From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jul 28 2020 - 07:36:02 CDT
I’d say don’t use hyperthreading in HPC in general, nothing special about GPUs. You can assign your tasks/threads to physical core only, e.g. using taskset, but determining the correct mapping can be tricky.
Bests
Norman Geist
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Ashkan Shekaari
Gesendet: Dienstag, 28. Juli 2020 14:25
An: namd-l <namd-l_at_ks.uiuc.edu>; Roshan Shrestha <roshanpra_at_gmail.com>
Betreff: Re: namd-l: Slow performance over multi-core processor and CUDA build
Dear Roshan,
DO NOT USE GPU along with cpu- hyperthreading
--
All the best,
Ashkan Shekaari,
Ph.D Candidate in Solid State Physics,
K. N. Toosi University of Technology,
Tehran, Iran
_____
From: "Roshan Shrestha" <roshanpra_at_gmail.com <mailto:roshanpra_at_gmail.com> >
To: "namd-l" <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> >
Sent: Tuesday, July 28, 2020 2:31:14 PM
Subject: namd-l: Slow performance over multi-core processor and CUDA build
Hi everyone,
I have a system with i7 9700k 8 core processor and rtx 2070 Nvidia GPU. My namd is cuda build; but I am extremely disappointed with its performance as it gives me like 0.21 ns/ day while with the same system gromacs give me the performance of more than 300 ns/day. I really can't fathom what's the issue here as namd2 is using the GPU when I see the GPU processes using nvidia-smi. The command I typically use to run the simulation is:
namd2 +p8 .... .conf | tee .... .log
Do I need to specify anything extra in the command? or in my configuration file. Thanks.
With best regards
--
Roshan Shrestha
M.Sc (Physics)
Central Department of Physics, Tribhuvan University
Kathmandu, Nepal
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