Molecular Dynamics

NVIDIA GPU Benchmarks AMBER 22

October 18, 2022
9 min read
EXX-Blog-NVIDIA-Ampere-Benchmark-for-Amber22.jpg
Updated: 10/18/2022 > [NEW] NVIDIA RTX 4090 AMBER Benchmarks
Last Update: 06/23/2022

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

    • NVIDIA Ada Lovelace GPUs (RTX 4090) outperformed all Ampere models (A100, RTX 3090, RTX 3080) by a long shot. We are excited to see how future Ada Lovelace GPUs (RTX 6000 Ada, RTX 4080) as well as NVIDIA's new data center Hopper GPU (H100) releasing 2023.
    • NVIDIA 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

512GB DDR4

Storage

2.84TB NVMe SSD

OS

Centos 7

CUDA Version

11.4

AMBER Version

22

GPU Benchmark Overview

Benchmark

RTX 4090

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

1659.42

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

1618.45

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

883.23

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

842.69

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

466.44

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

433.24

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

129.63

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

119.04

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

78.90

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

1482.22

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

929.62

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

36.90

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

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.


Have any questions?
Contact Exxact Today


EXX-Blog-NVIDIA-Ampere-Benchmark-for-Amber22.jpg
Molecular Dynamics

NVIDIA GPU Benchmarks AMBER 22

October 18, 20229 min read
Updated: 10/18/2022 > [NEW] NVIDIA RTX 4090 AMBER Benchmarks
Last Update: 06/23/2022

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

    • NVIDIA Ada Lovelace GPUs (RTX 4090) outperformed all Ampere models (A100, RTX 3090, RTX 3080) by a long shot. We are excited to see how future Ada Lovelace GPUs (RTX 6000 Ada, RTX 4080) as well as NVIDIA's new data center Hopper GPU (H100) releasing 2023.
    • NVIDIA 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

512GB DDR4

Storage

2.84TB NVMe SSD

OS

Centos 7

CUDA Version

11.4

AMBER Version

22

GPU Benchmark Overview

Benchmark

RTX 4090

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

1659.42

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

1618.45

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

883.23

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

842.69

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

466.44

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

433.24

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

129.63

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

119.04

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

78.90

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

1482.22

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

929.62

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

36.90

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

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.


Have any questions?
Contact Exxact Today