AMBER Archive (2000)

Subject: Re: amber on AMDs cluster

From: David Konerding (dek_at_konerding.com)
Date: Wed Jun 14 2000 - 12:18:16 CDT

>#proc #nodes nonsetup %cpu commun.
> [s] on master [s]
>
>1 1 137 100 0.0
>2 2 98 95 1.8
>2 1 92 98 1.7
>4 4 59 85 3.3
>4 2 56 91 2.4
>6 6 48 74 3.7
>6 3 44 79 3.5
>8 8 53 56 5.7
>8 4 37 74 3.2
>10 10 38 69 4.8
>10 5 36 67 4.3
>12 12 35 66 4.7
>12 6 34 62 3.9
>14 14 33 57 4.5
>14 7 31 60 4.0
>16 8 29 56 3.9

>As you can see the scaling is not perfect but it is not so bad,
>especially up to 8 processors on 4 nodes.

If I read this properly, you're getting a scaling of 48% for the second node (from 137
to 92 seconds), are you sure that is "not too bad"?

>A few more details : PROWAT is Amber 4.1 benchmark: plastocyanin in water
>(11585 atoms) with cut=12.0. Sander was compiled with g77 2.95.2 and MPICH
>1.2.0, with the following options :
>
>-fomit-frame-pointer -malign-double -fcaller-saves -fno-f2c
>-march=pentiumpro -funix-intrinsics-hide -O6

I did some experimenting with the various compiler flags, the current
fastest I've found (using egcs-1.1.2) is
-O3 -m486 -malign-double -ffast-math -fno-strength-reduce

-fomit-frame-pointer slowed things down, while -fno-strength-reduce speeded
things up. However, egcs-1.1.2 differs from gcc 2.95.2. I was planning to
compare the two compilers some time soon.

Dave