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

5 Seconds

Average Run Time

3 Minutes, 37 Seconds

Accolades

10k+ Downloads

Supported Platforms

Supported Architectures

x86_64

Public Result UploadsReported Installs*Test Completions*OpenBenchmarking.orgEventsNAMD CUDA Popularity Statisticspts/namd-cuda2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042004006008001000
* 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.
Data current as of Mon, 12 Apr 2021 06:14:19 GMT.

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 503 public results since 27 August 2020 with the latest data as of 8 April 2021.

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
# Matching Public Results
days/ns (Average)
99th
7
0.13088 +/- 0.00448
96th
5
0.13823 +/- 0.00451
93rd
12
0.14307 +/- 0.01791
93rd
9
0.14379 +/- 0.01358
92nd
7
0.14774 +/- 0.00150
90th
6
0.14954 +/- 0.00132
90th
7
0.14959 +/- 0.00169
89th
11
0.15353 +/- 0.01723
87th
6
0.15912 +/- 0.00255
86th
7
0.16204 +/- 0.00432
84th
3
0.16776 +/- 0.00854
Mid-Tier
75th
> 0.19195
71st
4
0.19607 +/- 0.00650
Median
50th
0.22867
25th
3
0.58687 +/- 0.00123
Low-Tier
25th
> 0.58662
24th
3
0.68751 +/- 0.03160
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms501 Results Range From 0 To 2 days/ns00.1670.3340.5010.6680.8351.0021.1691.3361.5031.671.8372.00460120180240300

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.

OpenBenchmarking.orgMinutesTime Required To Complete BenchmarkATPase Simulation - 327,506 AtomsRun-Time246810Min: 1 / Avg: 1.83 / Max: 6

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 1%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsATPase Simulation - 327,506 AtomsDeviation246810Min: 0 / Avg: 0.97 / Max: 3

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
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
Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).

 
VPBROADCASTQ VGATHERQPD VEXTRACTI128 VPBROADCASTD
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: 30 January 2021

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.

Recent Test Results

OpenBenchmarking.org Results Compare

1 System - 1 Benchmark Result

AMD Ryzen Threadripper 3970X 32-Core - ASRock TRX40 Creator - AMD Starship

Debian 10 - 4.19.0-16-amd64 - GNOME Shell 3.30.2

3 Systems - 99 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

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

1 System - 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

1 System - 1 Benchmark Result

Intel Core i7-9750H - Notebook P95_96_97Ex Rx - Intel Cannon Lake PCH

Ubuntu 20.10 - 5.8.0-48-generic - GNOME Shell 3.38.2

1 System - 1 Benchmark Result

AMD Ryzen 7 5800X 8-Core - Gigabyte B550 AORUS MASTER - AMD Starship

Linuxmint 20.1 - 5.11.0-051100-generic - Cinnamon 4.8.6

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

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

Most Popular Test Results

OpenBenchmarking.org Results Compare

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

3 Systems - 15 Benchmark Results

AMD Ryzen 5 2600 Six-Core - Gigabyte X470 AORUS ULTRA GAMING-CF - AMD 17h

Ubuntu 19.10 - 5.3.0-64-generic - KDE Plasma 5.18.3

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

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

8 Systems - 27 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

3 Systems - 52 Benchmark Results

Intel Core i7-5775C - CompuLab v1.0 - Intel Broadwell-U DMI

Ubuntu 20.10 - 5.8.0-26-generic - GNOME Shell 3.38.1

1 System - 55 Benchmark Results

AMD Ryzen 9 3950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 20.04 - 5.4.0-48-generic - GNOME Shell 3.36.4

23 Systems - 123 Benchmark Results

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

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