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 Thu, 04 Mar 2021 14:15:43 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 1,083 public results since 20 August 2020 with the latest data as of 4 March 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

AMD Ryzen Threadripper 3990X 64-Core

96th

0.42 ^{+/- 0.02}

AMD EPYC 7742 64-Core

95th

0.44 ^{+/- 0.02}

2 x AMD EPYC 7F72 24-Core

94th

0.45

2 x AMD EPYC 7601 32-Core

94th

0.45 ^{+/- 0.04}

AMD EPYC 7702 64-Core

92nd

0.48 ^{+/- 0.02}

AMD EPYC 7662 64-Core

92nd

0.49 ^{+/- 0.01}

AMD EPYC 7642 48-Core

89th

0.57

AMD EPYC 7552 48-Core

88th

0.58

AMD Ryzen Threadripper 3970X 32-Core

88th

0.59 ^{+/- 0.03}

2 x Intel Xeon Gold 5220R

87th

0.63 ^{+/- 0.02}

AMD EPYC 7542 32-Core

86th

0.72

AMD Ryzen Threadripper 3960X 24-Core

85th

0.74 ^{+/- 0.03}

2 x AMD EPYC 7282 16-Core

85th

0.76

AMD EPYC 7502 32-Core

84th

0.78

AMD EPYC 7502P 32-Core

83rd

0.78

AMD EPYC 7532 32-Core

82nd

0.79

AMD Ryzen Threadripper 2990WX 32-Core

81st

0.79 ^{+/- 0.01}

AMD EPYC 7452 32-Core

81st

0.85

AMD EPYC 7F72 24-Core

79th

0.86 ^{+/- 0.01}

AMD EPYC 7402P 24-Core

78th

0.94

2 x AMD EPYC 7272 12-Core

77th

0.95

AMD EPYC 7601 32-Core

77th

0.97

Mid-Tier

75th

> 0.99

Intel Core i9-10980XE

75th

0.99 ^{+/- 0.02}

Intel Core i9-7980XE

75th

0.99

AMD Ryzen 9 5950X 16-Core

73rd

1.08 ^{+/- 0.01}

AMD Ryzen 9 3950X 16-Core

71st

1.14 ^{+/- 0.03}

AMD EPYC 7F52 16-Core

70th

1.15 ^{+/- 0.01}

AMD EPYC 7352 24-Core

70th

1.15

AMD Ryzen Threadripper 2970WX 24-Core

69th

1.17 ^{+/- 0.03}

Intel Xeon Gold 6226R

68th

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

1.46 ^{+/- 0.01}

AMD Ryzen 9 3900XT 12-Core

56th

1.49 ^{+/- 0.09}

Intel Xeon Gold 5218

55th

1.52

AMD Ryzen 9 3900X 12-Core

55th

1.52 ^{+/- 0.04}

Intel Xeon Silver 4216

54th

1.56 ^{+/- 0.04}

Intel Core i7-7900X

54th

1.60

Intel Xeon Silver 4214R

52nd

1.74

Intel Core i9-9900KS

52nd

1.75 ^{+/- 0.07}

AMD Ryzen 7 5800X 8-Core

51st

1.84 ^{+/- 0.06}

AMD EPYC 7272 12-Core

51st

1.89 ^{+/- 0.06}

Median

50th

1.90

Intel Xeon E-2288G

49th

1.98 ^{+/- 0.03}

Intel Xeon E5-2687W v3

49th

1.99 ^{+/- 0.01}

Intel Core i9-9900K

48th

2.03 ^{+/- 0.11}

Intel Core i5-10600K

46th

2.13 ^{+/- 0.06}

AMD Ryzen 7 3800XT 8-Core

46th

2.13 ^{+/- 0.06}

AMD Ryzen 7 PRO 4750G

45th

2.17 ^{+/- 0.02}

Intel Core i7-8086K

45th

2.18

Intel Core i7-8700K

44th

2.20 ^{+/- 0.03}

AMD EPYC 7F32 8-Core

42nd

2.26 ^{+/- 0.03}

AMD Ryzen 7 3700X 8-Core

42nd

2.26 ^{+/- 0.01}

Intel Xeon Gold 5217

41st

2.34

Intel Xeon Silver 4210R

41st

2.37 ^{+/- 0.01}

AMD Ryzen 5 5600X 6-Core

40th

2.39 ^{+/- 0.01}

Intel Core i7-5960X

39th

2.45 ^{+/- 0.01}

AMD Ryzen 7 2700X Eight-Core

39th

2.47 ^{+/- 0.01}

AMD EPYC 7262 8-Core

39th

2.55

AMD Ryzen 7 1800X Eight-Core

38th

2.68 ^{+/- 0.05}

Intel Xeon Silver 4215R

38th

2.71

AMD EPYC 7232P 8-Core

36th

2.73

Intel Core i7-6800K

36th

2.76

Intel Xeon E-2278GEL

35th

2.81

Intel Core i7-8700B

35th

2.84 ^{+/- 0.02}

AMD Ryzen 5 3600X 6-Core

34th

2.87

Intel Core i5-9400F

34th

2.88 ^{+/- 0.01}

AMD Ryzen 7 2700 Eight-Core

34th

2.88 ^{+/- 0.04}

AMD EPYC 7252 8-Core

34th

2.88

AMD Ryzen 5 3600XT 6-Core

33rd

2.89 ^{+/- 0.14}

AMD Ryzen 7 1700 Eight-Core

32nd

2.97 ^{+/- 0.08}

Intel Core i5-8400

32nd

2.98 ^{+/- 0.02}

Intel Core i7-7740K

32nd

3.10

AMD Ryzen 7 1700X Eight-Core

31st

3.12 ^{+/- 0.04}

Intel Core i7-7700K

31st

3.14 ^{+/- 0.03}

Intel Core i7-4960X

31st

3.14 ^{+/- 0.01}

AMD Ryzen 5 2600X Six-Core

30th

3.17 ^{+/- 0.01}

Intel Core i7-10700T

29th

3.25 ^{+/- 0.10}

AMD Ryzen 5 2600 Six-Core

27th

3.43 ^{+/- 0.06}

Intel Core i3-10100

27th

3.49 ^{+/- 0.09}

Apple M1

26th

3.56

Low-Tier

25th

> 3.57

Intel Core i7-9750H

25th

3.58 ^{+/- 0.24}

Intel Xeon E3-1275 v6

25th

3.59 ^{+/- 0.16}

Intel Xeon E3-1270 v5

24th

3.68 ^{+/- 0.01}

Intel Core i7-4790K

23rd

3.82 ^{+/- 0.50}

Intel Xeon E3-1245 v5

23rd

3.88 ^{+/- 0.01}

Intel Xeon E3-1280 v5

23rd

3.90 ^{+/- 0.11}

Intel Core i5-10210U

21st

4.15 ^{+/- 0.03}

Intel Core i7-5775C

20th

4.18 ^{+/- 0.17}

Intel Core i7-9700TE

20th

4.19 ^{+/- 0.03}

Intel Core i5-7600K

18th

4.23 ^{+/- 0.01}

AMD Ryzen 3 3300X 4-Core

16th

4.31 ^{+/- 0.01}

AMD Ryzen 3 3100 4-Core

15th

4.49 ^{+/- 0.01}

Intel Core i3-8100

14th

4.58 ^{+/- 0.01}

AMD Ryzen 5 4500U

14th

4.60 ^{+/- 0.18}

Intel Core i7-3770K

13th

4.75 ^{+/- 0.01}

AMD Ryzen 5 3400G

13th

4.80 ^{+/- 0.04}

Intel Core i7-6700HQ

12th

4.84 ^{+/- 0.17}

Intel Xeon E3-1260L v5

11th

4.98 ^{+/- 0.10}

Intel Core i7-4770K

11th

5.00 ^{+/- 0.13}

Intel Core i5-6500

11th

5.00 ^{+/- 0.02}

Intel Xeon E5-2609 v4

11th

5.00

Intel Core i5-4670

10th

5.16 ^{+/- 0.04}

AMD Ryzen 5 2400G

9th

5.53 ^{+/- 0.49}

Intel Core i5-2500K

9th

5.83 ^{+/- 0.66}

Intel Xeon E3-1235L v5

9th

6.07 ^{+/- 0.02}

AMD Ryzen 3 1300X

8th

6.51 ^{+/- 0.04}

Intel Core i7-1065G7

7th

6.74 ^{+/- 0.08}

AMD Ryzen 3 2200G

7th

6.79 ^{+/- 0.58}

Intel Core i7-8550U

6th

6.84 ^{+/- 0.27}

Intel Core i7-8565U

5th

7.16 ^{+/- 0.23}

Intel Core i3-7100

5th

7.46 ^{+/- 0.32}

AMD FX-8150 Eight-Core

4th

8.88 ^{+/- 0.08}

Intel Core i3-4130

4th

9.50 ^{+/- 0.03}

Intel Core i5-5300U

3rd

11.13

Intel Core i7-5600U

3rd

11.14 ^{+/- 0.03}

Intel Core i7-4558U

3rd

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 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%.

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: 30 January 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.

10700T openSUSE 2 Systems - 78 Benchmark Results	Intel Core i7-10700T - Logic Supply RXM-181 - Intel Comet Lake PCH openSUSE 15.2 - 5.3.18-lp152.63-default - KDE Plasma 5.18.6
10700T openSUSE 1 System - 78 Benchmark Results	Intel Core i7-10700T - Logic Supply RXM-181 - Intel Comet Lake PCH openSUSE 15.2 - 5.3.18-lp152.63-default - KDE Plasma 5.18.6
Intel Core i5-10210U On Ubuntu 20.04 1 System - 9 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
Intel NUC10i5FNB (FNCML357.0047.2020.1118.1629 BIOS) On Ubuntu 20.04 1 System - 5 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
Intel Core i5-10210U Benchmarks 1 System - 7 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
Intel Core i5-10210U + Intel UHD 3GB + Intel NUC10i5FNB (FNCML357.0047.2020.1118.1629 BIOS) 1 System - 4 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
5.4.0-65-generic + Ubuntu 20.04 Tests 1 System - 8 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
Intel Core i5-10210U + Intel UHD 3GB + Intel NUC10i5FNB (FNCML357.0047.2020.1118.1629 BIOS) 1 System - 4 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
Ubuntu 20.04 Performance 1 System - 5 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
Ubuntu 20.04 Performance 1 System - 6 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
Intel Core i5-10210U On Ubuntu 20.04 1 System - 4 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14
Intel NUC10i5FNB (FNCML357.0047.2020.1118.1629 BIOS) On Ubuntu 20.04 1 System - 3 Benchmark Results	Intel Core i5-10210U - Intel NUC10i5FNB - Intel Device 02ef Ubuntu 20.04 - 5.4.0-65-generic - Xfce 4.14

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 3950X 16-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
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
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
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-sched - GNOME Shell 3.38.2
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 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	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 5 5600X Linux Performance 12 Systems - 229 Benchmark Results	Intel Core i5-10600K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH Ubuntu 20.04 - 5.9.0-050900-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 - 5.4.0-21-generic - GNOME Shell 3.36.0

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