From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Dec 10 2020 - 19:27:16 CST
Thanks for all of the responses, very helpful information! Rafael, we have two 2080ti's and are wondering if you thinkg using NVLINK with them would produce similar results with NAMD3 that you show here...?
Dr. Kelly L. McGuire
PhD Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
________________________________
From: Rafael Bernardi <rcbernardi_at_auburn.edu>
Sent: Wednesday, December 9, 2020 10:36 PM
To: Bennion, Brian <bennion1_at_llnl.gov>; namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Gumbart, JC <gumbart_at_physics.gatech.edu>; McGuire, Kelly <mcg05004_at_byui.edu>
Subject: Re: namd-l: Re: CPU vs GPU Question
Sorry about the mistake.
……………………………………………………………………...
Rafael C. Bernardi
Biophysics Cluster - Department of Physics at Auburn University
NIH Center for Macromolecular Modeling & Bioinformatics
rcbernardi_at_auburn.edu<mailto:rcbernardi_at_auburn.edu>
rcbernardi_at_ks.uiuc.edu<mailto:rcbernardi_at_ks.uiuc.edu>
www.ks.uiuc.edu/~rcbernardi<http://www.ks.uiuc.edu/~rcbernardi>
+1 (334) 844-4393
From: "Bennion, Brian" <bennion1_at_llnl.gov>
Date: Wednesday, December 9, 2020 at 11:35 PM
To: Rafael Bernardi <rcbernardi_at_auburn.edu>, "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, JC Gumbart <gumbart_at_physics.gatech.edu>, "McGuire, Kelly" <mcg05004_at_byui.edu>
Subject: Re: namd-l: Re: CPU vs GPU Question
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.
brian
________________________________
From: Rafael Bernardi <rcbernardi_at_auburn.edu>
Sent: Wednesday, December 9, 2020 9:26 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Gumbart, JC <gumbart_at_physics.gatech.edu>; McGuire, Kelly <mcg05004_at_byui.edu>
Cc: Bennion, Brian <bennion1_at_llnl.gov>
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_BYAPR01MB42477060A2E5129AB107CCD2FFCA0BYAPR01MB4247prod_--
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