From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Thu Jun 25 2020 - 11:10:51 CDT
Something else that I've done without paying attention is to run a CPU-only
NAMD binary and then wonder why GPUs weren't helping performance. What
build of NAMD does the top of your log report?
On Thu, Jun 25, 2020 at 6:53 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> 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 bandwidth.
> 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 <itamar.kass_at_gmail.com> wrote:
>> 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.
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
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