The de facto standard seems to be CUDA GPU Memtest. As @c2h5oh mentioned, it looks like it's based on memtest86 test patterns so I'm sure it does a good job. It runs relatively quickly on the high end GPUs I'm testing (30 minutes on a Quadro 6000 and 20 minutes on a Tesla C2075). It runs inside the OS (unlike, memtest) so monitoring is a bit different. You'll probably want to output stdout and stderr to a file to look at later. So consider running it something like this in case you lose your terminal output you can look up what the tests found:
cuda_memtest 2>cuda_memtest.stderr 1>cuda_memtest.stdout &
tail -f cuda_memtest.stdout &
tail -f cuda_memtest.stderr &
You'll also want to make sure that no one is using the system and/or cards. You can set the GPUs to exclusive mode using:
nvidia-smi --compute-mode=EXCLUSIVE_PROCESS
Here are some of the output from sample runs of both the Quadro and the Tesla in case you're interested in what test info is given:
[09/07/2012 11:56:22][hydro][0]:Running cuda memtest, version 1.2.2
[09/07/2012 11:56:23][hydro][0]:Warning: Getting serial number failed
[09/07/2012 11:56:23][hydro][0]:NVRM version: NVIDIA UNIX x86_64 Kernel Module 295.41 Fri Apr 6 23:18:58 PDT 2012
[09/07/2012 11:56:23][hydro][0]:num_gpus=1
[09/07/2012 11:56:23][hydro][0]:Device name=Quadro 6000, global memory size=6441992192
[09/07/2012 11:56:23][hydro][0]:major=2, minor=0
[09/07/2012 11:56:24][hydro][0]:Attached to device 0 successfully.
[09/07/2012 11:56:24][hydro][0]:Allocated 6040 MB
[09/07/2012 11:56:24][hydro][0]:Test0 [Walking 1 bit]
[09/07/2012 11:56:30][hydro][0]:Test0 finished in 5.7 seconds
[09/07/2012 11:56:30][hydro][0]:Test1 [Own address test]
[09/07/2012 11:56:33][hydro][0]:Test1 finished in 3.5 seconds
[09/07/2012 11:56:33][hydro][0]:Test2 [Moving inversions, ones&zeros]
[09/07/2012 11:57:05][hydro][0]:Test2 finished in 32.3 seconds
[09/07/2012 11:57:05][hydro][0]:Test3 [Moving inversions, 8 bit pat]
[09/07/2012 11:57:37][hydro][0]:Test3 finished in 31.9 seconds
[09/07/2012 11:57:37][hydro][0]:Test4 [Moving inversions, random pattern]
[09/07/2012 11:57:53][hydro][0]:Test4 finished in 15.9 seconds
[09/07/2012 11:57:53][hydro][0]:Test5 [Block move, 64 moves]
[09/07/2012 11:57:59][hydro][0]:Test5 finished in 6.3 seconds
[09/07/2012 11:57:59][hydro][0]:Test6 [Moving inversions, 32 bit pat]
[09/07/2012 12:18:46][hydro][0]:Test6 finished in 1246.6 seconds
[09/07/2012 12:18:46][hydro][0]:Test7 [Random number sequence]
[09/07/2012 12:19:06][hydro][0]:Test7 finished in 19.8 seconds
[09/07/2012 12:19:06][hydro][0]:Test8 [Modulo 20, random pattern]
[09/07/2012 12:19:06][hydro][0]:test8[mod test]: p1=0x13472f5f, p2=0xecb8d0a0
[09/07/2012 12:20:34][hydro][0]:Test8 finished in 88.0 seconds
[09/07/2012 12:20:34][hydro][0]:Test10 [Memory stress test]
[09/07/2012 12:20:34][hydro][0]:Test10 with pattern=0x55f6c69858704128
[09/07/2012 12:21:11][hydro][0]:Test10 finished in 36.8 seconds
[09/07/2012 12:21:11][hydro][0]:Test0 [Walking 1 bit]
[09/07/2012 12:21:16][hydro][0]:Test0 finished in 5.8 seconds
[09/06/2012 18:49:07][hydro][0]:Running cuda memtest, version 1.2.2
[09/06/2012 18:49:10][hydro][0]:Warning: Getting serial number failed
[09/06/2012 18:49:10][hydro][0]:NVRM version: NVIDIA UNIX x86_64 Kernel Module 295.41 Fri Apr 6 23:18:58 PDT 2012
[09/06/2012 18:49:10][hydro][0]:num_gpus=1
[09/06/2012 18:49:10][hydro][0]:Device name=Tesla C2075, global memory size=5636292608
[09/06/2012 18:49:10][hydro][0]:major=2, minor=0
[09/06/2012 18:49:11][hydro][0]:Attached to device 0 successfully.
[09/06/2012 18:49:11][hydro][0]:Allocated 5273 MB
[09/06/2012 18:49:11][hydro][0]:Test0 [Walking 1 bit]
[09/06/2012 18:49:22][hydro][0]:Test0 finished in 11.1 seconds
[09/06/2012 18:49:22][hydro][0]:Test1 [Own address test]
[09/06/2012 18:49:25][hydro][0]:Test1 finished in 3.1 seconds
[09/06/2012 18:49:25][hydro][0]:Test2 [Moving inversions, ones&zeros]
[09/06/2012 18:49:52][hydro][0]:Test2 finished in 27.4 seconds
[09/06/2012 18:49:52][hydro][0]:Test3 [Moving inversions, 8 bit pat]
[09/06/2012 18:50:20][hydro][0]:Test3 finished in 27.9 seconds
[09/06/2012 18:50:20][hydro][0]:Test4 [Moving inversions, random pattern]
[09/06/2012 18:50:34][hydro][0]:Test4 finished in 13.7 seconds
[09/06/2012 18:50:34][hydro][0]:Test5 [Block move, 64 moves]
[09/06/2012 18:50:39][hydro][0]:Test5 finished in 5.5 seconds
[09/06/2012 18:50:39][hydro][0]:Test6 [Moving inversions, 32 bit pat]
[09/06/2012 19:08:34][hydro][0]:Test6 finished in 1074.9 seconds
[09/06/2012 19:08:34][hydro][0]:Test7 [Random number sequence]
[09/06/2012 19:08:51][hydro][0]:Test7 finished in 17.1 seconds
[09/06/2012 19:08:51][hydro][0]:Test8 [Modulo 20, random pattern]
[09/06/2012 19:08:51][hydro][0]:test8[mod test]: p1=0x63136646, p2=0x9cec99b9
[09/06/2012 19:10:10][hydro][0]:Test8 finished in 78.4 seconds
[09/06/2012 19:10:10][hydro][0]:Test10 [Memory stress test]
[09/06/2012 19:10:10][hydro][0]:Test10 with pattern=0x26341d134a89ac2b
[09/06/2012 19:10:39][hydro][0]:Test10 finished in 29.0 seconds