Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX

From: Raman Preet Singh <>
Date: Mon, 9 Nov 2020 07:20:57 +0000

We have two workstations with octa core Ryzen processors. One workstation has a single NVIDIA GPU while the second has 3 NVIDIA GPUs. They seemed to work very well initially (8 CPU Ryzen cores + 1 GPU performance was higher than a 32 cores of Xeon E5 v2 processor processor for NAMD) but after a few months started hanging and showing a decrease in performance (but still better than 32 core Xeon E5 v2). This is the issue with both workstations after around 6-10 months. We often run simulations for several days at a stretch as required for typical MD simulations. I typically use Amber tools for analysis and Gromacs or NAMD for MD as we don't have Amber license.

Since you are looking at a relatively higher end processor family (Threadripper), things might work well. But do look at reviews on major online stores or post on Quora or Tom's. I have read reviews where AMD processors show problems due to heating but those not frequent reviews as people are content with low cost of AMD processors.


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From: Jordi Bujons <>
Sent: Sunday, November 8, 2020 11:50:17 PM
To: <>
Subject: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX


At our group we are considering buying a new machine equipped with one or
two 3080 or 3090 GPUs to run Amber 20. The computer store recommends to get
an AMD based computer, with a Ryzen 3960X CPU and a TRX40 motherboard that
supports the PCIe 4.0 bus present in Nvidia 3080/3090. I have seen several
comments on the list about the 3080 and 3090 GPUs, but does anybody has
experience with such a combination of CPU+GPU? Will Amber 20 take much
advantage of having PCIe 4.0 rather than PCIe 3.0?

Any comments will be appreciated.


Jordi Bujons, PhD
Dept. of Biological Chemistry (QB)
Institute of Advanced Chemistry of Catalonia (IQAC)
National Research Council of Spain (CSIC)
Address: Jordi Girona 18-26, 08034 Barcelona, Spain
Phone: <tel:%2B34%20934006100%20ext.%201291> +34 934006100 ext. 1291
FAX: <tel:%2B34%20932045904> +34 932045904

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Received on Sun Nov 08 2020 - 23:30:02 PST
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