Re: Slow performance over multi-core processor and CUDA build

From: Ashkan Shekaari (
Date: Tue Jul 28 2020 - 07:25:29 CDT

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" <> 
To: "namd-l" <> 
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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