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

22 September 2024

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

3 Seconds

Average Run Time

6 Minutes, 57 Seconds

Accolades

80k+ 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 17 January 2025.

Revision History

pts/namd-1.4.0 [View Source] Sun, 22 Sep 2024 14:31:41 GMT
Update against NAMD 3.0 upstream.

pts/namd-1.3.2 [View Source] Fri, 07 Jun 2024 20:08:12 GMT
Adjust NUMA tuning per https://github.com/phoronix-test-suite/test-profiles/pull/308 Closes: https://github.com/phoronix-test-suite/test-profiles/pull/308

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 3.0

Input: STMV with 1,066,628 Atoms

OpenBenchmarking.org metrics for this test profile configuration based on 355 public results since 23 September 2024 with the latest data as of 13 January 2025.

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 9755 128-Core

100th

9.623 ^{+/- 0.062}

2 x AMD EPYC 9745 128-Core

96th

8.239 ^{+/- 0.130}

2 x AMD EPYC 9825 144-Core

96th

8.184 ^{+/- 0.289}

2 x AMD EPYC 9575F 64-Core

93rd

5.926 ^{+/- 0.046}

2 x AMD EPYC 9684X 96-Core

92nd

5.673 ^{+/- 0.027}

2 x AMD EPYC 9654 96-Core

89th

5.140 ^{+/- 0.007}

AMD EPYC 9965 192-Core

88th

5.110 ^{+/- 0.011}

2 x AMD EPYC 9535 64-Core

87th

4.616 ^{+/- 0.056}

AMD EPYC 9655P 96-Core

79th

4.103 ^{+/- 0.300}

Intel Xeon 6980P

78th

3.978 ^{+/- 0.050}

Mid-Tier

75th

< 3.754

AMD EPYC 9575F 64-Core

75th

3.719 ^{+/- 0.195}

2 x AMD EPYC 9534 64-Core

73rd

3.112 ^{+/- 0.024}

AMD Ryzen Threadripper 7980X 64-Cores

69th

1.626 ^{+/- 0.010}

2 x AMD EPYC 9124 16-Core

68th

1.579 ^{+/- 0.001}

AMD Ryzen 9 9950X 16-Core

65th

0.981 ^{+/- 0.044}

AMD EPYC 4584PX 16-Core

64th

0.760 ^{+/- 0.003}

AMD EPYC 4564P 16-Core

63rd

0.757 ^{+/- 0.002}

AMD Ryzen 7 9800X3D 8-Core

60th

0.753 ^{+/- 0.005}

AMD Ryzen Threadripper 3990X 64-Core

58th

0.670 ^{+/- 0.002}

AMD EPYC 4484PX 12-Core

57th

0.652 ^{+/- 0.003}

AMD EPYC 4464P 12-Core

54th

0.613 ^{+/- 0.002}

Intel Core Ultra 9 285K

53rd

0.606 ^{+/- 0.014}

AMD Ryzen 9 7945HX

52nd

0.602 ^{+/- 0.004}

Intel Core i9-10980XE

51st

0.593 ^{+/- 0.001}

Median

50th

0.592

2 x Intel Xeon Gold 6144

47th

0.570 ^{+/- 0.002}

AMD Ryzen Threadripper 3970X 32-Core

42nd

0.558

AMD EPYC 4364P 8-Core

41st

0.497 ^{+/- 0.001}

Intel Core i9-14900K

39th

0.444 ^{+/- 0.006}

AMD Ryzen AI 9 HX 370

37th

0.414 ^{+/- 0.016}

AMD Ryzen 5 7600 6-Core

35th

0.398 ^{+/- 0.001}

Intel Core Ultra 5 245K

33rd

0.392 ^{+/- 0.001}

AMD Ryzen 7 7840HS

32nd

0.377 ^{+/- 0.007}

Intel Xeon Silver 4216

31st

0.351 ^{+/- 0.001}

AMD Ryzen AI 9 365

30th

0.334 ^{+/- 0.035}

AMD Ryzen 9 5950X 16-Core

27th

0.274 ^{+/- 0.015}

AMD EPYC 4124P 4-Core

27th

0.273

Low-Tier

25th

< 0.265

AMD Ryzen 9 5900X 12-Core

25th

0.262 ^{+/- 0.003}

Intel Core i5-12600K

23rd

0.212 ^{+/- 0.002}

AMD Ryzen 7 5800X 8-Core

22nd

0.193 ^{+/- 0.003}

AMD Ryzen 7 5800X3D 8-Core

21st

0.181

Intel Core i7-1185G7

20th

0.169

AMD EPYC 7F32 8-Core

19th

0.160 ^{+/- 0.002}

AMD Ryzen 9 5900HX

18th

0.150 ^{+/- 0.001}

Intel Core Ultra 7 155H

16th

0.132 ^{+/- 0.009}

Intel Core i7-10875H

12th

0.119 ^{+/- 0.003}

Intel Core Ultra 7 256V

9th

0.114 ^{+/- 0.013}

AMD Ryzen 7 PRO 6850U

7th

0.103 ^{+/- 0.001}

Intel Core i7-1065G7

6th

0.102 ^{+/- 0.004}

AMD Ryzen 7 PRO 5850U

5th

0.098

Detailed Performance Overview

Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD 3.0 - Input: STMV with 1,066,628 Atoms) has an average run-time of 9 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 0.1%.

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: 16 October 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