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 Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsNAMD Popularity Statisticspts/namd2018.092018.102018.112018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042021.052021.062021.072021.082021.094K8K12K16K20K
* 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 15 September 2021.

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 1,626 public results since 20 August 2020 with the latest data as of 13 September 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
# Compatible Public Results
days/ns (Average)
99th
28
0.24 +/- 0.03
96th
23
0.27 +/- 0.01
95th
4
0.28 +/- 0.01
94th
3
0.30 +/- 0.02
87th
10
0.45 +/- 0.02
86th
7
0.46 +/- 0.03
84th
32
0.49 +/- 0.02
84th
11
0.49 +/- 0.01
79th
3
0.59 +/- 0.01
77th
10
0.62 +/- 0.02
76th
34
0.67 +/- 0.01
Mid-Tier
75th
> 0.67
73rd
4
0.72 +/- 0.01
69th
3
0.85 +/- 0.06
68th
19
0.86 +/- 0.01
66th
22
0.94 +/- 0.01
64th
19
0.99 +/- 0.02
61st
56
1.08 +/- 0.01
59th
11
1.14 +/- 0.03
59th
13
1.15 +/- 0.01
56th
7
1.18 +/- 0.03
55th
24
1.24 +/- 0.03
54th
4
1.27 +/- 0.02
52nd
59
1.29 +/- 0.02
Median
50th
1.30
50th
17
1.30 +/- 0.01
47th
18
1.35 +/- 0.01
47th
3
1.36 +/- 0.03
46th
10
1.46 +/- 0.01
45th
20
1.49 +/- 0.09
44th
21
1.52 +/- 0.04
43rd
4
1.54 +/- 0.04
43rd
9
1.54 +/- 0.03
43rd
8
1.56 +/- 0.04
41st
7
1.75 +/- 0.07
39th
8
1.88 +/- 0.05
39th
19
1.88 +/- 0.12
38th
13
1.98 +/- 0.03
37th
9
1.98 +/- 0.01
37th
3
1.99 +/- 0.01
37th
3
2.00 +/- 0.10
36th
6
2.03 +/- 0.11
34th
16
2.12 +/- 0.06
34th
16
2.13 +/- 0.06
34th
6
2.17 +/- 0.02
33rd
4
2.20 +/- 0.03
32nd
17
2.25 +/- 0.03
31st
8
2.26 +/- 0.01
30th
4
2.37 +/- 0.01
29th
5
2.41 +/- 0.02
29th
17
2.42 +/- 0.05
29th
4
2.45 +/- 0.01
27th
16
2.73 +/- 0.01
26th
7
2.84 +/- 0.02
Low-Tier
25th
> 2.86
25th
7
2.88 +/- 0.01
25th
4
2.88 +/- 0.04
24th
9
2.89 +/- 0.14
24th
4
2.97 +/- 0.08
24th
3
2.98 +/- 0.02
23rd
3
3.14 +/- 0.03
23rd
3
3.14 +/- 0.01
22nd
5
3.17 +/- 0.01
22nd
11
3.25 +/- 0.10
20th
11
3.43 +/- 0.06
20th
9
3.49 +/- 0.09
19th
6
3.56
19th
9
3.58 +/- 0.24
19th
4
3.59 +/- 0.16
18th
3
3.68 +/- 0.01
18th
3
3.80 +/- 0.31
17th
4
3.82 +/- 0.50
17th
6
3.90 +/- 0.11
17th
9
3.95 +/- 0.12
16th
15
4.15 +/- 0.03
15th
5
4.16 +/- 0.16
15th
5
4.19 +/- 0.03
14th
3
4.23 +/- 0.01
12th
12
4.31 +/- 0.01
11th
6
4.49 +/- 0.01
11th
3
4.58 +/- 0.01
11th
10
4.60 +/- 0.18
10th
3
4.75 +/- 0.01
10th
8
4.80 +/- 0.04
9th
6
4.84 +/- 0.17
8th
3
4.98 +/- 0.10
8th
4
5.00 +/- 0.02
8th
4
5.09 +/- 0.15
7th
5
5.53 +/- 0.49
7th
4
5.83 +/- 0.66
6th
3
6.07 +/- 0.02
6th
3
6.51 +/- 0.04
5th
3
6.74 +/- 0.08
5th
10
6.79 +/- 0.58
5th
4
6.84 +/- 0.27
4th
3
7.16 +/- 0.23
4th
6
7.46 +/- 0.32
3rd
4
8.88 +/- 0.08
3rd
3
9.50 +/- 0.03
2nd
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
OpenBenchmarking.orgDistribution Of Public Results - ATPase Simulation - 327,506 Atoms1626 Results Range From 0 To 38 days/ns0481216202428323640444830060090012001500

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-Time612182430Min: 1 / Avg: 5.32 / Max: 28

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: 0.21 / 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 Atoms2468101216182024324864128714212835

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
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: 10 May 2021

This test profile binary relies on the shared libraries libm.so.6, libpthread.so.0, libdl.so.2, libz.so.1, libc.so.6.

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