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
Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsNAMD CUDA Popularity Statisticspts/namd-cuda2018.122019.022019.042019.062019.082019.102019.122020.022020.042020.062020.082020.102020.122021.022021.042021.062021.082021.102021.122022.022022.042022.062022.082022.102022.122023.022023.042023.062023.082023.102023.122024.022024.042024.062024.082024.102K4K6K8K10K
* 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 November 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
10
0.072 +/- 0.009
Zotac NVIDIA GeForce RTX 4070 Ti
91st
5
0.083
AMD Radeon RX 7900 XT
89th
3
0.090
AMD Radeon RX 7900 XTX
89th
3
0.090
NVIDIA GeForce RTX 3070
79th
14
0.124 +/- 0.016
Mid-Tier
75th
> 0.128
NVIDIA GeForce RTX 3060 Ti
70th
17
0.136 +/- 0.014
AMD Radeon RX 6800
70th
3
0.137
NVIDIA GeForce RTX 2080 SUPER
69th
12
0.137 +/- 0.016
NVIDIA GeForce RTX 2070 SUPER
63rd
13
0.146 +/- 0.004
Zotac NVIDIA GeForce RTX 2080
63rd
8
0.147 +/- 0.005
ASUS NVIDIA GeForce RTX 2070
57th
11
0.156 +/- 0.004
NVIDIA GeForce RTX 2060 SUPER
55th
14
0.159 +/- 0.005
eVGA NVIDIA GeForce RTX 3060
54th
10
0.164 +/- 0.015
NVIDIA GeForce GTX 1080 Ti
52nd
3
0.168 +/- 0.009
Median
50th
0.172
NVIDIA GeForce RTX 2060
50th
12
0.173 +/- 0.004
NVIDIA GeForce GTX 1080
39th
4
0.196 +/- 0.007
NVIDIA Quadro RTX 5000 with Max-Q Design
29th
4
0.230 +/- 0.018
Low-Tier
25th
> 0.246
Intel ADL GT2
19th
4
0.339 +/- 0.011
NVIDIA GeForce RTX 3070 Ti Laptop GPU
16th
13
0.347 +/- 0.002
Gigabyte NVIDIA GeForce RTX 3070
15th
4
0.354 +/- 0.009
ASUS NVIDIA GeForce GTX 1080 Ti
12th
16
0.382 +/- 0.006
NVIDIA Quadro P2000
7th
6
0.546 +/- 0.061
eVGA NVIDIA GeForce GTX 950
5th
4
0.693 +/- 0.028
NVIDIA T400
4th
3
0.845 +/- 0.008
NVIDIA GeForce 920M
1st
3
4.105 +/- 0.008
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms600 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: 2.08 / Max: 19

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 1.1%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsATPase Simulation - 327,506 AtomsDeviation48121620Min: 0 / Avg: 1.15 / 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
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)

Recent Test Results

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1 System - 1 Benchmark Result

AMD Ryzen 9 5900X 12-Core - 32GB - 0GB Virtual Disk + 9GB Virtual Disk + 1100GB Virtual Disk

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1 System - 113 Benchmark Results

AMD Ryzen 9 7900X3D 12-Core - ASUS ProArt B650-CREATOR - AMD Device 14d8

Ubuntu 24.04 - 6.8.0-47-generic - GNOME Shell 46.0

1 System - 1 Benchmark Result

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Ubuntu 20.04 - 5.15.0-117-generic - GNOME Shell 3.36.9

1 System - 116 Benchmark Results

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RockyLinux 9.4 - 6.1.102-1.el9.elrepo.x86_64 - KDE Plasma 5.27.11

2 Systems - 130 Benchmark Results

2 Systems - 6 Benchmark Results

AMD Ryzen 9 5950X 16-Core - ASUS ROG STRIX B550-E GAMING - AMD Starship

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2 Systems - 6 Benchmark Results

AMD Ryzen 9 5950X 16-Core - ASUS ROG STRIX B550-E GAMING - AMD Starship

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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 - 6 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 - 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

Most Popular Test Results

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13 Systems - 23 Benchmark Results

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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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Ubuntu 20.04 - 5.11.0-37-generic - GNOME Shell 3.36.9

3 Systems - 253 Benchmark Results

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Ubuntu 20.04 - 5.6.0-1034-oem - GNOME Shell 3.36.4

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