NAMD CUDA

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. This version of the NAMD test profile uses CUDA GPU acceleration.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark namd-cuda.

Project Site

ks.uiuc.edu

Test Created

22 December 2018

Last Updated

18 September 2020

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

4 Seconds

Average Run Time

8 Minutes, 35 Seconds

Accolades

20k+ Downloads

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 2 December 2024.

Revision History

pts/namd-cuda-1.1.1 [View Source] Fri, 18 Sep 2020 13:22:37 GMT
TestType should be Graphics not Processor, typo when spinning off from namd test profile.

pts/namd-cuda-1.1.0 [View Source] Thu, 27 Aug 2020 15:53:41 GMT
Update against upstream NAMD 2.14.

pts/namd-cuda-1.0.0 [View Source] Sat, 22 Dec 2018 09:28:34 GMT
Initial commit of CUDA version of NAMD benchmark.

Suites Using This Test

NVIDIA GPU Compute

Performance Metrics

Analyze Test Configuration:

NAMD CUDA 2.14

ATPase Simulation - 327,506 Atoms

OpenBenchmarking.org metrics for this test profile configuration based on 600 public results since 27 August 2020 with the latest data as of 4 November 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

days/ns (Average)

NVIDIA GeForce RTX 4080

96th

0.072 ^{+/- 0.009}

Zotac NVIDIA GeForce RTX 4070 Ti

91st

0.083

AMD Radeon RX 7900 XT

89th

0.090

AMD Radeon RX 7900 XTX

89th

0.090

NVIDIA GeForce RTX 3070

79th

0.124 ^{+/- 0.016}

Mid-Tier

75th

> 0.128

NVIDIA GeForce RTX 3060 Ti

70th

0.136 ^{+/- 0.014}

AMD Radeon RX 6800

70th

0.137

NVIDIA GeForce RTX 2080 SUPER

69th

0.137 ^{+/- 0.016}

NVIDIA GeForce RTX 2070 SUPER

63rd

0.146 ^{+/- 0.004}

Zotac NVIDIA GeForce RTX 2080

63rd

0.147 ^{+/- 0.005}

ASUS NVIDIA GeForce RTX 2070

57th

0.156 ^{+/- 0.004}

NVIDIA GeForce RTX 2060 SUPER

55th

0.159 ^{+/- 0.005}

eVGA NVIDIA GeForce RTX 3060

54th

0.164 ^{+/- 0.015}

NVIDIA GeForce GTX 1080 Ti

52nd

0.168 ^{+/- 0.009}

Median

50th

0.172

NVIDIA GeForce RTX 2060

50th

0.173 ^{+/- 0.004}

NVIDIA GeForce GTX 1080

39th

0.196 ^{+/- 0.007}

NVIDIA Quadro RTX 5000 with Max-Q Design

29th

0.230 ^{+/- 0.018}

Low-Tier

25th

> 0.246

Intel ADL GT2

19th

0.339 ^{+/- 0.011}

NVIDIA GeForce RTX 3070 Ti Laptop GPU

16th

0.347 ^{+/- 0.002}

Gigabyte NVIDIA GeForce RTX 3070

15th

0.354 ^{+/- 0.009}

ASUS NVIDIA GeForce GTX 1080 Ti

12th

0.382 ^{+/- 0.006}

NVIDIA Quadro P2000

7th

0.546 ^{+/- 0.061}

eVGA NVIDIA GeForce GTX 950

5th

0.693 ^{+/- 0.028}

NVIDIA T400

4th

0.845 ^{+/- 0.008}

NVIDIA GeForce 920M

1st

4.105 ^{+/- 0.008}

Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD CUDA 2.14 - ATPase Simulation - 327,506 Atoms) has an average run-time of 2 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 1.1%.

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 CVTSD2SS SUBSD MULSD ADDSD CVTTSD2SI CVTSS2SD CVTPD2PS MOVDQU MOVD PSRLDQ CVTSI2SD DIVSD MOVHPD UNPCKLPD COMISD SQRTSD PSHUFD PUNPCKLQDQ PUNPCKHQDQ MINSD MAXSD UCOMISD MULPD CVTPS2PD ADDPD UNPCKHPD CMPLTSD CVTDQ2PD DIVPD SUBPD CMPLTPD MOVMSKPD PADDQ PSUBQ CVTDQ2PS SQRTPD CMPEQPD CVTTPD2DQ CMPNLTSD CMPEQSD CMPNEQSD CMPLESD CMPLEPD PMULUDQ MAXPD MINPD MOVAPD PSHUFLW 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 VMASKMOVPS VPERMILPD

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

Advanced Vector Extensions 512 (AVX512)

Used by default on supported hardware.

(ZMM REGISTER USE)

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 VFNMADD213SS VFMADD213PD VFNMADD231PD VFNMADD132PD VFMSUB213PD VFNMADD213PD VFMADD231PD VFMADD132PD VFMADD213PS VFNMADD213PS VFNMADD132PS

Last automated analysis: 18 January 2022

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

x86_64

(Many Processors)

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