I recently found this article for C++AMP where you can temporaly disable TDR in Windows 8. Is there any way to apply this solution for CUDA?
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Windows WDDM Driver Timeout Detection and Recovery mechanism can be disabled or the timeout can be extended to be greater than the default 2 seconds.Timeout Detection and Recovery is documented on MSDN.
(Edited: The above link is dead. The information that it provided might now be available at https://learn.microsoft.com/en-us/windows-hardware/drivers/display/tdr-registry-keys)
Nsight Visual Studio Edition Nsight.Monitor has settings to disable or increase the timeout. Otherwise, you can use the registry keys in the MSDN article. Make sure to restart the computer after making changes.
I recommend that you increase TdrDelay before completely disabling TDR.
Tesla GPUs can use the Tesla Compute Cluster driver which does not have a timeout watchdog.