From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Thu Mar 05 2020 - 11:18:09 CST
Since you already have a system in mind, you can compare the time it takes to perform a 10ps simulation with different setups.
> one or both gpu, number of cores
* With NAMD 2.13 comes a large improvement in dual gpu/single node performance and we observe almost linear scaling when going from 1 to 2 GPUs.
* 16core/GPU is sufficient, from our experience 6-8core/GPU is the lower limit.
* For GPU runs, hyperthreading should not increase affect performance.
> pemap/commap options
* check the output of nvidia-smi topo matrix - leaving cpu/gpu affinity as default should be fine.
On Thu, Mar 5, 2020 at 10:12 AM Stefano Guglielmo <stefano.guglielmo_at_unito.it<mailto:stefano.guglielmo_at_unito.it>> wrote:
Dear NAMD users,
I am using a workstation with an AMD Ryzen Threadripper 2990WX 32-Core Processor, 128 GB RAM and two RTX 2080 Ti cards with NVlink; I am here to ask for suggestions on what could be the "best" options to run a single simulation on a 200K atom system with NAMD 2.13 (one or both gpu, number of cores, hyperthreading or not, pemap/commap options...)
Thanks in advance for your time
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178
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