Re: [AMBER-Developers] GPU Code Update

From: Jason Swails <>
Date: Sun, 12 Jan 2014 11:08:13 -0500

On Sun, Jan 12, 2014 at 12:56 AM, Ross Walker <> wrote:

> Hi Peeps,
> The new GPU-Tachyon code has now been merged into master - I.e. the trunk
> now contains the GPU Tachyon code. Thus from now on if you are editing
> PMEMD code
> (particularly GPU code) please edit the master branch and NOT gpu-tachyon.
> Scott you may want to make a new branch from master for the TI code and we
> can merge it in later or you can work directly in the master - your choice.
> GTX-Titan is now the gold standard for saved output now.
> The following are the new features of this code:
> 1) 25 to 30% speed improvement for single GPU
> 2) Peer to Peer support for parallel - gives MUCH better multi GPU
> performance (up to 200ns/day for JAC NVE on 2 GTX-Titans) BUT it very much
> depends on your motherboard chipset, GPU slot locations etc. - This is
> work in progress to make this simpler.
> 3) Monte Carlo Barostat Support (although currently broken, see below)

Indeed, when I tried running the MC barostat in the gpu-tachyon branch
before you merged it, I found that the energies exploded and the simulation
ended with the message that the nonbonded cells needed to be
recalculated. I'm wondering if the volume fluctuations in the MC barostat
are much larger than Scott expected volume fluctuations to be... Hopefully
this is an easy fix.

4) ScaledMD support
> 5) Extra points on multi GPUs (although currently broken, see below)
> 6) Jarzynski support
> 7) Fixes for NMR restraints on multi GPUs. (although currently issues -
> see below)
> 8) Support for SM1.3 hardware is now deprecated.
> 9) A potential issue with inaccuracy in long NPT runs due to cumulative
> roundoff error on both CPU and GPU (which has been there since before the
> ark) has been fixed.
> 10) Improved skinnb error message for massively shrinking box sizes during
> NPT.
> 11) aMD support for both raising minima and lowers barriers.
> 12) Multi-D REMD (Adrian and Jason please clarify support here?)

Correct, supporting both T-REMD and H-REMD.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Sun Jan 12 2014 - 08:30:02 PST
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