Re: AMBER: Implicit precision in sander vs architecture

From: Teletchéa Stéphane <>
Date: 20 Oct 2003 10:45:04 +0200

Le ven 17/10/2003 à 19:05, David E. Konerding a écrit :
> Yong Duan wrote:
> Yong is confusing the meaning of 64-bit as it is conventionally used in
> the marketing literature with the actual
> technical details of how integer data is implemented on digital hardware.
> 64-bit is normally used these days to describe the size of the address
> register and the amount of directly addressable memory.
> It's not as relevant when applied to the size of the arithmetical,
> integer, or floating point registers. For example, my
> 32-bit Intel PC can only address memory using a 32-bit range, but it
> natively implements a 64-bit integer and an 80-bit floating
> point type. No extra "work" or "passes" are being done when I add two
> 64-bit integers or multiple to 80-bit FP ones (on my hardware).
> Dave

This is actually exactly what i mean by precision :

From what i know, there are many different 'internal' precision for x86
32 bits for integer,
80 bits for floating point,
128 for SSE, ...

So that's why i'm surprised byt he different behaviour on different

I understand that :
- different architectures have different implicit precision, but what is
employed for each architecture ? Does it influence the quality of the
dynamics ?
- running locally or over a network induces another variables that
implies another source of divergence, has it been quantified, what is
best ?
- 32 bits machines does not have only 32 bits precision (for instance
80bits for floating point operations) but do 64 bits machines have
64bits precision for integer of float (or a bigger precision for
floating point ?)

Last : AMBER has been developped on 64bits architectures and then to
32bits if i understand correctly. Maybe amber has been 'tuned' to
reproduce correctly dynamics simulation, taking explicitly the roundoff
error in the code. I saw papers for T3E for example, many contributions
from SGI, ... Has something similar been done for 32-bits processors ?

Could this be the difference between the architectures ?

Again, i remember you my point : i have the 'impression' that long
dynamics run are more 'stable' (less conformational space is explored)
on 64-bits machines than on 32-bits machines. One could say on the
opposite 32-bits machines are exploring more conformational space ...

I hope i'm clearer now, there are two options :
1 - implicit precision differences induces errors that lead to
divergence but it has been more controlled on 64-bits machines (intrisic
robustness in precision)
2 - AMBER has been more developped for 64-bits machines, so the results
have been more correctly examined than for 32-bits machines.

Thanks a lot for your answers.

Stéphane Teletchéa


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Received on Mon Oct 20 2003 - 09:53:00 PDT
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