After having successfully build a static data structure (see here), I would want to avoid having to build it from scratch every time a user requests an operation on it. My naïv first idea was to dump the structure (using python's pickle) into a file and load this file for each query. Needless to say (as I figured out), this turns out to be too time-consuming, as the file is rather large.
Any ideas how I can easily speed up this thing? Splitting the file into multiple files? Or a program running on the server? (How difficult is this to implement?)
Thanks for your help!
You can dump it in a memory cache (such as memcached).
This method has the advantage of cache key invalidation. When underlying data changes you can invalidate your cached data.
EDIT
Here's the python implementation of memcached: python-memcached. Thanks NicDumZ.
If you can rebuild your Python runtime with the patches offered in the Unladen Swallow project, you should see speedups of 40% to 150% in pickling, 36% to 56% in unpickling, according to their benchmarks; maybe that might help.
My suggestion would be not to rely on having an object structure. Instead have a byte array (or mmap'd file etc) which you can do random access operations on and implement the cross-referencing using pointers inside that structure.
True, it will introduce the concept of pointers to your code, but it will mean that you don't need to unpickle it each time the handler process starts up, and it will also use a lot less memory (as there won't be the overhead of python objects).
As your database is going to be fixed during the lifetime of a handler process (I imagine), you won't need to worry about concurrent modifications or locking etc.
Even if you did what you suggest, you shouldn't have to rebuild it on every user request, just keep an instance in memory in your worker process(es), which means it won't take too long to build as you only build it when a new worker process starts.
The number one way to speed up your web application, especially when you have lots of mostly-static modules, classes and objects that need to be initialized: use a way of serving files that supports serving multiple requests from a single interpreter, such as mod_wsgi, mod_python, SCGI, FastCGI, Google App Engine, a Python web server... basically anything except a standard CGI script that starts a new Python process for every request. With this approach, you can make your data structure a global object that only needs to be read from a serialized format for each new process—which is much less frequent.
Related
I have a python process serving as a WSGI-apache server. I have many copies of this process running on each of several machines. About 200 megabytes of my process is read-only python data. I would like to place these data in a memory-mapped segment so that the processes could share a single copy of those data. Best would be to be able to attach to those data so they could be actual python 2.7 data objects rather than parsing them out of something like pickle or DBM or SQLite.
Does anyone have sample code or pointers to a project that has done this to share?
This post by #modelnine on StackOverflow provides a really great comprehensive answer to this question. As he mentioned, using threads rather than process-forking in your webserver can significantly lesson the impact of this. I ran into a similar problem trying to share extremely-large NumPy arrays between CLI Python processes using some type of shared memory a couple of years ago, and we ended up using a combination of a sharedmem Python extension to share data between the workers (which proved to leak memory in certain cases, but, it's fixable probably). A read-only mmap() technique might work for you, but I'm not sure how to do that in pure-python (NumPy has a memmapping technique explained here). I've never found any clear and simple answers to this question, but hopefully this can point you in some new directions. Let us know what you end up doing!
It's difficult to share actual python objects because they are bound to the process address space. However, if you use mmap, you can create very usable shared objects. I'd create one process to pre-load the data, and the rest could use it. I found quite a good blog post that describes how it can be done: http://blog.schmichael.com/2011/05/15/sharing-python-data-between-processes-using-mmap/
Since it's read-only data you won't need to share any updates between processes (since there won't be any updates) I propose you just keep a local copy of it in each process.
If memory constraints is an issue you can have a look at using multiprocessing.Value or multiprocessing.Array without locks for this: https://docs.python.org/2/library/multiprocessing.html#shared-ctypes-objects
Other than that you'll have to rely on an external process and some serialising to get this done, I'd have a look at Redis or Memcached if I were you.
One possibility is to create a C- or C++-extension that provides a Pythonic interface to your shared data. You could memory map 200MB of raw data, and then have the C- or C++-extension provide it to the WSGI-service. That is, you could have regular (unshared) python objects implemented in C, which fetch data from some kind of binary format in shared memory. I know this isn't exactly what you wanted, but this way the data would at least appear pythonic to the WSGI-app.
However, if your data consists of many many very small objects, then it becomes important that even the "entrypoints" are located in the shared memory (otherwise they will waste too much memory). That is, you'd have to make sure that the PyObject* pointers that make up the interface to your data, actually themselves point to the shared memory. I.e, the python objects themselves would have to be in shared memory. As far as I can read the official docs, this isn't really supported. However, you could always try "handcrafting" python objects in shared memory, and see if it works. I'm guessing it would work, until the Python interpreter tries to free the memory. But in your case, it won't, since it's long-lived and read-only.
I doubt this is even possible, but here is the problem and proposed solution (the feasibility of the proposed solution is the object of this question):
I have some "global data" that needs to be available for all requests. I'm persisting this data to Riak and using Redis as a caching layer for access speed (for now...). The data is split into about 30 logical chunks, each about 8 KB.
Each request is required to read 4 of these 8KB chunks, resulting in 32KB of data read in from Redis or Riak. This is in ADDITION to any request-specific data which would also need to be read (which is quite a bit).
Assuming even 3000 requests per second (this isn't a live server so I don't have real numbers, but 3000ps is a reasonable assumption, could be more), this means 96KBps of transfer from Redis or Riak in ADDITION to the already not-insignificant other calls being made from the application logic. Also, Python is parsing the JSON of these 8KB objects 3000 times every second.
All of this - especially Python having to repeatedly deserialize the data - seems like an utter waste, and a perfectly elegant solution would be to just have the deserialized data cached in an in-memory native object in Python, which I can refresh periodically as and when all this "static" data becomes stale. Once in a few minutes (or hours), instead of 3000 times per second.
But I don't know if this is even possible. You'd realistically need an "always running" application for it to cache any data in its memory. And I know this is not the case in the nginx+uwsgi+python combination (versus something like node) - python in-memory data will NOT be persisted across all requests to my knowledge, unless I'm terribly mistaken.
Unfortunately this is a system I have "inherited" and therefore can't make too many changes in terms of the base technology, nor am I knowledgeable enough of how the nginx+uwsgi+python combination works in terms of starting up Python processes and persisting Python in-memory data - which means I COULD be terribly mistaken with my assumption above!
So, direct advice on whether this solution would work + references to material that could help me understand how the nginx+uwsgi+python would work in terms of starting new processes and memory allocation, would help greatly.
P.S:
Have gone through some of the documentation for nginx, uwsgi etc but haven't fully understood the ramifications per my use-case yet. Hope to make some progress on that going forward now
If the in-memory thing COULD work out, I would chuck Redis, since I'm caching ONLY the static data I mentioned above, in it. This makes an in-process persistent in-memory Python cache even more attractive for me, reducing one moving part in the system and at least FOUR network round-trips per request.
What you're suggesting isn't directly feasible. Since new processes can be spun up and down outside of your control, there's no way to keep native Python data in memory.
However, there are a few ways around this.
Often, one level of key-value storage is all you need. And sometimes, having fixed-size buffers for values (which you can use directly as str/bytes/bytearray objects; anything else you need to struct in there or otherwise serialize) is all you need. In that case, uWSGI's built-in caching framework will take care of everything you need.
If you need more precise control, you can look at how the cache is implemented on top of SharedArea and do something customize. However, I wouldn't recommend that. It basically gives you the same kind of API you get with a file, and the only real advantages over just using a file are that the server will manage the file's lifetime; it works in all uWSGI-supported languages, even those that don't allow files; and it makes it easier to migrate your custom cache to a distributed (multi-computer) cache if you later need to. I don't think any of those are relevant to you.
Another way to get flat key-value storage, but without the fixed-size buffers, is with Python's stdlib anydbm. The key-value lookup is as pythonic as it gets: it looks just like a dict, except that it's backed up to an on-disk BDB (or similar) database, cached as appropriate in memory, instead of being stored in an in-memory hash table.
If you need to handle a few other simple types—anything that's blazingly fast to un/pickle, like ints—you may want to consider shelve.
If your structure is rigid enough, you can use key-value database for the top level, but access the values through a ctypes.Structure, or de/serialize with struct. But usually, if you can do that, you can also eliminate the top level, at which point your whole thing is just one big Structure or Array.
At that point, you can just use a plain file for storage—either mmap it (for ctypes), or just open and read it (for struct).
Or use multiprocessing's Shared ctypes Objects to access your Structure directly out of a shared memory area.
Meanwhile, if you don't actually need all of the cache data all the time, just bits and pieces every once in a while, that's exactly what databases are for. Again, anydbm, etc. may be all you need, but if you've got complex structure, draw up an ER diagram, turn it into a set of tables, and use something like MySQL.
"python in-memory data will NOT be persisted across all requests to my knowledge, unless I'm terribly mistaken."
you are mistaken.
the whole point of using uwsgi over, say, the CGI mechanism is to persist data across threads and save the overhead of initialization for each call. you must set processes = 1 in your .ini file, or, depending on how uwsgi is configured, it might launch more than 1 worker process on your behalf. log the env and look for 'wsgi.multiprocess': False and 'wsgi.multithread': True, and all uwsgi.core threads for the single worker should show the same data.
you can also see how many worker processes, and "core" threads under each, you have by using the built-in stats-server.
that's why uwsgi provides lock and unlock functions for manipulating data stores by multiple threads.
you can easily test this by adding a /status route in your app that just dumps a json representation of your global data object, and view it every so often after actions that update the store.
You said nothing about writing this data back, is it static? In this case, the solution is every simple, and I have no clue what is up with all the "it's not feasible" responses.
Uwsgi workers are always-running applications. So data absolutely gets persisted between requests. All you need to do is store stuff in a global variable, that is it. And remember it's per-worker, and workers do restart from time to time, so you need proper loading/invalidation strategies.
If the data is updated very rarely (rarely enough to restart the server when it does), you can save even more. Just create the objects during app construction. This way, they will be created exactly once, and then all the workers will fork off the master, and reuse the same data. Of course, it's copy-on-write, so if you update it, you will lose the memory benefits (same thing will happen if python decides to compact its memory during a gc run, so it's not super predictable).
I have never actually tried it myself, but could you possibly use uWSGI's SharedArea to accomplish what you're after?
I'm developing a Python command line utility that potentially involves rather large queries against a set of files. It's a reasonably finite list of queries (think indexed DB columns) To improve performance in-process I can generated sorted/structured lists, maps and trees once, and hit those repeatedly, rather than hit the file system each time.
However, these caches are lost when the process ends, and need to be rebuilt every time the script runs, which dramatically increases the runtime of my program. I'd like to identify the best way to share this data between multiple executions of my command, which may be concurrent, one after another, or with significant delays between executions.
Requirements:
Must be fast - any sort of per-execution processing should be minimized, this includes disk IO and object construction.
Must be OS agnostic (or at least be able to hook into similar underlying behaviors on Unix/Windows, which is more likely).
Must allow reasonably complex querying / filtering - I don't think a key/value map will be good enough
Does not need to be up-to-date - (briefly) stale data is perfectly fine, this is just a cache, the actual data is being written to disk separately.
Can't use a heavyweight daemon process, like MySQL or MemCached - I want to minimize installation costs, and asking each user to install these services is too much.
Preferences:
I'd like to avoid any sort long running daemon process at all, if possible.
While I'd like to be able to update the cache quickly, rebuilding the whole cache on update isn't the end of the world, fast reads are much more important than fast writes.
In my ideal fantasy world, I'd be able to directly keep Python objects around between executions, sort of like Java threads (like Tomcat requests) sharing singleton data store objects, but I realize that may not be possible. The closer I can get to that though, the better.
Candidates:
SQLite in memory
SQLite on it's own doesn't seem fast enough for my use case, since it's backed by disk and therefore will have to read from the file on every execution. Perhaps this isn't as bad as it seems, but it seems necessary to persistently store the database in memory. SQLite allows for DBs to use memory as storage but these DBs are destroyed upon program exit, and cannot be shared between instances.
Flat file database loaded into memory with mmap
On the opposite end of the spectrum, I could write the caches to disk, then load them into memory with mmap, can share the same memory space between separate executions. It's not clear to me what happens to the mmap if all processes exit however. It's ok if the mmap is eventually flushed from memory, but I'd want it to stick around for a little bit (30 seconds? a few minutes?) so a user can run commands one after another, and the cache can be reused. This example seems to imply that there needs to be an open mmap handle, but I haven't found any exact description of when memory mapped files get dropped from memory and need to be reloaded from disk.
I think I could implement this, if mmap objects do stick around after exit, but it feels very low level, and I imagine someone's already got a more elegant solution implemented. I'd hate to start building this only to realize I've been rebuilding SQLite. On the other hand, it feels like it would be very fast, and I could make optimizations given my specific use case.
Share Python objects between processes using Processing
The Processing package indicates "Objects can be shared between processes using ... shared memory". Looking through the rest of the docs, I didn't see any further mention of this behavior, but that sounds very promising. Can anyone direct me to more information?
Store data on a RAM disk
My concern here is OS-specific capabilities, but I could create a RAM disk and then simply read/write to it as I please (SQLite?). The fs.memoryfs package seems like a promising alternative to work with multiple OSs, but the comments imply a fair number of limitations.
I know pickle is an efficient way to store Python objects, so it might have speed advantages over any sort of manual data storage. Can I hook pickle into any of the above options? Would that be better than flat files or SQLite?
I know there's a lot of questions related to this, but I did a fair bit of digging and couldn't find anything directly addressing my question with regards to multiple command line executions.
I fully admit, I may be way overthinking this. I'm just trying to get a feel for my options, and if they're worthwhile or not.
Thank you so much for your help!
I would just do the simplest thing that might possibly work. ...which in your case would likely just be to dump to a pickle file. If you find it's not fast enough, try something more involved (like memcached or SQLite). Donald Knuth says "Premature optimization is the root of all evil"!
Here's the situation: I have a massive object that needs to be loaded into memory. So big that if it is loaded in twice it will go beyond the available memory on my machine (and no, I can't upgrade the memory). I also can't divide it up into any smaller pieces. For simplicity's sake, let's just say the object is 600 MB and I only have 1 GB of RAM. I need to use this object from a web app, which is running in multiple processes, and I don't control how they're spawned (a third party load balancer does that), so I can't rely on just creating the object in some master thread/process and then spawning off children. This also eliminates the possibility of using something like POSH because that relies on it's own custom fork call. I also can't use something like a SQLite memory database, mmap or the posix_ipc, sysv_ipc, and shm modules because those act as a file in memory, and this data has to be an object for me to use it. Using one of those I would have to read it as a file and then turn it into an object in each individual process and BAM, segmentation fault from going over the machine's memory limit because I just tried to load in a second copy.
There must be someway to store a Python object in memory (and not as a file/string/serialized/pickled) and have it be accessible from any process. I just don't know what it is. I've looked all over StackOverflow and Google and can't find the answer to this, so I'm hoping somebody can help me out.
http://docs.python.org/library/multiprocessing.html#sharing-state-between-processes
Look for shared memory, or Server process. After re-reading your post Server process sounds closer to what you want.
http://en.wikipedia.org/wiki/Shared_memory
There must be someway to store a Python object in memory (and not as a
file/string/serialized/pickled) and have it be accessible from any
process.
That isn't the way in works. Python object reference counting and an object's internal pointers do not make sense across multiple processes.
If the data doesn't have to be an actual Python object, you can try working on the raw data stored in mmap() or in a database or somesuch.
I would implement this as a C module that gets imported into each Python script. Then the interface to this large object would be implemented in C, or some combination of C and Python.
I'm writing a reasonably complex web application. The Python backend runs an algorithm whose state depends on data stored in several interrelated database tables which does not change often, plus user specific data which does change often. The algorithm's per-user state undergoes many small changes as a user works with the application. This algorithm is used often during each user's work to make certain important decisions.
For performance reasons, re-initializing the state on every request from the (semi-normalized) database data quickly becomes non-feasible. It would be highly preferable, for example, to cache the state's Python object in some way so that it can simply be used and/or updated whenever necessary. However, since this is a web application, there several processes serving requests, so using a global variable is out of the question.
I've tried serializing the relevant object (via pickle) and saving the serialized data to the DB, and am now experimenting with caching the serialized data via memcached. However, this still has the significant overhead of serializing and deserializing the object often.
I've looked at shared memory solutions but the only relevant thing I've found is POSH. However POSH doesn't seem to be widely used and I don't feel easy integrating such an experimental component into my application.
I need some advice! This is my first shot at developing a web application, so I'm hoping this is a common enough issue that there are well-known solutions to such problems. At this point solutions which assume the Python back-end is running on a single server would be sufficient, but extra points for solutions which scale to multiple servers as well :)
Notes:
I have this application working, currently live and with active users. I started out without doing any premature optimization, and then optimized as needed. I've done the measuring and testing to make sure the above mentioned issue is the actual bottleneck. I'm sure pretty sure I could squeeze more performance out of the current setup, but I wanted to ask if there's a better way.
The setup itself is still a work in progress; assume that the system's architecture can be whatever suites your solution.
Be cautious of premature optimization.
Addition: The "Python backend runs an algorithm whose state..." is the session in the web framework. That's it. Let the Django framework maintain session state in cache. Period.
"The algorithm's per-user state undergoes many small changes as a user works with the application." Most web frameworks offer a cached session object. Often it is very high performance. See Django's session documentation for this.
Advice. [Revised]
It appears you have something that works. Leverage to learn your framework, learn the tools, and learn what knobs you can turn without breaking a sweat. Specifically, using session state.
Second, fiddle with caching, session management, and things that are easy to adjust, and see if you have enough speed. Find out whether MySQL socket or named pipe is faster by trying them out. These are the no-programming optimizations.
Third, measure performance to find your actual bottleneck. Be prepared to provide (and defend) the measurements as fine-grained enough to be useful and stable enough to providing meaningful comparison of alternatives.
For example, show the performance difference between persistent sessions and cached sessions.
I think that the multiprocessing framework has what might be applicable here - namely the shared ctypes module.
Multiprocessing is fairly new to Python, so it might have some oddities. I am not quite sure whether the solution works with processes not spawned via multiprocessing.
I think you can give ZODB a shot.
"A major feature of ZODB is transparency. You do not need to write any code to explicitly read or write your objects to or from a database. You just put your persistent objects into a container that works just like a Python dictionary. Everything inside this dictionary is saved in the database. This dictionary is said to be the "root" of the database. It's like a magic bag; any Python object that you put inside it becomes persistent."
Initailly it was a integral part of Zope, but lately a standalone package is also available.
It has the following limitation:
"Actually there are a few restrictions on what you can store in the ZODB. You can store any objects that can be "pickled" into a standard, cross-platform serial format. Objects like lists, dictionaries, and numbers can be pickled. Objects like files, sockets, and Python code objects, cannot be stored in the database because they cannot be pickled."
I have read it but haven't given it a shot myself though.
Other possible thing could be a in-memory sqlite db, that may speed up the process a bit - being an in-memory db, but still you would have to do the serialization stuff and all.
Note: In memory db is expensive on resources.
Here is a link: http://www.zope.org/Documentation/Articles/ZODB1
First of all your approach is not a common web development practice. Even multi threading is being used, web applications are designed to be able to run multi-processing environments, for both scalability and easier deployment .
If you need to just initialize a large object, and do not need to change later, you can do it easily by using a global variable that is initialized while your WSGI application is being created, or the module contains the object is being loaded etc, multi processing will do fine for you.
If you need to change the object and access it from every thread, you need to be sure your object is thread safe, use locks to ensure that. And use a single server context, a process. Any multi threading python server will serve you well, also FCGI is a good choice for this kind of design.
But, if multiple threads are accessing and changing your object the locks may have a really bad effect on your performance gain, which is likely to make all the benefits go away.
This is Durus, a persistent object system for applications written in the Python
programming language. Durus offers an easy way to use and maintain a consistent
collection of object instances used by one or more processes. Access and change of a
persistent instances is managed through a cached Connection instance which includes
commit() and abort() methods so that changes are transactional.
http://www.mems-exchange.org/software/durus/
I've used it before in some research code, where I wanted to persist the results of certain computations. I eventually switched to pytables as it met my needs better.
Another option is to review the requirement for state, it sounds like if the serialisation is the bottle neck then the object is very large. Do you really need an object that large?
I know in the Stackoverflow podcast 27 the reddit guys discuss what they use for state, so that maybe useful to listen to.