Is uninterruptible sleep the cause of my Python program being really slow (and if so, how can I solve this?)?
As I mentioned in an answer to a prior question you asked, did you give the sqlite module apsw a try? From the website:
APSW is a Python wrapper for the SQLite embedded relational database engine. In contrast to other wrappers such as pysqlite it focuses on being a minimal layer over SQLite attempting just to translate the complete SQLite API into Python. The documentation has a section on the differences between APSW and pysqlite.
I tried it myself and it seems to indeed reflect better how SQL statements are executed by the "real" Sqlite (i.e. the client or the C library).
There is a performance issue with SQLite and Python. Read this thread for more information. There are a few suggestions there - try them, it might work - like adding an index to your join fields or using pysqlite.
http://www.mail-archive.com/python-list@python.org/msg253067.html