From: Ming Sun (msun_at_beamtx.com)
Date: Mon Feb 15 2021 - 07:15:00 CST
Hi All,
A follow-up of previous discussion on the NAMD performed performances. I’m wondering if anyone has done benchmark on NAMD3 on AWS p2 instances or another GPU workstation? What would be an optimal / okay number of CPU per GPU ? I am using NAMD2.14 these days. I did not see improvements switching from 4-GPU machine to an 8-GPU machine while the number of CPU does not increase, at least at my hand
Any thoughts on NAMD3/ 2.14 are greatly appreciated.
Thanks,
Ming
From: "Vermaas, Josh" <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>>
Date: Thursday, January 28, 2021 at 7:45 PM
To: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>, "Ropon-Palacios G." <biodano.geo_at_gmail.com<mailto:biodano.geo_at_gmail.com>>
Subject: Re: namd-l: Improve performance
For the best NAMD performance on a GPU, use NAMD 3. This blog from NVIDIA has been my goto for explaining the differences to folks that haven’t used NAMD 3 yet. https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!t0qj3lFBcdvpNQmDX-ncJjXBjvRhCU6N3PxAox6tPJy255RhbwUZMj34czWhJwpQBA$ <https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!tjYMkz_rYz0-mcygjKo9GeKdRm_0FZD8S4mIIgeJcpPHpSrKAvJF-wFdVk0GayNq_w$>
-Josh
From: <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of "Ropon-Palacios G." <biodano.geo_at_gmail.com<mailto:biodano.geo_at_gmail.com>>
Reply-To: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>, "Ropon-Palacios G." <biodano.geo_at_gmail.com<mailto:biodano.geo_at_gmail.com>>
Date: Thursday, January 28, 2021 at 7:18 PM
To: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>
Subject: namd-l: Improve performance
Dear namd users,
How can i improve namd2.14 performance on GPU?
I`m using namd2.14 for run membrane protein simulation, but namd only use nor more the 50% of GPU, as can I make to improve this performance.
For other hand, if during equilibration of protein-membrane is necessary keep water out membrane?
Thanks,
Best,
Geo.
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