Questions:
- Do I use root account to install the software?
Yes to compile the source or do an RPM as seen below.
See http://www.mysql.com/doc/L/i/Linux-RPM.html

- What account do I use to create Innodb?
Same - I am guessing here but I do all installs as root then give the needed
permissions to others.

- Who owns the data files?  root or mysql
Root - See http://www.mysql.com/doc/P/r/Privilege_system.html

- Any suggestion of the owner and group for the mysql files?
See http://www.mysql.com/doc/P/r/Privilege_system.html

- I think the process is to load the mysql software, then configure the
Innodb. Once the Innodb is configured, when you mean startup or shutdown
mysql server is this the same as shutdown the Innodb?
see http://www.mysql.com/doc/I/n/InnoDB_overview.html for some help on this


- When I query show databases, it give me mysql, test1, test2.  Are they
really databases or they are like schema owners in Oracle and Innodb is like
instance in Oracle.
Yes they are real. The MySQL one holds your user permissions
See http://www.mysql.com/doc/P/r/Privilege_system.html

P.S.  What is a good book to buy for the MYSQL database and any user group
in the United States I can belong.

Number one is Paul DuBois - Search Amazon or Ask Paul here<G>

Your in the Best Mysql Newsgroup<G> There are some heavy users here and they
can help out but Please try and read the manual<G>
http://www.mysql.com/doc/index.html

Also for commercial use you should take a look at
http://www.mysql.com/doc/B/u/Business_Services_Commercial_licenses.html

These are only my opinions but they work here<G>

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