Error 2006: “MySQL server has gone away” using Python, Bottle Microframework and Apache

Question

After accessing my web app using:
- Python 2.7
- the Bottle micro framework v. 0.10.6
- Apache 2.2.22
- mod_wsgi
- on Ubuntu Server 12.04 64bit; I'm receiving this error after several hours:

OperationalError: (2006, 'MySQL server has gone away')

I'm using MySQL - the native one included in Python. It usually happens when I don't access the server. I've tried closing all the connections, which I do, using this:

cursor.close()
db.close()

where db is the standard MySQLdb.Connection() call.

The my.cnf file looks something like this:

key_buffer      = 16M
max_allowed_packet  = 128M
thread_stack        = 192K
thread_cache_size       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10

It is the default configuration file except max_allowed_packet is 128M instead of 16M.

The queries to the database are quite simple, at most they retrieve approximately 100 records.

Can anyone help me fix this? One idea I did have was use try/except but I'm not sure if that would actually work.

Thanks in advance,

Jamie

Update: try/except calls didn't work.

Answer 1

This is MySQL error, not Python's.

The list of possible causes and possible solutions is here: MySQL 5.5 Reference Manual: C.5.2.9. MySQL server has gone away.

Possible causes include:

• You tried to run a query after closing the connection to the server. This indicates a logic error in the application that should be corrected.
• A client application running on a different host does not have the necessary privileges to connect to the MySQL server from that host.
• 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 also get these errors if you send a query to the server that is incorrect or too large. If mysqld receives a packet that is too large or out of order, it assumes that something has gone wrong with the client and closes the connection. If you need big queries (for example, if you are working with big BLOB columns), you can increase the query limit by setting the server's max_allowed_packet variable, which has a default value of 1MB. You may also need to increase the maximum packet size on the client end. More information on setting the packet size is given in Section C.5.2.10, “Packet too large”.
• You also get a lost connection if you are sending a packet 16MB or larger if your client is older than 4.0.8 and your server is 4.0.8 and above, or the other way around.
• and so on...

In other words, there are plenty of possible causes. Go through that list and check every possible cause.

Answer 2

Make sure you are not trying to commit to a closed MySqldb object

Answer 3

An answer to a (very closely related) question has been posted here: https://stackoverflow.com/a/982873/209532

It relates directly to the MySQLdb driver (MySQL-python (unmaintained) and mysqlclient (maintained fork)), but the approach is the the same for other driver the does not support automatic reconnect.

Answer 4

For me this was fixed using

MySQLdb.connect("127.0.0.1","root","","db" )

instead of

MySQLdb.connect("localhost","root","","db" )

and then

df.to_sql('df',sql_cnxn,flavor='mysql',if_exists='replace', chunksize=100)