Have you closed the DB connection immediately when you are done with the database or statement handles etc.? If you are running a resource-intensive script, you should make sure you deallocate things as quickly as you can to avoid holding something for too long. You should not rely on the automatic reference-count garbage collection in this case as it is possible that deallocation may not occur soon enough.

If you are having a variable with very large content, you should consider manually unset() the variables immediately when you are done with it. It may not be related to your case but just try.