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I have a i7-2600 which is currently rendering a scene to .avi and is about 8 hours in and half way. The CPU is at near 90% usage.

I also have a GTX 460 GPU (which I believe supports CUDA)

Is it a good idea to launch another instance of Blender and configure to render another scene with the GPU instead? Will this have a negative impact on the other instance of Blender rendering?

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This should work, but I don't know if you want to risk it because you are rendering directly to a video file.

If the animation render stops the avi file could be corrupted. Not to mention if your computer crashes it will be lost entirely.

This is why it is considered bad practice to render directly to a video file.

If you were rendering to an image sequence, then it wouldn't be a big deal even if your computer crashed completely because everything up to the previous frame would be on the hard drive.

To answer your question:
Performance wise, I tested this with a GTX 460 and a quad core intel xeon rendering two separate scenes in separate instances of blender.

There was a slight slowdown on the CPU scene when I started the GPU render, but it was barely noticeable. What made me certain that there was indeed a slowdown is that the time estimation for the CPU render jumped backwards about a second or two when the GPU render was started.

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