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ZODB commit stuck and make my whole application to freeze

Today I found a bug on my python application using ZODB.
Trying to find why my application freezes up, I figured that ZODB was the cause.
Setting the logging to debug, it seem that when commiting, that ZODB would find 2 connections and then start freezing.
INFO:ZEO.ClientStorage:('127.0.0.1', 8092) Connected to storage: ('localhost', 8092)
DEBUG:txn.140661100980032:new transaction
DEBUG:txn.140661100980032:commit
DEBUG:ZODB.Connection:Committing savepoints of size 1858621925
DEBUG:discord.gateway:Keeping websocket alive with sequence 59.
DEBUG:txn.140661100980032:commit <Connection at 7fee2d080fd0>
DEBUG:txn.140661100980032:commit <Connection at 7fee359e5cc0>
As I'm a ZODB beginner, any idea on a how to solve / how to dig deeper ?
It seems to be related to concurrent commits.
I believed that opening a new connection would initiate a dedicated transaction manager, but this is not the case. While initiating a new connection without specifying a transaction manager, the local one (shared with other connections on the thread) is used.
My code:
async def get_connection():
return ZEO.connection(8092)
async def _message_db_init_aux(self, channel, after=None, before=None):
connexion = await get_connection()
root = connexion.root()
messages = await some_function_which_return_a_list()
async for message in messages:
# If author.id doesn't exist on the data, let's initiate it as a Tree
if message.author.id not in root.data: # root.data is a BTrees.OOBTree.BTree()
root.data[message.author.id] = BTrees.OOBTree.BTree()
# Message is a defined classed inherited from persistant.Persistant
root.data[message.author.id][message.id] = Message(message.id, message.author.id, message.created_at)
transaction.commit()
connexion.close()

Don't re-use transaction managers across connections. Each connection has its own transaction manager, use that.
Your code currently creates the connection, then commits. Rather than create the connection, ask the database to create a transaction manager for you, which then manages its own connection. The transaction manager can be used as a context manager, meaning that changes to the database are automatically committed when the context ends.
Moreover, by using ZEO.connection() for each transaction, you are forcing ZEO to create a complete new client object, with a fresh cache and connection pool. By using ZEO.DB() instead, and caching the result, a single client is created from which connections can be pooled and reused, and with a local cache to speed up transactions.
I'd alter the code to:
def get_db():
"""Access the ZEO database client.
The database client is cached to take advantage of caching and connection pooling
"""
db = getattr(get_db, 'db', None)
if db is None:
get_db.db = db = ZEO.DB(8092)
return db
async def _message_db_init_aux(self, channel, after=None, before=None):
with self.get_db().transaction() as conn:
root = conn.root()
messages = await some_function_which_return_a_list()
async for message in messages:
# If author.id doesn't exist on the data, let's initiate it as a Tree
if message.author.id not in root.data: # root.data is a BTrees.OOBTree.BTree()
root.data[message.author.id] = BTrees.OOBTree.BTree()
# Message is a defined classed inherited from persistant.Persistant
root.data[message.author.id][message.id] = Message(
message.id, message.author.id, message.created_at
)
The .transaction() method on the database object creates a new connection under the hood, the moment the context is entered (with causing __enter__ to be called), and when the with block ends the transaction is committed and the connection is released to the pool again.
Note that I used a synchronous def get_db() method; the call signatures on the ZEO client code are entirely synchronous. They are safe to call from asynchronous code because under the hood, the implementation uses asyncio throughout, using callbacks and tasks on the same loop, and actual I/O is deferred to separate tasks.

When not precised, the local transaction manager is used.
If you open multiple connections on the same thread, you have to precise the transaction manager you want to use. By default
transaction.commit()
is the local transaction manager.
connection.transaction.manager.commit()
will use the transaction manager dedicated to the transaction (and not the local one).
For more informations, check http://www.zodb.org/en/latest/guide/transactions-and-threading.html

Django with Peewee Connection Pooling MySQL disconnect

I'm running a Django project with Peewee in Python 3.6 and trying to track down what's wrong with the connection pooling. I keep getting the following error on the development server (for some reason I never experience this issue on my local machine):
Lost connection to MySQL server during query
The repro steps are reliable and are:
Restart Apache on the instance.
Go to my Django page and press a button which triggers a DB operation.
Works fine.
Wait exactly 10 minutes (I've tested enough to get the exact number).
Press another button to trigger another DB operation.
Get the lost connection error above.
The code is structured such that I have all the DB operations inside an independent Python module which is imported into the Django module.
In the main class constructor I'm setting up the DB as such:
from playhouse.pool import PooledMySQLDatabase
def __init__(self, host, database, user, password, stale_timeout=300):
self.mysql_db = PooledMySQLDatabase(host=host, database=database, user=user, password=password, stale_timeout=stale_timeout)
db_proxy.initialize(self.mysql_db)
Every call which needs to make calls out to the DB are done like this:
def get_user_by_id(self, user_id):
db_proxy.connect(reuse_if_open=True)
user = (User.get(User.user_id == user_id))
db_proxy.close()
return {'id': user.user_id, 'first_name': user.first_name, 'last_name': user.last_name, 'email': user.email }
I looked at the wait_timeout value on the MySQL instance and its value is 3600 so that doesn't seem to be the issue (and I tried changing it anyway just to see).
Any ideas on what I could be doing wrong here?
Update:
I found that the /etc/my.cnf configuration file for MySQL has the wait-timeout value set to 600, which matches what I'm experiencing. I don't know why this value doesn't show when I runSHOW VARIABLES LIKE 'wait_timeout'; on the MySQL DB (that returns 3600) but it does seem likely the issue is coming from the wait timeout.
Given this I tried setting the stale timeout to 60, assuming that if it's less than the wait timeout it might fix the issue but it didn't make a difference.

You need to be sure you're recycling the connections properly -- that means that when a request begins you open a connection and when the response is delivered you close the connection. The pool is not recycling the conn most likely because you're never putting it back in the pool, so it looks like its still "in use". This can easily be done with middleware and is described here:
http://docs.peewee-orm.com/en/latest/peewee/database.html#django

I finally came up with a fix which works for my case, after trying numerous ideas. It's not ideal but it works. This post on Connection pooling pointed me in the right direction.
I created a Django middleware class and configured it to be the first in the list of Django middleware.
from peewee import OperationalError
from playhouse.pool import PooledMySQLDatabase
database = PooledMySQLDatabase(None)
class PeeweeConnectionMiddleware(object):
CONN_FAILURE_CODES = [ 2006, 2013, ]
def __init__(self, get_response):
self.get_response = get_response
def __call__(self, request):
if database.database: # Is DB initialized?
response = None
try:
database.connect(reuse_if_open=True)
with database.atomic() as transaction:
try:
response = self.get_response(request)
except:
transaction.rollback()
raise
except OperationalError as exception:
if exception.args[0] in self.CONN_FAILURE_CODES:
database.close_all()
database.connect()
response = None
with database.atomic() as transaction:
try:
response = self.get_response(request)
except:
transaction.rollback()
raise
else:
raise
finally:
if not database.is_closed():
database.close()
return response
else:
return self.get_response(request)

Correct way of keeping mysql connection [duplicate]

This question already has answers here:
How to enable MySQL client auto re-connect with MySQLdb?
(8 answers)
Closed 4 years ago.
I have an application running 24/7 which uses mysql. Different functions of it use mysql. One way to implement it is to create a global mysql instance in the application like this:
self.db = MySQLdb.connect(
host=self.settings.MYSQL_HOST_LOCAL,
user=self.settings.MYSQL_USER,
passwd=self.settings.MYSQL_PASS,
db=self.settings.MYSQL_DB,
use_unicode=True,
charset="utf8",
)
and execute commands using self.db.execute(...). By doing this, the application uses 1 connection. The other way is to create connection every time I need to execute a transaction.
Approach 1, prevents the application from creating and deleting connections over and over but it will face "mysql gone away" problem if it stays ideal. Approach 2, doesn't have a problem with "mysql gone away", but it has too much I/O.
I am pretty sure neither these approcaches are the right ones, but what is the right approach?

One way to do is to create a connection every time you need to execute. You can also create a function to do it for you. This is how it meant to be. It is not too much I/O..
You can also do the following:
while True:
try:
db_session.execute('SELECT * FROM table')
break
except SQLAlchemyError:
db_session.rollback()
If the connection has go away, this will raise an exception, the session will be rollbackd, it'll try again is likely to succeed. (The first solution is much better)

In Approach 1, according to the application scenario 'MySQL server has gone away' may happens because
You have encountered a timeout on the server side and the automatic reconnection in the client is disabled (the reconnect flag in the MYSQL structure is equal to 0).
You can add a decorator to any db handler function like this to reconnect MySQL db when exception 'MySQL server has gone away' raised.
class DB:
"""Database interface"""
def retry(func):
def call(self, *args, **kwargs):
lock.acquire()
try:
return func(self, *args, **kwargs)
except MySQLdb.Error, e:
if 'MySQL server has gone away' in str(e):
# reconnect MySQL
self.connect_mysql()
else:
# No need to retry for other reasons
pass
finally:
lock.release()
return call
def __init__(self):
pass
def connect_mysql(self):
# do connection
#retry
def db_handler_function(self):
# do something

Python and Django OperationalError (2006, 'MySQL server has gone away')

Original: I have recently started getting MySQL OperationalErrors from some of my old code and cannot seem to trace back the problem. Since it was working before, I thought it may have been a software update that broke something. I am using python 2.7 with django runfcgi with nginx. Here is my original code:
views.py
DBNAME = "test"
DBIP = "localhost"
DBUSER = "django"
DBPASS = "password"
db = MySQLdb.connect(DBIP,DBUSER,DBPASS,DBNAME)
cursor = db.cursor()
def list(request):
statement = "SELECT item from table where selected = 1"
cursor.execute(statement)
results = cursor.fetchall()
I have tried the following, but it still does not work:
views.py
class DB:
conn = None
DBNAME = "test"
DBIP = "localhost"
DBUSER = "django"
DBPASS = "password"
def connect(self):
self.conn = MySQLdb.connect(DBIP,DBUSER,DBPASS,DBNAME)
def cursor(self):
try:
return self.conn.cursor()
except (AttributeError, MySQLdb.OperationalError):
self.connect()
return self.conn.cursor()
db = DB()
cursor = db.cursor()
def list(request):
cursor = db.cursor()
statement = "SELECT item from table where selected = 1"
cursor.execute(statement)
results = cursor.fetchall()
Currently, my only workaround is to do MySQLdb.connect() in each function that uses mysql. Also I noticed that when using django's manage.py runserver, I would not have this problem while nginx would throw these errors. I doubt that I am timing out with the connection because list() is being called within seconds of starting the server up. Were there any updates to the software I am using that would cause this to break/is there any fix for this?
Edit: I realized that I recently wrote a piece of middle-ware to daemonize a function and this was the cause of the problem. However, I cannot figure out why. Here is the code for the middle-ware
def process_request_handler(sender, **kwargs):
t = threading.Thread(target=dispatch.execute,
args=[kwargs['nodes'],kwargs['callback']],
kwargs={})
t.setDaemon(True)
t.start()
return
process_request.connect(process_request_handler)

Sometimes if you see "OperationalError: (2006, 'MySQL server has gone away')", it is because you are issuing a query that is too large. This can happen, for instance, if you're storing your sessions in MySQL, and you're trying to put something really big in the session. To fix the problem, you need to increase the value of the max_allowed_packet setting in MySQL.
The default value is 1048576.
So see the current value for the default, run the following SQL:
select ##max_allowed_packet;
To temporarily set a new value, run the following SQL:
set global max_allowed_packet=10485760;
To fix the problem more permanently, create a /etc/my.cnf file with at least the following:
[mysqld]
max_allowed_packet = 16M
After editing /etc/my.cnf, you'll need to restart MySQL or restart your machine if you don't know how.

As per the MySQL documentation, your error message is raised when the client can't send a question to the server, most likely because the server itself has closed the connection. In the most common case the server will close an idle connection after a (default) of 8 hours. This is configurable on the server side.
The MySQL documentation gives a number of other possible causes which might be worth looking into to see if they fit your situation.
An alternative to calling connect() in every function (which might end up needlessly creating new connections) would be to investigate using the ping() method on the connection object; this tests the connection with the option of attempting an automatic reconnect. I struggled to find some decent documentation for the ping() method online, but the answer to this question might help.
Note, automatically reconnecting can be dangerous when handling transactions as it appears the reconnect causes an implicit rollback (and appears to be the main reason why autoreconnect is not a feature of the MySQLdb implementation).

This might be due to DB connections getting copied in your child threads from the main thread. I faced the same error when using python's multiprocessing library to spawn different processes. The connection objects are copied between processes during forking and it leads to MySQL OperationalErrors when making DB calls in the child thread.
Here's a good reference to solve this: Django multiprocessing and database connections

For me this was happening in debug mode.
So I tried Persistent connections in debug mode, checkout the link: Django - Documentation - Databases - Persistent connections.
In settings:
'default': {
'ENGINE': 'django.db.backends.mysql',
'NAME': 'dbname',
'USER': 'root',
'PASSWORD': 'root',
'HOST': 'localhost',
'PORT': '3306',
'CONN_MAX_AGE': None
},

Check if you are allowed to create mysql connection object in one thread and then use it in another.
If it's forbidden, use threading.Local for per-thread connections:
class Db(threading.local):
""" thread-local db object """
con = None
def __init__(self, ...options...):
super(Db, self).__init__()
self.con = MySQLdb.connect(...options...)
db1 = Db(...)
def test():
"""safe to run from any thread"""
cursor = db.con.cursor()
cursor.execute(...)

This error is mysterious because MySQL doesn't report why it disconnects, it just goes away.
It seems there are many causes of this kind of disconnection. One I just found is, if the query string too large, the server will disconnect. This probably relates to the max_allowed_packets setting.

I've been struggling with this issue too. I don't like the idea of increasing timeout on mysqlserver. Autoreconnect with CONNECTION_MAX_AGE doesn't work either as it was mentioned. Unfortunately I ended up with wrapping every method that queries the database like this
def do_db( callback, *arg, **args):
try:
return callback(*arg, **args)
except (OperationalError, InterfaceError) as e: # Connection has gone away, fiter it with message or error code if you could catch another errors
connection.close()
return callback(*arg, **args)
do_db(User.objects.get, id=123) # instead of User.objects.get(id=123)
As you can see I rather prefer catching the exception than pinging the database every time before querying it. Because catching an exception is a rare case. I would expect django to reconnect automatically but they seemed to refused that issue.

This error may occur when you try to use the connection after a time-consuming operation that doesn't go to the database. Since the connection is not used for some time, MySQL timeout is hit and the connection is silently dropped.
You can try calling close_old_connections() after the time-consuming non-DB operation so that a new connection is opened if the connection is unusable. Beware, do not use close_old_connections() if you have a transaction.

The most common issue regarding such warning, is the fact that your application has reached the wait_timeout value of MySQL.
I had the same problem with a Flask app.
Here's how I solved:
$ grep timeout /etc/mysql/mysql.conf.d/mysqld.cnf
# https://support.rackspace.com/how-to/how-to-change-the-mysql-timeout-on-a-server/
# wait = timeout for application session (tdm)
# inteactive = timeout for keyboard session (terminal)
# 7 days = 604800s / 4 hours = 14400s
wait_timeout = 604800
interactive_timeout = 14400
Observation: if you search for the variables via MySQL batch mode, the values will appear as it is. But If you perform SHOW VARIABLES LIKE 'wait%'; or SHOW VARIABLES LIKE 'interactive%';, the value configured for interactive_timeout, will appear to both variables, and I don't know why, but the fact is, that the values configured for each variable at '/etc/mysql/mysql.conf.d/mysqld.cnf', will be respected by MySQL.

How old is this code? Django has had databases defined in settings since at least .96. Only other thing I can think of is multi-db support, which changed things a bit, but even that was 1.1 or 1.2.
Even if you need a special DB for certain views, I think you'd probably be better off defining it in settings.

SQLAlchemy now has a great write-up on how you can use pinging to be pessimistic about your connection's freshness:
http://docs.sqlalchemy.org/en/latest/core/pooling.html#disconnect-handling-pessimistic
From there,
from sqlalchemy import exc
from sqlalchemy import event
from sqlalchemy.pool import Pool
#event.listens_for(Pool, "checkout")
def ping_connection(dbapi_connection, connection_record, connection_proxy):
cursor = dbapi_connection.cursor()
try:
cursor.execute("SELECT 1")
except:
# optional - dispose the whole pool
# instead of invalidating one at a time
# connection_proxy._pool.dispose()
# raise DisconnectionError - pool will try
# connecting again up to three times before raising.
raise exc.DisconnectionError()
cursor.close()
And a test to make sure the above works:
from sqlalchemy import create_engine
e = create_engine("mysql://scott:tiger#localhost/test", echo_pool=True)
c1 = e.connect()
c2 = e.connect()
c3 = e.connect()
c1.close()
c2.close()
c3.close()
# pool size is now three.
print "Restart the server"
raw_input()
for i in xrange(10):
c = e.connect()
print c.execute("select 1").fetchall()
c.close()

I had this problem and did not have the option to change my configuration. I finally figured out that the problem was occurring 49500 records in to my 50000-record loop, because that was the about the time I was trying again (after having tried a long time ago) to hit my second database.
So I changed my code so that every few thousand records, I touched the second database again (with a count() of a very small table), and that fixed it. No doubt "ping" or some other means of touching the database would work, as well.

Firstly, You should make sure the MySQL session & global enviroments wait_timeout and interactive_timeout values. And secondly Your client should try to reconnect to the server below those enviroments values.

Twisted web service - sql connection drops

I am working on a web service with Twisted that is responsible for calling up several packages I had previously used on the command line. The routines these packages handle were being prototyped on their own but now are ready to be integrated into our webservice.
In short, I have several different modules that all create a mysql connection property internally in their original command line forms. Take this for example:
class searcher:
def __init__(self,lat,lon,radius):
self.conn = getConnection()[1]
self.con=self.conn.cursor();
self.mgo = getConnection(True)
self.lat = lat
self.lon = lon
self.radius = radius
self.profsinrange()
self.cache = memcache.Client(["173.220.194.84:11211"])
The getConnection function is just a helper that returns a mongo or mysql cursor respectively. Again, this is all prototypical :)
The problem I am experiencing is when implemented as a consistently running server using Twisted's WSGI resource, the sql connection created in init times out, and subsequent requests don't seem to regenerate it. Example code for small server app:
from twisted.web import server
from twisted.web.wsgi import WSGIResource
from twisted.python.threadpool import ThreadPool
from twisted.internet import reactor
from twisted.application import service, strports
import cgi
import gnengine
import nn
wsgiThreadPool = ThreadPool()
wsgiThreadPool.start()
# ensuring that it will be stopped when the reactor shuts down
reactor.addSystemEventTrigger('after', 'shutdown', wsgiThreadPool.stop)
def application(environ, start_response):
start_response('200 OK', [('Content-type','text/plain')])
params = cgi.parse_qs(environ['QUERY_STRING'])
try:
lat = float(params['lat'][0])
lon = float(params['lon'][0])
radius = int(params['radius'][0])
query_terms = params['query']
s = gnengine.searcher(lat,lon,radius)
query_terms = ' '.join( query_terms )
json = s.query(query_terms)
return [json]
except Exception, e:
return [str(e),str(params)]
return ['error']
wsgiAppAsResource = WSGIResource(reactor, wsgiThreadPool, application)
# Hooks for twistd
application = service.Application('Twisted.web.wsgi Hello World Example')
server = strports.service('tcp:8080', server.Site(wsgiAppAsResource))
server.setServiceParent(application)
The first few requests work fine, but after mysqls wait_timeout expires, the dread error 2006 "Mysql has gone away" error surfaces. It had been my understanding that every request to the WSGI Twisted resource would run the application function, thereby regenerating the searcher object and re-leasing the connection. If this isn't the case, how can I make the requests processed as such? Is this kind of Twisted deployment not transactional in this sense? Thanks!
EDIT: Per request, here is the prototype helper function calling up the connection:
def getConnection(mong = False):
if mong == False:
connection = mysql.connect(host = db_host,
user = db_user,
passwd = db_pass,
db = db,
cursorclass=mysql.cursors.DictCursor)
cur = connection.cursor();
return (cur,connection)
else:
return pymongo.Connection('173.220.194.84',27017).gonation_test

i was developing a piece of software with twisted where i had to utilize a constant MySQL database connection. i did run into this problem and digging through the twisted documentation extensively and posting a few questions i was unable to find a proper solution.There is a boolean parameter you can pass when you are instantiating the adbapi.connectionPool class; however it never seemed to work and i kept getting the error irregardless. However, what i am guessing the reconnect boolean represents is the destruction of the connection object when SQL disconnect does occur.
adbapi.ConnectionPool("MySQLdb", cp_reconnect=True, host="", user="", passwd="", db="")
I have not tested this but i will re-post some results when i do or if anyone else has please share.
When i was developing the script i was using twisted 8.2.0 (i havent touched twisted in a while) and back then the framework had no such explicit keep alive method, so i developed a ping/keepalive extension employing event driven paradigm twisted builds upon in conjunction with direct MySQLdb module ping() method (see code comment).
As i was typing this response; however, i did look around the current twisted documentation i was still unable to find an explicit keep-alive method or parameter. My guess is because twisted itself does not have database connectivity libraries/classes. It uses the methods available to python and provides an indirect layer of interfacing with those modules; with some exposure for direct calls to the database library being used. This is accomplished by using the adbapi.runWithConnection method.
here is the module i wrote under twisted 8.2.0 and python 2.6; you can set the intervals between pings. what the script does is, every 20 minutes it pings the database and if it fails, it attempts to reconnect back to it every 60 seconds. I must warn that the script does NOT handle sudden/dropped connection; that you can handle through addErrback whenever you run a query through twisted, atleast thats how i did it. I have noticed that whenever database connection drops, you can only find out if it has when you are executing a query and the event raises an errback, and then at that point you deal with it. Basically, if i dont run a query for 10 minutes, and my database disconnects me, my application will not respond in real time. the application will realize the connection has been dropped when it runs the query that follows; so the database could have disconnected us 1 minute after the first query, 5, 9, etc....
I guess this sort of goes back to the original idea that i have stated, twisted utilizes python's own libraries or 3rd party libraries for database connectivity and because of that, some things are handled a bit differently.
from twisted.enterprise import adbapi
from twisted.internet import reactor, defer, task
class sqlClass:
def __init__(self, db_pointer):
self.dbpool=db_pointer
self.dbping = task.LoopingCall(self.dbping)
self.dbping.start(1200) #20 minutes = 1200 seconds; i found out that if MySQL socket is idled for 20 minutes or longer, MySQL itself disconnects the session for security reasons; i do believe you can change that in the configuration of the database server itself but it may not be recommended.
self.reconnect=False
print "database ping initiated"
def dbping(self):
def ping(conn):
conn.ping() #what happens here is that twisted allows us to access methods from the MySQLdb module that python posesses; i chose to use the native command instead of sending null commands to the database.
pingdb=self.dbpool.runWithConnection(ping)
pingdb.addCallback(self.dbactive)
pingdb.addErrback(self.dbout)
print "pinging database"
def dbactive(self, data):
if data==None and self.reconnect==True:
self.dbping.stop()
self.reconnect=False
self.dbping.start(1200) #20 minutes = 1200 seconds
print "Reconnected to database!"
elif data==None:
print "database is active"
def dbout(self, deferr):
#print deferr
if self.reconnect==False:
self.dbreconnect()
elif self.reconnect==True:
print "Unable to reconnect to database"
print "unable to ping MySQL database!"
def dbreconnect(self, *data):
self.dbping.stop()
self.reconnect=True
#self.dbping = task.LoopingCall(self.dbping)
self.dbping.start(60) #60
if __name__ == "__main__":
db = sqlClass(adbapi.ConnectionPool("MySQLdb", cp_reconnect=True, host="", user="", passwd="", db=""))
reactor.callLater(2, db.dbping)
reactor.run()
let me know how it works out for you :)