I have recently had a similar problem, and I could not find any software for stress-testing a GPU - there does not seem to be any available for Linux.
Your best bet probably is to load the GPU by drawing lots of stuff, then wait for lock-ups or rendering errors.
To load the GPU, you could use
- for 3D functionality: any 3D software - Phoronix Test Suite looks fine, or some 3D demo
- for 2D functionality: try gtkperf, it continually draws stuff using GTK+ (run it in a loop from a shell so it loops endlessly)
Of course, running these test may not help you. It's not guaranteed that testing will reproduce your problem, and even if it does, it might still not be the GPU (maybe heavy load on the GPU overloads the PSU, or a warm GPU causes dogdy contacts on the motherboard to come loose, that kind of stuff ... ). So you will still have to investigate the results and draw your own conclusions. Such is the nature of testing...