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, 10 May 2021 17:31:50 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 1,383 public results since 20 August 2020 with the latest data as of 4 May 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 7763 64-Core

100th

0.24 ^{+/- 0.03}

2 x Intel Xeon Platinum 8380

99th

0.27

2 x AMD EPYC 7742 64-Core

98th

0.27

2 x AMD EPYC 7713 64-Core

98th

0.27

2 x AMD EPYC 7702 64-Core

97th

0.29

2 x AMD EPYC 75F3 32-Core

95th

0.31

2 x AMD EPYC 7543 32-Core

95th

0.34

2 x AMD EPYC 7513 32-Core

94th

0.37

2 x Intel Xeon Platinum 8280

93rd

0.37

AMD EPYC 7763 64-Core

92nd

0.38

AMD Ryzen Threadripper 3990X 64-Core

91st

0.42 ^{+/- 0.02}

2 x AMD EPYC 7443 24-Core

90th

0.44

AMD EPYC 7742 64-Core

90th

0.44 ^{+/- 0.02}

2 x AMD EPYC 7F72 24-Core

89th

0.45

2 x AMD EPYC 7601 32-Core

88th

0.46 ^{+/- 0.03}

AMD EPYC 7713 64-Core

88th

0.46

AMD EPYC 7702 64-Core

86th

0.49 ^{+/- 0.02}

AMD EPYC 7662 64-Core

86th

0.49 ^{+/- 0.01}

2 x AMD EPYC 73F3 16-Core

84th

0.54

AMD EPYC 7642 48-Core

83rd

0.57

AMD EPYC 7552 48-Core

82nd

0.58

2 x AMD EPYC 7F52 16-Core

82nd

0.59 ^{+/- 0.01}

AMD EPYC 75F3 32-Core

81st

0.60

AMD Ryzen Threadripper 3970X 32-Core

80th

0.61 ^{+/- 0.06}

2 x Intel Xeon Gold 5220R

80th

0.62 ^{+/- 0.02}

AMD EPYC 7543 32-Core

79th

0.66

Intel Xeon Gold 6258R

79th

0.71

Intel Xeon Platinum 8280

78th

0.72 ^{+/- 0.01}

AMD EPYC 7542 32-Core

78th

0.72

AMD Ryzen Threadripper 3960X 24-Core

77th

0.74 ^{+/- 0.03}

2 x AMD EPYC 7282 16-Core

77th

0.76

AMD EPYC 7502 32-Core

76th

0.78

Mid-Tier

75th

> 0.78

AMD EPYC 74F3 24-Core

75th

0.78

AMD EPYC 7502P 32-Core

75th

0.78

AMD EPYC 7532 32-Core

74th

0.79

AMD Ryzen Threadripper 2990WX 32-Core

74th

0.79 ^{+/- 0.01}

2 x Intel Xeon Gold 5218R

73rd

0.85 ^{+/- 0.06}

AMD EPYC 7452 32-Core

73rd

0.85

AMD EPYC 7F72 24-Core

72nd

0.86 ^{+/- 0.01}

AMD EPYC 7402P 24-Core

70th

0.94

2 x AMD EPYC 7272 12-Core

70th

0.95

AMD EPYC 7601 32-Core

69th

0.97

Intel Core i9-10980XE

68th

0.99 ^{+/- 0.02}

Intel Core i9-7980XE

68th

0.99

AMD EPYC 73F3 16-Core

67th

1.05

AMD Ryzen 9 5950X 16-Core

65th

1.08 ^{+/- 0.01}

AMD Ryzen 9 3950X 16-Core

63rd

1.14 ^{+/- 0.03}

AMD EPYC 7F52 16-Core

63rd

1.15 ^{+/- 0.01}

AMD EPYC 7352 24-Core

62nd

1.15

AMD EPYC 7343 16-Core

62nd

1.15

AMD Ryzen Threadripper 2970WX 24-Core

61st

1.17 ^{+/- 0.03}

Intel Xeon Gold 5220R

61st

1.18

Intel Xeon Gold 6226R

61st

1.18 ^{+/- 0.03}

Intel Core i9-10900K

59th

1.24 ^{+/- 0.03}

2 x AMD EPYC 7262 8-Core

57th

1.28

AMD Ryzen 9 5900X 12-Core

56th

1.29 ^{+/- 0.01}

Intel Core i9-11900K

54th

1.30

AMD Ryzen Threadripper 2950X 16-Core

53rd

1.31 ^{+/- 0.02}

AMD EPYC 7302P 16-Core

51st

1.35 ^{+/- 0.01}

Intel Core i7-11700K

51st

1.36 ^{+/- 0.03}

2 x AMD EPYC 7252 8-Core

51st

1.37

Median

50th

1.40

AMD EPYC 7282 16-Core

50th

1.46 ^{+/- 0.01}

AMD Ryzen 9 3900XT 12-Core

48th

1.49 ^{+/- 0.09}

Intel Core i7-10700K

48th

1.52

AMD Ryzen 9 3900X 12-Core

47th

1.52 ^{+/- 0.04}

Intel Xeon Gold 5218

47th

1.54 ^{+/- 0.03}

Intel Xeon Silver 4216

46th

1.56 ^{+/- 0.04}

Intel Core i7-7900X

46th

1.60

Intel Xeon Silver 4214R

44th

1.74

Intel Core i9-9900KS

44th

1.75 ^{+/- 0.07}

Intel Core i5-11600K

43rd

1.85 ^{+/- 0.22}

AMD Ryzen 7 5800X 8-Core

43rd

1.87 ^{+/- 0.08}

AMD EPYC 7272 12-Core

43rd

1.88 ^{+/- 0.05}

AMD EPYC 72F3 8-Core

41st

1.96

Intel Xeon E-2288G

41st

1.98 ^{+/- 0.03}

Intel Xeon E5-2687W v3

41st

1.99 ^{+/- 0.01}

Intel Core i9-9900K

40th

2.03 ^{+/- 0.11}

Intel Core i5-10600K

38th

2.12 ^{+/- 0.06}

AMD Ryzen 7 3800XT 8-Core

38th

2.13 ^{+/- 0.06}

AMD Ryzen 7 PRO 4750G

38th

2.17 ^{+/- 0.02}

Intel Core i7-8086K

37th

2.18

Intel Core i7-8700K

36th

2.20 ^{+/- 0.03}

AMD EPYC 7F32 8-Core

35th

2.25 ^{+/- 0.03}

AMD Ryzen 7 3700X 8-Core

35th

2.26 ^{+/- 0.01}

Intel Xeon Gold 5217

34th

2.34

Intel Xeon Silver 4210R

34th

2.37 ^{+/- 0.01}

AMD Ryzen 5 5600X 6-Core

33rd

2.42 ^{+/- 0.05}

Intel Core i7-5960X

32nd

2.45 ^{+/- 0.01}

AMD Ryzen 7 2700X Eight-Core

32nd

2.47 ^{+/- 0.01}

AMD EPYC 7262 8-Core

32nd

2.55

AMD Ryzen 7 1800X Eight-Core

31st

2.68 ^{+/- 0.05}

Intel Xeon Silver 4215R

31st

2.71

AMD EPYC 7232P 8-Core

30th

2.73 ^{+/- 0.01}

Intel Core i7-6800K

29th

2.76

Intel Xeon E-2278GEL

29th

2.81

Intel Core i7-8700B

28th

2.84 ^{+/- 0.02}

AMD Ryzen 5 3600X 6-Core

28th

2.87

Intel Core i5-9400F

27th

2.88 ^{+/- 0.01}

AMD Ryzen 7 2700 Eight-Core

27th

2.88 ^{+/- 0.04}

AMD EPYC 7252 8-Core

27th

2.88

AMD Ryzen 5 3600XT 6-Core

27th

2.89 ^{+/- 0.14}

AMD Ryzen 7 1700 Eight-Core

26th

2.97 ^{+/- 0.08}

Intel Core i5-8400

26th

2.98 ^{+/- 0.02}

Intel Core i7-7740K

26th

3.10

Low-Tier

25th

> 3.10

AMD Ryzen 7 1700X Eight-Core

25th

3.12 ^{+/- 0.04}

Intel Core i7-7700K

25th

3.14 ^{+/- 0.03}

Intel Core i7-4960X

25th

3.14 ^{+/- 0.01}

AMD Ryzen 5 2600X Six-Core

25th

3.17 ^{+/- 0.01}

Intel Core i7-10700T

24th

3.25 ^{+/- 0.10}

AMD Ryzen 5 2600 Six-Core

22nd

3.43 ^{+/- 0.06}

Intel Core i3-10100

22nd

3.49 ^{+/- 0.09}

Apple M1

21st

3.56

Intel Core i7-9750H

20th

3.58 ^{+/- 0.24}

Intel Xeon E3-1275 v6

20th

3.59 ^{+/- 0.16}

Intel Xeon E3-1270 v5

20th

3.68 ^{+/- 0.01}

Intel Core i7-4790K

19th

3.82 ^{+/- 0.50}

Intel Xeon E3-1245 v5

19th

3.88 ^{+/- 0.01}

Intel Xeon E3-1280 v5

19th

3.90 ^{+/- 0.11}

Intel Core i5-10210U

17th

4.15 ^{+/- 0.03}

Intel Core i7-5775C

17th

4.16 ^{+/- 0.16}

Intel Core i7-9700TE

16th

4.19 ^{+/- 0.03}

Intel Core i5-7600K

15th

4.23 ^{+/- 0.01}

AMD Ryzen 3 3300X 4-Core

14th

4.31 ^{+/- 0.01}

AMD Ryzen 3 3100 4-Core

12th

4.49 ^{+/- 0.01}

Intel Core i3-8100

12th

4.58 ^{+/- 0.01}

AMD Ryzen 5 4500U

12th

4.60 ^{+/- 0.18}

Intel Core i7-3770K

11th

4.75 ^{+/- 0.01}

AMD Ryzen 5 3400G

11th

4.80 ^{+/- 0.04}

Intel Core i7-6700HQ

10th

4.84 ^{+/- 0.17}

Intel Xeon E3-1260L v5

9th

4.98 ^{+/- 0.10}

Intel Core i5-6500

9th

5.00 ^{+/- 0.02}

Intel Xeon E5-2609 v4

9th

5.00

Intel Core i5-4670

9th

5.09 ^{+/- 0.15}

AMD Ryzen 5 2400G

8th

5.53 ^{+/- 0.49}

Intel Core i5-2500K

8th

5.83 ^{+/- 0.66}

Intel Xeon E3-1235L v5

7th

6.07 ^{+/- 0.02}

AMD Ryzen 3 1300X

6th

6.51 ^{+/- 0.04}

Intel Core i7-1065G7

6th

6.74 ^{+/- 0.08}

AMD Ryzen 3 2200G

5th

6.79 ^{+/- 0.58}

Intel Core i7-8550U

5th

6.84 ^{+/- 0.27}

Intel Core i7-8565U

5th

7.16 ^{+/- 0.23}

Intel Core i3-7100

4th

7.46 ^{+/- 0.32}

AMD FX-8150 Eight-Core

4th

8.88 ^{+/- 0.08}

Intel Core i3-4130

3rd

9.50 ^{+/- 0.03}

Intel Core i5-5300U

3rd

11.13

Intel Core i7-5600U

3rd

11.14 ^{+/- 0.03}

Intel Core i7-4558U

2nd

11.45 ^{+/- 0.31}

Intel Core i5-2520M

2nd

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 6 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%.

Does It Scale Well With Increasing Cores?

Yes, based on the automated analysis of the collected public benchmark data, this test / test settings does generally scale well with increasing CPU core counts. Data based on publicly available results for this test / test settings, separated by vendor, result divided by the reference CPU clock speed, grouped by matching physical CPU core count, and normalized against the smallest core count tested from each vendor for each CPU having a sufficient number of test samples and statistically significant data.

Notable Instruction Set Usage

Notable instruction set extensions supported by this test, based on an automatic analysis by the Phoronix Test Suite / OpenBenchmarking.org analytics engine.

Instruction Set

Support

Instructions Detected

SSE2 (SSE2)

Used by default on supported hardware.

CVTSD2SS SUBSD MULSD ADDSD CVTTSD2SI CVTSS2SD CVTPD2PS MOVDQU MOVD MOVDQA PSRLDQ CVTSI2SD DIVSD MOVHPD UNPCKLPD COMISD SQRTSD PSHUFD PUNPCKLQDQ PUNPCKHQDQ MINSD MAXSD UCOMISD MULPD CVTPS2PD ADDPD UNPCKHPD CMPLTSD CVTDQ2PD DIVPD SUBPD CMPLTPD MOVMSKPD PADDQ CVTDQ2PS SQRTPD PMULUDQ CVTTPD2DQ MINPD CMPEQPD CMPNLTSD CMPEQSD CMPNEQSD CMPLEPD CMPLESD MAXPD PSUBQ PSHUFLW MOVAPD CVTSD2SI ANDPD XORPD ORPD ANDNPD MOVLPD CMPNLESD SHUFPD CMPUNORDPD CMPNLEPD CMPNLTPD CVTPS2DQ PSLLDQ MOVNTDQ MOVNTI

SSE3 (SSE3)

Used by default on supported hardware.

MOVDDUP LDDQU

SSSE3 (SSSE3)

Used by default on supported hardware.

PALIGNR PMADDUBSW PHADDD

SSE 4.2 (SSE4_2)

Used by default on supported hardware.
Found on Intel processors since at least 2010.
Found on AMD processors since Bulldozer (2011).

PCMPISTRM PCMPISTRI

Advanced Vector Extensions (AVX)

Used by default on supported hardware.
Found on Intel processors since Sandy Bridge (2011).
Found on AMD processors since Bulldozer (2011).

VINSERTF128 VZEROUPPER VEXTRACTF128 VBROADCASTSS VBROADCASTSD VPERM2F128 VPERMILPD VMASKMOVPS

Advanced Vector Extensions 2 (AVX2)

Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).

VPBROADCASTQ VGATHERQPD VEXTRACTI128 VPBROADCASTD

FMA (FMA)

Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Bulldozer (2011).

VFNMADD213SD VFMADD213SD VFMADD231SD VFMSUB213SD VFNMADD231SD VFMADD132SD VFNMADD132SD VFMSUB213SS VFMADD213SS VFMADD231SS VFMADD213PD VFNMADD231PD VFNMADD132PD VFMSUB213PD VFNMADD213PD VFMADD231PD VFMADD132PD VFMADD213PS VFNMADD213PS VFNMADD132PS

Last automated analysis: 10 May 2021

This test profile binary relies on the shared libraries libm.so.6, libpthread.so.0, libdl.so.2, libz.so.1, libc.so.6.

Linux 5.13 Rocket Lake Intel Performance Featured Kernel Comparison	5.12.0-051200-generic - 5.13.0-051300rc1-generic
Linux 5.13 AMD Ryzen 9 5950X Featured Kernel Comparison	5.11.18-051118-generic - 5.12.1-051201-generic - 5.12.0-051200daily20210503-generic
Windows 10 Tests 1 System - 124 Benchmark Results	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - 2 x 8192 MB 3600MHz F4-3600C16-8GTRG Microsoft Windows 10 Pro Build 21370 - 10.0 - 466.27
Linux 5.13 AMD Ryzen 9 5950X Featured Kernel Comparison	5.11.18-051118-generic - 5.12.1-051201-generic - 5.12.0-051200daily20210503-generic
clearlinux-ryzen3g-16gb-corsair 2 Systems - 169 Benchmark Results	AMD Ryzen 3 3200G - ASRock B450M-HDV R4.0 - AMD Raven Clear Linux OS 34550 - 5.10.19-1032.native - GNOME Shell 40.0
Xeon Platinum 8380 2P 1 System - 732 Benchmark Results	2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 20.04 - 5.11.6-051106-generic - GNOME Shell 3.36.4
AMD EPYC 72F3 Performance Benchmarks Featured Processor Comparison	AMD EPYC 7F32 8-Core - AMD EPYC 72F3 8-Core
Linux 5.12 Compiler LLVM Clang Build 1 System - 115 Benchmark Results	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.12.0-051200rc8daily20210425-generic - GNOME Shell 3.36.7
2021-04-14-0804 1 System - 176 Benchmark Results	AMD EPYC 7B12 - Google Compute Engine n2d-standard-16 - Intel 440FX 82441FX PMC Ubuntu 20.04 - 5.4.0-1040-gcp - GCC 9.3.0
Clear Linux vs. Ubuntu 21.04 Benchmarks 3 Systems - 101 Benchmark Results	Intel Core i9-10980XE - ASRock X299 Steel Legend - Intel Sky Lake-E DMI3 Registers Ubuntu 21.04 - 5.11.0-16-generic - GNOME Shell 3.38.4
Ubuntu 21.04 EPYC 2 Systems - 434 Benchmark Results	AMD EPYC 72F3 8-Core - Supermicro H12SSL-i v1.01 - AMD Starship Ubuntu 21.04 - 5.11.0-16-generic - GNOME Shell 3.38.4
Clear Linux April 2021 Intel Core i9 2 Systems - 102 Benchmark Results	Intel Core i9-10980XE - ASRock X299 Steel Legend - Intel Sky Lake-E DMI3 Registers Ubuntu 20.10 - 5.8.0-50-generic - GNOME Shell 3.38.1

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 9 5900X 12-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	Apple - Apple Mac mini - 8GB macOS 11.0 - 20.1.0 - OpenCL 1.2
Xeon E 8 Systems - 84 Benchmark Results	Intel Xeon E-2288G - Compulab SBC-ATCFL v1.2 - Intel Cannon Lake PCH Ubuntu 20.10 - 5.8.0-26-generic - GNOME Shell 3.38.1
Ubuntu 20.10 Kernels AMD Zen 3 6 Systems - 143 Benchmark Results	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.10 - 5.10.7-xanmod1 - GNOME Shell 3.38.1
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 33 - 5.8.11-300.fc33.x86_64 - GNOME Shell 3.38.0
md xeon 3 Systems - 14 Benchmark Results	Intel Core i7-10700T - Logic Supply RXM-181 - Intel Comet Lake PCH Ubuntu 20.10 - 5.8.0-43-generic - GNOME Shell 3.38.2
Linux 5.12 Scheduler Featured Kernel Comparison	AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.10 - 5.11.0-051100-generic - GNOME Shell 3.38.2
Ryzen 5 5600X Linux Performance 12 Systems - 229 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
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 20.10 - 5.8.0-22-generic - GNOME Shell 3.38.0
Ryzen 9 3900XT Ubuntu 20.04 LTS vs. Ubuntu 20.10 3 Systems - 406 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
10700T openSUSE 2 Systems - 78 Benchmark Results	Intel Core i7-10700T - Logic Supply RXM-181 - Intel Comet Lake PCH openSUSE 15.3 - 5.3.18-47-default - KDE Plasma 5.18.6

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

Does It Scale Well With Increasing Cores?

Notable Instruction Set Usage

Recent Test Results

Most Popular Test Results