Re: NAMD on 24 threads

From: Ashkan Shekaari (
Date: Mon Jul 27 2020 - 07:03:54 CDT

Dear Asma,

Are you using gpu along with cpu hyperthreading?
If so, you will not have speed-up. Therefore,
0- Change to linux os.
1- Turn off cpu-hyperthreading.
2- Download and install the latest cuda version of namd, not the multicore one.

All the best, 
Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "Asmi Mahmood" <> 
To: "namd-l" <> 
Sent: Monday, July 27, 2020 1:36:28 PM 
Subject: namd-l: NAMD on 24 threads 
I need some help in optimizing my system efficiency for Simulation. Previously i was running NAMD on system with 4 processor on windows 10 and get 10 ns results in 10 days. Now as i have upgraded my system to dual processor each with 12 core and 12 threads (total 24 processor) with NVIDIA quadro fx 580 i was expecting a greater efficiency but still not getting desirable results as 10 ns is taking 5 days. It is to mention that i am using OS window 7 on my upgraded system and NAMD 2.13 multicore 64 bit.. 
what is reason of so low speed on 24 processors? 
In addition, i am planing to upgrade OS to linux and wants use CUDA environment if can be done on my system. Please guide me with this GPU card can i use CUDA as it supports CUDA 1.1 (as in its specifications). If yes which NAMD version should i use. 
Asma Tariq 

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