I have exceeded the 250k click line in my Prosper installation and sure enough stats generation is getting slow... as in get cup of coffee slow :)
I decided to upgrade my Ubuntu Dapper 6.06 to MySQL 5.1. Ubuntu (or debian) don't include .deb packages for MySQL 5.1 since technically 5.1 isn't ready for public consumption yet.
I ended up building MySQL 5.1 from source. All works great but every time I'd reinstall Prosper, I'd get a cryptic Out of Resources error. After rebuilding MySQL many times with diff ./configure options, I finally figured out the problem.
Prosper202 creates a metric F-ton of partition files for one of the tables, and MySQL was exceeding its max open files limit. Of course the error says nothing like this.
So, as a tip, be sure to add:
open_files_limit = 4096
to your /etc/mysql/my.cnf file.
(4096 can be higher, but make sure your Linux distro allows a lot of open files first, otherwise you need to tweak a few other things).
Now restart mysql and reinstall prosper, and it will work great. It took me 12 hours to figure this out, let it save you some time.
And for the curious, here's what my ./configure settings came out to. (for building mysql 5.1 on ubuntu 6.06 LTS) There are some other debian-related tweaks you need to do to keep the apt-get package manager happy. I ended up putting this in /usr/local/bin where the distro install was in /usr/bin and /usr/sbin
./configure --with-plugin-partition --with-plugin-myisam --with-plugin-innobase --with-plugin-archive --with-plugin-heap --with-unix-socket-path=/var/run/mysqld/mysqld.sock --with-mysqld-user=mysql --enable-assembler