Re: How to best use GPUs

From: Giacomo Fiorin (
Date: Thu Jun 25 2020 - 07:51:45 CDT

Hi, regardless of GPU use, there is nothing to gain (and often something to
lose) in running more threads than physical cores available. Using all the
"hardware" threads (which are 2x the number of cores in most CPUs) only
makes sense for codes that spend a lot of time waiting for data to be
loaded into the CPU, and are essentially processing a multitude of
*independent* tasks. This is not the case for NAMD. Also, try to further
decrease the number of threads, which are certainly competing for CPU-GPU

It may be helpful to know that the 3.0 alpha version may be more efficient
in the single-GPU setup by running on it exclusively:


On Thu, Jun 25, 2020 at 6:08 AM Itamar Kass <> wrote:

> Hi,
> I am using NAMD 2.13 on a single Linux machine with 32CPU (64 threads) and
> 4 NVIDIA TITAN Xp cards. I run a protein solvated in TIP3 water (total
> system size ~220K).
> I have tried to run with few flags:
> namd2 +p64 +setcpuaffinity +devices 0,1,2,3 MD004.conf
> namd2 +p64 +setcpuaffinity +idlepoll +devices 0,1,2,3, MD004.conf
> namd2 +p64 +idlepoll +devices 0,1,2,3, MD004.conf
> But in all cases, it seems that the GPUs do not contribute anything to the
> run (I look at the GPU load while running and I compared the run time to a
> run without GPUs).
> In addition, I set:
> *outputEnergies 5000*
> Thanks in advance,
> Itamar
> --
> -----
> Itamar Kass, PhD.

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD

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