Molecular Dynamics

NVIDIA Ampere GPU Benchmarks AMBER 22

May 17, 2022

11 min read

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:

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.

Quick AMBER GPU Benchmark takeaways

Ampere GPUs (RTX 3090, RTX 3080 & A100) outperformed the Turing models (2080 Ti & RTX 6000) across the board. The A5000 competes alongside the RTX 6000.
For the larger simulations, such as STMV Production NPT 4fs, the A100 outperformed all others. It's here that the RTX A5000 did slightly better than the RTX 6000.
For smaller simulations, the RTX 3090 and RTX 3080 showed excellent performance, and in some cases, on par with the A100.
The A4000 performed closely to the RTX 3070 as to be expected
The A4500 looks to perform well. By comparison, it is roughly equivalent to the 3070. A tiny bit slower for small systems but faster for larger systems

Interested in getting faster results?
Learn more about the only AMBER Certified GPU Systems starting around $6,000

Exxact Workstation System Specs:

Make / Model	Supermicro AS -4124GS-TN
Nodes	1
Processor / Count	2x AMD EPYC 7552
Total Logical Cores	48
Memory	DDR4 512 GB
Storage	NVMe 3.84 TB
OS	Centos 7
CUDA Version	11.4
Amber	22

GPU Benchmark Overview

Benchmark	RTX A6000	RTX A5500	RTX A5000	RTX A4500	RTX A4000	A100 PCIe	A10	RTX 3090	RTX 3080	RTX 3070	RTX 6000
JAC Production NVE 4fs	1101.29	1061.73	1008.05	935.33	810	1199.22	895.05	1196.5	1101.24	950.17	1034.88
JAC Production NPT 4fs	1084.37	1042.13	992.14	911.08	803.02	1194.5	886.04	1157.76	1086.21	930.3	1004.03
JAC Production NVE 2fs	586.09	561.62	535.01	491.62	429.67	611.08	470.51	632.19	585.81	502.13	540.17
JAC Production NPT 2fs	560.05	535.28	505.58	469.85	412.73	610.09	455.36	595.28	557.6	479.15	515.86
FactorIX Production NVE 2fs	256.1	231.31	214.13	189.02	154.45	271.36	185.45	264.78	234.58	179.07	217.25
FactorIX Production NPT 2fs	241.63	215.41	206.78	181.35	150.12	252.87	180.45	248.65	217.5	170.09	206
Cellulose Production NVE 2fs	59.52	52.7	47.09	41.26	31.26	85.23	38.45	63.23	53.44	37.41	47.41
Cellulose Production NPT 2fs	55.5	49.88	45.71	39.48	30.34	77.98	36.72	58.3	49.69	35.75	45.24
STMV Production NPT 4fs	37.01	33.58	30.87	26.67	20.27	52.02	24.24	38.65	32.18	23.89	28.49
TRPCage GB 2fs	1166.26	1124.98	1235.49	1188.03	1244.75	1040.61	1096.59	1225.53	1332.27	1375.35	1189.25
Myoglobin GB 2fs	650.48	602.16	586.42	518.8	492.48	661.22	584.93	621.73	619.67	539.21	600.83
Nucleosome GB 2fs	20.37	15.23	15.6	13.47	11.02	29.66	14.49	21.08	17.72	12.76	16.81

AMBER 22 GPU Benchmark: JAC Production NVE 4fs

JAC_PRODUCTION_NVE_4FS_(1).png

AMBER 22 GPU Benchmark: JAC Production NPT 4fs

JAC_PRODUCTION_NPT_4FS_(1).png

AMBER 22 GPU Benchmark: JAC Production NVE 2fs

JAC_PRODUCTION_NVE_2FS_(1).png

AMBER 22 GPU Benchmark: JAC Production NPT 2fs

JAC_PRODUCTION_NPT_2FS_(1).png

AMBER 22 GPU Benchmark: FactorIX Production NVE and NPT 2fs

FACTORIX_PRODUCTION_NVE_2FS_(1).png

FACTORIX_PRODUCTION_NPT_2FS_(1).png

AMBER 22 GPU Benchmark: Cellulose Production NVE 2fs

CELLULOSE_PRODUCTION_NVE_2FS_(1).png

AMBER 22 GPU Benchmark: Cellulose Production NPT 2fs

CELLULOSE_PRODUCTION_NPT_2FS_(1).png

AMBER 22 GPU Benchmark: STMV Production NPT 4fs

STMV_PRODUCTION_NPT_4FS_(1).png

AMBER 22 GPU Benchmark: TRPCage GB 2fs

TRPCAGE_GB_2FS_(1).png

AMBER 22 GPU Benchmark: Myoglobin GB 2fs

MYOGLOBIN_GB_2FS_(1).png

AMBER 22 GPU Benchmark: Nucleosome GB 2fs

NUCLEOSOME_GB_2FS_(1).png

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, total 90,906 atoms. The larger cellulose system, 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?

If you’re not familiar with AMBER it refers to ‘Assisted Model Building with Energy Refinement‘, a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman’s group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields and is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Adrian Roitberg at 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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