[gmx-users] pentium III vs Pentium IVs

[Erik Lindahl]

Lynne E. Bilston wrote:

> Hi all,
>
> I'm about to buy a small cluster of machines for running MD 
> calculations on. I intend (at this stage) to put linux on them.
>
> I was wondering if people had any benchmark data to compare the 
> pentium IV machines to pentium IIIs etc? My systems of interest are 
> quite large (lipid/ion channel systems). A colleague uses p4's with 
> RDRAM for heavy-duty fluids calculation and if I don't need too much 
> RAM per machine, they are quite cheap now. Is 128MB enough?
>
> Or whether I should go with a smaller number of dual processor 
> machines, or more single processor machines?
>
> Also, thoughts on various flavours of mpi and linux would be welcome. 
> I gather from various discussions here that LAM seems to be less 
> problematic than mpi-ch. 


Hi Lynne,

I would recommend AMD Athlon CPUs instead of Intel. They are just as 
fast, if not faster, and considerably cheaper. And, when you don't run 
Gromacs they will still be very fast since they have a really good 
"normal" floating-point unit in contrast to the Pentium4.

The only reason to go with Pentium4 is if you need double-precision in 
your MD calculations.

We've just been researching systems to update our local cluster in the 
group here at Stanford; per processor it can actually be cheaper to go 
with single-cpu systems, but I would still recommend dual-cpu boxes if 
you want to run in parallel since the scaling is much better withing 
each node (no ethernet communication involved).

Dual Pentium4 ("Xeon") boxes are insanely expensive, but the Athlon MP 
systems are reasonable!

Cheers,

Erik