I am running a backend python-eve server with multiple functions being called to provide one service. I want to do profiling for this python backend server. I want to find out which among the multiple functionalities is taking time for execution. I have heard and used cprofiler but for a server that is continuously running, how do I do profiling? Moreover, I am using Pycharm IDE to work with the python code. So, it will be beneficial if there's a way I can do profiling using Pycharm.
While I do not have direct experience with python-eve, I wrote pprofile (pypi) mainly to use on Zope (also a long-running process).
The basic idea (at least on processes using worker threads, like Zope) is to start pprofile in statistic mode, let it collect samples for a while (how long heavily depends on how busy the process is and the level of detail you want to capture in the profiling result), and finally to build a profiling result archive, which in my case contains both the profiling result and all executed source code (so I'm extra-sure I'm annotating the correct version of the code).
I have so far not needed to do extra-long profiling session, like do one query to start profiling, then later another query to stop and fetch the result - or even to keep the result server-side and browse it somehow, and how to do this will likely heavily depend on server details.
You can find the extra customisation for Zope (allowing to fetch the python source out of Zope's Python Scripts, TAL expressions, and beyond pure python profiling it also collects object database loading durations, and even SQL queries run, to provide a broader picture) in pprofile.zope, just to give you an idea of what can be done.
Related
Edit for clarify my question:
I want to attach a python service on uwsgi using this feature (I can't understand the examples) and I also want to be able to communicate results between them. Below I present some context and also present my first thought on the communication matter, expecting maybe some advice or another approach to take.
I have an already developed python application that uses multiprocessing.Pool to run on demand tasks. The main reason for using the pool of workers is that I need to share several objects between them.
On top of that, I want to have a flask application that triggers tasks from its endpoints.
I've read several questions here on SO looking for possible drawbacks of using flask with python's multiprocessing module. I'm still a bit confused but this answer summarizes well both the downsides of starting a multiprocessing.Pool directly from flask and what my options are.
This answer shows an uWSGI feature to manage daemon/services. I want to follow this approach so I can use my already developed python application as a service of the flask app.
One of my main problems is that I look at the examples and do not know what I need to do next. In other words, how would I start the python app from there?
Another problem is about the communication between the flask app and the daemon process/service. My first thought is to use flask-socketIO to communicate, but then, if my server stops I need to deal with the connection... Is this a good way to communicate between server and service? What are other possible solutions?
Note:
I'm well aware of Celery, and I pretend to use it in a near future. In fact, I have an already developed node.js app, on which users perform actions that should trigger specific tasks from the (also) already developed python application. The thing is, I need a production-ready version as soon as possible, and instead of modifying the python application, that uses multiprocessing, I thought it would be faster to create a simple flask server to communicate with node.js through HTTP. This way I would only need to implement a flask app that instantiates the python app.
Edit:
Why do I need to share objects?
Simply because the creation of the objects in questions takes too long. Actually, the creation takes an acceptable amount of time if done once, but, since I'm expecting (maybe) hundreds to thousands of requests simultaneously having to load every object again would be something I want to avoid.
One of the objects is a scikit classifier model, persisted on a pickle file, which takes 3 seconds to load. Each user can create several "job spots" each one will take over 2k documents to be classified, each document will be uploaded on an unknown point in time, so I need to have this model loaded in memory (loading it again for every task is not acceptable).
This is one example of a single task.
Edit 2:
I've asked some questions related to this project before:
Bidirectional python-node communication
Python multiprocessing within node.js - Prints on sub process not working
Adding a shared object to a manager.Namespace
As stated, but to clarify: I think the best solution would be to use Celery, but in order to quickly have a production ready solution, I trying to use this uWSGI attach daemon solution
I can see the temptation to hang on to multiprocessing.Pool. I'm using it in production as part of a pipeline. But Celery (which I'm also using in production) is much better suited to what you're trying to do, which is distribute work across cores to a resource that's expensive to set up. Have N cores? Start N celery workers, which of which can load (or maybe lazy-load) the expensive model as a global. A request comes in to the app, launch a task (e.g., task = predict.delay(args), wait for it to complete (e.g., result = task.get()) and return a response. You're trading a little bit of time learning celery for saving having to write a bunch of coordination code.
I need you guys :D
I have a web page, on this page I have check some items and pass their value as variable to python script.
problem is:
I Need to write a python script and in that script I need to put this variables into my predefined shell commands and run them.
It is one gnuplot and one other shell commands.
I never do anything in python can you guys send me some advices ?
THx
I can't fully address your questions due to lack of information on the web framework that you are using but here are some advice and guidance that you will find useful. I did had a similar problem that will require me to run a shell program that pass arguments derived from user requests( i was using the django framework ( python ) )
Now there are several factors that you have to consider
How long will each job takes
What is the load that you are expecting (are there going to be loads of jobs)
Will there be any side effects from your shell command
Here are some explanation that why this will be important
How long will each job takes.
Depending on your framework and browser, there is a limitation on the duration that a connection to the server is kept alive. In other words, you will have to take into consideration that the time for the server to response to a user request do not exceed the connection time out set by the server or the browser. If it takes too long, then you will get a server connection time out. Ie you will get an error response as there is no response from the server side.
What is the load that you are expecting.
You will have probably figure that if a work that you are requesting is huge,it will take out more resources than you will need. Also, if you have multiple requests at the same time, it will take a huge toll on your server. For instance, if you do proceed with using subprocess for your jobs, it will be important to note if you job is blocking or non blocking.
Side effects.
It is important to understand what are the side effects of your shell process. For instance, if your shell process involves writing and generating lots of temp files, you will then have to consider the permissions that your script have. It is a complex task.
So how can this be resolve!
subprocesswhich ship with base python will allow you to run shell commands using python. If you want more sophisticated tools check out the fabric library. For passing of arguments do check out optparse and sys.argv
If you expect a huge work load or a long processing time, do consider setting up a queue system for your jobs. Popular framework like celery is a good example. You may look at gevent and asyncio( python 3) as well. Generally, instead of returning a response on the fly, you can retur a job id or a url in which the user can come back later on and have a look
Point to note!
Permission and security is vital! The last thing you want is for people to execute shell command that will be detrimental to your system
You can also increase connection timeout depending on the framework that you are using.
I hope you will find this useful
Cheers,
Biobirdman
I'm trying to do some machinery automation with python, but I've run into a problem.
I have code that does the actual control, code that logs, code the provides a GUI, and some other modules all being called from a single script.
The issue is that an error in one module halts all the others. So, for instance a bug in the GUI will kill the control systems.
I want to be able to have the modules run independently, so one can crash, be restarted, be patched, etc without halting the others.
The only way I can find to make that work is to store the variables in an SQL database, or files or something.
Is there a way for one python script to sort of ..debug another? so that one script can read or change the variables in the other? I can't find a way to do that that also allows to scripts to be started and stopped independently.
Does anyone have any ideas or advice?
A fairly effective way to do this is to use message passing. Each of your modules are independent, but they can send and receive messages to each other. A very good reference on the many ways to achieve this in Python is the Python wiki page for parallel processing.
A generic strategy
Split your program into pieces where there are servers and clients. You could then use middleware such as 0MQ, Apache ActiveMQ or RabbitMQ to send data between different parts of the system.
In this case, your GUI could send a message to the log parser server telling it to begin work. Once it's done, the log parser will send a broadcast message to anyone interested telling the world the a reference to the results. The GUI could be a subscriber to the channel that the log parser subscribes to. Once it receives the message, it will open up the results file and display whatever the user is interested in.
Serialization and deserialization speed is important also. You want to minimise the overhead for communicating. Google Protocol Buffers and Apache Thrift are effective tools here.
You will also need some form of supervision strategy to prevent a failure in one of the servers from blocking everything. supervisord will restart things for you and is quite easy to configure. Again, it is only one of many options in this space.
Overkill much?
It sounds like you have created a simple utility. The multiprocessing module is an excellent way to have different bits of the program running fairly independently. You still apply the same strategy (message passing, no shared shared state, supervision), but with different tactics.
You want multiply independent processes, and you want them to talk to each other. Hence: read what methods of inter-process communication are available on your OS. I recommend sockets (generic, will work over a n/w and with diff OSs). You can easily invent a simple (maybe http-like) protocol on top of TCP, maybe with json for messages. There is a bunch of classes coming with Python distribution to make it easy (SocketServer.ThreadingMixIn, SocketServer.TCPServer, etc.).
I have a long-running twisted server.
In a large system test, at one particular point several minutes into the test, when some clients enter a particular state and a particular outside event happens, then this server takes several minutes of 100% CPU and does its work very slowly. I'd like to know what it is doing.
How do you get a profile for a particular span of time in a long-running server?
I could easily send the server start and stop messages via HTTP if there was a way to enable or inject the profiler at runtime?
Given the choice, I'd like stack-based/call-graph profiling but even leaf sampling might give insight.
yappi profiler can be started and stopped at runtime.
There are two interesting tools that came up that try to solve that specific problem, where you might not necessarily have instrumented profiling in your code in advance but want to profile production code in a pinch.
pyflame will attach to an existing process using the ptrace(2) syscall and create "flame graphs" of the process. It's written in Python.
py-spy works by reading the process memory instead and figuring out the Python call stack. It also provides a flame graph but also a "top-like" interface to show which function is taking the most time. It's written in Rust and Python.
Not a very Pythonic answer, but maybe straceing the process gives some insight (assuming you are on a Linux or similar).
Using strictly Python, for such things I'm using tracing all calls, storing their results in a ringbuffer and use a signal (maybe you could do that via your HTTP message) to dump that ringbuffer. Of course, tracing slows down everything, but in your scenario you could switch on the tracing by an HTTP message as well, so it will only be enabled when your trouble is active as well.
Pyliveupdate is a tool designed for the purpose: profiling long running programs without restarting them. It allows you to dynamically selecting specific functions to profiling or stop profiling without instrument your code ahead of time -- it dynamically instrument code to do profiling.
Pyliveupdate have three key features:
Profile specific Python functions' (by function names or module names) call time.
Add / remove profilings without restart programs.
Show profiling results with call summary and flamegraphs.
Check out a demo here: https://asciinema.org/a/304465.
I noticed that sqlite3 isn´t really capable nor reliable when i use it inside a multiprocessing enviroment. Each process tries to write some data into the same database, so that a connection is used by multiple threads. I tried it with the check_same_thread=False option, but the number of insertions is pretty random: Sometimes it includes everything, sometimes not. Should I parallel-process only parts of the function (fetching data from the web), stack their outputs into a list and put them into the table all together or is there a reliable way to handle multi-connections with sqlite?
First of all, there's a difference between multiprocessing (multiple processes) and multithreading (multiple threads within one process).
It seems that you're talking about multithreading here. There are a couple of caveats that you should be aware of when using SQLite in a multithreaded environment. The SQLite documentation mentions the following:
Do not use the same database connection at the same time in more than
one thread.
On some operating systems, a database connection should
always be used in the same thread in which it was originally created.
See here for a more detailed information: Is SQLite thread-safe?
I've actually just been working on something very similar:
multiple processes (for me a processing pool of 4 to 32 workers)
each process worker does some stuff that includes getting information
from the web (a call to the Alchemy API for mine)
each process opens its own sqlite3 connection, all to a single file, and each
process adds one entry before getting the next task off the stack
At first I thought I was seeing the same issue as you, then I traced it to overlapping and conflicting issues with retrieving the information from the web. Since I was right there I did some torture testing on sqlite and multiprocessing and found I could run MANY process workers, all connecting and adding to the same sqlite file without coordination and it was rock solid when I was just putting in test data.
So now I'm looking at your phrase "(fetching data from the web)" - perhaps you could try replacing that data fetching with some dummy data to ensure that it is really the sqlite3 connection causing you problems. At least in my tested case (running right now in another window) I found that multiple processes were able to all add through their own connection without issues but your description exactly matches the problem I'm having when two processes step on each other while going for the web API (very odd error actually) and sometimes don't get the expected data, which of course leaves an empty slot in the database. My eventual solution was to detect this failure within each worker and retry the web API call when it happened (could have been more elegant, but this was for a personal hack).
My apologies if this doesn't apply to your case, without code it's hard to know what you're facing, but the description makes me wonder if you might widen your considerations.
sqlitedict: A lightweight wrapper around Python's sqlite3 database, with a dict-like interface and multi-thread access support.
If I had to build a system like the one you describe, using SQLITE, then I would start by writing an async server (using the asynchat module) to handle all of the SQLITE database access, and then I would write the other processes to use that server. When there is only one process accessing the db file directly, it can enforce a strict sequence of queries so that there is no danger of two processes stepping on each others toes. It is also faster than continually opening and closing the db.
In fact, I would also try to avoid maintaining sessions, in other words, I would try to write all the other processes so that every database transaction is independent. At minimum this would mean allowing a transaction to contain a list of SQL statements, not just one, and it might even require some if then capability so that you could SELECT a record, check that a field is equal to X, and only then, UPDATE that field. If your existing app is closing the database after every transaction, then you don't need to worry about sessions.
You might be able to use something like nosqlite http://code.google.com/p/nosqlite/