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

14 Minutes, 14 Seconds

Accolades

50k+ Downloads + 5k+ Public Benchmark Results

Supported Platforms

Supported Architectures

x86_64

Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsNAMD Popularity Statisticspts/namd2018.092018.112019.012019.032019.052019.072019.092019.112020.012020.032020.052020.072020.092020.112021.012021.032021.052021.072021.092021.112022.012022.032022.052022.072022.092022.112023.012023.032023.052023.072023.092023.116K12K18K24K30K
* 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 3 December 2023.

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

HPC - High Performance Computing

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 4,059 public results since 20 August 2020 with the latest data as of 4 December 2023.

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
7
0.12 +/- 0.01
100th
53
0.13 +/- 0.01
98th
22
0.17 +/- 0.01
98th
4
0.19 +/- 0.02
97th
9
0.22 +/- 0.01
95th
71
0.23 +/- 0.01
94th
6
0.24 +/- 0.01
94th
20
0.24 +/- 0.02
93rd
14
0.26 +/- 0.01
90th
35
0.27 +/- 0.01
90th
16
0.27 +/- 0.01
89th
86
0.28 +/- 0.01
87th
4
0.28 +/- 0.01
87th
6
0.29 +/- 0.01
86th
12
0.30 +/- 0.02
85th
11
0.31 +/- 0.01
84th
8
0.31 +/- 0.02
84th
9
0.33 +/- 0.04
82nd
29
0.38 +/- 0.02
80th
7
0.39 +/- 0.04
80th
9
0.39 +/- 0.01
80th
5
0.40 +/- 0.01
79th
4
0.41 +/- 0.03
77th
19
0.45 +/- 0.01
Mid-Tier
75th
> 0.47
75th
4
0.48 +/- 0.02
75th
32
0.49 +/- 0.02
75th
11
0.49 +/- 0.01
73rd
9
0.53 +/- 0.03
73rd
31
0.54 +/- 0.02
71st
3
0.59 +/- 0.01
70th
23
0.59 +/- 0.01
69th
13
0.61 +/- 0.02
69th
10
0.62 +/- 0.02
69th
40
0.63 +/- 0.08
67th
42
0.67 +/- 0.01
65th
14
0.74 +/- 0.04
65th
3
0.75 +/- 0.03
65th
8
0.76 +/- 0.01
63rd
16
0.78 +/- 0.01
61st
59
0.82 +/- 0.04
61st
3
0.82 +/- 0.01
61st
27
0.83 +/- 0.03
60th
3
0.85 +/- 0.06
59th
19
0.86 +/- 0.01
58th
19
0.91 +/- 0.04
57th
5
0.92 +/- 0.11
57th
18
0.94 +/- 0.01
56th
3
0.98 +/- 0.01
56th
23
0.99 +/- 0.02
55th
49
1.02 +/- 0.02
54th
7
1.04 +/- 0.04
54th
8
1.05 +/- 0.01
53rd
109
1.08 +/- 0.04
Median
50th
1.11
50th
22
1.11 +/- 0.03
49th
17
1.14 +/- 0.01
49th
9
1.15 +/- 0.10
49th
19
1.15 +/- 0.03
49th
8
1.15 +/- 0.01
48th
7
1.18 +/- 0.03
48th
23
1.18 +/- 0.02
47th
6
1.19 +/- 0.01
47th
24
1.20 +/- 0.03
46th
10
1.22 +/- 0.07
46th
28
1.26 +/- 0.05
46th
4
1.27 +/- 0.02
44th
84
1.29 +/- 0.04
43rd
4
1.31 +/- 0.03
43rd
25
1.34 +/- 0.09
42nd
15
1.35 +/- 0.01
42nd
3
1.36 +/- 0.03
41st
10
1.46 +/- 0.01
41st
3
1.48 +/- 0.09
41st
22
1.50 +/- 0.09
40th
26
1.51 +/- 0.01
40th
28
1.52 +/- 0.03
39th
4
1.54 +/- 0.04
39th
9
1.54 +/- 0.03
39th
16
1.55 +/- 0.04
39th
9
1.55 +/- 0.04
38th
7
1.58 +/- 0.01
38th
19
1.60 +/- 0.01
37th
8
1.65 +/- 0.03
36th
8
1.73 +/- 0.09
36th
7
1.75 +/- 0.07
35th
7
1.79 +/- 0.19
35th
17
1.81 +/- 0.05
34th
22
1.84 +/- 0.03
34th
38
1.84 +/- 0.11
33rd
8
1.88 +/- 0.05
33rd
20
1.93 +/- 0.07
33rd
18
1.94 +/- 0.06
32nd
11
1.96 +/- 0.29
32nd
10
1.96 +/- 0.01
32nd
3
1.99 +/- 0.01
31st
6
2.03 +/- 0.11
31st
19
2.04 +/- 0.06
31st
10
2.05 +/- 0.06
31st
9
2.06 +/- 0.01
29th
15
2.12 +/- 0.06
29th
9
2.13 +/- 0.05
29th
15
2.14 +/- 0.06
29th
3
2.16 +/- 0.02
28th
7
2.20 +/- 0.07
28th
4
2.20 +/- 0.03
28th
13
2.26 +/- 0.02
27th
26
2.27 +/- 0.04
26th
4
2.37 +/- 0.01
26th
33
2.42 +/- 0.08
Low-Tier
25th
> 2.44
25th
15
2.47 +/- 0.06
25th
12
2.57 +/- 0.27
24th
7
2.64 +/- 0.23
24th
5
2.65 +/- 0.01
24th
13
2.73 +/- 0.01
23rd
11
2.79 +/- 0.07
23rd
5
2.81 +/- 0.16
22nd
13
2.87 +/- 0.18
22nd
7
2.88 +/- 0.01
22nd
9
2.89 +/- 0.14
22nd
4
2.89 +/- 0.02
21st
22
2.89 +/- 0.01
21st
3
2.98 +/- 0.02
21st
4
2.99 +/- 0.26
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
13
3.15 +/- 0.32
19th
4
3.17 +/- 0.02
19th
14
3.20 +/- 0.31
19th
11
3.25 +/- 0.10
18th
3
3.37 +/- 0.02
18th
5
3.38 +/- 0.37
18th
4
3.43 +/- 0.08
18th
10
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
16th
5
3.69 +/- 0.16
16th
4
3.71 +/- 0.05
15th
4
3.82 +/- 0.50
15th
6
3.90 +/- 0.11
14th
9
3.95 +/- 0.12
14th
3
4.04 +/- 0.30
14th
9
4.14 +/- 0.42
13th
15
4.15 +/- 0.03
13th
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
5
5.01 +/- 0.03
9th
4
5.09 +/- 0.15
9th
5
5.15 +/- 0.03
8th
6
5.52 +/- 0.44
8th
26
5.61 +/- 0.02
7th
4
5.83 +/- 0.66
7th
5
5.89 +/- 0.05
7th
3
6.07 +/- 0.02
6th
3
6.51 +/- 0.04
6th
14
6.58 +/- 0.13
6th
4
6.60 +/- 0.28
6th
4
6.80 +/- 0.73
6th
8
6.86 +/- 0.88
5th
7
7.80 +/- 0.93
5th
4
8.01 +/- 0.95
4th
4
8.88 +/- 0.08
4th
3
9.50 +/- 0.03
4th
53
10.33 +/- 0.05
2nd
5
11.14 +/- 0.03
2nd
4
11.45 +/- 0.31
2nd
3
11.95 +/- 0.05
2nd
3
13.49 +/- 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 Atoms4092 Results Range From 0 To 82 days/ns714212835424956637077848001600240032004000

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: 5.82 / Max: 37

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.3%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsATPase Simulation - 327,506 AtomsDeviation3691215Min: 0 / Avg: 0.27 / Max: 7

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 Atoms246810121618202428324048566496128714212835

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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