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/namd2018.092018.102018.112018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.10130260390520650

* 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 768 public samples since 20 August 2020 with the latest data as of 22 November 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
1.83
Low-Tier
25th
> 3.43
23rd
3.56
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms768 Results Range From 0 To 26 days/ns0369121518212427303336120240360480600

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: 6.47 / Max: 30

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: 0.2 / Max: 3

Recent Test Results

Compare

1 System - 59 Benchmark Results

Intel Core i5-8250U - HP 841C - 2 x 8192 MB 2400MHz Kingston HP26D4S9S8MH-8

Microsoft Windows 10 Famille Build 18363 - 10.0 - 441.87

1 System - 24 Benchmark Results

2 x Intel Xeon L5639 - QEMU Standard PC - Intel 82G33

Ubuntu 20.04 - 5.4.0-53-generic - KDE Plasma 5.18.5

1 System - 1 Benchmark Result

AMD Ryzen 9 3900X 12-Core - ASUS ROG STRIX X570-E GAMING - AMD Device 1480

Debian 9.13 - 4.9.0-14-amd64 - GNOME Shell 3.22.3

1 System - 2 Benchmark Results

Intel Core i5-8250U - HP 841C - 2 x 8192 MB 2400MHz Kingston HP26D4S9S8MH-8

Microsoft Windows 10 Famille Build 18363 - 10.0 - 441.87

1 System - 1 Benchmark Result

Intel Core i5-3470 - ASUS P8P67 EVO - Intel Xeon E3-1200 v2

Arch Linux - 5.9.9-arch1-1 - GCC 10.2.0 + Clang 11.0.0Target

5 Systems - 99 Benchmark Results

Intel Core i7-1165G7 - Dell 0GG9PT - Intel Tiger Lake-LP

Ubuntu 20.10 - 5.9.2-050902-generic - GNOME Shell 3.38.1

1 System - 214 Benchmark Results

Intel Xeon Platinum 8275CL - Amazon EC2 c5.2xlarge - Intel 440FX 82441FX PMC

Ubuntu 20.04 - 5.4.0-1029-aws - GCC 9.3.0

3 Systems - 17 Benchmark Results

Apple M1 - Apple Mac mini - 8GB

macOS 11.0.1 - 20.1.0 - OpenCL 1.2

1 System - 80 Benchmark Results

AMD EPYC 7401P 24-Core - Supermicro H11SSW-NT - AMD 17h

Ubuntu 20.04 - 5.4.0-53-generic - GCC 9.3.0

1 System - 1 Benchmark Result

Intel Core i7-8750H - ASUS X580GD v1.0 - Intel Cannon Lake PCH

Ubuntu 20.04 - 5.4.0-54-generic - GNOME Shell 3.36.4

1 System - 1 Benchmark Result

AMD Ryzen 5 4600U - LENOVO LNVNB161216 - 2 x 8192 MB 3200MHz Samsung M471A1G44AB0-CWE

Microsoft Windows 10 Pro Build 19042 - 10.0 - 27.20.1028.1

4 Systems - 99 Benchmark Results

AMD Ryzen 5 4500U - LENOVO LNVNB161216 - AMD Renoir Root Complex

Ubuntu 20.10 - 5.9.1-050901-generic - GNOME Shell 3.38.1

Most Popular Test Results

Compare

3 Systems - 268 Benchmark Results

Intel Core i5-2520M - HP 161C - Intel 2nd Generation Core DRAM

Ubuntu 18.04 - 4.18.0-20-generic - GNOME Shell 3.28.3

11 Systems - 217 Benchmark Results

Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH

Ubuntu 20.04 - 5.9.0-050900-generic - GNOME Shell 3.36.4

4 Systems - 99 Benchmark Results

VirtualApple - Apple Mac mini - 8GB

macOS 11.0 - 20.1.0 - OpenCL 1.2

3 Systems - 174 Benchmark Results

Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH

Fedora 33 - 5.8.11-300.fc33.x86_64 - GNOME Shell 3.38.0

2 Systems - 403 Benchmark Results

Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH

Ubuntu 20.10 - 5.8.0-22-generic - GNOME Shell 3.38.0

3 Systems - 11 Benchmark Results

AMD Ryzen 7 3800XT 8-Core - ASRock X570 Pro4 - AMD Starship

Ubuntu 20.04 - 5.4.0-42-generic - GNOME Shell 3.36.1

3 Systems - 406 Benchmark Results

AMD Ryzen 9 3900XT 12-Core - MSI MEG X570 GODLIKE - AMD Starship

Ubuntu 20.04 - 5.4.0-48-generic - GNOME Shell 3.36.4

3 Systems - 202 Benchmark Results

Intel Core i7-7700K - MSI Z270-A PRO - Intel Xeon E3-1200 v6

Ubuntu 20.04 - 5.4.0-28-generic - GNOME Shell 3.36.1

3 Systems - 100 Benchmark Results

AMD Ryzen Threadripper 3990X 64-Core - System76 Thelio Major - AMD Starship

Ubuntu 20.04 - 5.4.0-47-generic - GNOME Shell 3.36.4

Find More Test Results


User Comments

Post A Comment