I got this error after a script I wrote went AWOL and inserted 10000 rows into a table simultaneously. Seemed like a failsafe to me - not sure if that relates to your problem...
You might want to check MySQL's timeout variables:
show variables like '%timeout%';
You're probably interested in waittimeout (less likely but possible: interactivetimeout). On Debian and Ubuntu, the defaults are 28800 (MySQL kills connections after 8 hours), but maybe the default for your platform is different or whoever administrates the server has configured things differently.
AFAICT, pool_recycle doesn't actually keep the connections alive, it expires them on its own before MySQL kills them. I'm not familiar with pylons, but if causing the connections to intermittently do a "SELECT 1;" is an option, that will keep them alive at the cost of basically no server load and minimal network traffic. One final thought: are you somehow managing to use a connection that pylons thinks it has expired?
@Jon Bright - I can't say for certain; I don't know the internals of Pylons well enough yet. I haven't had a chance to poke through the documentation yet either (busy busy). I don't think the SELECT 1; thing is an option though, seems kind of kludgey too :).
I think I fixed it. It's turns out I had a simple config error. My ini file read:
sqlalchemy.default.url = [connection string here]
sqlalchemy.pool_recycle = 1800
The problem is that my environment.py file declared that the engine would only map keys with the prefix: sqlalchemy.default so pool_recycle was ignored.
The solution is to simply change the second line in the ini to:
sqlalchemy.default.pool_recycle = 1800