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I am running mysql-standard-4.0.20-pc-linux-i686 and mysql-standard-4.1.12-pc-linux-gnu-i686 on the same machine, installed binaries.
I had a heck of a time running both of these versions at once. And not for the typical reasons: port collision, sock file, etc… I have that all figured out, I should be able to run two versions of MySQL on the same machine. I am running 4.0 out of /usr/local/mysql and trying to run 4.1 out of /usr/local/mysql-4.1 and cannot get it working for the life of my, using the mysqld_safe script.