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 14 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 287 public results since 16 February 2024 with the latest data as of 13 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

97th

6.446 ^{+/- 0.038}

AMD Ryzen Threadripper PRO 7995WX 96-Cores

93rd

2.495 ^{+/- 0.001}

2 x Intel Xeon Max 9468

90th

1.989 ^{+/- 0.096}

AMD Ryzen Threadripper 7980X 64-Cores

83rd

1.636 ^{+/- 0.022}

AMD EPYC 8534P 64-Core

81st

1.582 ^{+/- 0.011}

Intel Xeon Max 9468

79th

1.449 ^{+/- 0.003}

Intel Xeon Max 9480

77th

1.433 ^{+/- 0.132}

Mid-Tier

75th

< 1.384

INTEL XEON PLATINUM 8592

75th

1.356 ^{+/- 0.080}

2 x Intel Xeon Platinum 8280

74th

1.334 ^{+/- 0.007}

2 x Intel Xeon Platinum 8490H

69th

1.155 ^{+/- 0.036}

Intel Xeon Platinum 8490H

67th

1.084 ^{+/- 0.050}

AMD Ryzen 9 7950X 16-Core

62nd

0.761 ^{+/- 0.034}

AMD Ryzen Threadripper 3990X 64-Core

58th

0.671 ^{+/- 0.002}

Intel Xeon Gold 5416S

57th

0.646 ^{+/- 0.004}

AMD Ryzen 9 7900 12-Core

56th

0.622 ^{+/- 0.003}

Intel Core i9-10980XE

54th

0.598 ^{+/- 0.007}

AMD Ryzen Threadripper 3970X 32-Core

53rd

0.569

AMD Ryzen Threadripper PRO 5965WX 24-Cores

52nd

0.531 ^{+/- 0.001}

Median

50th

0.524

2 x AMD EPYC 7303 16-Core

50th

0.522 ^{+/- 0.006}

Intel Core i9-14900K

46th

0.465 ^{+/- 0.003}

AMD Ryzen 7 8700G

42nd

0.425 ^{+/- 0.039}

AMD Ryzen 5 7600 6-Core

39th

0.382 ^{+/- 0.006}

AMD Ryzen 7 7840HS

37th

0.372 ^{+/- 0.035}

Intel Xeon Silver 4216

36th

0.354 ^{+/- 0.004}

AMD EPYC 7551 32-Core

34th

0.351 ^{+/- 0.003}

AMD Ryzen 7 7840U

29th

0.229 ^{+/- 0.023}

Intel Xeon E E-2488

26th

0.209 ^{+/- 0.001}

Low-Tier

25th

< 0.206

Intel Core i7-1185G7

24th

0.168

AMD Ryzen 7 3800XT 8-Core

22nd

0.165

AMD Ryzen 9 5900HX

21st

0.162

AMD EPYC 7F32 8-Core

20th

0.160 ^{+/- 0.001}

Intel Core Ultra 7 155H

18th

0.156 ^{+/- 0.003}

Intel Core i7-1165G7

17th

0.150 ^{+/- 0.005}

Intel Core i7-1280P

15th

0.129

AMD Ryzen 7 PRO 6850U

13th

0.111 ^{+/- 0.003}

Intel Core i7-1065G7

10th

0.105 ^{+/- 0.004}

Intel Core i7-5960X

10th

0.104 ^{+/- 0.001}

AMD Ryzen 5 5500U

8th

0.098 ^{+/- 0.001}

AMD Ryzen 7 PRO 5850U

6th

0.094 ^{+/- 0.002}

AMD Ryzen 7 4700U

6th

0.094

Intel Core i7-8565U

3rd

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 0.4%.

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