NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark namd.

Project Site

ks.uiuc.edu

Test Created

19 September 2018

Last Updated

28 August 2020

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

3 Seconds

Average Run Time

5 Minutes, 50 Seconds

Accolades

40k+ Downloads

Supported Platforms

Supported Architectures

x86_64

* Data based on those opting to upload their test results to OpenBenchmarking.org and users enabling the opt-in anonymous statistics reporting while running benchmarks from an Internet-connected platform.
Data current as of Mon, 18 Jan 2021 20:57:30 GMT.

Revision History

pts/namd-1.2.1 [View Source] Fri, 28 Aug 2020 06:28:19 GMT
Fix checksum on NAMD 2.14 Linux build as apparently it changed upstream.

pts/namd-1.2.0 [View Source] Thu, 20 Aug 2020 10:53:15 GMT
Update against new upstream NAMD 2.14 release.

pts/namd-1.1.0 [View Source] Sat, 29 Feb 2020 08:14:38 GMT
Overdue been meaning to bump upstream from beta to final 2.13.

pts/namd-1.0.2 [View Source] Tue, 15 Oct 2019 17:14:19 GMT
Add macOS support.

pts/namd-1.0.1 [View Source] Thu, 17 Jan 2019 11:31:07 GMT
Add Windows support.

pts/namd-1.0.0 [View Source] Wed, 19 Sep 2018 13:38:38 GMT
Initial commit finally of NAMD benchmark...

Suites Using This Test

Multi-Core

CPU Massive

Server CPU Tests

Molecular Dynamics

Scientific Computing

HPC - High Performance Computing

Performance Metrics

Analyze Test Configuration:

NAMD 2.14

ATPase Simulation - 327,506 Atoms

OpenBenchmarking.org metrics for this test profile configuration based on 905 public results since 20 August 2020 with the latest data as of 17 January 2021.

Below is an overview of the generalized performance for components where there is sufficient statistically significant data based upon user-uploaded results. It is important to keep in mind particularly in the Linux/open-source space there can be vastly different OS configurations, with this overview intended to offer just general guidance as to the performance expectations.

Component

Percentile Rank

# Matching Public Results

days/ns (Average)

2 x AMD EPYC 7742 64-Core

100th

0.27

2 x AMD EPYC 7702 64-Core

99th

0.29

2 x Intel Xeon Platinum 8280

98th

0.37 ^{+/- 0.01}

AMD Ryzen Threadripper 3990X 64-Core

97th

0.42 ^{+/- 0.02}

AMD EPYC 7742 64-Core

96th

0.44 ^{+/- 0.03}

2 x AMD EPYC 7601 32-Core

95th

0.45 ^{+/- 0.04}

2 x AMD EPYC 7F72 24-Core

95th

0.45

AMD EPYC 7702 64-Core

93rd

0.48 ^{+/- 0.02}

AMD EPYC 7662 64-Core

93rd

0.49 ^{+/- 0.01}

AMD EPYC 7642 48-Core

91st

0.57

AMD EPYC 7552 48-Core

90th

0.58

AMD Ryzen Threadripper 3970X 32-Core

89th

0.59 ^{+/- 0.03}

2 x Intel Xeon Gold 5220R

88th

0.63 ^{+/- 0.02}

AMD EPYC 7542 32-Core

87th

0.72

AMD Ryzen Threadripper 3960X 24-Core

87th

0.74 ^{+/- 0.03}

2 x AMD EPYC 7282 16-Core

86th

0.76

AMD EPYC 7502 32-Core

85th

0.78

AMD EPYC 7502P 32-Core

84th

0.78

AMD EPYC 7532 32-Core

84th

0.79

AMD Ryzen Threadripper 2990WX 32-Core

83rd

0.79 ^{+/- 0.01}

AMD EPYC 7452 32-Core

82nd

0.85

AMD EPYC 7F72 24-Core

81st

0.86 ^{+/- 0.01}

AMD EPYC 7402P 24-Core

79th

0.94

2 x AMD EPYC 7272 12-Core

78th

0.95

AMD EPYC 7601 32-Core

78th

0.97

Intel Core i9-10980XE

76th

0.99 ^{+/- 0.02}

Intel Core i9-7980XE

76th

0.99

Mid-Tier

75th

> 1.07

AMD Ryzen 9 5950X 16-Core

75th

1.08 ^{+/- 0.01}

AMD Ryzen 9 3950X 16-Core

72nd

1.14 ^{+/- 0.03}

AMD EPYC 7F52 16-Core

71st

1.15 ^{+/- 0.01}

AMD EPYC 7352 24-Core

71st

1.15

AMD Ryzen Threadripper 2970WX 24-Core

70th

1.17 ^{+/- 0.03}

Intel Xeon Gold 6226R

69th

1.18 ^{+/- 0.03}

Intel Core i9-10900K

67th

1.24 ^{+/- 0.03}

2 x AMD EPYC 7262 8-Core

65th

1.28

AMD Ryzen 9 5900X 12-Core

63rd

1.29 ^{+/- 0.01}

AMD Ryzen Threadripper 2950X 16-Core

61st

1.31 ^{+/- 0.02}

AMD EPYC 7302P 16-Core

60th

1.35

2 x AMD EPYC 7252 8-Core

59th

1.37

AMD EPYC 7282 16-Core

58th

1.47

AMD Ryzen 9 3900XT 12-Core

56th

1.49 ^{+/- 0.09}

Intel Xeon Gold 5218

55th

1.52

AMD Ryzen 9 3900X 12-Core

54th

1.52 ^{+/- 0.04}

Intel Xeon Silver 4216

53rd

1.56 ^{+/- 0.04}

Intel Core i9-7960X

53rd

1.56

Intel Core i7-7900X

53rd

1.60

Intel Xeon Silver 4214R

51st

1.74

Intel Core i9-9900KS

51st

1.75 ^{+/- 0.07}

Median

50th

1.78

AMD Ryzen 7 5800X 8-Core

50th

1.84 ^{+/- 0.06}

AMD EPYC 7272 12-Core

49th

1.94

Intel Xeon E5-2687W v3

48th

1.99 ^{+/- 0.01}

Intel Core i9-9900K

47th

2.03 ^{+/- 0.11}

Intel Xeon E-2288G

46th

2.05 ^{+/- 0.22}

Intel Core i5-10600K

45th

2.13 ^{+/- 0.06}

AMD Ryzen 7 3800XT 8-Core

45th

2.13 ^{+/- 0.06}

Intel Core i7-8086K

44th

2.18

Intel Core i7-8700K

42nd

2.20 ^{+/- 0.03}

AMD Ryzen 7 3700X 8-Core

41st

2.26 ^{+/- 0.01}

AMD EPYC 7F32 8-Core

41st

2.27 ^{+/- 0.03}

Intel Xeon Gold 5217

40th

2.34

Intel Xeon Silver 4210R

40th

2.37 ^{+/- 0.01}

AMD Ryzen 5 5600X 6-Core

39th

2.39 ^{+/- 0.01}

Intel Core i7-5960X

38th

2.45 ^{+/- 0.01}

AMD Ryzen 7 2700X Eight-Core

38th

2.47 ^{+/- 0.01}

AMD EPYC 7262 8-Core

37th

2.55

AMD Ryzen 7 1800X Eight-Core

36th

2.68 ^{+/- 0.05}

Intel Xeon Silver 4215R

36th

2.71

AMD EPYC 7232P 8-Core

35th

2.73 ^{+/- 0.01}

Intel Core i7-6800K

34th

2.76

Intel Core i7-8700B

33rd

2.84 ^{+/- 0.02}

AMD Ryzen 5 3600X 6-Core

32nd

2.87

Intel Core i5-9400F

32nd

2.88 ^{+/- 0.01}

AMD Ryzen 7 2700 Eight-Core

32nd

2.88 ^{+/- 0.04}

AMD EPYC 7252 8-Core

32nd

2.88

AMD Ryzen 5 3600XT 6-Core

31st

2.89 ^{+/- 0.14}

AMD Ryzen 7 1700 Eight-Core

30th

2.97 ^{+/- 0.08}

Intel Core i5-8400

30th

2.98 ^{+/- 0.02}

Intel Core i7-7740K

29th

3.10

AMD Ryzen 7 1700X Eight-Core

28th

3.12 ^{+/- 0.04}

Intel Core i7-7700K

28th

3.14 ^{+/- 0.03}

Intel Core i7-4960X

28th

3.14 ^{+/- 0.01}

AMD Ryzen 5 2600X Six-Core

28th

3.17 ^{+/- 0.01}

Intel Core i7-10700T

27th

3.21 ^{+/- 0.01}

Intel Core i7-9750H

26th

3.41 ^{+/- 0.12}

AMD Ryzen 5 2600 Six-Core

26th

3.45

Low-Tier

25th

> 3.45

Intel Core i3-10100

25th

3.49 ^{+/- 0.09}

Apple M1

24th

3.56

Intel Xeon E3-1275 v6

23rd

3.59 ^{+/- 0.16}

Intel Xeon E3-1270 v5

23rd

3.68 ^{+/- 0.01}

Intel Core i7-4790K

22nd

3.82 ^{+/- 0.50}

Intel Xeon E3-1245 v5

21st

3.88 ^{+/- 0.01}

Intel Xeon E3-1280 v5

21st

3.90 ^{+/- 0.11}

Intel Core i7-5775C

20th

4.18 ^{+/- 0.17}

Intel Core i7-9700TE

20th

4.19 ^{+/- 0.03}

Intel Core i5-7600K

20th

4.23 ^{+/- 0.01}

AMD Ryzen 3 3300X 4-Core

18th

4.31 ^{+/- 0.01}

AMD Ryzen 3 3100 4-Core

16th

4.49 ^{+/- 0.01}

Intel Core i3-8100

16th

4.58 ^{+/- 0.01}

AMD Ryzen 5 4500U

15th

4.60 ^{+/- 0.18}

AMD Ryzen 5 3400G

14th

4.75

Intel Core i7-3770K

14th

4.75 ^{+/- 0.01}

Intel Core i7-6700HQ

14th

4.84 ^{+/- 0.17}

Intel Xeon E3-1260L v5

13th

4.98 ^{+/- 0.10}

Intel Core i7-4770K

13th

5.00 ^{+/- 0.13}

Intel Core i7-1165G7

13th

5.00 ^{+/- 0.91}

Intel Core i5-6500

13th

5.00 ^{+/- 0.02}

Intel Xeon E5-2609 v4

13th

5.00

Intel Core i5-4670

12th

5.16 ^{+/- 0.04}

AMD Ryzen 5 2400G

10th

5.53 ^{+/- 0.49}

Intel Core i5-2500K

10th

5.83 ^{+/- 0.66}

Intel Xeon E3-1235L v5

10th

6.07 ^{+/- 0.02}

Intel Core i5-3470

9th

6.46 ^{+/- 1.15}

AMD Ryzen 3 1300X

9th

6.51 ^{+/- 0.04}

Intel Core i7-1065G7

8th

6.74 ^{+/- 0.08}

AMD Ryzen 3 2200G

8th

6.79 ^{+/- 0.71}

Intel Core i7-8550U

7th

6.84 ^{+/- 0.27}

Intel Core i7-8565U

6th

7.16 ^{+/- 0.23}

Intel Core i3-7100

6th

7.46 ^{+/- 0.32}

AMD FX-8150 Eight-Core

5th

8.88 ^{+/- 0.08}

Intel Core i3-4130

5th

9.50 ^{+/- 0.03}

Intel Core i5-5300U

4th

11.13

Intel Core i7-5600U

4th

11.14 ^{+/- 0.03}

Intel Core i7-4558U

3rd

11.45 ^{+/- 0.31}

Intel Core i5-2520M

3rd

11.95 ^{+/- 0.05}

AMD Ryzen 3 3200U

2nd

14.04 ^{+/- 0.20}

Intel Core i7-3517U

2nd

14.05 ^{+/- 1.86}

Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD 2.14 - ATPase Simulation - 327,506 Atoms) has an average run-time of 7 minutes. By default this test profile is set to run at least 3 times but may increase if the standard deviation exceeds pre-defined defaults or other calculations deem additional runs necessary for greater statistical accuracy of the result.

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.2%.

Ryzen 3 2200G 2021 3 Systems - 191 Benchmark Results	AMD Ryzen 3 2200G - ASUS PRIME B350M-E - AMD Raven Ubuntu 20.10 - 5.8.0-38-generic - GNOME Shell 3.38.1
os bench 2 Systems - 17 Benchmark Results	2 x Intel Celeron J3455 - Intel 440BX - Intel 440BX Ubuntu 18.04 - 4.15.0-130-generic - GCC 7.5.0
namd5800xbench 1 System - 1 Benchmark Result	AMD Ryzen 7 5800X 8-Core - ASUS ROG STRIX X470-F GAMING - AMD Starship Ubuntu 20.04 - 5.10.0-051000-generic - GNOME Shell 3.36.4
namd1800xbench 1 System - 1 Benchmark Result	AMD Ryzen 7 1800X Eight-Core - ASUS ROG STRIX X470-F GAMING - AMD 17h Ubuntu 20.04 - 5.8.0-38-generic - GNOME Shell 3.36.4
a 2 Systems - 1 Benchmark Result	Intel Core i5-9300H - LENOVO LNVNB161216 - Intel Cannon Lake PCH Arch rolling - 5.10.3-106-tkg-MuQSS - KDE Plasma 5.20.5
a 1 System - 1 Benchmark Result	Intel Core i5-9300H - LENOVO LNVNB161216 - Intel Cannon Lake PCH Arch rolling - 5.10.3-106-tkg-MuQSS - KDE Plasma 5.20.5
vd3-5106-4 1 System - 14 Benchmark Results	AMD Ryzen 9 3900X 12-Core - ASUS PRIME X570-PRO - AMD Starship EndeavourOS rolling - 5.10.6-vd-2.4 - Xfce 4.16
vd3-5106-1 1 System - 14 Benchmark Results	AMD Ryzen 9 3900X 12-Core - ASUS PRIME X570-PRO - AMD Starship EndeavourOS rolling - 5.10.6-vd-2.1 - Xfce 4.16
vd3-5106-2 1 System - 14 Benchmark Results	AMD Ryzen 9 3900X 12-Core - ASUS PRIME X570-PRO - AMD Starship EndeavourOS rolling - 5.10.6-vd-2.2 - Xfce 4.16
vd3-5106-4 1 System - 14 Benchmark Results	AMD Ryzen 9 3900X 12-Core - ASUS PRIME X570-PRO - AMD Starship EndeavourOS rolling - 5.10.6-vd-2.4 - Xfce 4.16
gogz-win81-00vm-sci-comp-11jan2021 1 System - 3 Benchmark Results	AMD Ryzen Threadripper 3960X 24-Core - Intel 440BX - 1 x 8192 MB 0MHz VMW-8192MB Microsoft Windows 10 Home Build 18362 - 10.0 - 8.16.7.5
gnsft-win10-hvmb-sci-comp-11jan2021 1 System - 3 Benchmark Results	AMD Ryzen Threadripper 3960X 24-Core - Intel 440BX - 1 x 16384 MB 0MHz Microsoft Windows 10 Home Build 17134 - 10.0 - 8.16.7.5

Sandy 3 Systems - 268 Benchmark Results	Intel Core i5-2520M - HP 161C - Intel 2nd Generation Core DRAM Ubuntu 18.04 - 4.18.0-20-generic - GNOME Shell 3.28.3
Ryzen 9 5900X / Ryzen 9 5950X Linux Performance 11 Systems - 217 Benchmark Results	AMD Ryzen 5 3600X 6-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.9.0-050900-generic - GNOME Shell 3.36.4
Apple M1 vs. AMD Renoir vs. Intel Tiger Lake 4 Systems - 99 Benchmark Results	VirtualApple - Apple Mac mini - 8GB macOS 11.0 - 20.1.0 - OpenCL 1.2
Fedora 32 vs. Fedora 33 Beta Benchmarks 3 Systems - 174 Benchmark Results	Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH Fedora 32 - 5.8.11-200.fc32.x86_64 - GNOME Shell 3.36.6
Core i9 10900K - Ubuntu 20.04 LTS vs. Ubuntu 20.10 2 Systems - 403 Benchmark Results	Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH Ubuntu 20.04 - 5.4.0-48-generic - GNOME Shell 3.36.4
Ryzen 7 3800XT New Tests End Of August 3 Systems - 11 Benchmark Results	AMD Ryzen 7 3800XT 8-Core - ASRock X570 Pro4 - AMD Starship Ubuntu 20.04 - 5.4.0-42-generic - GNOME Shell 3.36.1
Ryzen 9 3900XT Ubuntu 20.04 LTS vs. Ubuntu 20.10 3 Systems - 406 Benchmark Results	AMD Ryzen 9 3900XT 12-Core - MSI MEG X570 GODLIKE - AMD Starship Ubuntu 20.04 - 5.4.0-48-generic - GNOME Shell 3.36.4
Core i5 9400F Linux 5.9 Kernel Featured Kernel Comparison	Intel Core i5-9400F - MSI B360M GAMING PLUS - Intel Cannon Lake PCH Ubuntu 20.04 - 5.8.3-050803-generic - GNOME Shell 3.36.0
Ryzen 7 1700 Summer Featured Kernel Comparison	AMD Ryzen 7 1700 Eight-Core - MSI B350 TOMAHAWK - AMD 17h Ubuntu 19.10 - 5.9.0-050900rc2-generic - GNOME Shell 3.34.1
Ryzen 3 3300X Linux 5.9 Kernel Test Featured Kernel Comparison	AMD Ryzen 3 3300X 4-Core - MSI B350M GAMING PRO - AMD Starship Ubuntu 20.04 - 5.9.0-050900rc4daily20200911-generic - GNOME Shell 3.36.4
7700K Intel 2020 3 Systems - 202 Benchmark Results	Intel Core i7-7700K - MSI Z270-A PRO - Intel Xeon E3-1200 v6 Ubuntu 20.04 - 5.9.0-050900rc8daily20201011-generic - GNOME Shell 3.36.4
TR 3990X Okt 3 Systems - 100 Benchmark Results	AMD Ryzen Threadripper 3990X 64-Core - System76 Thelio Major - AMD Starship Ubuntu 20.04 - 5.4.0-47-generic - GNOME Shell 3.36.4

NAMD

Project Site

Test Created

Last Updated

Test Maintainer

Test Type

Average Install Time

Average Run Time

Accolades

Supported Platforms

Supported Architectures

Revision History

Suites Using This Test

Performance Metrics

NAMD 2.14

ATPase Simulation - 327,506 Atoms

Recent Test Results

Most Popular Test Results

User Comments