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

Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsNAMD CUDA Popularity Statisticspts/namd-cuda2018.122019.022019.042019.062019.082019.102019.122020.022020.042020.062020.082020.102020.122021.022021.042021.062021.082021.102021.122022.022022.042022.062022.082022.102022.122023.022023.042023.062023.082023.102023.122024.022024.042024.062K4K6K8K10K
* 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 8 June 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 593 public results since 27 August 2020 with the latest data as of 29 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
days/ns (Average)
96th
10
0.072 +/- 0.009
79th
14
0.124 +/- 0.016
Mid-Tier
75th
> 0.128
70th
17
0.136 +/- 0.014
69th
12
0.137 +/- 0.016
64th
13
0.146 +/- 0.004
63rd
8
0.147 +/- 0.005
57th
11
0.156 +/- 0.004
56th
14
0.159 +/- 0.005
54th
10
0.164 +/- 0.015
53rd
3
0.168 +/- 0.009
Median
50th
0.172
50th
12
0.173 +/- 0.004
39th
4
0.196 +/- 0.007
Low-Tier
25th
> 0.246
19th
4
0.339 +/- 0.011
12th
16
0.382 +/- 0.006
7th
6
0.546 +/- 0.061
5th
4
0.693 +/- 0.028
4th
3
0.845 +/- 0.008
1st
3
4.105 +/- 0.008
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms593 Results Range From 0 To 30 days/ns369121518212427303336130260390520650

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-Time510152025Min: 1 / Avg: 2.07 / Max: 19

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 1.2%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsATPase Simulation - 327,506 AtomsDeviation48121620Min: 0 / Avg: 1.16 / Max: 14

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
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)

Recent Test Results

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Intel Core i7-12700H - System76 Oryx Pro - Intel Alder Lake PCH

Pop 22.04 - 6.8.0-76060800daily20240311-generic - GNOME Shell 42.9

1 System - 1 Benchmark Result

Intel Core i7-12700H - System76 Oryx Pro - Intel Alder Lake PCH

Pop 22.04 - 6.8.0-76060800daily20240311-generic - GNOME Shell 42.9

1 System - 7 Benchmark Results

Intel Core i7-12700H - System76 Oryx Pro - Intel Alder Lake PCH

Pop 22.04 - 6.8.0-76060800daily20240311-generic - GNOME Shell 42.9

1 System - 8 Benchmark Results

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Pop 22.04 - 6.8.0-76060800daily20240311-generic - GNOME Shell 42.9

1 System - 4 Benchmark Results

Intel Core i7-12700H - System76 Oryx Pro - Intel Alder Lake PCH

Pop 22.04 - 6.8.0-76060800daily20240311-generic - GNOME Shell 42.9

1 System - 8 Benchmark Results

Intel Core i7-12700H - System76 Oryx Pro - Intel Alder Lake PCH

Pop 22.04 - 6.8.0-76060800daily20240311-generic - GNOME Shell 42.9

1 System - 134 Benchmark Results

AMD Ryzen 7 7700X 8-Core - MSI PRO B650-P WIFI - AMD Device 14d8

Ubuntu 23.04 - 6.2.0-39-generic - GNOME Shell 44.3

1 System - 133 Benchmark Results

AMD Ryzen Threadripper 7960X 24-Cores - ASRock TRX50 WS - AMD Device 14a4

Ubuntu 22.04 - 6.5.0-26-generic - GNOME Shell 42.9

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Ubuntu 20.04 - 5.4.0-42-generic - GNOME Shell 3.36.4

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

3 Systems - 67 Benchmark Results

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