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.

Learn more about this test at the upstream project site: http://www.ks.uiuc.edu/Research/namd/.

This benchmark test profile is maintained by Michael Larabel. This OpenBenchmarking.org test profile was created on 22 December 2018 and last updated on 18 September 2020. To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark namd-cuda.

This test has an average install time of 7 seconds and an average run-time of 3 minutes, 37 seconds.

10k+ Downloads

Installation StatsTest Completion StatsOpenBenchmarking.orgEventsNAMD CUDA Popularitypts/namd-cuda2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.091632486480

* Data based on those opting to upload their test results to OpenBenchmarking.org and users enabling the opt-in anonymous statistics reporting.

Revision History

pts/namd-cuda-1.1.1   [View Source]   18 Sep 2020 13:22 EDT
TestType should be Graphics not Processor, typo when spinning off from namd test profile.

pts/namd-cuda-1.1.0   [View Source]   27 Aug 2020 15:53 EDT
Update against upstream NAMD 2.14.

pts/namd-cuda-1.0.0   [View Source]   22 Dec 2018 09:28 EST
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 209 public samples since 27 August 2020 with the latest data as of 11 October 2020.

Additional benchmark metrics will come after OpenBenchmarking.org has collected a sufficient data-set.

OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms209 Results Range From 0 To 1 days/ns00.0830.1660.2490.3320.4150.4980.5810.6640.7470.830.9130.996306090120150

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: 1.32 / Max: 4

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: 0.67 / Max: 3

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