Just throwing in my two cents, but I've had frequent problems with
phpMyAdmin exceeding timeout limits (and once even memory limits) on a
shared hosts...

So, trying to compare phpMyAdmin with what you're trying to do isn't really
fair. All it does are imports and exports (in terms of large processes).

However, you *should* be fine with just pumping up both the allocated RAM
and exec. time for PHP, if you truly want to have this done through CakePHP.

But what you're describing is neither a limitation for CakePHP or PHP
itself. You just have a butt load of data to deal with and memory issues are
going to be a problem with a butt load of data.

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