Re: Optimizing heatbugs in Obj-C

[Jan Kreft]

Paul,

On Mon, 10 Apr 2000, Paul E. Johnson wrote:

> I found a study of Marcus's fast code for Java Heatbugs to be very
> instructive and if any of you have comparable tips about writing faster
> models, I would be glad to hear them. I guess I've said that before

from my own experience, I would say that the model design and the
algorithms used are paramount. My first version of BacSim took 3 days to
compute what the current version does in 10 min.

What did I change? The main idea was to separate the two different
processes in the model, diffusion and growth, on the basis of their
different time-scale. That is, you decouple the two processes, keeping
growth in a frozen state while simulating diffusion, and diffusion in a
pseudo-steady state while simulating growth.

Then, you are free to choose the fastest algorithm known to simulate
diffusion, and it makes a huge difference. Ironically, the faster process
takes most of the time of the CPU. Actually, I didn't choose the fastest
algorithm but the fastest that I felt I could fully understand. An expert
in the field could use a sophisticated adaptive grid that would be fine
only were the gradients are steep. I guess that would speed things up
10-fold or more.

In general, there is a trade-off between speed and memory-use. Fast
algorithms typically use a lot of memory to solve a system of equations
simultaneously while slow algorithms are iterative and hence require less
memory. On modern machines, there's always enough memory.

Dunno whether that applies to your sort of models at all, but hope someone
finds this useful.

Cheers, Jan.

Dr. Jan-Ulrich Kreft                    Phone  +44 (0)29 20875278
Cardiff School of Biosciences           Fax    +44 (0)29 20874305
Cardiff University                      E-mail address@hidden
PO Box 915, Cardiff CF10 3TL, UK


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