NAMD

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.

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 19 September 2018 and last updated on 28 August 2020. To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark namd.

This test has an average install time of 3 seconds and an average run-time of 5 minutes, 42 seconds.

40k+ Downloads

Installation StatsTest Completion StatsOpenBenchmarking.orgEventsNAMD Popularitypts/namd2018.092018.102018.112018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.09130260390520650

* 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-1.2.1   [View Source]   28 Aug 2020 06:28 EDT
Fix checksum on NAMD 2.14 Linux build as apparently it changed upstream.

pts/namd-1.2.0   [View Source]   20 Aug 2020 10:53 EDT
Update against new upstream NAMD 2.14 release.

pts/namd-1.1.0   [View Source]   29 Feb 2020 08:14 EST
Overdue been meaning to bump upstream from beta to final 2.13.

pts/namd-1.0.2   [View Source]   15 Oct 2019 17:14 EDT
Add macOS support.

pts/namd-1.0.1   [View Source]   17 Jan 2019 11:31 EST
Add Windows support.

pts/namd-1.0.0   [View Source]   19 Sep 2018 13:38 EDT
Initial commit finally of NAMD benchmark...

Suites Using This Test

Multi-Core

CPU Massive

Server CPU Tests

Molecular Dynamics

Scientific Computing

Performance Metrics

Analyze Test Configuration:

NAMD 2.14

ATPase Simulation - 327,506 Atoms

OpenBenchmarking.org metrics for this test profile configuration based on 534 public samples since 20 August 2020 with the latest data as of 23 October 2020.

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
days/ns (Average)
Mid-Tier
75th
> 0.98
Median
50th
2.03
Low-Tier
25th
> 4.00
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms534 Results Range From 0 To 26 days/ns036912151821242730333680160240320400

Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD 2.14 - ATPase Simulation - 327,506 Atoms) has an average run-time of 8 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-Time816243240Min: 1 / Avg: 7.51 / Max: 36

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.2%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsATPase Simulation - 327,506 AtomsDeviation246810Min: 0 / Avg: 0.25 / Max: 4

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