Re: Re: CPU vs GPU Question

From: Bennion, Brian (
Date: Wed Dec 09 2020 - 23:35:11 CST

Thank you for the info. It isn't me that is curious about a single machine timings, it was Kelly.
However, it has sparked a light to go back to see if I can get namd3 running on some of our newer amd and intel clusters. in the past the interconnect just never worked well with namd.


From: Rafael Bernardi <>
Sent: Wednesday, December 9, 2020 9:26 PM
To: <>; Gumbart, JC <>; McGuire, Kelly <>
Cc: Bennion, Brian <>
Subject: Re: namd-l: Re: CPU vs GPU Question

Hello Brian,

If what you want is a node to run NAMD3 don’t worry so much about buying CPUs. To be honest I would just buy any AMD EPYC because of the motherboards with PCIe 4.0 support.

I just got a machine with 2x EPYC 7302, so 32 cores in total. I was running some benchmarks today, and using only 2 CPU cores, 2 RTX 3090 with NVLINK, I can get:

STMV (1.06M atoms)

4fs timestep, NVE, and Amber-like parameters (8A cutoff, etc) = 76 ns/day

4fs timestep, NPT, and Amber-like parameters (8A cutoff, etc) = 52 ns/day

4fs timestep, NPT, with regular (safe) parameters (12A cutoff, etc) = 30 ns/day

2fs timestep, NPT, with regular (safe) parameters (12A cutoff, etc) = 16 ns/day

I hope these numbers give you an idea about what you can do with a new local machine. The other nice thing is that you can have a machine with 4x 3090s, installed as 2 pairs of NVLINKed 3090s. That way you can run two simulations at these performances at the same time.

Also, I wouldn’t use any of the Amber-like parameters with CHARMM force field in a production dynamics. That was done just as good way to compare the speed of NAMD vs AMBER (software). If you want to read more about that JC Gumbart wrote a great paper testing these parameters for a membrane system--_000_SJ0PR09MB67347DAE886482B8FA8DBFC8F6CB0SJ0PR09MB6734namp_--

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