Timemout in python multithread/multiprocess worker - python

I'm trying to write program which executes time consuming tasks in parallel. I'd like to limit task execution time using signal within worker. Is it going to work? Any better approach?

Depending on you goal, trying to implement a multi-task operation on your own might be extremely time consuming and error prone. I would suggest you look into pre-made frameworks, such as Celery, which handle these exact tasks and allow, among other things, to set timeouts on tasks and so-forth.

Related

Python asyncio. Can too many asynchronous calls decrease performance?

As far as we know, it is bad if we start too many threads, and it may significantly decrease performance and increase memory usage. However, I can't find anywhere if the situation is the same if we call too many async functions.
As far as I know, asyncio is a kind of abstraction for parallel computing, and it may use or may not use actual threading.
In my project, multiple asynchronous tasks are run, and each such task (currently, it is done using threading) may start other threads. It is a risky situation. I'm thinking of two ways how to solve the issue with too many threads. The first one is to limit the number of 'software' threads to the number of 'hardware' threads. Another one is to use asyncio. Is the second option reasonable in such a case?
As far as I know, asyncio is a kind of abstraction for parallel computing and it may use or may not use actual threading.
Please do not confuse parallelism with asynchronous. In Python, you can achieve parallelism only using multiprocessing.
In my project, multiple asynchronous tasks are run, and each such task may start other threads.
All asynchronous tasks are run in one event loop and use only one thread.
I'm thinking of two ways how to solve the issue with too many threads. The first one is to limit the number of 'software' threads to the number of 'hardware' threads. Another one is to use asyncio. Is the second option reasonable in such a case?
In this answer I have demonstrated situations where we can use async functions. It mainly depends on the operations you do. If your application works with threading and does not need multiprocessing, it can be converted to asynchronous tasks.

How to submit a large set of long running parallel tasks to dask?

I have a computational workload that I originally ran with concurrent.futures.ProcessPoolExecutor which I converted to use dask so that I could make use of dask's integrations with distributed computing systems for scaling beyond one machine. The workload consists of two task types:
Task A: takes string/float inputs and produces a matrix (around 2000 x 2000). Task duration is usually 60 seconds or less.
Task B: takes the matrix from task A and uses it and some other small inputs to solve an ordinary differential equation. The solution is written to disk (so no return value). Task duration can be up to fifteen minutes.
There can multiple B tasks for each A task.
Originally, my code looked like this:
a_results = client.map(calc_a, a_inputs)
all_b_inputs = [(a_result, b_input) for b_input in b_inputs for a_result in a_results]
b_results = client.map(calc_b, all_b_inputs)
dask.distributed.wait(b_results)
because that was the clean translation from the concurrent.futures code (I actually kept the code so that it could be run either with dask or concurrent.futures so I could compare). client here is a distributed.Client instance.
I have been experiencing some stability issues with this code, especially for large numbers of tasks, and I think I might not be using dask in the best way. Recently, I changed my code to use Delayed instead like this:
a_results = [dask.delayed(calc_a)(a) for a in a_inputs]
b_results = [dask.delayed(calc_b)(a, b) for a in a_inputs for b in b_inputs]
client.compute(b_results)
I did this because I thought perhaps the scheduler could work through the tasks more efficiently if it examined the entire graph before starting anything rather than beginning to schedule the A tasks before knowing about the B tasks. This change seems to help some but I still see some stability issues.
I can create separate questions for the stability problems, but I first wanted to find out if I am using dask in the best way for this use case or if I should modify how I am submitting the tasks. Just to describe the problems briefly, the worst problem to me is that over time my workers drop to 0% CPU and tasks stop completing. Other problems include things like getting KilledWorker exceptions and seeing log messages about an unresponsive loop and time outs. Usually the scheduler runs fine for at least a few hours, completing thousands of tasks before these issues show up (which makes debugging difficult since the feedback loop is so long).
Some questions I have been wondering about:
I can have thousands of tasks to run. Can I submit these all to dask to start out or do I need to submit them in batches? My thought was that the dask scheduler would be better at scheduling tasks than my batching code.
If I do need to batch things myself, can I query the scheduler to find out the maximum number of workers so I can write something that will submit batches of the right size? Or do I need to make the batch size an input to my batching code?
In the end, my results all get written to disk and nothing gets returned. With the way I am running tasks, are resources getting held onto longer than necessary?
My B tasks are long but they could be split by scheduling tasks that solve for solutions at intermediate time steps and feeding those in as the inputs to subsequent solving tasks. I think I need to do this any way because I would like to use an HPC cluster with a timed queue and I think I need to use the lifetime parameter to retire workers to keep them from running over the time limit and that works best with short-lived tasks (to avoid losing work when shut down early). Is there an optimal way to split the B task?
There are lots of questions here, but with regards to the code snippets you provided, both look correct, but the futures version will scale better in my experience. The reason for that is that by default, whenever one of the delayed tasks fails, the computation of all delayed tasks halts, while futures can proceed as long as they are not directly affected by the failure.
Another observation is that delayed values will tend to hold on to resources after completion, while for futures you can at least .release() them once they have been completed (or use fire_and_forget).
Finally, with very large task lists, it might be worth to make them a bit more resilient to restarts. One basic option is to create simple text files after successful completion of a task, and then on restart check which tasks need to be re-computed. Fancier options include prefect and joblib.memory, but if you don't need all the bells and whistles, the text file route is often fastest.

schedule tasks based purely on idleness, instead of data communication

Using distributed to schedule lots of interdependent tasks, running on google compute engine. When I start an extra instance with workers halfway, no tasks get scheduled to it (though it registers fine with the scheduler). I presume this is because (from http://distributed.readthedocs.io/en/latest/scheduling-state.html#distributed.scheduler.decide_worker):
"If the task requires data communication, then we choose to minimize the number of bytes sent between workers. This takes precedence over worker occupancy."
Once I'm halfway running the task tree, all remaining tasks depend on the result of tasks which have already run. So, if I interpret the above quote right, nothing will ever be scheduled on the new workers, no matter how idle they are, as the dependent data is never already there but always on a 'old' worker.
However, I do make sure the amount of data to transfer is fairly minimal, usually just a small string. So in this case it would make much more sense to let idleness prevail over data communication. Would it be possible to allow this (e.g. setting a 'scheduler policy'? Or maybe even have a data-vs-idleness tradeoff coefficent which could be tuned?
Update after comment #1:
Complicating factor: every task is using the resources framework to make sure it either runs on the set of workers for cpu-bound tasks ("CPU=1") or on the set of workers for network-bound tasks ("NET=1"). This separation was made to avoid overloading up/download servers and restrict up/download tasks to a certain max, while still being able to scale the other tasks. However, according to http://distributed.readthedocs.io/en/latest/work-stealing.html, task stealing will not happen in these cases? Is there a way to allow task stealing while keeping the resource restrictions?
Update 2: I see there is an open issue for that: https://github.com/dask/distributed/issues/1389. Are there plans to implement this?
While Dask prefers to schedule work to reduce communication it also acknowledges that this isn't always best. Generally Dask runs a task on the machine where it will finish first, taking into account both communication costs and existing task backlogs on overloaded workers.
For more information on load balancing you might consider reading this documentation page:
http://distributed.readthedocs.io/en/latest/work-stealing.html

Using Celery for Realtime, Synchronous External API Querying with Gevent

I'm working on a web application that will receive a request from a user and have to hit a number of external APIs to compose the answer to that request. This could be done directly from the main web thread using something like gevent to fan out the request.
Alternatively, I was thinking, I could put incoming requests into a queue and use workers to distribute the load. The idea would be to try to keep it real time, while splitting up the requests amongst several workers. Each of these workers would be querying only one of the many external APIs. The response they receive would then go through a series transformations, be saved into a DB, be transformed to a common schema and saved in a common DB to finally be composed into one big response that would be returned through the web request. The web request is most likely going to be blocking all this time, with a user waiting, so keeping
the queueing and dequeueing as fast as possible is important.
The external API calls can easily be turned into individual tasks. I think the linking
from one api task to a transformation to a DB saving task could be done using a chain, etc, and the final result combining all results returned to the web thread using a chord.
Some questions:
Can this (and should this) be done using celery?
I'm using django. Should I try to use django-celery over plain celery?
Each one of those tasks might spawn off other tasks - such as logging what just
happened or other types of branching off. Is this possible?
Could tasks be returning the data they get - i.e. potentially Kb of data through celery (redis as underlying in this case) or should they write to the DB, and just pass pointers to that data around?
Each task is mostly I/O bound, and was initially just going to use gevent from the web thread to fan out the requests and skip the whole queuing design, but it turns out that it would be reused for a different component. Trying to keep the whole round trip through the Qs real time will probably require many workers making sure the queueus are mostly empty. Or is it? Would running the gevent worker pool help with this?
Do I have to write gevent specific tasks or will using the gevent pool deal with network IO automagically?
Is it possible to assign priority to certain tasks?
What about keeping them in order?
Should I skip celery and just use kombu?
It seems like celery is geared more towards "tasks" that can be deferred and are
not time sensitive. Am I nuts for trying to keep this real time?
What other technologies should I look at?
Update: Trying to hash this out a bit more. I did some reading on Kombu and it seems to be able to do what I'm thinking of, although at a much lower level than celery. Here is a diagram of what I had in mind.
What seems to be possible with raw queues as accessible with Kombu is the ability for a number of workers to subscribe to a broadcast message. The type and number does not need to be known by the publisher if using a queue. Can something similar be achieved using Celery? It seems like if you want to make a chord, you need to know at runtime what tasks are going to be involved in the chord, whereas in this scenario you can simply add listeners to the broadcast, and simply make sure they announce they are in the running to add responses to the final queue.
Update 2: I see there is the ability to broadcast Can you combine this with a chord? In general, can you combine celery with raw kombu? This is starting to sound like a question about smoothies.
I will try to answer as many of the questions as possible.
Can this (and should this) be done using celery?
Yes you can
I'm using django. Should I try to use django-celery over plain celery?
Django has a good support for celery and would make the life much easier during development
Each one of those tasks might spawn off other tasks - such as logging
what just happened or other types of branching off. Is this possible?
You can start subtasks from withing a task with ignore_result = true for only side effects
Could tasks be returning the data they get - i.e. potentially Kb of
data through celery (redis as underlying in this case) or should they
write to the DB, and just pass pointers to that data around?
I would suggest putting the results in db and then passing id around would make your broker and workers happy. Less data transfer/pickling etc.
Each task is mostly I/O bound, and was initially just going to use
gevent from the web thread to fan out the requests and skip the whole
queuing design, but it turns out that it would be reused for a
different component. Trying to keep the whole round trip through the
Qs real time will probably require many workers making sure the
queueus are mostly empty. Or is it? Would running the gevent worker
pool help with this?
Since the process is io bound then gevent will definitely help here. However, how much the concurrency should be for gevent pool'd worker, is something that I'm looking for answer too.
Do I have to write gevent specific tasks or will using the gevent pool
deal with network IO automagically?
Gevent does the monkey patching automatically when you use it in pool. But the libraries that you use should play well with gevent. Otherwise, if your parsing some data with simplejson (which is written in c) then that would block other gevent greenlets.
Is it possible to assign priority to certain tasks?
You cannot assign specific priorities to certain tasks, but route them to different queue and then have those queues being listened to by varying number of workers. The more the workers for a particular queue, the higher would be the priority of that tasks on that queue.
What about keeping them in order?
Chain is one way to maintain order. Chord is a good way to summarize. Celery takes care of it, so you dont have to worry about it. Even when using gevent pool, it would at the end be possible to reason about the order of the tasks execution.
Should I skip celery and just use kombu?
You can, if your use case will not change to something more complex over time and also if you are willing to manage your processes through celeryd + supervisord by yourself. Also, if you don't care about the task monitoring that comes with tools such as celerymon, flower, etc.
It seems like celery is geared more towards "tasks" that can be
deferred and are not time sensitive.
Celery supports scheduled tasks as well. If that is what you meant by that statement.
Am I nuts for trying to keep this real time?
I don't think so. As long as your consumers are fast enough, it will be as good as real time.
What other technologies should I look at?
Pertaining to celery, you should choose result store wisely. My suggestion would be to use cassandra. It is good for realtime data (both write and query wise). You can also use redis or mongodb. They come with their own set of problems as result store. But then a little tweaking in configuration can go a long way.
If you mean something completely different from celery, then you can look into asyncio (python3.5) and zeromq for achieving the same. I can't comment more on that though.

Parallel processing within a queue (using Pool within Celery)

I'm using Celery to queue jobs from a CGI application I made. The way I've set it up, Celery makes each job run one- or two-at-a-time by setting CELERYD_CONCURRENCY = 1 or = 2 (so they don't crowd the processor or thrash from memory consumption). The queue works great, thanks to advice I got on StackOverflow.
Each of these jobs takes a fair amount of time (~30 minutes serial), but has an embarrassing parallelizability. For this reason, I was using Pool.map to split it and do the work in parallel. It worked great from the command line, and I got runtimes around 5 minutes using a new many-cored chip.
Unfortunately, there is some limitation that does not allow daemonic process to have subprocesses, and when I run the fancy parallelized code within the CGI queue, I get this error:
AssertionError: daemonic processes are not allowed to have children
I noticed other people have had similar questions, but I can't find an answer that wouldn't require abandoning Pool.map altogether, and making more complicated thread code.
What is the appropriate design choice here? I can easily run my serial jobs using my Celery queue. I can also run my much faster parallelized jobs without a queue. How should I approach this, and is it possible to get what I want (both the queue and the per-job parallelization)?
A couple of ideas I've had (some are quite hacky):
The job sent to the Celery queue simply calls the command line program. That program can use Pool as it pleases, and then saves the result figures & data to a file (just as it does now). Downside: I won't be able to check on the status of the job or see if it terminated successfully. Also, system calls from CGI may cause security issues.
Obviously, if the queue is very full of jobs, I can make use of the CPU resources (by setting CELERYD_CONCURRENCY = 6 or so); this will allow many people to be "at the front of the queue" at once.Downside: Each job will spend a lot of time at the front of the queue; if the queue isn't full, there will be no speedup. Also, many partially finished jobs will be stored in memory at the same time, using much more RAM.
Use Celery's #task to parallelize within sub-jobs. Then, instead of setting CELERYD_CONCURRENCY = 1, I would set it to 6 (or however many sub jobs I'd like to allow in memory at a time). Downside: First of all, I'm not sure whether this will successfully avoid the "task-within-task" problem. But also, the notion of queue position may be lost, and many partially finished jobs may end up in memory at once.
Perhaps there is a way to call Pool.map and specify that the threads are non-daemonic? Or perhaps there is something more lightweight I can use instead of Pool.map? This is similar to an approach taken on another open StackOverflow question. Also, I should note that the parallelization I exploit via Pool.map is similar to linear algebra, and there is no inter-process communication (each just runs independently and returns its result without talking to the others).
Throw away Celery and use multiprocessing.Queue. Then maybe there'd be some way to use the same "thread depth" for every thread I use (i.e. maybe all of the threads could use the same Pool, avoiding nesting)?
Thanks a lot in advance.
What you need is a workflow management system (WFMS) that manages
task concurrency
task dependency
task nesting
among other things.
From a very high level view, a WFMS sits on top of a task pool like celery, and submits the tasks which are ready to execute to the pool. It is also responsible for opening up a nest and submitting the tasks in the nest accordingly.
I've developed a system to do just that. It's called pomsets. Try it out, and feel free to send me any questions.
I using a multiprocessed deamons based on Twisted with forking and Gearman jobs query normally.
Try to look at Gearman.

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