How to best use GPUs

From: Itamar Kass (
Date: Thu Jun 25 2020 - 05:06:46 CDT


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 Kass, PhD.

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