when running CPU intensive tasks you generally will find the CPU temperature goes up (because the system turns off the CPU when it's not being used, reducing power, and reducing heat generation - which it stops doing when it's in use)
as for the overheat alarm triggering at 50'C, if you go in to the BIOS setup utility for your motherbard (normally DEL or F2 sometimes F8 as soon as the computer is turned on) it should let you turn the alarm temperature up or disable it so it doesn't keep pestering you about it, most motherboards only allow about 70'C as the highest setting so set it to that - it's also about the right setting to use for a 2.8GHz P4 (depending on exact model the 2.8GHz P4s have maximum temperatures between 70 and 80) but with a P4 overheats aren't an issue anyway as the CPU is not capable of overheating