I'm playing around with some measurement instruments through PyVisa (Python wrapper for VISA). Specifically I need to read the measurement value from four instruments, similar to this:
current1 = instrument1.ask("READ?")
current2 = instrument2.ask("READ?")
current3 = instrument3.ask("READ?")
current4 = instrument4.ask("READ?")
For my application, speed is a must. Individually, I can get between 50 and 200 measurements per second from the four instruments, but unfortunately my current code evaluates the four instruments serially.
From what I've read, there's some options with Threading and Multiprocessing in Python, but it's not obvious what the best, and fastest, option for me.
Best case scenario I will be spawning ~4x50 threads per second, so overhead is a bit of a concern.
The task is in no way CPU intensive, it is simply a matter of waiting for the readout from the instrument.
Any advice on what the proper course of action might be?
Many thanks in advance!
Try using the multiprocessing module in python. Because of the way the python interpreter is written, the threading module for python actually slows down your application when using multiple threads on a computer with multiple processors. This is due to something called the Global Interpreter Lock (GIL) which only allows one python thread per process to be run at a time. This makes things like memory management and concurrency easier for the interpreter.
I would suggest trying to create a process for each instrument (producer process) and send the results to a shared queue that gets processed by a single process (consumer process).
I would also limit the number of processes that you create to the number of processors on your computer. Creating too many processes introduces a lot of overhead.
If you really feel like you need the 200 threads you suggested in your post, I would program this in Java or C++.
I'm not sure if this fits your requirements I'm not too familiar with pyVisa, however have you looked into pypy's stackless examples the speed increase is pretty impressive, and you're able to spawn almost infinite amount of 'threadlets' without much hindrance to your system / program.
pypy is kinda limited in terms of supporting various packages but looks like pyVisa isn't one of them.
https://pypi.python.org/pypi/PyVISA
Related
Does the presence of python GIL imply that in python multi threading the same operation is not so different from repeating it in a single thread?.
For example, If I need to upload two files, what is the advantage of doing them in two threads instead of uploading them one after another?.
I tried a big math operation in both ways. But they seem to take almost equal time to complete.
This seems to be unclear to me. Can someone help me on this?.
Thanks.
Python's threads get a slightly worse rap than they deserve. There are three (well, 2.5) cases where they actually get you benefits:
If non-Python code (e.g. a C library, the kernel, etc.) is running, other Python threads can continue executing. It's only pure Python code that can't run in two threads at once. So if you're doing disk or network I/O, threads can indeed buy you something, as most of the time is spent outside of Python itself.
The GIL is not actually part of Python, it's an implementation detail of CPython (the "reference" implementation that the core Python devs work on, and that you usually get if you just run "python" on your Linux box or something.
Jython, IronPython, and any other reimplementations of Python generally do not have a GIL, and multiple pure-Python threads can execute simultaneously.
The 0.5 case: Even if you're entirely pure-Python and see little or no performance benefit from threading, some problems are really convenient in terms of developer time and difficulty to solve with threads. This depends in part on the developer, too, of course.
It really depends on the library you're using. The GIL is meant to prevent Python objects and its internal data structures to be changed at the same time. If you're doing an upload, the library you use to do the actual upload might release the GIL while it's waiting for the actual HTTP request to complete (I would assume that is the case with the HTTP modules in the standard library, but I didn't check).
As a side note, if you really want to have things running in parallel, just use multiple processes. It will save you a lot of trouble and you'll end up with better code (more robust, more scalable, and most probably better structured).
It depends on the native code module that's executing. Native modules can release the GIL and then go off and do their own thing allowing another thread to lock the GIL. The GIL is normally held while code, both python and native, are operating on python objects. If you want more detail you'll probably need to go and read quite a bit about it. :)
See:
What is a global interpreter lock (GIL)? and Thread State and the Global Interpreter Lock
Multithreading is a concept where two are more tasks need be completed simultaneously, for example, I have word processor in this application there are N numbers of a parallel task have to work. Like listening to keyboard, formatting input text, sending a formatted text to display unit. In this context with sequential processing, it is time-consuming and one task has to wait till the next task completion. So we put these tasks in threads and simultaneously complete the task. Three threads are always up and waiting for the inputs to arrive, then take that input and produce the output simultaneously.
So multi-threading works faster if we have multi-core and processors. But in reality with single processors, threads will work one after the other, but we feel it's executing with greater speed, Actually, one instruction executes at a time and a processor can execute billions of instructions at a time. So the computer creates illusion that multi-task or thread working parallel. It just an illusion.
I'm slightly confused about whether multithreading works in Python or not.
I know there has been a lot of questions about this and I've read many of them, but I'm still confused. I know from my own experience and have seen others post their own answers and examples here on StackOverflow that multithreading is indeed possible in Python. So why is it that everyone keep saying that Python is locked by the GIL and that only one thread can run at a time? It clearly does work. Or is there some distinction I'm not getting here?
Many posters/respondents also keep mentioning that threading is limited because it does not make use of multiple cores. But I would say they are still useful because they do work simultaneously and thus get the combined workload done faster. I mean why would there even be a Python thread module otherwise?
Update:
Thanks for all the answers so far. The way I understand it is that multithreading will only run in parallel for some IO tasks, but can only run one at a time for CPU-bound multiple core tasks.
I'm not entirely sure what this means for me in practical terms, so I'll just give an example of the kind of task I'd like to multithread. For instance, let's say I want to loop through a very long list of strings and I want to do some basic string operations on each list item. If I split up the list, send each sublist to be processed by my loop/string code in a new thread, and send the results back in a queue, will these workloads run roughly at the same time? Most importantly will this theoretically speed up the time it takes to run the script?
Another example might be if I can render and save four different pictures using PIL in four different threads, and have this be faster than processing the pictures one by one after each other? I guess this speed-component is what I'm really wondering about rather than what the correct terminology is.
I also know about the multiprocessing module but my main interest right now is for small-to-medium task loads (10-30 secs) and so I think multithreading will be more appropriate because subprocesses can be slow to initiate.
The GIL does not prevent threading. All the GIL does is make sure only one thread is executing Python code at a time; control still switches between threads.
What the GIL prevents then, is making use of more than one CPU core or separate CPUs to run threads in parallel.
This only applies to Python code. C extensions can and do release the GIL to allow multiple threads of C code and one Python thread to run across multiple cores. This extends to I/O controlled by the kernel, such as select() calls for socket reads and writes, making Python handle network events reasonably efficiently in a multi-threaded multi-core setup.
What many server deployments then do, is run more than one Python process, to let the OS handle the scheduling between processes to utilize your CPU cores to the max. You can also use the multiprocessing library to handle parallel processing across multiple processes from one codebase and parent process, if that suits your use cases.
Note that the GIL is only applicable to the CPython implementation; Jython and IronPython use a different threading implementation (the native Java VM and .NET common runtime threads respectively).
To address your update directly: Any task that tries to get a speed boost from parallel execution, using pure Python code, will not see a speed-up as threaded Python code is locked to one thread executing at a time. If you mix in C extensions and I/O, however (such as PIL or numpy operations) and any C code can run in parallel with one active Python thread.
Python threading is great for creating a responsive GUI, or for handling multiple short web requests where I/O is the bottleneck more than the Python code. It is not suitable for parallelizing computationally intensive Python code, stick to the multiprocessing module for such tasks or delegate to a dedicated external library.
Yes. :)
You have the low level thread module and the higher level threading module. But it you simply want to use multicore machines, the multiprocessing module is the way to go.
Quote from the docs:
In CPython, due to the Global Interpreter Lock, only one thread can
execute Python code at once (even though certain performance-oriented
libraries might overcome this limitation). If you want your
application to make better use of the computational resources of
multi-core machines, you are advised to use multiprocessing. However,
threading is still an appropriate model if you want to run multiple
I/O-bound tasks simultaneously.
Threading is Allowed in Python, the only problem is that the GIL will make sure that just one thread is executed at a time (no parallelism).
So basically if you want to multi-thread the code to speed up calculation it won't speed it up as just one thread is executed at a time, but if you use it to interact with a database for example it will.
I feel for the poster because the answer is invariably "it depends what you want to do". However parallel speed up in python has always been terrible in my experience even for multiprocessing.
For example check this tutorial out (second to top result in google): https://www.machinelearningplus.com/python/parallel-processing-python/
I put timings around this code and increased the number of processes (2,4,8,16) for the pool map function and got the following bad timings:
serial 70.8921644706279
parallel 93.49704207479954 tasks 2
parallel 56.02441442012787 tasks 4
parallel 51.026168536394835 tasks 8
parallel 39.18044807203114 tasks 16
code:
# increase array size at the start
# my compute node has 40 CPUs so I've got plenty to spare here
arr = np.random.randint(0, 10, size=[2000000, 600])
.... more code ....
tasks = [2,4,8,16]
for task in tasks:
tic = time.perf_counter()
pool = mp.Pool(task)
results = pool.map(howmany_within_range_rowonly, [row for row in data])
pool.close()
toc = time.perf_counter()
time1 = toc - tic
print(f"parallel {time1} tasks {task}")
I'm slightly confused about whether multithreading works in Python or not.
I know there has been a lot of questions about this and I've read many of them, but I'm still confused. I know from my own experience and have seen others post their own answers and examples here on StackOverflow that multithreading is indeed possible in Python. So why is it that everyone keep saying that Python is locked by the GIL and that only one thread can run at a time? It clearly does work. Or is there some distinction I'm not getting here?
Many posters/respondents also keep mentioning that threading is limited because it does not make use of multiple cores. But I would say they are still useful because they do work simultaneously and thus get the combined workload done faster. I mean why would there even be a Python thread module otherwise?
Update:
Thanks for all the answers so far. The way I understand it is that multithreading will only run in parallel for some IO tasks, but can only run one at a time for CPU-bound multiple core tasks.
I'm not entirely sure what this means for me in practical terms, so I'll just give an example of the kind of task I'd like to multithread. For instance, let's say I want to loop through a very long list of strings and I want to do some basic string operations on each list item. If I split up the list, send each sublist to be processed by my loop/string code in a new thread, and send the results back in a queue, will these workloads run roughly at the same time? Most importantly will this theoretically speed up the time it takes to run the script?
Another example might be if I can render and save four different pictures using PIL in four different threads, and have this be faster than processing the pictures one by one after each other? I guess this speed-component is what I'm really wondering about rather than what the correct terminology is.
I also know about the multiprocessing module but my main interest right now is for small-to-medium task loads (10-30 secs) and so I think multithreading will be more appropriate because subprocesses can be slow to initiate.
The GIL does not prevent threading. All the GIL does is make sure only one thread is executing Python code at a time; control still switches between threads.
What the GIL prevents then, is making use of more than one CPU core or separate CPUs to run threads in parallel.
This only applies to Python code. C extensions can and do release the GIL to allow multiple threads of C code and one Python thread to run across multiple cores. This extends to I/O controlled by the kernel, such as select() calls for socket reads and writes, making Python handle network events reasonably efficiently in a multi-threaded multi-core setup.
What many server deployments then do, is run more than one Python process, to let the OS handle the scheduling between processes to utilize your CPU cores to the max. You can also use the multiprocessing library to handle parallel processing across multiple processes from one codebase and parent process, if that suits your use cases.
Note that the GIL is only applicable to the CPython implementation; Jython and IronPython use a different threading implementation (the native Java VM and .NET common runtime threads respectively).
To address your update directly: Any task that tries to get a speed boost from parallel execution, using pure Python code, will not see a speed-up as threaded Python code is locked to one thread executing at a time. If you mix in C extensions and I/O, however (such as PIL or numpy operations) and any C code can run in parallel with one active Python thread.
Python threading is great for creating a responsive GUI, or for handling multiple short web requests where I/O is the bottleneck more than the Python code. It is not suitable for parallelizing computationally intensive Python code, stick to the multiprocessing module for such tasks or delegate to a dedicated external library.
Yes. :)
You have the low level thread module and the higher level threading module. But it you simply want to use multicore machines, the multiprocessing module is the way to go.
Quote from the docs:
In CPython, due to the Global Interpreter Lock, only one thread can
execute Python code at once (even though certain performance-oriented
libraries might overcome this limitation). If you want your
application to make better use of the computational resources of
multi-core machines, you are advised to use multiprocessing. However,
threading is still an appropriate model if you want to run multiple
I/O-bound tasks simultaneously.
Threading is Allowed in Python, the only problem is that the GIL will make sure that just one thread is executed at a time (no parallelism).
So basically if you want to multi-thread the code to speed up calculation it won't speed it up as just one thread is executed at a time, but if you use it to interact with a database for example it will.
I feel for the poster because the answer is invariably "it depends what you want to do". However parallel speed up in python has always been terrible in my experience even for multiprocessing.
For example check this tutorial out (second to top result in google): https://www.machinelearningplus.com/python/parallel-processing-python/
I put timings around this code and increased the number of processes (2,4,8,16) for the pool map function and got the following bad timings:
serial 70.8921644706279
parallel 93.49704207479954 tasks 2
parallel 56.02441442012787 tasks 4
parallel 51.026168536394835 tasks 8
parallel 39.18044807203114 tasks 16
code:
# increase array size at the start
# my compute node has 40 CPUs so I've got plenty to spare here
arr = np.random.randint(0, 10, size=[2000000, 600])
.... more code ....
tasks = [2,4,8,16]
for task in tasks:
tic = time.perf_counter()
pool = mp.Pool(task)
results = pool.map(howmany_within_range_rowonly, [row for row in data])
pool.close()
toc = time.perf_counter()
time1 = toc - tic
print(f"parallel {time1} tasks {task}")
I'm working on simulating a mesh network with a large number of nodes. The nodes pass data between different master nodes throughout the network.
Each master comes live once a second to receive the information, but the slave nodes don't know when the master is up or not, so when they have information to send, they try and do so every 5 ms for 1 second to make sure they can find the master.
Running this on a regular computer with 1600 nodes results in 1600 threads and the performance is extremely bad.
What is a good approach to handling the threading so each node acts as if it is running on its own thread?
In case it matters, I'm building the simulation in python 2.7, but I'm open to changing to something else if that makes sense.
For one, are you really using regular, default Python threads available in the default Python 2.7 interpreter (CPython), and is all of your code in Python? If so, you are probably not actually using multiple CPU cores because of the global interpreter lock CPython has (see https://wiki.python.org/moin/GlobalInterpreterLock). You could maybe try running your code under Jython, just to check if performance will be better.
You should probably rethink your application architecture and switch to manually scheduling events instead of using threads, or maybe try using something like greenlets (https://stackoverflow.com/a/15596277/1488821), but that would probably mean less precise timings because of lack of parallelism.
To me, 1600 threads sounds like a lot but not excessive given that it's a simulation. If this were a production application it would probably not be production-worthy.
A standard machine should have no trouble handling 1600 threads. As to the OS this article could provide you with some insights.
When it comes to your code a Python script is not a native application but an interpreted script and as such will require more CPU resources to execute.
I suggest you try implementing the simulation in C or C++ instead which will produce a native application which should execute more efficiently.
Do not use threading for that. If sticking to Python, let the nodes perform their actions one by one. If the performance you get doing so is OK, you will not have to use C/C++. If the actions each node perform are simple, that may work. Anyway, there is no reason to use threads in Python at all. Python threads are usable mostly for making blocking I/O not to block your program, not for multiple CPU kernels utilization.
If you want to really use parallel processing and to write your nodes as if they were really separated and exchanging only using messages, you may use Erlang (http://www.erlang.org/). It is a functional language very well suited for executing parallel processes and making them exchange messages. Erlang processes do not map to OS threads, and you may create thousands of them. However, Erlang is a purely functional language and may seem extremely strange if you have never used such languages. And it also is not very fast, so, like Python, it is unlikely to handle 1600 actions every 5ms unless the actions are rather simple.
Finally, if you do not get desired performance using Python or Erlang, you may move to C or C++. However, still do not use 1600 threads. In fact, using threads to gain performance is reasonable only if the number of threads does not dramatically exceed number of CPU kernels. A reactor pattern (with several reactor threads) is what you may need in that case (http://en.wikipedia.org/wiki/Reactor_pattern). There is an excellent implementation of the reactor pattern in boost.asio library. It is explained here: http://www.gamedev.net/blog/950/entry-2249317-a-guide-to-getting-started-with-boostasio/
Some random thoughts here:
I did rather well with several hundred threads working like this in Java; it can be done with the right language. (But I haven't tried this in Python.)
In any language, you could run the master node code in one thread; just have it loop continuously, running the code for each master in each cycle. You'll lose the benefits of multiple cores that way, though. On the other hand, you'll lose the problems of multithreading, too. (You could have, say, 4 such threads, utilizing the cores but getting the multithreading headaches back. It'll keep the thread-overhead down, too, but then there's blocking...)
One big problem I had was threads blocking each other. Enabling 100 threads to call the same method on the same object at the same time without waiting for each other requires a bit of thought and even research. I found my multithreading program at first often used only 25% of a 4-core CPU even when running flat out. This might be one reason you're running slow.
Don't have your slave nodes repeat sending data. The master nodes should come alive in response to data coming in, or have some way of storing it until they do come alive, or some combination.
It does pay to have more threads than cores. Once you have two threads, they can block each other (and will if they share any data). If you have code to run that won't block, you want to run it in its own thread so it won't be waiting for code that does block to unblock and finish. I found once I had a few threads, they started to multiply like crazy--hence my hundreds-of-threads program. Even when 100 threads block at one spot despite all my brilliance, there's plenty of other threads to keep the cores busy!
In my script, I have a function foo which basically uses pynotify to notify user about something repeatedly after a time interval say 15 minutes.
def foo:
while True:
"""Does something"""
time.sleep(900)
My main script has to interact with user & does all other things so I just cant call the foo() function. directly.
Whats the better way of doing it and why?
Using fork or threads?
I won't tell you which one to use, but here are some of the advantages of each:
Threads can start more quickly than processes, and threads use fewer operating system resources than processes, including memory, file handles, etc. Threads also give you the option of communicating through shared variables (although many would say this is more of a disadvantage than an advantage - See below).
Processes each have their own separate memory and variables, which means that processes generally communicate by sending messages to each other. This is much easier to do correctly than having threads communicate via shared memory. Processes can also run truly concurrently, so that if you have multiple CPU cores, you can keep all of them busy using processes. In Python*, the global interpreter lock prevents threads from making much use of more than a single core.
* - That is, CPython, which the implementation of Python that you get if you go to http://python.org and download Python. Other Python implementations (such as Jython) do not necessarily prohibit Python from running threads on multiple CPUs simultaneously. Thanks to #EOL for the clarification.
For these kinds of problems, neither threads nor forked processes seem the right approach. If all you want to do is to once every 15 minutes notify the user of something, why not use an event loop like GLib's or Twisted's reactor ? This allows you to schedule operations that should run once in a while, and get on with the rest of your program.
Using multiple processes lets you exploit multiple CPU cores at the same time, while, in CPython, using threads doesn't (threads take turns using a single CPU core) -- so, if you have CPU intensive work and absolutely want to use threads, you should consider Jython or IronPython; with CPython, this consideration is often enough to sway the choice towards the multiprocessing module and away from the threading one (they offer pretty similar interfaces, because multiprocessing was designed to be easily put in place in lieu of threading).
Net of this crucial consideration, threads might often be a better choice (performance-wise) on Windows (where making a new process is a heavy task), but less often on Unix variants (Linux, BSD versions, OpenSolaris, MacOSX, ...), since making a new process is faster there (but if you're using IronPython or Jython, you should check, on the platforms you care about, that this still applies in the virtual machines in question -- CLR with either .NET or Mono for IronPython, your JVM of choice for Jython).
Processes are much simpler. Just turn them loose and let the OS handle it.
Also, processes are often much more efficient. Processes do not share a common pool of I/O resources; they are completely independent.
Python's subprocess.Popen handles everything.
If by fork you mean os.fork then I would avoid using that. It is not cross platform and too low level - you would need to implement communication between the processes yourself.
If you want to use a separate process then use either the subprocess module or if you are on Python 2.6 or later the new multiprocessing module. This has a very similar API to the threading module, so you could start off using threads and then easily switch to processes, or vice-versa.
For what you want to do I think I would use threads, unless """does something""" is CPU intensive and you want to take advantage of multiple cores, which I doubt in this particular case.