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I’m running a Rackspace Cloud CentOS 5.5 instance.

It shipped with:

[root@server ~]# php -v
PHP 5.1.6 (cli) (built: Nov 29 2010 16:47:46) 
Copyright (c) 1997-2006 The PHP Group
Zend Engine v2.1.0, Copyright (c) 1998-2006 Zend Technologies

and

[root@server ~]# mysql --version
mysql  Ver 14.12 Distrib 5.0.77, for redhat-linux-gnu (x86_64) using readline 5.1

I want to upgrade it to at least PHP 5.2, and 5.3 if possible.

What are the proper steps for ensuring a smooth upgrade (with no data loss in MySQL, dependencies upgraded accordingly, etc.), and how would that upgrade actually be performed?

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Upgrading like that always has a risk of data loss. Therefore it's an extremely good idea to make backups of your files and database. After doing that, peruse php upgrade and mysql upgrade

Edit: It might be possible to go directly from 5.1 to 5.3, but to be safe you can go from 5.1->5.2, then from 5.2->5.3.

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