Re: [AMBER-Developers] IPS in pmemd

From: Ross Walker <>
Date: Thu, 19 Jul 2012 20:09:15 -0700

Hi Dave,

> 1. Thinking behind allowing only IPS=1? IPS=2 would seem to be the
> "sweet
> spot", but maybe performance is really not much different between these
> two.
> Have people checked on this?

Romelia is in charge of the ips implementation so will be able to answer you
in more detail. I believe the choice of only having ips=1 was to avoid
having an if statement inside the nonbond loop. It should be pretty easy to
support ips=2 or 3, I think the main issue at the time was just lack of
resources (= people) to actually test the impact of having that on various
different architectures, with different compilers etc. I didn't think there
was any down side to having ips for VDW but if you think there is an
appreciable advantage to having ips=2 we could add that. Certainly the
individual cutoff for vdw and eel are in the code already so it should be
possible to have this without too much of a hit.

> 2. How well does it scale, and how much has it been tested? I'm seeing
> failures on BlueGene at 128 threads (not crazy results, but marked lack
> of
> energy conservation in NVE), compared to identical input (JAC
> benchmark) but
> using 32 or 64 threads. I'll debug as I have time (although am very
> busy for
> the next month), but reports from others on experience at high
> processor
> counts would be helpful.

Romelia is going to have to provide the details here. My understanding was
she'd tested this on large processor counts and looked at scaling etc as
well as making sure the results matched. It has definitely NOT been tested
on any bluegene system. Do you know if it shows this same issue on other
systems? - Is it just isolated to ips? - I don't think anybody has been
testing high processor counts for pmemd in general for a while. :-S

I note the manual does not list the IPS restrictions for pmemd. :-( I'll get
that updated.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Thu Jul 19 2012 - 20:30:02 PDT
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