The same technology that would allow for the needed massively parallel chips would allow for massively parallel GPUs and CPUs. 3D graphics tend to be pretty embarrassingly parallel, so I don't think the uploads are going to necessarily be relegated to some grueling terminal.

General algorithms on a massively parallel CPU are harder to design and implement, but with a 1,000,000 fold increase in subjective time you probably have the luxury of developing great parallel algorithms. Most scientific problems in general are amenable to parallelism.

Edited for stupidity, thanks wedrifid.