I have different threads and after processing they put data in a common list. Is there anything built in python for a list or a numpy array to be accessed by only a single thread. Secondly, if it is not what is an elegant way of doing it?
According to Thread synchronisation mechanisms in Python, reading a single item from a list and modifying a list in place are guaranteed to be atomic. If this is right (although it seems to be partially contradicted by the very existence of the Queue module), then if your code is all of the form:
try:
val = mylist.pop()
except IndexError:
# wait for a while or exit
else:
# process val
And everything put into mylist is done by .append(), then your code is already threadsafe. If you don't trust that one document on that score, use a queue.queue, which does all synchronisation for you, and has a better API than list for concurrent programs - particularly, it gives you the option of blocking indefinitely, or for a timeout, waiting for .pop() to work if you don't have anything else the thread could be getting on with in the mean time.
For numpy arrays, and in general any case where you need more than a producer/consumer queue, use a Lock or RLock from threading - these implement the context manager protocol, so using them is quite simple:
with mylock:
# Process as necessarry
And python will guarantee that the lock gets released once you fall off the end of the with block - including in tricky cases like if something you do raises an exception.
Finally, consider whether multiprocessing is a better fit for your application than threading - threads in Python aren't guaranteed to actually run concurrently, and in CPython only can if the drop to C-level code. multiprocessing gets around that issue, but may have some extra overhead - if you haven't already, you should read the docs to determine which one suits your needs better.
threading provides Lock objects if you need to protect an entire critical section, or the Queue module provides a queue that is threadsafe.
How about the standard library Queue?
Related
I have a piece of code where I have a processing thread and a monitor thread. In the processing thread, I have a call to collections.deque.popleft function. I wanted to know if this function releases GIL because I want run my monitor thread even when the processing function is blocked on the popleft function
Instead of answering this specific question I'll answer a different question:
What is the Global Interpreter Lock (GIL), and when will it block my program?
In short, the GIL protects the interpreter's state from becoming corrupted by concurrent threads.
For a sense of what it is for, Consider the low level implementation of dict, which somewhere has an array of keys, organized for quick lookup. When you write some code like:
myDict['foo'] = 'bar'
the python interpreter needs to adjust its collection of keys. That might involve things like making more room for the additional key as well as adding the particular key to that array.
If multiple, concurrent threads are modifying that dict, then one thread might reallocate the array while another is in the middle of modifying it, which could cause some unpredictable, probably bad behavior (anything from corrupted data, segfault or heartbleed like memory content leak of sensitive data or arbitrary code execution)
Since that's not the sort of state you can reasonably describe or prevent at the level of your python application, the run-time goes to great lengths to prevent those sorts of problems from occuring. The way it does it is that certain parts of the interpreter, such as the modification of a dict, is surrounded by a PyGILState_Ensure()/PyGILState_Release() pair, so that critical operations always reach a consistent state.
Note however that the scope of this lock is very narrow; it doesn't attempt to protect from general data races, it won't protect you from writing a program with multiple threads overwriting each other's work in a common container (say, a collections.deque), only that even if you do write such a program, it wont' cause the interpreter to crash, you'll always have a valid, working deque. You can add additional application locks, as in queue.Queue to give good concurrent semantics to your application.
Since every operation that the GIL protects is a change in the interpreter state, it never blocks on external events; since those events won't cause the interpreter state to be changed, a signaling condition variable cannot corrupt memory.
The only time you might have a problem is when you have several unblocked threads, since they are potentially all executing code in the low level interpreter, they'll compete for the GIL, and only one thread can hold it, blocking other threads that also want to do some computation.
Unless you are writing C extensions, you probably don't need to worry about it, and unless you have multiple, compute bound threads, in python, you won't be affected by it, either.
Yes -- deque is thread-safe (thanks #hemanths) http://docs.python.org/2/library/collections.html#collections.deque
No, because collections.deque is not thread-safe. Use a Queue, or make your own deque subclass.
I'm trying to solve a problem, where I have many (on the order of ten thousand) URLs, and need to download the content from all of them. I've been doing this in a "for link in links:" loop up till now, but the amount of time it's taking is now too long. I think it's time to implement a multithreaded or multiprocessing approach. My question is, what is the best approach to take?
I know about the Global Interpreter Lock, but since my problem is network-bound, not CPU-bound, I don't think that will be an issue. I need to pass data back from each thread/process to the main thread/process. I don't need help implementing whatever approach (Terminate multiple threads when any thread completes a task covers that), I need advice on which approach to take. My current approach:
data_list = get_data(...)
output = []
for datum in data:
output.append(get_URL_data(datum))
return output
There's no other shared state.
I think the best approach would be to have a queue with all the data in it, and have several worker threads pop from the input queue, get the URL data, then push onto an output queue.
Am I right? Is there anything I'm missing? This is my first time implementing multithreaded code in any language, and I know it's generally a Hard Problem.
For your specific task I would recommend a multiprocessing worker pool. You simply define a pool and tell it how many processes you want to use (one per processor core by default) as well as a function you want to run on each unit of work. Then you ready every unit of work (in your case this would be a list of URLs) in a list and give it to the worker pool.
Your output will be a list of the return values of your worker function for every item of work in your original array. All the cool multi-processing goodness will happen in the background. There is of course other ways of working with the worker pool as well, but this is my favourite one.
Happy multi-processing!
The best approach I can think of in your use case will be to use a thread pool and maintain a work queue. The threads in the thread pool get work from the work queue, do the work and then go get some more work. This way you can finely control the number of threads working on your URLs.
So, create a WorkQueue, which in your case is basically a list containing the URLs that need to be downloaded.
Create a thread pool, which create the number of threads you specify, fetches work from the WorkQueue and assigns it to a thread. Each time a thread finishes and returns you check if the work queues has more work and accordingly assign work to that thread again. You may also want to put a hook so that every time work is added to the work queue, your threads assigns it to a free thread if available.
The fastest and most efficient method of doing IO bound tasks like this is an asynchronous event loop. The libcurl can do this, and there is a Python wrapper for that called pycurl. Using it's "multi" interface you can do high-performance client activities. I have done over 1000 simultaneous fetchs as fast as one.
However, the API is quite low-level and difficult to use. There is a simplifying wrapper here, which you can use as an example.
I'm trying to write a Python 2.6 (OSX) program using multiprocessing, and I want to populate a Queue with more than the default of 32767 items.
from multiprocessing import Queue
Queue(2**15) # raises OSError
Queue(32767) works fine, but any higher number (e.g. Queue(32768)) fails with OSError: [Errno 22] Invalid argument
Is there a workaround for this issue?
One approach would be to wrap your multiprocessing.Queue with a custom class (just on the producer side, or transparently from the consumer perspective). Using that you would queue up items to be dispatched to the Queue object that you're wrapping, and only feed things from the local queue (Python list() object) into the multiprocess.Queue as space becomes available, with exception handling to throttle when the Queue is full.
That's probably the easiest approach since it should have the minimum impact on the rest of your code. The custom class should behave just like a Queue while hiding the underlying multiprocessing.Queue behind your abstraction.
(One approach might be to have your producer use threads, one thread to manage the dispatch from a threading Queue to your multiprocessing.Queue and any other threads actually just feeding the threading Queue).
I've already answered the original question but I do feel like adding that Redis lists are quite reliable and the Python module's support for them are extremely easy to use for implementing a Queue like object. These have the advantage of allowing one to scale out over multiple nodes (across a network) as well as just over multiple processes.
Basically to use those you'd just pick a key (string) for your queue name have your producers push into it and have your workers (task consumers) loop on blocking pops from that key.
The Redis BLPOP, and BRPOP commands all take a list of keys (lists/queues) and an optional timeout value. They return a tuple (key,value) or None (on timeout). So you can easily write up an event driven system that's very similar to the familiar structure of select() (but at a much higher level). The only thing you have to watch for are missing keys and invalid key types (just wrap your queue operations with exception handlers, of course). (If some other application stops on your shared Redis server removing keys or replacing keys that you were using as queues with string/integer or other types of values ... well, you have a different problem at that point). :)
Another advantage of this model is that Redis does persist its data to the disk. So your work queue could survive system restarts if you chose to allow it.
(Of course you could implement a simple Queue as a table in SQLlite or any other SQL system if you really wanted to do so; just using some sort of auto-incrementing index for the sequencing and a column to mark each item has having been "done" (consumed); but that does involve somewhat more complexity than using what Redis gives you "out of the box").
Working for me on MacOSX
>>> import Queue
>>> Queue.Queue(30000000)
<Queue.Queue instance at 0x1006035f0>
I'm learning to use the Queue module, and am a bit confused about how a queue consumer thread can be made to know that the queue is complete. Ideally I'd like to use get() from within the consumer thread and have it throw an exception if the queue has been marked "done". Is there a better way to communicate this than by appending a sentinel value to mark the last item in the queue?
original (most of this has changed; see updates below)
Based on some of the suggestions (thanks!) of Glenn Maynard and others, I decided to roll up a descendant of Queue.Queue that implements a close method. It's available in the form of a primitive (unpackaged) module. I'll clean this up a bit and package it properly when I have a bit more time. For now the module only contains the CloseableQueue class and the Closed exception class. I'm planning to expand it to also include subclasses of Queue.LifoQueue and Queue.PriorityQueue.
It's in a pretty preliminary state currently, which is to say that although it passes its test suite, I haven't actually used it for anything yet. Your mileage may vary. I'll keep this answer updated with exciting news.
The CloseableQueue class differs a bit from Glenn's suggestion in that closing the queue will prevent future puts, but not prevent future gets until the queue is emptied. This made the most sense to me; it seemed like functionality to clear the queue could be added as a separate mixin* that would be orthogonal to the closeability functionality. So basically with CloseableQueue, by closing the queue you indicate that the last element has been put. There's also an option to do this atomically by passing last=True to the final put call. Subsequent calls to put, and subsequent calls to get once the queue is emptied, as well as outstanding blocked calls matching those descriptions, will raise the Closed exception.
This is mostly useful for situations where a single producer is generating data for one or more consumers, but it could also be useful for a multi-multi arrangement where consumers are waiting for a particular item or set of items. In particular it doesn't provide a way to determine that all of a number of producers have finished production. Getting that working would entail the provision of some way to register producers (.open()?), as well as a way to indicate that producer registration is itself closed.
Suggestions and/or code reviews are quite welcome. I haven't written a whole lot of concurrency code, but hopefully the test suite is thorough enough that the fact that the code passes it is an indication of the code's quality, rather than the suite's lack thereof. I was able to reuse a bunch of the code from the Queue module's test suite: the file itself is included in this module and used as a basis for various subclasses and routines, including regression testing. This probably (hopefully) helped to avoid complete ineptitude in the testing department. The code itself just overrides Queue.get and Queue.put with fairly minimal changes, and adds the close and closed methods.
I've sort of intentionally avoided using any new-fangled fanciness like context managers in both the code itself and in the test suite in an effort to keep the code as backwards-compatible as is the Queue module itself, which is considerably backwards indeed. I'll probably add __enter__ and __exit__ methods at some point; otherwise, the contextlib's closing function should be applicable to a CloseableQueue instance.
*: Here I use the term "mixin" loosely. As the Queue module's classes are old-style, mixins would need to be mixed using class factory functions; some restrictions apply; offer void where prohibited by Guido.
update
The CloseableQueue module now provides CloseableLifoQueue and CloseablePriorityQueue classes. I've also added some convenience functions to support iteration. Still need to rework it as a proper package. There's a class factory function to allow for convenient subclassing of other Queue.Queue-derived classes.
update 2
CloseableQueue is now available via PyPI, e.g. with
$ easy_install CloseableQueue
Comments and criticism are welcome, especially from this answer's anonymous downvoter.
Queue's don't inherently have the idea of being complete or done. They can be used indefinitely. To close it up when you are done, you will indeed need to put None or some other magic value at the end and write the logic to check for it, as you described. The ideal way would probably be subclassing the Queue object.
See http://en.wikipedia.org/wiki/Queue_(data_structure) to learn more about queue in general.
A sentinel is a natural way to shut down a queue, but there are a couple things to watch out for.
First, remember that you may have more than one consumer, so you need to send a sentinel once for each running consumer, and guarantee that each consumer will only consume one sentinel, to ensure that each consumer receives its shutdown sentinel.
Second, remember that Queue defines an interface, and that when possible, code should behave regardless of the underlying Queue. You might have a PriorityQueue, or you might have some other class that exposes the same interface and returns values in some other order.
Unfortunately, it's hard to deal with both of these. To deal with the general case of different queues, a consumer that's shutting down must continue to consume values after receiving its shutdown sentinel until the queue is empty. That means that it may consume another thread's sentinel. This is a weakness of the Queue interface: it should have a Queue.shutdown call to cause an exception to be thrown by all consumers, but that's missing.
So, in practice:
if you're sure you're only ever using a regular Queue, simply send one sentinel per thread.
if you may be using a PriorityQueue, ensure that the sentinel has the lowest priority.
Queue is a FIFO (first in first out) register so remember that the consumer can be faster than producer. When consumers thread detect that the queue is empty normally realise one of following actions:
Send to API: switch to next thread.
Send to API: sleep some ms and than check again the queue.
Send to API: wait on event (like new message in queue).
If you wont that consumers thread terminate after job is complete than put in queue a sentinel value to terminate task.
The best practice way of doing this would be to have the queue itself notify a client that it has reached the 'done' state. The client can then take any action that is appropriate.
What you have suggested; checking the queue to see if it is done periodically, would be highly undesirable. Polling is an antipattern in multithreaded programming, you should always be using notifications.
EDIT:
So your saying that the queue itself knows that it's 'done' based on some criteria and needs to notify the clients of that fact. I think you are correct and the best way to do this is by throwing when a client calls get() and the queue is in the done state. If your throwing this would negate the need for a sentinel value on the client side. Internally the queue can detect that it is 'done' in any way it pleases e.g. queue is empty, it's state was set to done etc I don't see any need for a sentinel value.
I need to dynamically load code (comes as source), run it and get the results. The code that I load always includes a run method, which returns the needed results. Everything looks ridiculously easy, as usual in Python, since I can do
exec(source) #source includes run() definition
result = run(params)
#do stuff with result
The only problem is, the run() method in the dynamically generated code can potentially not terminate, so I need to only run it for up to x seconds. I could spawn a new thread for this, and specify a time for .join() method, but then I cannot easily get the result out of it (or can I). Performance is also an issue to consider, since all of this is happening in a long while loop
Any suggestions on how to proceed?
Edit: to clear things up per dcrosta's request: the loaded code is not untrusted, but generated automatically on the machine. The purpose for this is genetic programming.
The only "really good" solutions -- imposing essentially no overhead -- are going to be based on SIGALRM, either directly or through a nice abstraction layer; but as already remarked Windows does not support this. Threads are no use, not because it's hard to get results out (that would be trivial, with a Queue!), but because forcibly terminating a runaway thread in a nice cross-platform way is unfeasible.
This leaves high-overhead multiprocessing as the only viable cross-platform solution. You'll want a process pool to reduce process-spawning overhead (since presumably the need to kill a runaway function is only occasional, most of the time you'll be able to reuse an existing process by sending it new functions to execute). Again, Queue (the multiprocessing kind) makes getting results back easy (albeit with a modicum more caution than for the threading case, since in the multiprocessing case deadlocks are possible).
If you don't need to strictly serialize the executions of your functions, but rather can arrange your architecture to try two or more of them in parallel, AND are running on a multi-core machine (or multiple machines on a fast LAN), then suddenly multiprocessing becomes a high-performance solution, easily paying back for the spawning and IPC overhead and more, exactly because you can exploit as many processors (or nodes in a cluster) as you can use.
You could use the multiprocessing library to run the code in a separate process, and call .join() on the process to wait for it to finish, with the timeout parameter set to whatever you want. The library provides several ways of getting data back from another process - using a Value object (seen in the Shared Memory example on that page) is probably sufficient. You can use the terminate() call on the process if you really need to, though it's not recommended.
You could also use Stackless Python, as it allows for cooperative scheduling of microthreads. Here you can specify a maximum number of instructions to execute before returning. Setting up the routines and getting the return value out is a little more tricky though.
I could spawn a new thread for this, and specify a time for .join() method, but then I cannot easily get the result out of it
If the timeout expires, that means the method didn't finish, so there's no result to get. If you have incremental results, you can store them somewhere and read them out however you like (keeping threadsafety in mind).
Using SIGALRM-based systems is dicey, because it can deliver async signals at any time, even during an except or finally handler where you're not expecting one. (Other languages deal with this better, unfortunately.) For example:
try:
# code
finally:
cleanup1()
cleanup2()
cleanup3()
A signal passed up via SIGALRM might happen during cleanup2(), which would cause cleanup3() to never be executed. Python simply does not have a way to terminate a running thread in a way that's both uncooperative and safe.
You should just have the code check the timeout on its own.
import threading
from datetime import datetime, timedelta
local = threading.local()
class ExecutionTimeout(Exception): pass
def start(max_duration = timedelta(seconds=1)):
local.start_time = datetime.now()
local.max_duration = max_duration
def check():
if datetime.now() - local.start_time > local.max_duration:
raise ExecutionTimeout()
def do_work():
start()
while True:
check()
# do stuff here
return 10
try:
print do_work()
except ExecutionTimeout:
print "Timed out"
(Of course, this belongs in a module, so the code would actually look like "timeout.start()"; "timeout.check()".)
If you're generating code dynamically, then generate a timeout.check() call at the start of each loop.
Consider using the stopit package that could be useful in some cases you need timeout control. Its doc emphasizes the limitations.
https://pypi.python.org/pypi/stopit
a quick google for "python timeout" reveals a TimeoutFunction class
Executing untrusted code is dangerous, and should usually be avoided unless it's impossible to do so. I think you're right to be worried about the time of the run() method, but the run() method could do other things as well: delete all your files, open sockets and make network connections, begin cracking your password and email the result back to an attacker, etc.
Perhaps if you can give some more detail on what the dynamically loaded code does, the SO community can help suggest alternatives.