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 Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsNAMD CUDA Popularity Statisticspts/namd-cuda2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042021.052021.062021.072021.082004006008001000
* 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 current as of 4 August 2021.

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 424 public results since 27 August 2020 with the latest data as of 3 August 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
# Compatible Public Results
days/ns (Average)
96th
10
0.12761 +/- 0.00641
91st
7
0.13477 +/- 0.00697
88th
27
0.14017 +/- 0.01352
86th
11
0.14115 +/- 0.01349
81st
9
0.14496 +/- 0.00567
80th
8
0.14665 +/- 0.00545
80th
10
0.14767 +/- 0.00339
78th
13
0.15041 +/- 0.01747
Mid-Tier
75th
> 0.15419
73rd
8
0.15746 +/- 0.00376
72nd
5
0.15957 +/- 0.00444
72nd
9
0.16048 +/- 0.00486
69th
3
0.16776 +/- 0.00854
Median
50th
0.19265
47th
4
0.19607 +/- 0.00650
Low-Tier
25th
> 0.24290
12th
3
0.58687 +/- 0.00123
10th
3
0.68751 +/- 0.03160
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms424 Results Range From 0 To 30 days/ns036912151821242730333690180270360450

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-Time3691215Min: 1 / Avg: 1.6 / Max: 8

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.7%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsATPase Simulation - 327,506 AtomsDeviation246810Min: 0 / Avg: 0.7 / Max: 4

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: 10 May 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

2 Systems - 1 Benchmark Result

2 x AMD EPYC 7713 64-Core - Supermicro H12DSG-O-CPU - AMD Starship

CentOS 8.3.2011 - 4.18.0-240.22.1.el8_3.x86_64 - X Server

1 System - 101 Benchmark Results

AMD Ryzen 9 5950X 16-Core - Gigabyte X570 AORUS ULTRA - AMD Starship

Debian 10 - 4.19.0-8-amd64 - GNOME Shell 3.30.2

1 System - 103 Benchmark Results

AMD Ryzen 9 5900 12-Core - Alienware 0TYR0X - AMD Starship

Ubuntu 20.04 - 5.8.0-63-generic - GNOME Shell 3.36.9

1 System - 1 Benchmark Result

AMD Ryzen 9 5900X 12-Core - Gigabyte B550 AORUS ELITE V2 - AMD Starship

Ubuntu 20.04 - 5.8.0-59-generic - GNOME Shell 3.36.4

1 System - 1 Benchmark Result

Intel Core i7-8700 - ASUS PRIME Z390-P - Intel Cannon Lake PCH

Ubuntu 20.04 - 5.8.0-59-generic - GNOME Shell 3.36.9

1 System - 171 Benchmark Results

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

1 System - 39 Benchmark Results

Intel 0000 - Gigabyte H81-D3 - Intel 4th Gen Core DRAM

Ubuntu 20.04 - 5.8.0-53-generic - GNOME Shell 3.36.7

1 System - 1 Benchmark Result

AMD Ryzen 9 3900X 12-Core - ASUS ROG STRIX B550-I GAMING - AMD Starship

ManjaroLinux 21.0.3 - 5.10.32-1-MANJARO - GNOME Shell 3.38.4

25 Systems - 134 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

1 System - 55 Benchmark Results

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

Most Popular Test Results

OpenBenchmarking.org Results Compare

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 - 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

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

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

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

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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