NVIDIA GPU Benchmarks AMBER 22

Updated: 03/21/2023 > [NEW] NVIDIA RTX 6000 Ada Generation Benchmarks

Updated: 02/07/2023 > [NEW] NVIDIA H100 (PCIe)and RTX 4070 Ti AMBER Benchmarks

Updated: 10/18/2022 > [NEW] NVIDIA RTX 4090 AMBER Benchmarks

Last Update: 06/23/2022 > Benchmarks Uploaded

AMBER 22 GPU Benchmarks for Molecular Dynamics with NVIDIA Professional and Data Center GPUs

The following Amber 22 Benchmarks were performed on an Exxact AMBER Certified MD System using the AMBER 22 Benchmark Suite with the following GPUs:

• NVIDIA H100 (PCIe) [NEW]
• NVIDIA GeForce RTX 4090**
• NVIDIA GeForce RTX 4070 Ti** [NEW]
• NVIDIA GeForce RTX 3090**
• NVIDIA GeForce RTX 3080**
• NVIDIA GeForce RTX 3070**
• NVIDIA A100 (PCIe)
• NVIDIA A10
• RTX 6000 Ada [NEW]
• RTX A6000
• RTX A5500
• RTX A5000
• RTX A4500
• RTX A4000

*All benchmarks were performed using a single GPU configuration using Amber 22 Update 1 & AmberTools 22 Update 1. NVIDIA CUDA 11.4 was also used for these benchmarks.

**NVIDIA GeForce RTX GPUs were tested on an Exxact workstation and can have a maximum of a 2-way configuration. All other NVIDIA Professional GPUs are tested in an Exxact server and support 8-way GPU configuration.
***Since AMBER computations are only performed by GPUs via CUDA, the variation between CPUs from workstation and server systems should have little effect on comparisons between benchmarks.

Quick AMBER GPU Benchmark takeaways

• NVIDIA Ada Lovelace GPUs (RTX 4090, RTX 6000 Ada, RTX 4070Ti) outperform all Ampere models (A100, RTX 3090, RTX 3080) by a long shot.
  • NVIDIA RTX 4090 is a definite winner as the single most powerful GPU in our tests.
  • RTX 6000 Ada has the same GPU dies as 4090. Built for peak reliability, the RTX 6000 Ada is a hair behind in performance.
  • The upgrade to an RTX 4070Ti shows considerable performance gain from the RTX 3090
• NVIDIA H100 is on par as 3rd most powerful (behind the RTX 4090 and RTX 6000 Ada) winning in only a couple of tests. However, the H100 offers far more scalability due to its data center nature! Leverage up to 8x NVIDIA H100s in a server or 4x in a workstation for unparalleled performance, something you cannot do with the 4090.
• For the larger simulations, such as STMV Production NPT 4fs, the H100's larger memory capacity, and the RTX 4090's higher clock speed pulls away from the others.
• For smaller simulations, the RTX 4070Ti showed excellent performance, a leg up on even the NVIDIA A100.

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Exxact Test Bench System Specs:

GPU Benchmark Overview

AMBER 22 GPU Benchmark: JAC Production NVE 4fs

AMBER 22 GPU Benchmark: JAC Production NPT 4fs

AMBER 22 GPU Benchmark: JAC Production NVE 2fs

AMBER 22 GPU Benchmark: JAC Production NPT 2fs

AMBER 22 GPU Benchmark: FactorIX Production NVE 2fs

AMBER 22 GPU Benchmark: FactorIX Production NPT 2fs

AMBER 22 GPU Benchmark: Cellulose Production NVE 2fs

AMBER 22 GPU Benchmark: Cellulose Production NPT 2fs

AMBER 22 GPU Benchmark: STMV Production NPT 4fs

AMBER 22 GPU Benchmark: TRPCage GB 2fs

AMBER 22 GPU Benchmark: Myoglobin GB 2fs

AMBER 22 GPU Benchmark: Nucleosome GB 2fs

Note about AMBER Benchmarks (From Dave Cerutti)

We take as benchmarks four periodic systems spanning a range of system sizes and compositions. The smallest Dihydrofolate Reductase (DHFR) case is a 159-residue protein in water, weighing in at 23,588 atoms. Next, from the human blood clotting system, Factor IX is a 379-residue protein also in a box of water, totaling 90,906 atoms. The larger cellulose system, with 408,609 atoms, has a greater content of macromolecules in it: the repeating sugar polymer constitutes roughly a sixth of the atoms in the system. Finally, the very large simulation of satellite tobacco mosaic virus (STMV), a gargantuan 1,067,095 atom system, also has an appreciable macromolecule content but is otherwise another collection of proteins in water. (source http://ambermd.org/GPUPerformance.php)

What is AMBER Molecular Dynamics Package?

AMBER is a molecular dynamics software package that simulates molecular mechanical force fields. AMBER (Assisted Model Building with Energy Refinement) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman’s group at the University of California, San Francisco. The AMBER MD software package is maintained by active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Adrian Roitberg at the University of Florida, Ken Merz at Michigan State University, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals.

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