COVID Moonshot on CPUs?

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COVID Moonshot on CPUs?

Postby JimF » Wed Aug 26, 2020 2:10 am

Insofar as I can see, all of the COVID Moonshot "small molecule inhibitors" are being studied with the GPUs (Core 22), mainly from the Chodera lab. Is any part of COVID Moonshot being done on CPUs?

That is, I see references to COVID work on the CPUs, so is that being done seperately from Moonshot, or are they a part of it too?
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Re: COVID Moonshot on CPUs?

Postby bruce » Wed Aug 26, 2020 7:34 am

The Moonshot research is fundamentally quite different than traditional folding projects. There has been a lot of development work on FAHCore_22 using custom analysis methods in OpenMM on a GPU so the critical parts of the research currently runs only on GPUs.

The COVID projects that use FAHCore_a7 (on a CPU) do provide a lot of supporting information so don't sell yourself short if you have only CPU hardware.
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Re: COVID Moonshot on CPUs?

Postby JimF » Wed Aug 26, 2020 7:46 am

Thanks. I am perfectly happy folding on CPUs quite apart from Moonshot. I ask just because "small molecules" usually implies CPU to me, so I was not sure how they were dividing that up.
But I have two Ryzen 3950Xs on FAH, and they can do other COVID or anything else. The cancer, etc. is fine with me. Core A8 should really make them fly.
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Re: COVID Moonshot on CPUs?

Postby puuteknikko » Wed Aug 26, 2020 3:57 pm

JimF wrote:Thanks. I am perfectly happy folding on CPUs quite apart from Moonshot. I ask just because "small molecules" usually implies CPU to me, so I was not sure how they were dividing that up.
But I have two Ryzen 3950Xs on FAH, and they can do other COVID or anything else. The cancer, etc. is fine with me. Core A8 should really make them fly.

I really hope A8 is out in the public rather sooner than later. It could make a nice boost in the output as there's a lot of proper AVX2 capable hardware out there.
Ryzen 3900X, 12c/24t @ 3.8GHz
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Re: COVID Moonshot on CPUs?

Postby JimF » Wed Aug 26, 2020 4:42 pm

puuteknikko wrote:I really hope A8 is out in the public rather sooner than later. It could make a nice boost in the output as there's a lot of proper AVX2 capable hardware out there.

I am getting 650 k on P14802 now (Ubuntu 18.04.5). But 900 k will be even nicer.
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Re: COVID Moonshot on CPUs?

Postby puuteknikko » Wed Aug 26, 2020 9:13 pm

Nice figures there. I'm getting around 330k for 14802 on my system, the beta core gives around 450k for 16810.
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Re: COVID Moonshot on CPUs?

Postby JohnChodera » Thu Aug 27, 2020 1:38 am

> Insofar as I can see, all of the COVID Moonshot "small molecule inhibitors" are being studied with the GPUs (Core 22), mainly from the Chodera lab. Is any part of COVID Moonshot being done on CPUs?

The initial phase was all done with the gromacs a7 CPU core (by the Voelz lab) to prioritize hits for synthesis using absolute alchemical free energy calculations. Right now, we're using GPUs with core22 to run relative free energy calculations. It's possible we will eventually split those calculations into small molecule+protein on the GPU and small molecule in solvent on the CPU, but that will likely not come for at least another month if we go that route.

> I really hope A8 is out in the public rather sooner than later. It could make a nice boost in the output as there's a lot of proper AVX2 capable hardware out there.

It's being tested right now! Hopefully will launch soon!

Thanks so much for your support!

~ John Chodera // MSKCC
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