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

16 February 2024

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

3 Seconds

Average Run Time

6 Minutes, 57 Seconds

Accolades

60k+ Downloads + 5k+ Public Benchmark Results

Supported Platforms

Supported Architectures

x86_64

* Uploading of benchmark result data to OpenBenchmarking.org is always optional (opt-in) via the Phoronix Test Suite for users wishing to share their results publicly.
** 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.
*** Test profile page view reporting began March 2021.
Data updated weekly as of 22 May 2024.

Revision History

pts/namd-1.3.1 [View Source] Fri, 16 Feb 2024 14:24:47 GMT
Update against NAMD 3.0b6 but no Windows binaries yet.

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

HPC - High Performance Computing

CPU Massive

Server CPU Tests

Molecular Dynamics

Scientific Computing

Performance Metrics

Analyze Test Configuration:

NAMD 3.0b6

Input: STMV with 1,066,628 Atoms

OpenBenchmarking.org metrics for this test profile configuration based on 421 public results since 16 February 2024 with the latest data as of 26 May 2024.

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

# Compatible Public Results

ns/day (Average)

2 x AMD EPYC 9684X 96-Core

98th

6.440 ^{+/- 0.040}

2 x AMD EPYC 9754 128-Core

96th

5.925 ^{+/- 0.204}

2 x Intel Xeon Platinum 8462Y

93rd

3.009 ^{+/- 0.040}

AMD Ryzen Threadripper PRO 7995WX 96-Cores

92nd

2.495 ^{+/- 0.001}

2 x Intel Xeon Gold 6442Y

91st

2.352 ^{+/- 0.006}

2 x Intel Xeon Max 9468

87th

1.992 ^{+/- 0.079}

2 x Intel Xeon Gold 6444Y

87th

1.981 ^{+/- 0.010}

2 x INTEL XEON PLATINUM 8592

86th

1.947 ^{+/- 0.269}

Intel Xeon Platinum 8462Y

81st

1.717 ^{+/- 0.002}

AMD Ryzen Threadripper 7980X 64-Cores

80th

1.636 ^{+/- 0.022}

AMD EPYC 8534P 64-Core

78th

1.561 ^{+/- 0.033}

Mid-Tier

75th

< 1.479

Intel Xeon Max 9468

74th

1.450 ^{+/- 0.002}

Intel Xeon Max 9480

73rd

1.433 ^{+/- 0.118}

2 x Intel Xeon Platinum 8468

72nd

1.423 ^{+/- 0.057}

INTEL XEON PLATINUM 8592

70th

1.348 ^{+/- 0.083}

Intel Xeon Gold 6414U

70th

1.343 ^{+/- 0.001}

2 x Intel Xeon Platinum 8280

68th

1.334 ^{+/- 0.007}

Intel Xeon Gold 6421N

67th

1.327 ^{+/- 0.003}

2 x Intel Xeon Platinum 8490H

63rd

1.155 ^{+/- 0.034}

Intel Xeon Platinum 8471N

61st

1.110 ^{+/- 0.013}

Intel Xeon Platinum 8490H

60th

1.082 ^{+/- 0.050}

AMD Ryzen 9 7950X 16-Core

55th

0.761 ^{+/- 0.034}

AMD EPYC 4584PX 16-Core

55th

0.758

AMD EPYC 4564P 16-Core

53rd

0.753 ^{+/- 0.008}

AMD Ryzen Threadripper 3990X 64-Core

51st

0.671 ^{+/- 0.002}

Median

50th

0.650

Intel Xeon Gold 5416S

50th

0.646 ^{+/- 0.004}

AMD Ryzen 9 7900 12-Core

49th

0.622 ^{+/- 0.003}

AMD EPYC 4464P 12-Core

49th

0.608

Intel Core i9-10980XE

48th

0.598 ^{+/- 0.007}

AMD Ryzen Threadripper 3970X 32-Core

47th

0.569

AMD Ryzen Threadripper PRO 5965WX 24-Cores

46th

0.531 ^{+/- 0.001}

2 x AMD EPYC 7303 16-Core

45th

0.522 ^{+/- 0.006}

AMD EPYC 4364P 8-Core

44th

0.493 ^{+/- 0.002}

AMD EPYC 4344P 8-Core

43rd

0.486

Intel Core i9-14900K

40th

0.465 ^{+/- 0.003}

AMD Ryzen 7 8700G

38th

0.425 ^{+/- 0.039}

AMD EPYC 4244P 6-Core

37th

0.390

AMD Ryzen 5 7600 6-Core

35th

0.382 ^{+/- 0.006}

AMD Ryzen 7 7840HS

34th

0.375 ^{+/- 0.035}

AMD Ryzen 5 8400F 6-Core

34th

0.370

Intel Xeon Silver 4216

32nd

0.354 ^{+/- 0.004}

AMD EPYC 7551 32-Core

31st

0.351 ^{+/- 0.003}

AMD EPYC 4124P 4-Core

26th

0.274 ^{+/- 0.001}

AMD EPYC 4484PX 12-Core

26th

0.270

Low-Tier

25th

< 0.270

Intel Core i5-14400F

24th

0.211

Intel Xeon E E-2488

22nd

0.208 ^{+/- 0.002}

AMD Ryzen 7 5700G

20th

0.180 ^{+/- 0.006}

Intel Core i7-1185G7

19th

0.168

AMD Ryzen 7 3800XT 8-Core

18th

0.165

AMD Ryzen 9 5900HX

17th

0.162

AMD EPYC 7F32 8-Core

16th

0.160 ^{+/- 0.001}

Intel Core i7-1165G7

14th

0.150 ^{+/- 0.005}

Intel Core Ultra 7 155H

14th

0.149 ^{+/- 0.010}

Intel Core i7-1280P

12th

0.129

Intel Core Ultra 7 165U

12th

0.127

AMD Ryzen 7 PRO 6850U

10th

0.111 ^{+/- 0.003}

Intel Core i7-1065G7

8th

0.105 ^{+/- 0.004}

Intel Core i7-5960X

8th

0.104 ^{+/- 0.001}

AMD Ryzen 5 5500U

7th

0.098 ^{+/- 0.001}

AMD Ryzen 7 PRO 5850U

6th

0.094 ^{+/- 0.002}

AMD Ryzen 7 4700U

5th

0.094

Intel Xeon E3-1280 v5

4th

0.065

Intel Core i7-8565U

2nd

0.044 ^{+/- 0.002}

Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD 3.0b6 - Input: STMV with 1,066,628 Atoms) has an average run-time of 11 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 0.6%.

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.

MOVDQA MOVDQU PUNPCKLQDQ MOVUPD PSRLDQ MOVD CVTSI2SD DIVSD MULSD COMISD ADDSD CVTTSD2SI CVTSD2SS ADDPD CVTSS2SD SUBSD MOVAPD ANDPD CMPNLESD UNPCKLPD SUBPD SQRTSD XORPD MULPD CVTPD2PS MOVHPD MAXSD MOVLPD UNPCKHPD SHUFPD CVTPS2PD MINSD PSHUFD CVTDQ2PD DIVPD PSUBQ PADDQ CVTDQ2PS SQRTPD CMPNLTSD ANDNPD ORPD PMULUDQ MAXPD CMPEQPD CMPNEQPD CMPLESD CMPLEPD CMPLTPD MINPD UCOMISD CMPLTSD MOVMSKPD

Last automated analysis: 18 February 2024

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

Tested CPU Architectures

This benchmark has been successfully tested on the below mentioned architectures. The CPU architectures listed is where successful OpenBenchmarking.org result uploads occurred, namely for helping to determine if a given test is compatible with various alternative CPU architectures.

CPU Architecture

Kernel Identifier

Verified On

Intel / AMD x86 64-bit