Memory leak in Google ndb library - python

I think there is a memory leak in the ndb library but I can not find where.
Is there a way to avoid the problem described below?
Do you have a more accurate idea of testing to figure out where the problem is?
That's how I reproduced the problem :
I created a minimalist Google App Engine application with 2 files.
app.yaml:
application: myapplicationid
version: demo
runtime: python27
api_version: 1
threadsafe: yes
handlers:
- url: /.*
script: main.APP
libraries:
- name: webapp2
version: latest
main.py:
# -*- coding: utf-8 -*-
"""Memory leak demo."""
from google.appengine.ext import ndb
import webapp2
class DummyModel(ndb.Model):
content = ndb.TextProperty()
class CreatePage(webapp2.RequestHandler):
def get(self):
value = str(102**100000)
entities = (DummyModel(content=value) for _ in xrange(100))
ndb.put_multi(entities)
class MainPage(webapp2.RequestHandler):
def get(self):
"""Use of `query().iter()` was suggested here:
https://code.google.com/p/googleappengine/issues/detail?id=9610
Same result can be reproduced without decorator and a "classic"
`query().fetch()`.
"""
for _ in range(10):
for entity in DummyModel.query().iter():
pass # Do whatever you want
self.response.headers['Content-Type'] = 'text/plain'
self.response.write('Hello, World!')
APP = webapp2.WSGIApplication([
('/', MainPage),
('/create', CreatePage),
])
I uploaded the application, called /create once.
After that, each call to / increases the memory used by the instance. Until it stops due to the error Exceeded soft private memory limit of 128 MB with 143 MB after servicing 5 requests total.
Exemple of memory usage graph (you can see the memory growth and crashes) :
Note: The problem can be reproduced with another framework than webapp2, like web.py

After more investigations, and with the help of a google engineer, I've found two explanation to my memory consumption.
Context and thread
ndb.Context is a "thread local" object and is only cleared when a new request come in the thread. So the thread hold on it between requests. Many threads may exist in a GAE instance and it may take hundreds of requests before a thread is used a second time and it's context cleared.
This is not a memory leak, but contexts size in memory may exceed the available memory in a small GAE instance.
Workaround:
You can not configure the number of threads used in a GAE instance. So it is best to keep each context smallest possible. Avoid in-context cache, and clear it after each request.
Event queue
It seems that NDB does not guarantee that event queue is emptied after a request. Again this is not a memory leak. But it leave Futures in your thread context, and you're back to the first problem.
Workaround:
Wrap all your code that use NDB with #ndb.toplevel.

There is a known issue with NDB. You can read about it here and there is a work around here:
The non-determinism observed with fetch_page is due to the iteration order of eventloop.rpcs, which is passed to datastore_rpc.MultiRpc.wait_any() and apiproxy_stub_map.__check_one selects the last rpc from the iterator.
Fetching with page_size of 10 does an rpc with count=10, limit=11, a standard technique to force the backend to more accurately determine whether there are more results. This returns 10 results, but due to a bug in the way the QueryIterator is unraveled, an RPC is added to fetch the last entry (using obtained cursor and count=1). NDB then returns the batch of entities without processing this RPC. I believe that this RPC will not be evaluated until selected at random (if MultiRpc consumes it before a necessary rpc), since it doesn't block client code.
Workaround: use iter(). This function does not have this issue (count and limit will be the same). iter() can be used as a workaround for the performance and memory issues associated with fetch page caused by the above.

A possible workaround is to use context.clear_cache() and gc.collect() on get method.
def get(self):
for _ in range(10):
for entity in DummyModel.query().iter():
pass # Do whatever you want
self.response.headers['Content-Type'] = 'text/plain'
self.response.write('Hello, World!')
context = ndb.get_context()
context.clear_cache()
gc.collect()

Related

What happens when two functions try to use the same List to update at the same time in Python [duplicate]

In my application, the state of a common object is changed by making requests, and the response depends on the state.
class SomeObj():
def __init__(self, param):
self.param = param
def query(self):
self.param += 1
return self.param
global_obj = SomeObj(0)
#app.route('/')
def home():
flash(global_obj.query())
render_template('index.html')
If I run this on my development server, I expect to get 1, 2, 3 and so on. If requests are made from 100 different clients simultaneously, can something go wrong? The expected result would be that the 100 different clients each see a unique number from 1 to 100. Or will something like this happen:
Client 1 queries. self.param is incremented by 1.
Before the return statement can be executed, the thread switches over to client 2. self.param is incremented again.
The thread switches back to client 1, and the client is returned the number 2, say.
Now the thread moves to client 2 and returns him/her the number 3.
Since there were only two clients, the expected results were 1 and 2, not 2 and 3. A number was skipped.
Will this actually happen as I scale up my application? What alternatives to a global variable should I look at?
You can't use global variables to hold this sort of data. Not only is it not thread safe, it's not process safe, and WSGI servers in production spawn multiple processes. Not only would your counts be wrong if you were using threads to handle requests, they would also vary depending on which process handled the request.
Use a data source outside of Flask to hold global data. A database, memcached, or redis are all appropriate separate storage areas, depending on your needs. If you need to load and access Python data, consider multiprocessing.Manager. You could also use the session for simple data that is per-user.
The development server may run in single thread and process. You won't see the behavior you describe since each request will be handled synchronously. Enable threads or processes and you will see it. app.run(threaded=True) or app.run(processes=10). (In 1.0 the server is threaded by default.)
Some WSGI servers may support gevent or another async worker. Global variables are still not thread safe because there's still no protection against most race conditions. You can still have a scenario where one worker gets a value, yields, another modifies it, yields, then the first worker also modifies it.
If you need to store some global data during a request, you may use Flask's g object. Another common case is some top-level object that manages database connections. The distinction for this type of "global" is that it's unique to each request, not used between requests, and there's something managing the set up and teardown of the resource.
This is not really an answer to thread safety of globals.
But I think it is important to mention sessions here.
You are looking for a way to store client-specific data. Every connection should have access to its own pool of data, in a threadsafe way.
This is possible with server-side sessions, and they are available in a very neat flask plugin: https://pythonhosted.org/Flask-Session/
If you set up sessions, a session variable is available in all your routes and it behaves like a dictionary. The data stored in this dictionary is individual for each connecting client.
Here is a short demo:
from flask import Flask, session
from flask_session import Session
app = Flask(__name__)
# Check Configuration section for more details
SESSION_TYPE = 'filesystem'
app.config.from_object(__name__)
Session(app)
#app.route('/')
def reset():
session["counter"]=0
return "counter was reset"
#app.route('/inc')
def routeA():
if not "counter" in session:
session["counter"]=0
session["counter"]+=1
return "counter is {}".format(session["counter"])
#app.route('/dec')
def routeB():
if not "counter" in session:
session["counter"] = 0
session["counter"] -= 1
return "counter is {}".format(session["counter"])
if __name__ == '__main__':
app.run()
After pip install Flask-Session, you should be able to run this. Try accessing it from different browsers, you'll see that the counter is not shared between them.
Another example of a data source external to requests is a cache, such as what's provided by Flask-Caching or another extension.
Create a file common.py and place in it the following:
from flask_caching import Cache
# Instantiate the cache
cache = Cache()
In the file where your flask app is created, register your cache with the following code:
# Import cache
from common import cache
# ...
app = Flask(__name__)
cache.init_app(app=app, config={"CACHE_TYPE": "filesystem",'CACHE_DIR': Path('/tmp')})
Now use throughout your application by importing the cache and executing as follows:
# Import cache
from common import cache
# store a value
cache.set("my_value", 1_000_000)
# Get a value
my_value = cache.get("my_value")
While totally accepting the previous upvoted answers, and discouraging use of global variables for production and scalable Flask storage, for the purpose of prototyping or really simple servers, running under the flask 'development server'...
...
The Python built-in data types, and I personally used and tested the global dict, as per Python documentation are thread safe. Not process safe.
The insertions, lookups, and reads from such a (server global) dict will be OK from each (possibly concurrent) Flask session running under the development server.
When such a global dict is keyed with a unique Flask session key, it can be rather useful for server-side storage of session specific data otherwise not fitting into the cookie (max size 4 kB).
Of course, such a server global dict should be carefully guarded for growing too large, being in-memory. Some sort of expiring the 'old' key/value pairs can be coded during request processing.
Again, it is not recommended for production or scalable deployments, but it is possibly OK for local task-oriented servers where a separate database is too much for the given task.
...

Flask - Data is being shared between users - BAD [duplicate]

In my application, the state of a common object is changed by making requests, and the response depends on the state.
class SomeObj():
def __init__(self, param):
self.param = param
def query(self):
self.param += 1
return self.param
global_obj = SomeObj(0)
#app.route('/')
def home():
flash(global_obj.query())
render_template('index.html')
If I run this on my development server, I expect to get 1, 2, 3 and so on. If requests are made from 100 different clients simultaneously, can something go wrong? The expected result would be that the 100 different clients each see a unique number from 1 to 100. Or will something like this happen:
Client 1 queries. self.param is incremented by 1.
Before the return statement can be executed, the thread switches over to client 2. self.param is incremented again.
The thread switches back to client 1, and the client is returned the number 2, say.
Now the thread moves to client 2 and returns him/her the number 3.
Since there were only two clients, the expected results were 1 and 2, not 2 and 3. A number was skipped.
Will this actually happen as I scale up my application? What alternatives to a global variable should I look at?
You can't use global variables to hold this sort of data. Not only is it not thread safe, it's not process safe, and WSGI servers in production spawn multiple processes. Not only would your counts be wrong if you were using threads to handle requests, they would also vary depending on which process handled the request.
Use a data source outside of Flask to hold global data. A database, memcached, or redis are all appropriate separate storage areas, depending on your needs. If you need to load and access Python data, consider multiprocessing.Manager. You could also use the session for simple data that is per-user.
The development server may run in single thread and process. You won't see the behavior you describe since each request will be handled synchronously. Enable threads or processes and you will see it. app.run(threaded=True) or app.run(processes=10). (In 1.0 the server is threaded by default.)
Some WSGI servers may support gevent or another async worker. Global variables are still not thread safe because there's still no protection against most race conditions. You can still have a scenario where one worker gets a value, yields, another modifies it, yields, then the first worker also modifies it.
If you need to store some global data during a request, you may use Flask's g object. Another common case is some top-level object that manages database connections. The distinction for this type of "global" is that it's unique to each request, not used between requests, and there's something managing the set up and teardown of the resource.
This is not really an answer to thread safety of globals.
But I think it is important to mention sessions here.
You are looking for a way to store client-specific data. Every connection should have access to its own pool of data, in a threadsafe way.
This is possible with server-side sessions, and they are available in a very neat flask plugin: https://pythonhosted.org/Flask-Session/
If you set up sessions, a session variable is available in all your routes and it behaves like a dictionary. The data stored in this dictionary is individual for each connecting client.
Here is a short demo:
from flask import Flask, session
from flask_session import Session
app = Flask(__name__)
# Check Configuration section for more details
SESSION_TYPE = 'filesystem'
app.config.from_object(__name__)
Session(app)
#app.route('/')
def reset():
session["counter"]=0
return "counter was reset"
#app.route('/inc')
def routeA():
if not "counter" in session:
session["counter"]=0
session["counter"]+=1
return "counter is {}".format(session["counter"])
#app.route('/dec')
def routeB():
if not "counter" in session:
session["counter"] = 0
session["counter"] -= 1
return "counter is {}".format(session["counter"])
if __name__ == '__main__':
app.run()
After pip install Flask-Session, you should be able to run this. Try accessing it from different browsers, you'll see that the counter is not shared between them.
Another example of a data source external to requests is a cache, such as what's provided by Flask-Caching or another extension.
Create a file common.py and place in it the following:
from flask_caching import Cache
# Instantiate the cache
cache = Cache()
In the file where your flask app is created, register your cache with the following code:
# Import cache
from common import cache
# ...
app = Flask(__name__)
cache.init_app(app=app, config={"CACHE_TYPE": "filesystem",'CACHE_DIR': Path('/tmp')})
Now use throughout your application by importing the cache and executing as follows:
# Import cache
from common import cache
# store a value
cache.set("my_value", 1_000_000)
# Get a value
my_value = cache.get("my_value")
While totally accepting the previous upvoted answers, and discouraging use of global variables for production and scalable Flask storage, for the purpose of prototyping or really simple servers, running under the flask 'development server'...
...
The Python built-in data types, and I personally used and tested the global dict, as per Python documentation are thread safe. Not process safe.
The insertions, lookups, and reads from such a (server global) dict will be OK from each (possibly concurrent) Flask session running under the development server.
When such a global dict is keyed with a unique Flask session key, it can be rather useful for server-side storage of session specific data otherwise not fitting into the cookie (max size 4 kB).
Of course, such a server global dict should be carefully guarded for growing too large, being in-memory. Some sort of expiring the 'old' key/value pairs can be coded during request processing.
Again, it is not recommended for production or scalable deployments, but it is possibly OK for local task-oriented servers where a separate database is too much for the given task.
...

Sharing a variable between Celery tasks [duplicate]

In my application, the state of a common object is changed by making requests, and the response depends on the state.
class SomeObj():
def __init__(self, param):
self.param = param
def query(self):
self.param += 1
return self.param
global_obj = SomeObj(0)
#app.route('/')
def home():
flash(global_obj.query())
render_template('index.html')
If I run this on my development server, I expect to get 1, 2, 3 and so on. If requests are made from 100 different clients simultaneously, can something go wrong? The expected result would be that the 100 different clients each see a unique number from 1 to 100. Or will something like this happen:
Client 1 queries. self.param is incremented by 1.
Before the return statement can be executed, the thread switches over to client 2. self.param is incremented again.
The thread switches back to client 1, and the client is returned the number 2, say.
Now the thread moves to client 2 and returns him/her the number 3.
Since there were only two clients, the expected results were 1 and 2, not 2 and 3. A number was skipped.
Will this actually happen as I scale up my application? What alternatives to a global variable should I look at?
You can't use global variables to hold this sort of data. Not only is it not thread safe, it's not process safe, and WSGI servers in production spawn multiple processes. Not only would your counts be wrong if you were using threads to handle requests, they would also vary depending on which process handled the request.
Use a data source outside of Flask to hold global data. A database, memcached, or redis are all appropriate separate storage areas, depending on your needs. If you need to load and access Python data, consider multiprocessing.Manager. You could also use the session for simple data that is per-user.
The development server may run in single thread and process. You won't see the behavior you describe since each request will be handled synchronously. Enable threads or processes and you will see it. app.run(threaded=True) or app.run(processes=10). (In 1.0 the server is threaded by default.)
Some WSGI servers may support gevent or another async worker. Global variables are still not thread safe because there's still no protection against most race conditions. You can still have a scenario where one worker gets a value, yields, another modifies it, yields, then the first worker also modifies it.
If you need to store some global data during a request, you may use Flask's g object. Another common case is some top-level object that manages database connections. The distinction for this type of "global" is that it's unique to each request, not used between requests, and there's something managing the set up and teardown of the resource.
This is not really an answer to thread safety of globals.
But I think it is important to mention sessions here.
You are looking for a way to store client-specific data. Every connection should have access to its own pool of data, in a threadsafe way.
This is possible with server-side sessions, and they are available in a very neat flask plugin: https://pythonhosted.org/Flask-Session/
If you set up sessions, a session variable is available in all your routes and it behaves like a dictionary. The data stored in this dictionary is individual for each connecting client.
Here is a short demo:
from flask import Flask, session
from flask_session import Session
app = Flask(__name__)
# Check Configuration section for more details
SESSION_TYPE = 'filesystem'
app.config.from_object(__name__)
Session(app)
#app.route('/')
def reset():
session["counter"]=0
return "counter was reset"
#app.route('/inc')
def routeA():
if not "counter" in session:
session["counter"]=0
session["counter"]+=1
return "counter is {}".format(session["counter"])
#app.route('/dec')
def routeB():
if not "counter" in session:
session["counter"] = 0
session["counter"] -= 1
return "counter is {}".format(session["counter"])
if __name__ == '__main__':
app.run()
After pip install Flask-Session, you should be able to run this. Try accessing it from different browsers, you'll see that the counter is not shared between them.
Another example of a data source external to requests is a cache, such as what's provided by Flask-Caching or another extension.
Create a file common.py and place in it the following:
from flask_caching import Cache
# Instantiate the cache
cache = Cache()
In the file where your flask app is created, register your cache with the following code:
# Import cache
from common import cache
# ...
app = Flask(__name__)
cache.init_app(app=app, config={"CACHE_TYPE": "filesystem",'CACHE_DIR': Path('/tmp')})
Now use throughout your application by importing the cache and executing as follows:
# Import cache
from common import cache
# store a value
cache.set("my_value", 1_000_000)
# Get a value
my_value = cache.get("my_value")
While totally accepting the previous upvoted answers, and discouraging use of global variables for production and scalable Flask storage, for the purpose of prototyping or really simple servers, running under the flask 'development server'...
...
The Python built-in data types, and I personally used and tested the global dict, as per Python documentation are thread safe. Not process safe.
The insertions, lookups, and reads from such a (server global) dict will be OK from each (possibly concurrent) Flask session running under the development server.
When such a global dict is keyed with a unique Flask session key, it can be rather useful for server-side storage of session specific data otherwise not fitting into the cookie (max size 4 kB).
Of course, such a server global dict should be carefully guarded for growing too large, being in-memory. Some sort of expiring the 'old' key/value pairs can be coded during request processing.
Again, it is not recommended for production or scalable deployments, but it is possibly OK for local task-oriented servers where a separate database is too much for the given task.
...

Python-loop leaks memory [duplicate]

I think there is a memory leak in the ndb library but I can not find where.
Is there a way to avoid the problem described below?
Do you have a more accurate idea of testing to figure out where the problem is?
That's how I reproduced the problem :
I created a minimalist Google App Engine application with 2 files.
app.yaml:
application: myapplicationid
version: demo
runtime: python27
api_version: 1
threadsafe: yes
handlers:
- url: /.*
script: main.APP
libraries:
- name: webapp2
version: latest
main.py:
# -*- coding: utf-8 -*-
"""Memory leak demo."""
from google.appengine.ext import ndb
import webapp2
class DummyModel(ndb.Model):
content = ndb.TextProperty()
class CreatePage(webapp2.RequestHandler):
def get(self):
value = str(102**100000)
entities = (DummyModel(content=value) for _ in xrange(100))
ndb.put_multi(entities)
class MainPage(webapp2.RequestHandler):
def get(self):
"""Use of `query().iter()` was suggested here:
https://code.google.com/p/googleappengine/issues/detail?id=9610
Same result can be reproduced without decorator and a "classic"
`query().fetch()`.
"""
for _ in range(10):
for entity in DummyModel.query().iter():
pass # Do whatever you want
self.response.headers['Content-Type'] = 'text/plain'
self.response.write('Hello, World!')
APP = webapp2.WSGIApplication([
('/', MainPage),
('/create', CreatePage),
])
I uploaded the application, called /create once.
After that, each call to / increases the memory used by the instance. Until it stops due to the error Exceeded soft private memory limit of 128 MB with 143 MB after servicing 5 requests total.
Exemple of memory usage graph (you can see the memory growth and crashes) :
Note: The problem can be reproduced with another framework than webapp2, like web.py
After more investigations, and with the help of a google engineer, I've found two explanation to my memory consumption.
Context and thread
ndb.Context is a "thread local" object and is only cleared when a new request come in the thread. So the thread hold on it between requests. Many threads may exist in a GAE instance and it may take hundreds of requests before a thread is used a second time and it's context cleared.
This is not a memory leak, but contexts size in memory may exceed the available memory in a small GAE instance.
Workaround:
You can not configure the number of threads used in a GAE instance. So it is best to keep each context smallest possible. Avoid in-context cache, and clear it after each request.
Event queue
It seems that NDB does not guarantee that event queue is emptied after a request. Again this is not a memory leak. But it leave Futures in your thread context, and you're back to the first problem.
Workaround:
Wrap all your code that use NDB with #ndb.toplevel.
There is a known issue with NDB. You can read about it here and there is a work around here:
The non-determinism observed with fetch_page is due to the iteration order of eventloop.rpcs, which is passed to datastore_rpc.MultiRpc.wait_any() and apiproxy_stub_map.__check_one selects the last rpc from the iterator.
Fetching with page_size of 10 does an rpc with count=10, limit=11, a standard technique to force the backend to more accurately determine whether there are more results. This returns 10 results, but due to a bug in the way the QueryIterator is unraveled, an RPC is added to fetch the last entry (using obtained cursor and count=1). NDB then returns the batch of entities without processing this RPC. I believe that this RPC will not be evaluated until selected at random (if MultiRpc consumes it before a necessary rpc), since it doesn't block client code.
Workaround: use iter(). This function does not have this issue (count and limit will be the same). iter() can be used as a workaround for the performance and memory issues associated with fetch page caused by the above.
A possible workaround is to use context.clear_cache() and gc.collect() on get method.
def get(self):
for _ in range(10):
for entity in DummyModel.query().iter():
pass # Do whatever you want
self.response.headers['Content-Type'] = 'text/plain'
self.response.write('Hello, World!')
context = ndb.get_context()
context.clear_cache()
gc.collect()

How to log memory usage of an Django app per request

Do you know about an efficient way to log memory usage of a django app per request ?
I have an apache/mod_wsgi/django stack, which runs usually well, but sometimes one process ends up eating a huge lot of memory. The servers ends up being short on mem, swapping a lot, and services are dramatically slowed down.
This situation is quite hard to fix because I don't know which request is to be blamed for this behavior, I can't reproduce it.
I'd like to have something deployed in production which logs the memory usage of the process before and after each request, with minimal overhead.
Before I start reinventing the wheel, do the community of my fellow djangoists know any existing solution to address this problem ?
Advices, middleware, snippet or maybe apache log configuration appreciated.
What (I think) I don't need is:
a set of dev-stage profiling/debugging tools, I already know some and I'd use them if I knew what to profile/debug, it looks a little bit too much to be forever monitoring services running in production. On top of that, what is usually displayed by those tol is a mem usage report of the code shred to pieces, It would really be helpful to just pinpoint the faulty request.
generic advices on how to optimize mem usage of a django app, well it's always good to read, but the idea here is rather «how to efficiently track down requests which need to be optimized».
My closest search results:
Django / WSGI - How to profile partial request? My profiling tools are per-request but app runs out of memory before then
Django memory usage going up with every request
Average php memory usage per request?
A Django middleware for tracking memory usage and generating a usable result immediately, needs to hook both process request and process response. In other words, look at difference between start and finish of request and log a warning if exceeds some threshold.
A complete middleware example is:
import os
import psutil
import sys
THRESHOLD = 2*1024*1024
class MemoryUsageMiddleware(object):
def process_request(self, request):
request._mem = psutil.Process(os.getpid()).memory_info()
def process_response(self, request, response):
mem = psutil.Process(os.getpid()).memory_info()
diff = mem.rss - request._mem.rss
if diff > THRESHOLD:
print >> sys.stderr, 'MEMORY USAGE %r' % ((diff, request.path),)
return response
This requires the 'psutil' module to be installed for doing memory calculation.
Is brute force and can lead to false positives in a multithread system. Because of lazy loading, you will also see it trigger on first few requests against new process as stuff loads up.
This may not fully cover your question, but I recommend trying nginx+uwsgi instead of apache2+mod_wsgi. In my tests it turned out to be much more stable (mod_wsgi choked at some point completely), much faster and uses a lot less memory (it may just fix all your issues altogether).
About tracking memory usage, you can create a simple middleware:
class SaveMemoryUsageMiddleware(object):
def process_response(self, request, response):
# track memory usage here and append to file or db
return response
and add it to your middlewares.
For memory tracking code I recommend checking out:
Total memory used by Python process?
However, it would probably be better if you could avoid doing this on production. Just for dev and tests to track down real problem.

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