[FIXED] Python multiprocess: run several instances of a class, keep all child processes in memory

Issue

First, I'd like to thank the StackOverflow community for the tremendous help it provided me over the years, without me having to ask a single question. I could not find anything that I can relate to my problem, though it is probably due to my lack of understanding of the subject, rather than the absence of a response on the website. My apologies in advance if this is a duplicate.

I am relatively new to multiprocess; some time ago I succeeded in using multiprocessing.pools in a very simple way, where I didn't need any feedback between the child processes. Now I am facing a much more complicated problem, and I am just lost in the documentation about multiprocessing. I hence ask for you help, your kindness and your patience.

I am trying to build a parallel tempering monte-carlo algorithm, from a class.

The basic class very roughly goes as follows:

import numpy as np

class monte_carlo:

    def __init__(self):
        self.x=np.ones((1000,3))
        self.E=np.mean(self.x)
        self.Elist=[]

    def simulation(self,temperature):
        self.T=temperature
        for i in range(3000):
            self.MC_step()
            if i%10==0:
                self.Elist.append(self.E)
        return

    def MC_step(self):
        x=self.x.copy()
        k = np.random.randint(1000)
        x[k] = (x[k] + np.random.uniform(-1,1,3))
        temp_E=np.mean(self.x)
        if np.random.random()<np.exp((self.E-temp_E)/self.T):
            self.E=temp_E
            self.x=x
        return

Obviously, I simplified a great deal (actual class is 500 lines long!), and built fake functions for simplicity: __init__ takes a bunch of parameters as arguments, there are many more lists of measurement else than self.Elist, and also many arrays derived from self.X that I use to compute them. The key point is that each instance of the class contains a lot of informations that I want to keep in memory, and that I don't want to copy over and over again, to avoid dramatic slowing down. Else I would just use the multiprocessing.pool module.

Now, the parallelization I want to do, in pseudo-code:

def proba(dE,pT):
    return np.exp(-dE/pT)  
          
Tlist=[1.1,1.2,1.3]
N=len(Tlist)
G=[]
for _ in range(N):
    G.append(monte_carlo())

for _ in range(5):

    for i in range(N): # this loop should be ran in multiprocess
        G[i].simulation(Tlist[i])
    
    for i in range(N//2): 
        dE=G[i].E-G[i+1].E
        pT=G[i].T + G[i+1].T
        p=proba(dE,pT) # (proba is a function, giving a probability depending on dE)
        if np.random.random() < p: 
             T_temp = G[i].T
             G[i].T = G[i+1].T
             G[i+1].T = T_temp

Synthesis: I want to run several instances of my monte-carlo class in parallel child processes, with different values for a parameter T, then periodically pause everything to change the different T's, and run again the child processes/class instances, from where they paused. Doing this, I want each class-instance/child-process to stay independent from one another, save its current state with all internal variables while it is paused, and do as few copies as possible. This last point is critical, as the arrays inside the class are quite big (some are 1000x1000), and a copy will therefore very quickly become quite time-costly.

Thanks in advance, and sorry if I am not clear...

Edit: I am using a distant machine with many (64) CPUs, running on Debian GNU/Linux 10 (buster).

Edit2: I made a mistake in my original post: in the end, the temperatures must be exchanged between the class-instances, and not inside the global Tlist.

Edit3: Charchit answer works perfectly for the test code, on both my personal machine and the distant machine I am usually using for running my codes. I hence check this as the accepted answer. However, I want to report here that, inserting the actual, more complicated code, instead of the oversimplified monte_carlo class, the distant machine gives me some strange errors:

Unable to init server: Could not connect: Connection refused

(CMC_temper_all.py:55509): Gtk-WARNING **: ##:##:##:###: Locale not supported by C library.
    Using the fallback 'C' locale.
Unable to init server: Could not connect: Connection refused

(CMC_temper_all.py:55509): Gdk-CRITICAL **: ##:##:##:###: 

gdk_cursor_new_for_display: assertion 'GDK_IS_DISPLAY (display)' failed

(CMC_temper_all.py:55509): Gdk-CRITICAL **: ##:##:##:###: gdk_cursor_new_for_display: assertion 'GDK_IS_DISPLAY (display)' failed

The "##:##:##:###" are (or seems like) IP adresses. Without the call to set_start_method('spawn') this error shows only once, in the very beginning, while when I use this method, it seems to show at every occurrence of result.get()... The strangest thing is that the code seems otherwise to work fine, does not crash, produces the datafiles I then ask it to, etc...

I think this would deserve to publish a new question, but I put it here nonetheless in case someone has a quick answer. If not, I will resort to add one by one the variables, methods, etc... that are present in my actual code but not in the test example, to try and find the origin of the bug. My best guess for now is that the memory space required by each child-process with the actual code, is too large for the distant machine to accept it, due to some restrictions implemented by the admin.

Solution

What you are looking for is sharing state between processes. As per the documentation, you can either create shared memory, which is restrictive about the data it can store and is not thread-safe, but offers better speed and performance; or you can use server processes through managers. The latter is what we are going to use since you want to share whole objects of user-defined datatypes. Keep in mind that using managers will impact speed of your code depending on the complexity of the arguments that you pass and receive, to and from the managed objects.

Managers, proxies and pickling

As mentioned, managers create server processes to store objects, and allow access to them through proxies. I have answered a question with better details on how they work, and how to create a suitable proxy here. We are going to use the same proxy defined in the linked answer, with some variations. Namely, I have replaced the factory functions inside the __getattr__ to something that can be pickled using pickle. This means that you can run instance methods of managed objects created with this proxy without resorting to using multiprocess. The result is this modified proxy:

from multiprocessing.managers import NamespaceProxy, BaseManager
import types
import numpy as np


class A:
    def __init__(self, name, method):
        self.name = name
        self.method = method

    def get(self, *args, **kwargs):
        return self.method(self.name, args, kwargs)


class ObjProxy(NamespaceProxy):
    """Returns a proxy instance for any user defined data-type. The proxy instance will have the namespace and
    functions of the data-type (except private/protected callables/attributes). Furthermore, the proxy will be
    pickable and can its state can be shared among different processes. """

    def __getattr__(self, name):
        result = super().__getattr__(name)
        if isinstance(result, types.MethodType):
            return A(name, self._callmethod).get
        return result

Solution

Now we only need to make sure that when we are creating objects of monte_carlo, we do so using managers and the above proxy. For that, we create a class constructor called create. All objects for monte_carlo should be created with this function. With that, the final code looks like this:

from multiprocessing import Pool
from multiprocessing.managers import NamespaceProxy, BaseManager
import types
import numpy as np


class A:
    def __init__(self, name, method):
        self.name = name
        self.method = method

    def get(self, *args, **kwargs):
        return self.method(self.name, args, kwargs)


class ObjProxy(NamespaceProxy):
    """Returns a proxy instance for any user defined data-type. The proxy instance will have the namespace and
    functions of the data-type (except private/protected callables/attributes). Furthermore, the proxy will be
    pickable and can its state can be shared among different processes. """

    def __getattr__(self, name):
        result = super().__getattr__(name)
        if isinstance(result, types.MethodType):
            return A(name, self._callmethod).get
        return result


class monte_carlo:

    def __init__(self, ):
        self.x = np.ones((1000, 3))
        self.E = np.mean(self.x)
        self.Elist = []
        self.T = None

    def simulation(self, temperature):
        self.T = temperature
        for i in range(3000):
            self.MC_step()
            if i % 10 == 0:
                self.Elist.append(self.E)
        return

    def MC_step(self):
        x = self.x.copy()
        k = np.random.randint(1000)
        x[k] = (x[k] + np.random.uniform(-1, 1, 3))
        temp_E = np.mean(self.x)
        if np.random.random() < np.exp((self.E - temp_E) / self.T):
            self.E = temp_E
            self.x = x
        return

    @classmethod
    def create(cls, *args, **kwargs):
        # Register class
        class_str = cls.__name__
        BaseManager.register(class_str, cls, ObjProxy, exposed=tuple(dir(cls)))
        # Start a manager process
        manager = BaseManager()
        manager.start()

        # Create and return this proxy instance. Using this proxy allows sharing of state between processes.
        inst = eval("manager.{}(*args, **kwargs)".format(class_str))
        return inst


def proba(dE,pT):
    return np.exp(-dE/pT)


if __name__ == "__main__":
    Tlist = [1.1, 1.2, 1.3]
    N = len(Tlist)
    G = []

    # Create our managed instances
    for _ in range(N):
        G.append(monte_carlo.create())

    for _ in range(5):

        #  Run simulations in the manager server
        results = []
        with Pool(8) as pool:

            for i in range(N):  # this loop should be ran in multiprocess
                results.append(pool.apply_async(G[i].simulation, (Tlist[i], )))

            # Wait for the simulations to complete
            for result in results:
                result.get()

        for i in range(N // 2):
            dE = G[i].E - G[i + 1].E
            pT = G[i].T + G[i + 1].T
            p = proba(dE, pT)  # (proba is a function, giving a probability depending on dE)
            if np.random.random() < p:
                T_temp = Tlist[i]
                Tlist[i] = Tlist[i + 1]
                Tlist[i + 1] = T_temp

    print(Tlist)

This meets the criteria you wanted. It does not create any copies at all, rather, all arguments to the simulation method call are serialized inside the pool and sent to the manager server where the object is actually stored. It gets executed there, and the results (if any) are serialized and returned in the main process. All of this, with only using the builtins!

Output

[1.2, 1.1, 1.3]

Edit

Since you are using Linux, I encourage you to use multiprocessing.set_start_method inside the if __name__ ... clause to set the start method to "spawn". Doing this will ensure that the child processes do not have access to variables defined inside the clause.

Answered By - Charchit