Python multiprocessing pool with shared data - python

I'm attempting to speed up a multivariate fixed-point iteration algorithm using multiprocessing however, I'm running issues dealing with shared data. My solution vector is actually a named dictionary rather than a vector of numbers. Each element of the vector is actually computed using a different formula. At a high level, I have an algorithm like this:
current_estimate = previous_estimate
while True:
for state in all_states:
current_estimate[state] = state.getValue(previous_estimate)
if norm(current_estimate, previous_estimate) < tolerance:
break
else:
previous_estimate, current_estimate = current_estimate, previous_estimate
I'm trying to parallelize the for-loop part with multiprocessing. The previous_estimate variable is read-only and each process only needs to write to one element of current_estimate. My current attempt at rewriting the for-loop is as follows:
# Class and function definitions
class A(object):
def __init__(self,val):
self.val = val
# representative getValue function
def getValue(self, est):
return est[self] + self.val
def worker(state, in_est, out_est):
out_est[state] = state.getValue(in_est)
def worker_star(a_b_c):
""" Allow multiple arguments for a pool
Taken from http://stackoverflow.com/a/5443941/3865495
"""
return worker(*a_b_c)
# Initialize test environment
manager = Manager()
estimates = manager.dict()
all_states = []
for i in range(5):
a = A(i)
all_states.append(a)
estimates[a] = 0
pool = Pool(process = 2)
prev_est = estimates
curr_est = estimates
pool.map(worker_star, itertools.izip(all_states, itertools.repeat(prev_est), itertools.repreat(curr_est)))
The issue I'm currently running into is that the elements added to the all_states array are not the same as those added to the manager.dict(). I keep getting key value errors when trying to access elements of the dictionary using elements of the array. And debugging, I found that none of the elements are the same.
print map(id, estimates.keys())
>>> [19558864, 19558928, 19558992, 19559056, 19559120]
print map(id, all_states)
>>> [19416144, 19416208, 19416272, 19416336, 19416400]

This is happening because the objects you're putting into the estimates DictProxy aren't actually the same objects as those that live in the regular dict. The manager.dict() call returns a DictProxy, which is proxying access to a dict that actually lives in a completely separate manager process. When you insert things into it, they're really being copied and sent to a remote process, which means they're going to have a different identity.
To work around this, you can define your own __eq__ and __hash__ functions on A, as described in this question:
class A(object):
def __init__(self,val):
self.val = val
# representative getValue function
def getValue(self, est):
return est[self] + self.val
def __hash__(self):
return hash(self.__key())
def __key(self):
return (self.val,)
def __eq__(x, y):
return x.__key() == y.__key()
This means the key look ups for items in the estimates will just use the value of the val attribute to establish identity and equality, rather than the id assigned by Python.

Related

Iteratively create subclass and store objects as class attribute

I have a class that does some complex calculation and generates some result MyClass.myresults.
MyClass.myresults is actually a class itself with different attributes (e.g. MyClass.myresults.mydf1, MyClass.myresults.mydf2.
Now, I need to run MyClass iteratively following a list of scenarios(scenarios=[1,2,[2,4], 5].
This happens with a simple loop:
for iter in scenarios:
iter = [iter] if isinstance(iter, int) else iter
myclass = MyClass() #Initialize MyClass
myclass.DoStuff(someInput) #Do stuff and get results
results.StoreScenario(myclass.myresults, iter)
and at the end of each iteration store MyClass.myresults.
I would like to create a separate class (Results) that at each iteration creates a subclass scenario_1, scenario_2, scenario_2_4 and stores within it MyClass.myresults.
class Results:
# no initialization, is an empty container to which I would like to add attributes iteratively
class StoreScenario:
def __init__(self, myresults, iter):
self.'scenario_'.join(str(iter)) = myresults #just a guess, I am assuming this is wrong
Suggestions on different approaches are more than welcome, I am quite new to classes and I am not sure if this is an acceptable approach or if I am doing something awful (clunky, memory inefficient, or else).
There's two problems of using this approach, The first one is, Result class (separate class) only stores modified values of your class MyClass, I mean, they should be the same class.
The second problem is memory efficiency, you create the same object twice for storing actual values and modified values at each iteration.
The suggested approach is using a hashmap or a dictionary in python. Using dictionary you are able to store copies of modified object very efficient and there's no need to create another class.
class MyClass:
def __init__(self):
# some attributes ...
self.scenarios_result = {}
superObject = MyClass()
for iter in scenarios:
iter = [iter] if isinstance(iter, int) else iter
myclass = MyClass() #Initialize MyClass
myclass.DoStuff(someInput) #Do stuff and get results
# results.StoreScenario(myclass.myresults, iter)
superObject.scenarios_result[iter] = myclass
So I solved it using setattr:
class Results:
def __init__(self):
self.scenario_results= type('ScenarioResults', (), {}) # create an empty object
def store_scenario(self, data, scenarios):
scenario_key = 'scenario_' + '_'.join(str(x) for x in scenarios)
setattr(self.simulation_results, scenario_key,
subclass_store_scenario(data))
class subclass_store_scenario:
def __init__(self, data):
self.some_stuff = data.result1.__dict__
self.other_stuff = data.result2.__dict__
This allows me to call things like:
results.scenario_results.scenario_1.some_stuff.something
results.scenario_results.scenario_1.some_stuff.something_else
This is necessary for me as I need to compute other measures, summary or scenario-specific, which I can then iteratively assign using again setattr:
def construct_measures(self, some_data, configuration):
for scenario in self.scenario_results:
#scenario is a reference to the self.scenario_results class.
#we can simply add attributes to it
setattr(scenario , 'some_measure',
self.computeSomething(
some_data.input1, some_data.input2))

Efficient growing pools of objects

Is there an established module, or good practice, to work efficiently with large object pools in Python 3?
What I mean by "object pool" is some class capable of:
fetching new instances of specified type, while dynamically extending the memory allocation under the hood when necessary;
maintaining a consistent indexing for previously fetched objects.
Here is a basic example:
class Value:
__slots__ = ('a','b')
def __init__(self,a=None,b=None):
self.a = a
self.b = b
class BasicPool:
def __init__(self):
self.data = []
def __getitem__(self,k):
return self.data[k]
def fetch(self):
v = Value()
self.data.append(v)
return v
class BlockPool:
def __init__(self,bsize=100):
self.bsize = bsize
self.next = bsize
self.data = []
def __getitem__(self,k):
b,k = divmod(k,self.bsize)
return self.data[b][k]
def fetch(self):
self.next += 1
if self.next >= self.bsize:
self.data.append([ Value() for _ in range(self.bsize) ])
self.next = 0
return self.data[-1][self.next]
The BasicPool doesn't do anything smart: whenever a new instance is requested, it is instanciated and appended to an underlying list. On the other hand, the BlockPool grows a list of pre-allocated blocks of instances. Surprisingly though, it seems that preallocation is not beneficial in practice:
from timeit import default_timer as timer
def benchmark(P):
N = int(1e6)
start = timer()
for _ in range(N): P.fetch()
print( timer() - start )
print( 'Basic pool:' )
for _ in range(5): benchmark(BasicPool())
# Basic pool:
# 1.2352294209995307
# 0.5003506309985823
# 0.48115064000012353
# 0.48508202800076106
# 1.1760561199989752
print( 'Block pool:' )
for _ in range(5): benchmark(BlockPool())
# Block pool:
# 0.7272855400005938
# 1.4875716509995982
# 0.726611527003115
# 0.7369502859983186
# 1.4867010340021807
As you can see, the BasicPool is always faster than the BlockPool (I also don't know the cause of these large variations). Pools of objects must be a fairly common need in Python; is the best approach really to use the builtin list.append? Are there smarter containers that can be used to further improve runtime performance, or is this dominated by the instanciation time anyway?
The whole point of the geometric growth of the array underlying a list is to reduce the reallocation overhead to a constant factor. That constant can easily be smaller than that for manually making blocks (principally because of the slow, interpreted manipulation of self.next and self.data in the latter). (Asymptotically, the cost of BlockPool.fetch is still the append, of course.) Moreover, your benchmark doesn’t include the additional cost of destroying the blocks, nor that of the two-step indexing on read.
So list is surely as good as it gets (without writing your own C code). You can improve BasicPool a bit by inheriting from list rather than containing one, eliminating a dictionary lookup per fetch and the interpreted __getitem__ wrapper entirely.

Shared python generator

I am trying to reproduce the reactive extensions "shared" observable concept with Python generators.
Say I have an API that gives me an infinite stream that I can use like this:
def my_generator():
for elem in the_infinite_stream():
yield elem
I could use this generator multiple times like so:
stream1 = my_generator()
stream2 = my_generator()
And the_infinite_stream() will be called twice (once for each generator).
Now say that the_infinite_stream() is an expensive operation. Is there a way to "share" the generator between multiple clients? It seems like tee would do that, but I have to know in advance how many independent generators I want.
The idea is that in other languages (Java, Swift) using the reactive extensions (RxJava, RxSwift) "shared" streams, I can conveniently duplicate the stream on the client side. I am wondering how to do that in Python.
Note: I am using asyncio
I took tee implementation and modified it such you can have various number of generators from infinite_stream:
import collections
def generators_factory(iterable):
it = iter(iterable)
deques = []
already_gone = []
def new_generator():
new_deque = collections.deque()
new_deque.extend(already_gone)
deques.append(new_deque)
def gen(mydeque):
while True:
if not mydeque: # when the local deque is empty
newval = next(it) # fetch a new value and
already_gone.append(newval)
for d in deques: # load it to all the deques
d.append(newval)
yield mydeque.popleft()
return gen(new_deque)
return new_generator
# test it:
infinite_stream = [1, 2, 3, 4, 5]
factory = generators_factory(infinite_stream)
gen1 = factory()
gen2 = factory()
print(next(gen1)) # 1
print(next(gen2)) # 1 even after it was produced by gen1
print(list(gen1)) # [2, 3, 4, 5] # the rest after 1
To cache only some amount of values you can change already_gone = [] into already_gone = collections.deque(maxlen=size) and add size=None parameter to generators_factory.
Consider simple class attributes.
Given
def infinite_stream():
"""Yield a number from a (semi-)infinite iterator."""
# Alternatively, `yield from itertools.count()`
yield from iter(range(100000000))
# Helper
def get_data(iterable):
"""Print the state of `data` per stream."""
return ", ".join([f"{x.__name__}: {x.data}" for x in iterable])
Code
class SharedIterator:
"""Share the state of an iterator with subclasses."""
_gen = infinite_stream()
data = None
#staticmethod
def modify():
"""Advance the shared iterator + assign new data."""
cls = SharedIterator
cls.data = next(cls._gen)
Demo
Given a tuple of client streams (A, B and C),
# Streams
class A(SharedIterator): pass
class B(SharedIterator): pass
class C(SharedIterator): pass
streams = A, B, C
let us modify and print the state of one iterator shared between them:
# Observe changed state in subclasses
A.modify()
print("1st access:", get_data(streams))
B.modify()
print("2nd access:", get_data(streams))
C.modify()
print("3rd access:", get_data(streams))
Output
1st access: A: 0, B: 0, C: 0
2nd access: A: 1, B: 1, C: 1
3rd access: A: 2, B: 2, C: 2
Although any stream can modify the iterator, the class attribute is shared between sub-classes.
See Also
Docs on asyncio.Queue - an async alternative to shared container
Post on the Observer Pattern + asyncio
You can call "tee" repeatedly to create multiple iterators as needed.
it = iter([ random.random() for i in range(100)])
base, it_cp = itertools.tee(it)
_, it_cp2 = itertools.tee(base)
_, it_cp3 = itertools.tee(base)
Sample: http://tpcg.io/ZGc6l5.
You can use single generator and "subscriber generators":
subscribed_generators = []
def my_generator():
while true:
elem = yield
do_something(elem) # or yield do_something(elem) depending on your actual use
def publishing_generator():
for elem in the_infinite_stream():
for generator in subscribed_generators:
generator.send(elem)
subscribed_generators.extend([my_generator(), my_generator()])
# Next is just ane example that forces iteration over `the_infinite_stream`
for elem in publishing_generator():
pass
Instead of generator-function you may also create a class with methods: __next__, __iter__, send, throw. That way you can modify MyGenerator.__init__ method to automatically add new instances of it to subscribed_generators.
This is somewhat similar to event-based approach with a "dumb implementation":
for elem in the_infinite_stream is similar to emitting event
for generator ...: generator.send is similar to sending event to each subscriber.
So one way to implement a "more complex but structured solution" would be to use event-based approach:
For example you can use asyncio.Event
Or some third-party solution like aiopubsub
For any of those approaches you should emit event for each element from the_infinite_stream, and your instances of my_generator should be subscribed to those events.
And other approaches can also be used and the best choice depends: on details of your task, on how are you using event-loop in asyncio. For example:
You can implement the_infinite_stream (or wrapper for it) as some class with "cursors" (objects that track current position in the stream for different subscribers); then each my_generator registers new cursor and uses it to get next item in the infinite stream. In this approach event-loop will not automatically revisit my_generator instances, which might be required if those instances "are not equal" (for example have some "priority balancing")
Intermediate generator calling all the instances of my_generator (as described earlier). In this approach each instance of my_generator is automatically revisited by event-loop. Most likely this approach is thread-safe.
Event-based approaches:
using asyncio.Event. Similar to use of intermediate generator. Not
thread-safe
aiopubsub.
something that uses Observer pattern
Make the_infinite_generator (or wrapper for it) to be "Singleton" that "caches" latest event. Some approaches were described in other answers. Another "caching" solutions can be used:
emit the same element once for each instance of the_infinite_generator (use class with custom __new__ method that tracks instances, or use the same instance of class that has a method returning "shifted" iterator over the_infinite_loop) until someone calls special method on
instance of the_infinite_generator (or on class): infinite_gen.next_cycle. In
this case there should always be some "last finalizing
generator/processor" that at the end of each event-loop's cycle will
do the_infinite_generator().next_cycle()
Similar to previous but same event is allowed to fire multiple times in the same my_generator instance (so they should watch for this case). In this approach the_infinite_generator().next_cycle() can be called "periodically" with loop.call_later or loop.cal_at. This approach might be needed if "subscribers" should be able to handle/analyze: delays, rate-limits, timeouts between events, etc.
Many other solutions are possible. It's hard to propose something specific without looking at your current implementation and without knowing what is the desired behavior of generators that use the_infinite_loop
If I understand your description of "shared" streams correctly, that you really need "one" the_infinite_stream generator and a "handler" for it. Example that tries to do this:
class StreamHandler:
def __init__(self):
self.__real_stream = the_infinite_stream()
self.__sub_streams = []
def get_stream(self):
sub_stream = [] # or better use some Queue/deque object. Using list just to show base principle
self.__sub_streams.append(sub_stream)
while True:
while sub_stream:
yield sub_stream.pop(0)
next(self)
def __next__(self):
next_item = next(self.__real_stream)
for sub_stream in self.__sub_steams:
sub_stream.append(next_item)
some_global_variable = StreamHandler()
# Or you can change StreamHandler.__new__ to make it singleton, or you can create an instance at the point of creation of event-loop
def my_generator():
for elem in some_global_variable.get_stream():
yield elem
But if all your my_generator objects are initialized at the same point of infinite stream, and "equally" iterated inside the loop, then this approach will introduce "unnecessary" memory overhead for each "sub_stream" (used as queue). Unnecessary: because those queues will always be the same (but that can be optimized: if there are some existing "empty" sub_stream than it can be re-used for new sub_streams with some changes to "pop-logic"). And many-many other implementations and nuances can be discussed
If you have a single generator, you can use one queue per "subscriber" and route events to each subscriber as the primary generator produces results.
This has the advantage of allowing the subscribers to move at their own pace, and it can be dropped in existing code with very little changes to the original source.
For example:
def my_gen():
...
m1 = Muxer(my_gen)
m2 = Muxer(my_gen)
consumer1(m1).start()
consumer2(m2).start()
As items are pulled from the primary generator they are inserted into queues for each listener. Listeners can subscribe any time by constructing a new Muxer():
import queue
from threading import Lock
from collections import namedtuple
class Muxer():
Entry = namedtuple('Entry', 'genref listeners, lock')
already = {}
top_lock = Lock()
def __init__(self, func, restart=False):
self.restart = restart
self.func = func
self.queue = queue.Queue()
with self.top_lock:
if func not in self.already:
self.already[func] = self.Entry([func()], [], Lock())
ent = self.already[func]
self.genref = ent.genref
self.lock = ent.lock
self.listeners = ent.listeners
self.listeners.append(self)
def __iter__(self):
return self
def __next__(self):
try:
e = self.queue.get_nowait()
except queue.Empty:
with self.lock:
try:
e = self.queue.get_nowait()
except queue.Empty:
try:
e = next(self.genref[0])
for other in self.listeners:
if not other is self:
other.queue.put(e)
except StopIteration:
if self.restart:
self.genref[0] = self.func()
raise
return e
Original source code, including test suite:
https://gist.github.com/earonesty/cafa4626a2def6766acf5098331157b3
The unit tests run many threads concurrently processing the same generated events in sequence. The code is order preserving, with a lock acquired during the single generator's access.
Caveats: the version here uses a singleton to gate access, otherwise it would be possible to accidentally evade its control over the contained generators. It also allows the contained generators to be "restartable", which was a useful feature for me a the time. There is no "close()" feature, simply because I didn't need it. This is an appropriate use case for __del__ however, since the last reference to a listener is the right time to clean up.

lambda,map on object arrays in python - Return List of objects

How to return a list of objects and not list here.
I want to return a list of test objects and not a list of str..
class test:
val = ""
def __init__(self,v):
self.val = v
def tolower(self,k):
k = k.val.lower()
return k
def test_run():
tests_lst = []
tests_lst.append(test("TEST-0"))
tests_lst.append(test("TEST-1"))
tests_lst.append(test("TEST-2"))
i_want_object_of_test = map(lambda x:x.val.lower(),tests_lst)
if __name__ == '__main__':
test_run()
OUTPUT:
['test-0', 'test-1', 'test-2']
i want a list of test objects where each object's val has changed to lower case.
The question is unclear. I'll answer by what I understand.
What I understand is that you are trying to create a new list of test objects, with the values as lower case.
You can do this either by changing the state of each of the objects in a for loop (changing state is usually not recommended):
for test_obj in test_lst:
test_obj.val = test_obj.val.lower()
A way to do it through a list comprehension is to create new test instances:
i_want_object_of_test = [test(test_obj.val.lower()) for test_obj in test_lst]
Besides, there are a few problems with your test class:
It is an old style class, you should always inherit from object in your classes: class test(object):
You define a class variable by putting val = ""' in your class defenition, you then override it in each instance.
Your tolower method gets another test instance (k) and returns its value as lower case. I assume you want to either return a new test object or change the current one in place. Either way the method should only use self.

Python dynamically generate dependencies between class instances

Suppose I have the following classes:
class base(object):
def __init__(self, name):
self.name = name
self.last_x = 0.0
def calc(self, x):
return x
class A(base):
def calc(self, x):
return f_A(x)
class B(base):
def calc(self, x):
return f_B(x)
...
Each of the lettered classes is basically a wrapper for a corresponding lettered function f_A, f_B. The class instances include a state variable self.last_x as well as the lettered functions are assumed to be state-dependent (i.e. a Markov Chain type process).
What I would like to do is to define dependency chains between instances of these classes in order to try out different functional convolutions. For example, if we wanted to calculate a chain [a, b] on a numerical input value x we would have to do
a = A('firstnode')
b = B('secondnode')
res = b.calc(a.calc(x))
The goal is to do this with arbitrarily long chains, while also being able to access results from each intermediate calculation. I.e. if the chain is [a, b, c] I would like to make accessible results of [a] and [a, b] as well (which is why I included a name string for each node in my current implementation).
What would be the right way to setup my classes and data structures for this use case?
So far I have a fairly heavy-handed solution involving multiple dictionaries to keep track of things, but it feels inelegant and I think I might be missing out on something obvious.
Unfortunately you're improperly reusing names (thus hiding their previous values). E.g, after:
a = A('firstnode')
calling a.calc will try to call this instance (since the assignment has replaced the fact that previously name a was bound to a function) and fail. Best would be to use more sensible naming. If for some reason that's not practical, you need to bind the function names internally at class definition time:
class A(base):
def calc(self, x, a=a):
return a(x)
where the a=a does the trick, and so forth.
Having passed that hurdle, the second one is that you want the last result of each class to be saved, but, you don't save it. So, change the code to e.g
class A(base):
def calc(self, x, a=a):
self.last_result = a(x)
return self.last_result
Once that is done, performing your desired operation on a list of class instances is the least of your problems. E.g
def doit(instances, x):
curr = x
for inst in instances: curr=inst.calc(curr)
return curr
and after this
[inst.last_result for inst in instances]
will give you the intermediate results you're looking for.

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