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

15 Minutes, 56 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 3 December 2023.

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 536 public results since 27 August 2020 with the latest data as of 26 November 2023.

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

98th

0.068 ^{+/- 0.008}

NVIDIA GeForce RTX 3070

82nd

0.124 ^{+/- 0.016}

Mid-Tier

75th

> 0.133

NVIDIA GeForce RTX 3060 Ti

73rd

0.136 ^{+/- 0.014}

NVIDIA GeForce RTX 2080 SUPER

72nd

0.137 ^{+/- 0.016}

NVIDIA GeForce RTX 2070 SUPER

66th

0.146 ^{+/- 0.004}

Zotac NVIDIA GeForce RTX 2080

66th

0.147 ^{+/- 0.005}

ASUS NVIDIA GeForce RTX 2070

59th

0.156 ^{+/- 0.004}

NVIDIA GeForce RTX 2060 SUPER

57th

0.159 ^{+/- 0.005}

eVGA NVIDIA GeForce RTX 3060

56th

0.164 ^{+/- 0.015}

NVIDIA GeForce GTX 1080 Ti

54th

0.168 ^{+/- 0.009}

NVIDIA GeForce RTX 2060

52nd

0.173 ^{+/- 0.004}

Median

50th

0.179

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

> 0.243

Intel ADL GT2

17th

0.339 ^{+/- 0.011}

Gigabyte NVIDIA GeForce RTX 3070

16th

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 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 1.2%.

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)

LENOVO 23252UG (G2ETA2WW 2.62 BIOS) On Debian 11 1 System - 2 Benchmark Results	Intel Core i5-3320M - LENOVO 23252UG - Intel 3rd Gen Core DRAM Debian 11 - 5.10.0-18-amd64 - Xfce 4.16
namd_without_disturbance 1 System - 1 Benchmark Result	2 x Intel Xeon Gold 6326 - GIGABYTE MD72-HB3-00 v01000100 - Intel Device 0998 Ubuntu 20.04 - 5.15.0-89-generic - GNOME Shell 3.36.9
unigineheaven1 1 System - 1 Benchmark Result	2 x Intel Xeon Gold 6326 - GIGABYTE MD72-HB3-00 v01000100 - Intel Device 0998 Ubuntu 20.04 - 5.15.0-89-generic - GNOME Shell 3.36.9
AMD Ryzen 7 5700U Performance 1 System - 3 Benchmark Results	AMD Ryzen 7 5700U - LENOVO LNVNB161216 - AMD Renoir Root Complex Debian 11 - 5.10.60 - GNOME Shell 3.38.6
namd-214 2 Systems - 8 Benchmark Results	Intel Xeon w9-3495X - ASUS Pro WS W790E-SAGE SE - Intel Device 7aa7 Ubuntu 22.04 - 6.3.0-060300-generic - GNOME Shell 42.9
NAMD-214 1 System - 4 Benchmark Results	Intel Xeon w9-3495X - ASUS Pro WS W790E-SAGE SE - Intel Device 7aa7 Ubuntu 22.04 - 6.3.0-060300-generic - GNOME Shell 42.9
HP 89C0 (U97 Ver. 01.08.00 BIOS) On Fedora Linux 39 1 System - 9 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
Fedora Linux 39 Benchmarks 1 System - 7 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
Fedora Linux 39 Performance 1 System - 5 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
HP 89C0 (U97 Ver. 01.08.00 BIOS) On Fedora Linux 39 1 System - 8 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
i7-12700hrtx3060 Featured Disk Comparison	128GB HFM128GDJTNG-8310A + 1024GB SAMSUNG MZVL21T0HCLR-00B07 - 1024GB SAMSUNG MZVL21T0HCLR-00B07 + 128GB HFM128GDJTNG-8310A
pisystem 1 System - 1 Benchmark Result	Intel Core i9-12900K - Gigabyte Z790 GAMING X AX - Intel Device 7a27 Ubuntu 22.04 - 6.2.0-35-generic - GNOME Shell 42.9
Latitude System 1/5 Test 1 System - 168 Benchmark Results	2 x AMD EPYC 9354 32-Core - Supermicro H13DSG-O-CPU v1.10 - AMD Device 14a4 Ubuntu 22.04 - 6.2.0-34-generic - GNOME Shell 42.9
atomicrulez_ubuntu_2310_namd-cuda 1 System - 1 Benchmark Result	Intel Core i9-10850K - ASUS ROG MAXIMUS XII APEX - Intel Comet Lake PCH Ubuntu 23.10 - 6.5.0-5-generic - GNOME Shell 45.0
oo080800x06092023 1 System - 1 Benchmark Result	Intel Core i5-4210U - Acer ZORO_BH - Intel Haswell-ULT DRAM Ubuntu 20.04 - 5.15.0-83-generic - Xfce 4.14

NVIDIA GeForce RTX 30 Linux GPU Compute Benchmarks Featured Graphics Comparison	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.8.0-48-generic - GNOME Shell 3.36.7
HP Zbook 3 Systems - 253 Benchmark Results	Intel Core i9-10885H - HP 8736 - Intel Comet Lake PCH Ubuntu 20.04 - 5.6.0-1034-oem - GNOME Shell 3.36.4
NVIDIA Linux GPU Benchmarks 2021 12 Systems - 59 Benchmark Results	AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.10 - 5.8.0-41-generic - GNOME Shell 3.38.2
NVIDIA CUDA OpenCL Compute Tests Pre-Ampere 13 Systems - 23 Benchmark Results	AMD Ryzen 9 3950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.4.0-42-generic - GNOME Shell 3.36.4
nvidia linux 17 Systems - 41 Benchmark Results	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.11.0-37-generic - GNOME Shell 3.36.9
RTX 30 Compute September Featured Graphics Comparison	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 21.10 - 5.13.0-14-generic - GNOME Shell 40.2
nvidia geforce gtx 3090 3 Systems - 67 Benchmark Results	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.11.0-37-generic - GNOME Shell 3.36.9
ngc rtx 3090 3 Systems - 100 Benchmark Results	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.8.0-48-generic - GNOME Shell 3.36.7
nvidia-linux-gpu-performance-20212 Featured Graphics Comparison	AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.10 - 5.8.0-41-generic - GNOME Shell 3.38.2
NVIDIA GeForce RTX 3090 3 Systems - 177 Benchmark Results	AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 21.10 - 5.13.0-22-generic - GNOME Shell 40.5
March 2021 Linux Vulkan, RT, Compute Featured Graphics Comparison	AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.10 - 5.8.0-44-generic - GNOME Shell 3.38.2
nvidia linux 17 Systems - 41 Benchmark Results	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.11.0-37-generic - GNOME Shell 3.36.9
GTX 1080 Ti 3 Systems - 75 Benchmark Results	Intel Core i9-10980XE - ASRock X299 Steel Legend - Intel Sky Lake-E DMI3 Registers Ubuntu 20.04 - 5.4.0-48-generic - GNOME Shell 3.36.3
NVIDIA GPU Compute OpenCL CUDA Benchmarks Featured Graphics Comparison	AMD Ryzen 9 3950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.4.0-45-generic - GNOME Shell 3.36.4
NVIDIA GPU Compute Benchmarks Featured Graphics Comparison	AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 21.04 - 5.11.0-17-generic - GNOME Shell 3.38.4

NAMD CUDA

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 CUDA 2.14

ATPase Simulation - 327,506 Atoms

Notable Instruction Set Usage

Tested CPU Architectures

Recent Test Results

Most Popular Test Results