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

7 June 2024

Test Maintainer

Michael Larabel 

Test Type

Processor

Average Install Time

3 Seconds

Average Run Time

6 Minutes, 57 Seconds

Accolades

60k+ Downloads + 5k+ Public Benchmark Results + Recently Updated Test Profile

Supported Platforms

Supported Architectures

x86_64

Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsNAMD Popularity Statisticspts/namd2018.092018.112019.012019.032019.052019.072019.092019.112020.012020.032020.052020.072020.092020.112021.012021.032021.052021.072021.092021.112022.012022.032022.052022.072022.092022.112023.012023.032023.052023.072023.092023.112024.012024.032024.057K14K21K28K35K
* 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 6 June 2024.
ATPase with 327,506 Atoms49.8%STMV with 1,066,628 Atoms50.2%Input Option PopularityOpenBenchmarking.org

Revision History

pts/namd-1.3.2   [View Source]   Fri, 07 Jun 2024 20:08:12 GMT
Adjust NUMA tuning per https://github.com/phoronix-test-suite/test-profiles/pull/308 Closes: https://github.com/phoronix-test-suite/test-profiles/pull/308

pts/namd-1.3.1   [View Source]   Fri, 16 Feb 2024 14:24:47 GMT
Update against NAMD 3.0b6 but no Windows binaries yet.

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

HPC - High Performance Computing

CPU Massive

Server CPU Tests

Molecular Dynamics

Scientific Computing


Performance Metrics

Analyze Test Configuration:

NAMD 3.0b6

Input: ATPase with 327,506 Atoms

OpenBenchmarking.org metrics for this test profile configuration based on 443 public results since 16 February 2024 with the latest data as of 9 June 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
ns/day (Average)
98th
24
20.84 +/- 0.08
90th
3
7.59 +/- 0.50
88th
4
6.84 +/- 0.01
83rd
5
6.20 +/- 0.37
79th
7
5.89 +/- 0.17
Mid-Tier
75th
< 4.86
74th
3
4.65 +/- 0.01
68th
12
3.04 +/- 0.27
63rd
17
2.83 +/- 0.14
62nd
5
2.78 +/- 0.02
57th
3
2.30 +/- 0.05
52nd
3
1.94 +/- 0.01
Median
50th
1.83
47th
4
1.65 +/- 0.01
44th
20
1.59 +/- 0.03
40th
9
1.45 +/- 0.15
36th
3
1.29 +/- 0.01
35th
13
1.26 +/- 0.12
34th
4
1.23 +/- 0.01
Low-Tier
25th
< 0.68
24th
11
0.66 +/- 0.01
21st
5
0.60 +/- 0.02
18th
3
0.54 +/- 0.01
17th
5
0.52 +/- 0.01
15th
3
0.50 +/- 0.01
14th
12
0.47 +/- 0.03
8th
4
0.35 +/- 0.01
7th
6
0.32 +/- 0.01
6th
3
0.31 +/- 0.01
3rd
3
0.15 +/- 0.01
OpenBenchmarking.orgDistribution Of Public Results - Input: ATPase with 327,506 Atoms439 Results Range From 0 To 21 ns/day2468101214161820222450100150200250

Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD 3.0b6 - Input: ATPase with 327,506 Atoms) has an average run-time of 5 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 BenchmarkInput: ATPase with 327,506 AtomsRun-Time510152025Min: 1 / Avg: 4.43 / Max: 22

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.9%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsInput: ATPase with 327,506 AtomsDeviation510152025Min: 0 / Avg: 0.92 / Max: 21

Does It Scale Well With Increasing Cores?

Yes, based on the automated analysis of the collected public benchmark data, this test / test settings does generally scale well with increasing CPU core counts. Data based on publicly available results for this test / test settings, separated by vendor, result divided by the reference CPU clock speed, grouped by matching physical CPU core count, and normalized against the smallest core count tested from each vendor for each CPU having a sufficient number of test samples and statistically significant data.

OpenBenchmarking.orgRelative Core Scaling To BaseNAMD CPU Core ScalingInput: ATPase with 327,506 Atoms68121632643691215

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 MOVDQU PUNPCKLQDQ MOVUPD PSRLDQ MOVD CVTSI2SD DIVSD MULSD COMISD ADDSD CVTTSD2SI CVTSD2SS ADDPD CVTSS2SD SUBSD MOVAPD ANDPD CMPNLESD UNPCKLPD SUBPD SQRTSD XORPD MULPD CVTPD2PS MOVHPD MAXSD MOVLPD UNPCKHPD SHUFPD CVTPS2PD MINSD PSHUFD CVTDQ2PD DIVPD PSUBQ PADDQ CVTDQ2PS SQRTPD CMPNLTSD ANDNPD ORPD PMULUDQ MAXPD CMPEQPD CMPNEQPD CMPLESD CMPLEPD CMPLTPD MINPD UCOMISD CMPLTSD MOVMSKPD
Last automated analysis: 18 February 2024

This test profile binary relies on the shared libraries libpthread.so.0, libdl.so.2, libm.so.6, libmvec.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)