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.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark namd.

Project Site

ks.uiuc.edu

Test Created

19 September 2018

Last Updated

28 August 2020

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

3 Seconds

Average Run Time

5 Minutes, 50 Seconds

Accolades

40k+ Downloads

Supported Platforms

Supported Architectures

x86_64

Public Result UploadsReported Installs*Test Completions*OpenBenchmarking.orgEventsNAMD Popularity Statisticspts/namd2018.092018.102018.112018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012K4K6K8K10K
* 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.
Data current as of Mon, 18 Jan 2021 20:57:30 GMT.

Revision History

pts/namd-1.2.1   [View Source]   Fri, 28 Aug 2020 06:28:19 GMT
Fix checksum on NAMD 2.14 Linux build as apparently it changed upstream.

pts/namd-1.2.0   [View Source]   Thu, 20 Aug 2020 10:53:15 GMT
Update against new upstream NAMD 2.14 release.

pts/namd-1.1.0   [View Source]   Sat, 29 Feb 2020 08:14:38 GMT
Overdue been meaning to bump upstream from beta to final 2.13.

pts/namd-1.0.2   [View Source]   Tue, 15 Oct 2019 17:14:19 GMT
Add macOS support.

pts/namd-1.0.1   [View Source]   Thu, 17 Jan 2019 11:31:07 GMT
Add Windows support.

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

Suites Using This Test

Multi-Core

CPU Massive

Server CPU Tests

Molecular Dynamics

Scientific Computing

HPC - High Performance Computing


Performance Metrics

Analyze Test Configuration:

NAMD 2.14

ATPase Simulation - 327,506 Atoms

OpenBenchmarking.org metrics for this test profile configuration based on 905 public results since 20 August 2020 with the latest data as of 17 January 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
# Matching Public Results
days/ns (Average)
96th
4
0.44 +/- 0.03
95th
4
0.45 +/- 0.04
93rd
27
0.48 +/- 0.02
93rd
6
0.49 +/- 0.01
88th
7
0.63 +/- 0.02
81st
18
0.86 +/- 0.01
76th
14
0.99 +/- 0.02
Mid-Tier
75th
> 1.07
75th
21
1.08 +/- 0.01
72nd
11
1.14 +/- 0.03
71st
9
1.15 +/- 0.01
69th
7
1.18 +/- 0.03
67th
20
1.24 +/- 0.03
63rd
39
1.29 +/- 0.01
56th
20
1.49 +/- 0.09
54th
20
1.52 +/- 0.04
53rd
8
1.56 +/- 0.04
51st
7
1.75 +/- 0.07
Median
50th
1.78
50th
8
1.84 +/- 0.06
48th
3
1.99 +/- 0.01
47th
6
2.03 +/- 0.11
46th
9
2.05 +/- 0.22
45th
12
2.13 +/- 0.06
45th
16
2.13 +/- 0.06
42nd
4
2.20 +/- 0.03
41st
6
2.26 +/- 0.01
41st
9
2.27 +/- 0.03
40th
4
2.37 +/- 0.01
39th
10
2.39 +/- 0.01
38th
4
2.45 +/- 0.01
35th
11
2.73 +/- 0.01
33rd
7
2.84 +/- 0.02
32nd
7
2.88 +/- 0.01
32nd
4
2.88 +/- 0.04
31st
9
2.89 +/- 0.14
30th
4
2.97 +/- 0.08
30th
3
2.98 +/- 0.02
28th
3
3.14 +/- 0.03
28th
3
3.14 +/- 0.01
28th
5
3.17 +/- 0.01
27th
4
3.21 +/- 0.01
26th
4
3.41 +/- 0.12
Low-Tier
25th
> 3.45
25th
9
3.49 +/- 0.09
24th
6
3.56
23rd
4
3.59 +/- 0.16
23rd
3
3.68 +/- 0.01
22nd
4
3.82 +/- 0.50
21st
3
3.88 +/- 0.01
21st
6
3.90 +/- 0.11
20th
4
4.18 +/- 0.17
20th
5
4.19 +/- 0.03
20th
3
4.23 +/- 0.01
18th
12
4.31 +/- 0.01
16th
6
4.49 +/- 0.01
16th
3
4.58 +/- 0.01
15th
10
4.60 +/- 0.18
14th
3
4.75 +/- 0.01
14th
6
4.84 +/- 0.17
13th
3
4.98 +/- 0.10
13th
3
5.00 +/- 0.13
13th
13
5.00 +/- 0.91
13th
4
5.00 +/- 0.02
12th
3
5.16 +/- 0.04
10th
5
5.53 +/- 0.49
10th
4
5.83 +/- 0.66
10th
3
6.07 +/- 0.02
9th
4
6.46 +/- 1.15
9th
3
6.51 +/- 0.04
8th
3
6.74 +/- 0.08
8th
7
6.79 +/- 0.71
7th
4
6.84 +/- 0.27
6th
3
7.16 +/- 0.23
6th
6
7.46 +/- 0.32
5th
4
8.88 +/- 0.08
5th
3
9.50 +/- 0.03
4th
5
11.14 +/- 0.03
3rd
4
11.45 +/- 0.31
3rd
3
11.95 +/- 0.05
2nd
4
14.04 +/- 0.20
2nd
3
14.05 +/- 1.86
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms905 Results Range From 0 To 38 days/ns04812162024283236404448160320480640800

Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD 2.14 - ATPase Simulation - 327,506 Atoms) has an average run-time of 7 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-Time714212835Min: 1 / Avg: 6.56 / Max: 34

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: 0.22 / Max: 4

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