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

4 Minutes, 46 Seconds

Accolades

50k+ Downloads

Supported Platforms

Supported Architectures

x86_64

Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsNAMD Popularity Statisticspts/namd2018.092018.112019.012019.032019.052019.072019.092019.112020.012020.032020.052020.072020.092020.112021.012021.032021.052021.072021.092021.112022.012022.032022.052022.072022.092022.115K10K15K20K25K
* 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 current as of 28 November 2022.

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

HPC - High Performance Computing

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 3,007 public results since 20 August 2020 with the latest data as of 30 November 2022.

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
days/ns (Average)
100th
9
0.12 +/- 0.01
100th
9
0.16 +/- 0.01
96th
69
0.23 +/- 0.01
96th
8
0.23 +/- 0.01
96th
4
0.24 +/- 0.01
93rd
8
0.27 +/- 0.01
93rd
35
0.27 +/- 0.01
91st
79
0.28 +/- 0.01
90th
4
0.28 +/- 0.01
89th
6
0.29 +/- 0.01
88th
11
0.30 +/- 0.01
86th
8
0.31 +/- 0.02
84th
29
0.38 +/- 0.02
82nd
5
0.40 +/- 0.01
79th
19
0.45 +/- 0.01
77th
4
0.48 +/- 0.02
77th
32
0.49 +/- 0.02
76th
11
0.49 +/- 0.01
Mid-Tier
75th
> 0.52
75th
30
0.54 +/- 0.02
72nd
3
0.59 +/- 0.01
71st
23
0.59 +/- 0.01
70th
10
0.62 +/- 0.02
69th
39
0.67 +/- 0.01
66th
14
0.74 +/- 0.04
64th
16
0.78 +/- 0.01
63rd
11
0.80 +/- 0.03
61st
3
0.85 +/- 0.06
61st
56
0.85 +/- 0.08
61st
19
0.86 +/- 0.01
59th
22
0.94 +/- 0.01
57th
3
0.98 +/- 0.01
57th
22
0.99 +/- 0.02
57th
8
1.03 +/- 0.02
56th
8
1.05 +/- 0.01
54th
89
1.09 +/- 0.02
52nd
17
1.14 +/- 0.01
52nd
17
1.15 +/- 0.03
52nd
9
1.15 +/- 0.10
51st
6
1.15 +/- 0.01
Median
50th
1.18
50th
7
1.18 +/- 0.03
50th
5
1.19 +/- 0.01
50th
21
1.20 +/- 0.02
49th
26
1.24 +/- 0.03
48th
8
1.25 +/- 0.05
48th
4
1.27 +/- 0.02
47th
75
1.29 +/- 0.03
45th
4
1.31 +/- 0.03
45th
22
1.31 +/- 0.02
44th
18
1.35 +/- 0.01
44th
3
1.36 +/- 0.03
43rd
10
1.46 +/- 0.01
42nd
22
1.50 +/- 0.09
41st
26
1.52 +/- 0.04
40th
4
1.54 +/- 0.04
40th
9
1.54 +/- 0.03
40th
16
1.55 +/- 0.04
40th
9
1.55 +/- 0.04
39th
7
1.58 +/- 0.01
38th
8
1.65 +/- 0.03
38th
3
1.66 +/- 0.21
37th
7
1.74 +/- 0.09
37th
7
1.75 +/- 0.07
36th
10
1.84 +/- 0.02
35th
29
1.86 +/- 0.11
35th
8
1.88 +/- 0.05
34th
20
1.93 +/- 0.07
34th
10
1.93 +/- 0.28
34th
16
1.95 +/- 0.06
34th
10
1.96 +/- 0.01
33rd
3
1.99 +/- 0.01
32nd
6
2.03 +/- 0.11
32nd
10
2.05 +/- 0.06
31st
16
2.12 +/- 0.06
31st
7
2.12 +/- 0.06
31st
16
2.13 +/- 0.06
30th
6
2.17 +/- 0.02
30th
4
2.20 +/- 0.03
29th
11
2.26 +/- 0.02
28th
26
2.27 +/- 0.04
27th
4
2.37 +/- 0.01
26th
30
2.43 +/- 0.08
Low-Tier
25th
> 2.53
25th
8
2.59 +/- 0.38
25th
11
2.59 +/- 0.28
25th
7
2.64 +/- 0.23
24th
17
2.73 +/- 0.01
24th
12
2.80 +/- 0.07
22nd
7
2.88 +/- 0.01
22nd
4
2.88 +/- 0.04
22nd
5
2.88 +/- 0.02
22nd
9
2.89 +/- 0.14
21st
4
2.97 +/- 0.08
21st
3
2.98 +/- 0.02
21st
5
3.02 +/- 0.08
20th
3
3.11 +/- 0.01
20th
5
3.12 +/- 0.02
20th
3
3.14 +/- 0.03
20th
3
3.14 +/- 0.01
20th
9
3.15 +/- 0.40
20th
5
3.17 +/- 0.01
20th
14
3.20 +/- 0.31
19th
11
3.25 +/- 0.10
19th
5
3.38 +/- 0.37
18th
11
3.43 +/- 0.06
18th
9
3.49 +/- 0.09
17th
13
3.56
17th
4
3.59 +/- 0.16
17th
10
3.61 +/- 0.25
17th
5
3.69 +/- 0.16
16th
4
3.71 +/- 0.05
16th
4
3.82 +/- 0.50
15th
6
3.90 +/- 0.11
15th
9
3.95 +/- 0.12
15th
8
4.02 +/- 0.25
15th
3
4.04 +/- 0.30
14th
15
4.15 +/- 0.03
14th
5
4.16 +/- 0.16
13th
5
4.19 +/- 0.03
13th
3
4.23 +/- 0.01
12th
12
4.31 +/- 0.01
11th
3
4.58 +/- 0.01
11th
10
4.60 +/- 0.18
10th
7
4.70 +/- 0.57
10th
7
4.71 +/- 0.26
10th
3
4.75 +/- 0.01
10th
8
4.80 +/- 0.04
10th
6
4.84 +/- 0.17
9th
4
5.00 +/- 0.02
9th
4
5.09 +/- 0.15
9th
5
5.15 +/- 0.03
8th
6
5.52 +/- 0.44
8th
25
5.61 +/- 0.02
7th
4
5.83 +/- 0.66
6th
5
5.89 +/- 0.05
6th
3
6.07 +/- 0.02
5th
3
6.51 +/- 0.04
5th
14
6.58 +/- 0.13
5th
4
6.60 +/- 0.28
5th
4
6.80 +/- 0.73
5th
8
6.86 +/- 0.88
4th
7
7.80 +/- 0.93
3rd
4
8.88 +/- 0.08
3rd
3
9.50 +/- 0.03
3rd
5
11.14 +/- 0.03
2nd
4
11.45 +/- 0.31
2nd
3
11.95 +/- 0.05
2nd
4
14.04 +/- 0.20
2nd
3
14.05 +/- 1.86
1st
3
23.42 +/- 0.06
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms3004 Results Range From 0 To 82 days/ns714212835424956637077846001200180024003000

Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD 2.14 - ATPase Simulation - 327,506 Atoms) has an average run-time of 6 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: 5.73 / Max: 37

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: 0.23 / Max: 4

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.

IntelAMDOpenBenchmarking.orgRelative Core Scaling To BaseNAMD CPU Core ScalingATPase Simulation - 327,506 Atoms24681012161820242832404864128714212835

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.
 
CVTSD2SS SUBSD MULSD ADDSD CVTTSD2SI CVTSS2SD CVTPD2PS MOVDQU MOVD MOVDQA PSRLDQ CVTSI2SD DIVSD MOVHPD UNPCKLPD COMISD SQRTSD PSHUFD PUNPCKLQDQ PUNPCKHQDQ MINSD MAXSD UCOMISD MULPD CVTPS2PD ADDPD UNPCKHPD CMPLTSD CVTDQ2PD DIVPD SUBPD CMPLTPD MOVMSKPD PADDQ CVTDQ2PS SQRTPD PMULUDQ CVTTPD2DQ MINPD CMPEQPD CMPNLTSD CMPEQSD CMPNEQSD CMPLEPD CMPLESD MAXPD PSUBQ PSHUFLW MOVAPD CVTSD2SI ANDPD XORPD ORPD ANDNPD MOVLPD CMPNLESD SHUFPD CMPUNORDPD CMPNLEPD CMPNLTPD CVTPS2DQ PSLLDQ MOVNTDQ MOVNTI
SSE3 (SSE3)
Used by default on supported hardware.
 
MOVDDUP LDDQU
SSSE3 (SSSE3)
Used by default on supported hardware.
 
PALIGNR PMADDUBSW PHADDD
SSE 4.2 (SSE4_2)
Used by default on supported hardware.
Found on Intel processors since at least 2010.
Found on AMD processors since Bulldozer (2011).

 
PCMPISTRM PCMPISTRI
Used by default on supported hardware.
Found on Intel processors since Sandy Bridge (2011).
Found on AMD processors since Bulldozer (2011).

 
VINSERTF128 VZEROUPPER VEXTRACTF128 VBROADCASTSS VBROADCASTSD VPERM2F128 VPERMILPD VMASKMOVPS
Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).

 
VPBROADCASTQ VGATHERQPD VEXTRACTI128 VPBROADCASTD
Advanced Vector Extensions 512 (AVX512)
Used by default on supported hardware.
 
(ZMM REGISTER USE)
FMA (FMA)
Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Bulldozer (2011).

 
VFNMADD213SD VFMADD213SD VFMADD231SD VFMSUB213SD VFNMADD231SD VFMADD132SD VFNMADD132SD VFMSUB213SS VFMADD213SS VFMADD231SS VFMADD213PD VFNMADD231PD VFNMADD132PD VFMSUB213PD VFNMADD213PD VFMADD231PD VFMADD132PD VFMADD213PS VFNMADD213PS VFNMADD132PS
Last automated analysis: 18 January 2022

This test profile binary relies on the shared libraries libm.so.6, libpthread.so.0, libdl.so.2, 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)
ARMv8 64-bit
arm64
Apple M1, Apple M1 Max, Apple M1 Pro

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