Re: amber-developers: Altivec wrapper for PMEMD

From: Robert Duke <>
Date: Tue, 15 Jun 2004 12:47:11 -0700

Mengjuei -
Thanks much for working on this apple/pmemd stuff. I have no apple
resources whatsoever, so I am going to stay out of the fray; please just
thoroughly test before checkin. I would also recommend that maybe we make
the conditional something like APPLE_VEC (or something else that
indicates the scope of the usage) instead of vecLib.
Regards - Bob Duke

----- Original Message -----
From: "Mengjuei Hsieh" <>
To: <>
Sent: Tuesday, June 15, 2004 4:40 AM
Subject: amber-developers: Altivec wrapper for PMEMD

> Hi,
> Although there are few people playing AMBER on Macintosh here, this is
> for your information.
> I attached a wrapper for vrsqrtf (1/r^.5) in altivec (available in Apple
> G4/G5 machine) on MacOS X. You can call vrsqrtd_wrapper(input array,
> array, number of item in the array) from PMEMD. This wrapper accepts
> precision input and output while altivec is still thinking in single
> precision, so beware of those accuracy issues.
> And the patch file for PMEMD as a minimal modification (just an added-in
> modification, it won't delete any line or modify any loop in the code).
> Installation:
> 1. You need to compile an object file vector.o first
> cp vector.c amber8/src/pmemd/
> cd amber8/src/pmemd/
> gcc -c -O3 -fast -funroll-loops -mcpu=G5 -faltivec vector.c
> 2. Patch short_ene_bigcache_opt.f90, this command also make a backup.
> cd amber8/src/pmemd/src
> patch -b -p0 < patch.foraltivec.txt
> 3. Use the config.h.nopar attached here and make a new binary
> cp config.h.nopar amber8/src/pmemd/config.h
> cd amber8/src/pmemd/
> make clean; make
> Benchmark:
> I don't have any G5 machine around at the time I wrote this new
> However it boosts my powerbook g4-400 (yes, it's damned slow) on jac for
> about 20%.
> Best,
> --
> Mengjuei Hsieh, Luo group, Molecular Biology and Biochemistry,
> California Irvine. Tel: 49562, Address: 3144 Natural Science I building,
> UCI, Irvine CA 92697-3900. Group Homepage:
Received on Wed Apr 05 2006 - 23:50:01 PDT
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