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

From: Charo del Genio <>
Date: Fri, 13 Nov 2020 12:17:28 +0000

On 11/11/2020 13:47, Jordi Bujons wrote:
> Hello,
> Thanks for the comments. I guess that AMD Ryzen Threadripper and EPYC CPUs
> are quite similar, so that similar performance for the GPU can be expected.
> However, I read about some issues with these CPUs, like the RDRAND bug (
> estroyed-my-weekend/ ) or some problems to boot linux (
> Zen2MCE ). The RDRAND bug is also mentioned in the Release Notes of Gromacs
> 2020.4
> (
> ml ):
> "On AMD Ryzen 3000 series CPUs, the hardware random number generator
> (RDRAND) can behave incorrectly, always returning -1 (0xFFFFFFFF). When this
> hardware bug is detected at runtime, GROMACS will switch to its
> software-based pseudo-random number generator instead."
> I wonder if this might also affect AMBER, or if AMD has already solved this
> bug and it is not a problem now. Do you know anything about this?
> Jordi

Hi Jordi,
        I realized I forgot to answer back after my last email. In short, no, on our cluster we don't have any special options. We're running RHEL8, and the latest AMD processors should be supported out of
the box from RHEL 7.6.6. Alternatively, if you are going to be the only user of your machine, or if the only users are going to be just you and your immediate group, I would suggest you install
Gentoo, which, as a distribution, allows you easy, complete and fine-tuned control on everything.

Finally, about the RDRAND bug, AMD released updates for their motherboard BIOSes and for the CPU microcodes, so that's solved. And also, frankly, I wouldn't trust HW RNGs for other reasons, including
the existence of backdoors within them, so probably you should just disable the RDRAND support anyway.



Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
Design Hub
Coventry University Technology Park
Coventry CV1 5FB
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Received on Fri Nov 13 2020 - 04:30:03 PST
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