Here's one method that doesn't rely on either gravitational time dilation or simulation:
If you look at the basic equations of quantum mechanics, you notice that if you scale all masses by a common factor, you'll get essentially the same physics, just at different length and time scales. In particular, when all masses are multiplied by a factor $\lambda$, all lengths get scaled by a factor $1/\lambda$ and all processes go faster by a factor $\lambda$, The latter being exactly what you want. (Caveat: I don't know enough about nuclear physics/QCD to say for sure that this is the case there, too, but I suspect it is; indeed I seem to remember having read somewhere that the mass scaling is a requirement for the standard renormalization procedures — the way how infinities are avoided in quantum field theories — to work.)
Now the question is of course how you could scale all masses. Well, according to Higgs theory, the fundamental particles get their rest masses from interaction with the Higgs field (all other mass contributions are ultimately just kinetic/potential energies which automatically scale the right way). So one might think that if you find a way to manipulate the Higgs field, you should be able to scale masses that way.
How to apply it to your specific requirements
A speed-up to one second per year would be a factor of about $3\cdot 10^8$, that is, you'd have to scale masses up by that amount. This would also scale down sizes by the same amount, so a human would shrink to about half a dozen nanometers. That is, you could easily put a complete city into a matchbox.
However there's a caveat: Your human would now weight about $10^{10}\,\rm kg$. I guess that would locally give quite strong gravitational fields (gravitation does not follow the scaling law; correspondingly quantizing it the standard way does not work). So quite possibly you'd not be able to achieve that large acceleration without adverse gravitational effects, unless you're also able to locally manipulate the gravitational constant so that also the gravitation plays nice with it. Note also that a strong gravitational field would add a slowdown counteracting your speedup; this is another reason to decrease it.
So in summary: You'd need to be able to manipulate the Higgs field to get the speedup (combined with a shrinking), and additionally to locally manipulate the gravitational constant (to avoid the gravitational effects of the increased masses). But if you can do both, you'll get a sped-up city in a matchbox.
Further caveats to the speed-up
The speed-up inevitably means that any radiation coming from outside will be seen as very low frequency in your town. That means you'll have to ensure sufficient thermal insulation in order to prevent your town from freezing. Similarly, any radiation coming from your town will be shifted up in energy; with one second per year, even visible light will turn into gamma radiation. So to protect yourself, you better surround that city with appropriate radiation shielding.
If you settle with less extreme speed-ups (say, just one day per second), you'll reduce the problems with the radiation from the city; however it will still be very hot when viewed from outside; better make that matchbox out of fireproof material.