple example:
from multiprocessing import Process
p1 = Process(target=taskA, args=(*args, **kwargs))
p2 = Process(target=taskB, args=(*args, **kwargs))
p1.start()
p2.start()
merits: task can be run simultaneously in the background, you can control tasks(end, stop them etc), tasks can exchange data, can be synchronized if they compete the same resources etc.
drawbacks: too heavy!OS will frequently switch between them, they have their own data space even if data is redundant. If you have a lot tasks (say 100 or more), it's not what you want.
threading
threading is like process, just lightweight. check out this post. Their usage is quite similar:
import threading
p1 = threading.Thread(target=taskA, args=(*args, **kwargs))
p2 = threading.Thread(target=taskB, args=(*args, **kwargs))
p1.start()
p2.start()
coroutines
libraries like greenlet and gevent provides something called coroutines, which is supposed to be faster than threading. No examples provided, please google how to use them if you're interested.
merits: more flexible and lightweight
drawbacks: extra library needed, learning curve.
Why do you want to run the two processes at the same time? Is it because you think they will go faster (there is a good chance that they wont). Why not run the tasks in the same loop, e.g.
for i in range(10000):
doTaskA()
doTaskB()
The obvious answer to your question is to use threads - see the python threading module. However threading is a big subject and has many pitfalls, so read up on it before you go down that route.
Alternatively you could run the tasks in separate proccesses, using the python multiprocessing module. If both tasks are CPU intensive this will make better use of multiple cores on your computer.
There are other options such as coroutines, stackless tasklets, greenlets, CSP etc, but Without knowing more about Task A and Task B and why they need to be run at the same time it is impossible to give a more specific answer.
from threading import Thread
def loopA():
for i in range(10000):
#Do task A
def loopB():
for i in range(10000):
#Do task B
threadA = Thread(target = loopA)
threadB = Thread(target = loobB)
threadA.run()
threadB.run()
# Do work indepedent of loopA and loopB
threadA.join()
threadB.join()
You could use threading or multiprocessing.
How about: A loop for i in range(10000): Do Task A, Do Task B ? Without more information i dont have a better answer.
I find that using the "pool" submodule within "multiprocessing" works amazingly for executing multiple processes at once within a Python Script.
See Section: Using a pool of workers
Look carefully at "# launching multiple evaluations asynchronously may use more processes" in the example. Once you understand what those lines are doing, the following example I constructed will make a lot of sense.
import numpy as np
from multiprocessing import Pool
def desired_function(option, processes, data, etc...):
# your code will go here. option allows you to make choices within your script
# to execute desired sections of code for each pool or subprocess.
return result_array # "for example"
result_array = np.zeros("some shape") # This is normally populated by 1 loop, lets try 4.
processes = 4
pool = Pool(processes=processes)
args = (processes, data, etc...) # Arguments to be passed into desired function.
multiple_results = []
for i in range(processes): # Executes each pool w/ option (1-4 in this case).
multiple_results.append(pool.apply_async(param_process, (i+1,)+args)) # Syncs each.
results = np.array(res.get() for res in multiple_results) # Retrieves results after
# every pool is finished!
for i in range(processes):
result_array = result_array + results[i] # Combines all datasets!
The code will basically run the desired function for a set number of processes. You will have to carefully make sure your function can distinguish between each process (hence why I added the variable "option".) Additionally, it doesn't have to be an array that is being populated in the end, but for my example, that's how I used it. Hope this simplifies or helps you better understand the power of multiprocessing in Python!
I have a large program (specifically, a function) that I'm attempting to parallelize using a JoinableQueue and the multiprocessing map_async method. The function that I'm working with does several operations on multidimensional arrays, so I break up each array into sections, and each section evaluates independently; however I need to stitch together one of the arrays early on, but the "stitch" happens before the "evaluate" and I need to introduce some kind of delay in the JoinableQueue. I've searched all over for a workable solution but I'm very new to multiprocessing and most of it goes over my head.
This phrasing may be confusing- apologies. Here's an outline of my code (I can't put all of it because it's very long, but I can provide additional detail if needed)
import numpy as np
import multiprocessing as mp
from multiprocessing import Pool, Pipe, JoinableQueue
def main_function(section_number):
#define section sizes
array_this_section = array[:,start:end+1,:]
histogram_this_section = np.zeros((3, dataset_size, dataset_size))
#start and end are defined according to the size of the array
#dataset_size is to show that the histogram is a different size than the array
for m in range(1,num_iterations+1):
#do several operations- each section of the array
#corresponds to a section on the histogram
hist_queue.put(histogram_this_section)
#each process sends their own part of the histogram outside of the pool
#to be combined with every other part- later operations
#in this function must use the full histogram
hist_queue.join()
full_histogram = full_hist_queue.get()
full_hist_queue.task_done()
#do many more operations
hist_queue = JoinableQueue()
full_hist_queue = JoinableQueue()
if __name__ == '__main__':
pool = mp.Pool(num_sections)
args = np.arange(num_sections)
pool.map_async(main_function, args, chunksize=1)
#I need the map_async because the program is designed to display an output at the
#end of each iteration, and each output must be a compilation of all processes
#a few variable definitions go here
for m in range(1,num_iterations+1):
for i in range(num_sections):
temp_hist = hist_queue.get() #the code hangs here because the queue
#is attempting to get before anything
#has been put
hist_full += temp_hist
for i in range(num_sections):
hist_queue.task_done()
for i in range(num_sections):
full_hist_queue.put(hist_full) #the full histogram is sent back into
#the pool
full_hist_queue.join()
#etc etc
pool.close()
pool.join()
I'm pretty sure that your issue is how you're creating the Queues and trying to share them with the child processes. If you just have them as global variables, they may be recreated in the child processes instead of inherited (the exact details depend on what OS and/or context you're using for multiprocessing).
A better way to go about solving this issue is to avoid using multiprocessing.Pool to spawn your processes and instead explicitly create Process instances for your workers yourself. This way you can pass the Queue instances to the processes that need them without any difficulty (it's technically possible to pass the queues to the Pool workers, but it's awkward).
I'd try something like this:
def worker_function(section_number, hist_queue, full_hist_queue): # take queues as arguments
# ... the rest of the function can work as before
# note, I renamed this from "main_function" since it's not running in the main process
if __name__ == '__main__':
hist_queue = JoinableQueue() # create the queues only in the main process
full_hist_queue = JoinableQueue() # the workers don't need to access them as globals
processes = [Process(target=worker_function, args=(i, hist_queue, full_hist_queue)
for i in range(num_sections)]
for p in processes:
p.start()
# ...
If the different stages of your worker function are more or less independent of one another (that is, the "do many more operations" step doesn't depend directly on the "do several operations" step above it, just on full_histogram), you might be able to keep the Pool and instead split up the different steps into separate functions, which the main process could call via several calls to map on the pool. You don't need to use your own Queues in this approach, just the ones built in to the Pool. This might be best especially if the number of "sections" you're splitting the work up into doesn't correspond closely with the number of processor cores on your computer. You can let the Pool match the number of cores, and have each one work on several sections of the data in turn.
A rough sketch of this would be something like:
def worker_make_hist(section_number):
# do several operations, get a partial histogram
return histogram_this_section
def worker_do_more_ops(section_number, full_histogram):
# whatever...
return some_result
if __name__ == "__main__":
pool = multiprocessing.Pool() # by default the size will be equal to the number of cores
for temp_hist in pool.imap_unordered(worker_make_hist, range(number_of_sections)):
hist_full += temp_hist
some_results = pool.starmap(worker_do_more_ops, zip(range(number_of_sections),
itertools.repeat(hist_full)))
I have a problem running multiple processes in python3 .
My program does the following:
1. Takes entries from an sqllite database and passes them to an input_queue
2. Create multiple processes that take items off the input_queue, run it through a function and output the result to the output queue.
3. Create a thread that takes items off the output_queue and prints them (This thread is obviously started before the first 2 steps)
My problem is that currently the 'function' in step 2 is only run as many times as the number of processes set, so for example if you set the number of processes to 8, it only runs 8 times then stops. I assumed it would keep running until it took all items off the input_queue.
Do I need to rewrite the function that takes the entries out of the database (step 1) into another process and then pass its output queue as an input queue for step 2?
Edit:
Here is an example of the code, I used a list of numbers as a substitute for the database entries as it still performs the same way. I have 300 items on the list and I would like it to process all 300 items, but at the moment it just processes 10 (the number of processes I have assigned)
#!/usr/bin/python3
from multiprocessing import Process,Queue
import multiprocessing
from threading import Thread
## This is the class that would be passed to the multi_processing function
class Processor:
def __init__(self,out_queue):
self.out_queue = out_queue
def __call__(self,in_queue):
data_entry = in_queue.get()
result = data_entry*2
self.out_queue.put(result)
#Performs the multiprocessing
def perform_distributed_processing(dbList,threads,processor_factory,output_queue):
input_queue = Queue()
# Create the Data processors.
for i in range(threads):
processor = processor_factory(output_queue)
data_proc = Process(target = processor,
args = (input_queue,))
data_proc.start()
# Push entries to the queue.
for entry in dbList:
input_queue.put(entry)
# Push stop markers to the queue, one for each thread.
for i in range(threads):
input_queue.put(None)
data_proc.join()
output_queue.put(None)
if __name__ == '__main__':
output_results = Queue()
def output_results_reader(queue):
while True:
item = queue.get()
if item is None:
break
print(item)
# Establish results collecting thread.
results_process = Thread(target = output_results_reader,args = (output_results,))
results_process.start()
# Use this as a substitute for the database in the example
dbList = [i for i in range(300)]
# Perform multi processing
perform_distributed_processing(dbList,10,Processor,output_results)
# Wait for it all to finish.
results_process.join()
A collection of processes that service an input queue and write to an output queue is pretty much the definition of a process pool.
If you want to know how to build one from scratch, the best way to learn is to look at the source code for multiprocessing.Pool, which is pretty simply Python, and very nicely written. But, as you might expect, you can just use multiprocessing.Pool instead of re-implementing it. The examples in the docs are very nice.
But really, you could make this even simpler by using an executor instead of a pool. It's hard to explain the difference (again, read the docs for both modules), but basically, a future is a "smart" result object, which means instead of a pool with a variety of different ways to run jobs and get results, you just need a dumb thing that doesn't know how to do anything but return futures. (Of course in the most trivial cases, the code looks almost identical either way…)
from concurrent.futures import ProcessPoolExecutor
def Processor(data_entry):
return data_entry*2
def perform_distributed_processing(dbList, threads, processor_factory):
with ProcessPoolExecutor(processes=threads) as executor:
yield from executor.map(processor_factory, dbList)
if __name__ == '__main__':
# Use this as a substitute for the database in the example
dbList = [i for i in range(300)]
for result in perform_distributed_processing(dbList, 8, Processor):
print(result)
Or, if you want to handle them as they come instead of in order:
def perform_distributed_processing(dbList, threads, processor_factory):
with ProcessPoolExecutor(processes=threads) as executor:
fs = (executor.submit(processor_factory, db) for db in dbList)
yield from map(Future.result, as_completed(fs))
Notice that I also replaced your in-process queue and thread, because it wasn't doing anything but providing a way to interleave "wait for the next result" and "process the most recent result", and yield (or yield from, in this case) does that without all the complexity, overhead, and potential for getting things wrong.
Don't try to rewrite the whole multiprocessing library again. I think you can use any of multiprocessing.Pool methods depending on your needs - if this is a batch job you can even use the synchronous multiprocessing.Pool.map() - only instead of pushing to input queue, you need to write a generator that yields input to the threads.
I'm sorry if this is too simple for some people, but I still don't get the trick with python's multiprocessing. I've read
http://docs.python.org/dev/library/multiprocessing
http://pymotw.com/2/multiprocessing/basics.html
and many other tutorials and examples that google gives me... many of them from here too.
Well, my situation is that I have to compute many numpy matrices and I need to store them in a single numpy matrix afterwards. Let's say I want to use 20 cores (or that I can use 20 cores) but I haven't managed to successfully use the pool resource since it keeps the processes alive till the pool "dies". So I thought on doing something like this:
from multiprocessing import Process, Queue
import numpy as np
def f(q,i):
q.put( np.zeros( (4,4) ) )
if __name__ == '__main__':
q = Queue()
for i in range(30):
p = Process(target=f, args=(q,))
p.start()
p.join()
result = q.get()
while q.empty() == False:
result += q.get()
print result
but then it looks like the processes don't run in parallel but they run sequentially (please correct me if I'm wrong) and I don't know if they die after they do their computation (so for more than 20 processes the ones that did their part leave the core free for another process). Plus, for a very large number (let's say 100.000), storing all those matrices (which may be really big too) in a queue will use a lot of memory, rendering the code useless since the idea is to put every result on each iteration in the final result, like using a lock (and its acquire() and release() methods), but if this code isn't for parallel processing, the lock is useless too...
I hope somebody may help me.
Thanks in advance!
You are correct, they are executing sequentially in your example.
p.join() causes the current thread to block until it is finished executing. You'll either want to join your processes individually outside of your for loop (e.g., by storing them in a list and then iterating over it) or use something like numpy.Pool and apply_async with a callback. That will also let you add it to your results directly rather than keeping the objects around.
For example:
def f(i):
return i*np.identity(4)
if __name__ == '__main__':
p=Pool(5)
result = np.zeros((4,4))
def adder(value):
global result
result += value
for i in range(30):
p.apply_async(f, args=(i,), callback=adder)
p.close()
p.join()
print result
Closing and then joining the pool at the end ensures that the pool's processes have completed and the result object is finished being computed. You could also investigate using Pool.imap as a solution to your problem. That particular solution would look something like this:
if __name__ == '__main__':
p=Pool(5)
result = np.zeros((4,4))
im = p.imap_unordered(f, range(30), chunksize=5)
for x in im:
result += x
print result
This is cleaner for your specific situation, but may not be for whatever you are ultimately trying to do.
As to storing all of your varied results, if I understand your question, you can just add it off into a result in the callback method (as above) or item-at-a-time using imap/imap_unordered (which still stores the results, but you'll clear it as it builds). Then it doesn't need to be stored for longer than it takes to add to the result.