Script execution timeout.

So I must be missing something, how are we supposed to use
Flex to build business apps which often have to parse hundreds of
thousands of rows of data with a 60 second hard limit on code
execution? Nothing I can find will get around this limitation and
there is simply no way to do complex calculations within the time
allowed.

The problem that I'm in front of is as follows.
~500 rows of data. Each row is a calculated sum based on
multiplying a value in one row of another ~500x500 table with
another value and adding it to the running total.
I can do this in PhP on the server and it takes about two
min' to run. The problem is that the user needs to be able to
update a value, that value effects every other value in the table.
So to resubmit this calculation back to the server is very time
consuming and has the potential to overload the servers hardware.
It may just be my frustration at the task before me, but
running into these timeout limits is like smacking into a brick
wall at 100mph. I've not looked at AIR and shall do so, but there's
no way I can come up with to break up the task into smaller chunks
since every value is dependent on every other one. And even if I
got it to work, I would have to work out minimum requirements for
the web app due to hardware performance differences.

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