You run a benchmark till it's over. If you want to have a solid benchmark, run it at least 3 times, reboot before each run, average them.
Whoever said you will fry your video card after an hour, avoid their advice about computer stuff. The only time you may have an issue is if you are overclocking or troubleshooting an issue and you are doing a stress test. But then you already have an idea things may fail.