Comments on: Gordon Bell Prize Awarded To Molecular Dynamics-Quantum Mechanics Mashup On “Frontier” Supercomputer https://www.nextplatform.com/2024/12/19/gordon-bell-prize-awarded-to-molecular-dynamics-quantum-mechanics-mashup-on-frontier-supercomputer/ In-depth coverage of high-end computing at large enterprises, supercomputing centers, hyperscale data centers, and public clouds. Fri, 10 Jan 2025 18:03:08 +0000 hourly 1 https://wordpress.org/?v=6.7.1 By: Tom Womack https://www.nextplatform.com/2024/12/19/gordon-bell-prize-awarded-to-molecular-dynamics-quantum-mechanics-mashup-on-frontier-supercomputer/#comment-243195 Mon, 23 Dec 2024 10:47:23 +0000 https://www.nextplatform.com/?p=145157#comment-243195 In reply to Hubert.

Anton 3 is extremely hard-wired to doing electrostatics, whilst this work is much more about subtle quantum interactions – their big trick is to avoid having to do a calculation for every possible subset of four electrons, instead you do it for every subset of three electrons and can store the whole interactions for a thousand electrons in 40GB of GPU memory.

I’ve only ever used quantum chemistry tools as an input into a separate optimiser, modelling the ligand as a quantum object while doing the protein surrounding it with constraints much more like a ball-and-stick model, and where what we were trying to do is fit experimental X-ray diffraction data; I left the company fifteen years ago but it’s still there at the website in my link.

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By: Hubert https://www.nextplatform.com/2024/12/19/gordon-bell-prize-awarded-to-molecular-dynamics-quantum-mechanics-mashup-on-frontier-supercomputer/#comment-243001 Sat, 21 Dec 2024 01:13:45 +0000 https://www.nextplatform.com/?p=145157#comment-243001 Glad to see the Gordon Bell Prize awarded to this Ab Initio (from first principles) bioMolecular Dynamics (AIMD) computational research. If I understand, the approach is based on a post-Hartree-Fock (HF) Schrödinger equation wave-function-based (WF) second-order Møller-Plesset (MP2) perturbation method, that would normally scale as (N⁵) with problem size. The 2 million electron case was then tackled through parallelization over GPUs with a third-order many body expansion (MBE3) fragmentation approach that improves scaling to (N), and a resolution-of-the-identity (RI) approximation that replaces expensive four-center integrals with reusable three-center versions, followed by Verlet symplectic integration over asynchronous steps (Figs. 2, 4, and 7).

To me, the clincher comes with the results (in bold text) at the top-right of page 10: the computation of one time step takes “1.55 ZettaFLOPs on 9,400 nodes” of Frontier, and that takes 25.6 minutes of wall time (1,540 seconds) as the supermachine executes just North of 1 ExaFLOP per second … that’s what I call putting a supercomputer through its paces (bravo!)! And from this, and the needs of 1-km resolution climate modeling, it is becoming increasingly clear that we need to develop and qualify FP64 ZettaFlopping supermachines quick (let’s not rest on our ExaFlopping laurels!)!

One lingering question (for me, as a non-expert) is whether the specialized architecture of Anton 3 ( https://www.nextplatform.com/2023/12/04/the-bespoke-supercomputing-architecture-that-stood-test-of-time/ ) could help with such biologically-oriented AIMD computation, or if it is aimed at a slightly different conceptualization of the underlying processes, with a differing field of applicability? Either way, this work is very impressive imho, congratulations to the Barca (down under) team for winning this presitigous award, and let’s get ZettaFlopping soon, please!

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