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.
OpenBenchmarking.org metrics for this test profile configuration based on 287 public results since 16 February 2024 with the latest data as of 13 May 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.
Based on OpenBenchmarking.org data, the selected test / test configuration (NAMD 3.0b6 - Input: STMV with 1,066,628 Atoms) has an average run-time of 11 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.
Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.4%.
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.
Notable instruction set extensions supported by this test, based on an automatic analysis by the Phoronix Test Suite / OpenBenchmarking.org analytics engine.
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.
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.
2 Systems - 48 Benchmark Results |
2 x Intel Xeon Platinum 8280 - GIGABYTE S451-3R0-00 MD61-SC2-00 v01000100 - Intel Sky Lake-E DMI3 Registers Ubuntu 21.04 - 5.11.0-49-generic - GNOME Shell 3.38.4 |
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1 System - 2 Benchmark Results |
2 x Intel Xeon E5-2660 0 - Insyde RMIBV389 - Intel Xeon E5 Rocky Linux 8.8 - 4.18.0-477.15.1.el8_8.x86_64 - GCC 8.5.0 20210514 |
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2 Systems - 137 Benchmark Results |
Intel Core i9-14900K - ASUS PRIME Z790-P WIFI - Intel Raptor Lake-S PCH Clear Linux OS 41680 - 6.8.9-1432.native - GNOME Shell 46.1 |
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1 System - 37 Benchmark Results |
QEMU Virtual 2.5+ - QEMU Standard PC - Intel 440FX 82441FX PMC openSUSE Leap 15.5 - 5.14.21-150500.55.59-default - Xfce |
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2 Systems - 145 Benchmark Results |
2 x Intel Xeon Gold 6252 - Intel S2600WFD - Intel Sky Lake-E DMI3 Registers Ubuntu 24.04 - 6.8.0-31-generic - GCC 13.2.0 |
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2 Systems - 147 Benchmark Results |
2 x Intel $0000% - Intel M50CYP2SB2U - Intel Ice Lake IEH Ubuntu 24.04 - 6.8.0-31-generic - GCC 13.2.0 |
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1 System - 39 Benchmark Results |
Intel Xeon D-2775TE - Lenovo SB27B33636 v06 - Intel Device 0998 Ubuntu 22.04 - 5.15.0-105-generic - 1.3.255 |
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1 System - 35 Benchmark Results |
Intel Xeon Gold 5416S - Dell 075K3T - Intel Device 1bce Ubuntu 22.04 - 5.15.0-105-generic - 1.3.255 |
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1 System - 10 Benchmark Results |
AMD Ryzen 9 7945HX - Shenzhen Meigao Electronic Equipment DRFXI - AMD Device 14d8 Ubuntu 23.10 - 6.5.0-28-generic - KDE Plasma 5.27.8 |
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1 System - 432 Benchmark Results |
2 x AMD EPYC 7303 16-Core - AMD DAYTONA_X - AMD Starship Ubuntu 22.04 - 5.15.0-47-generic - GNOME Shell 42.9 |
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1 System - 912 Benchmark Results |
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6 Systems - 119 Benchmark Results
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AMD Ryzen 9 7950X 16-Core - ASUS ROG STRIX X670E-E GAMING WIFI - AMD Device 14d8 Ubuntu 24.04 - 6.8.0-31-generic - GNOME Shell 46.0
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4 Systems - 242 Benchmark Results
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Intel Core i9-14900K - ASUS PRIME Z790-P WIFI - Intel Device 7a27 Ubuntu 23.10 - 6.5.0-28-generic - GNOME Shell 45.2
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2 Systems - 256 Benchmark Results
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AMD Ryzen 9 7950X 16-Core - ASUS ROG STRIX X670E-E GAMING WIFI - AMD Device 14d8 Ubuntu 22.04 - 6.5.0-28-generic - GNOME Shell 42.9
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1 System - 236 Benchmark Results
|
AMD Ryzen 9 7900 12-Core - ASRockRack 1U4LW-B650/2L2T B650D4U-2L2T/BCM - AMD Device 14d8 Ubuntu 24.04 - 6.8.0-31-generic - GNOME Shell 46.0 |
Featured Graphics Comparison |
AMD Ryzen 9 5900HX - ASUS ROG Strix G513QY_G513QY G513QY v1.0 - AMD Renoir Ubuntu 22.10 - 5.19.0-46-generic - GNOME Shell 43.0 |
2 Systems - 54 Benchmark Results |
AMD EPYC 8534P 64-Core - AMD Cinnabar - AMD Device 14a4 Ubuntu 23.10 - 6.5.0-15-generic - GNOME Shell |
4 Systems - 125 Benchmark Results |
2 x INTEL XEON PLATINUM 8592+ - Quanta Cloud QuantaGrid D54Q-2U S6Q-MB-MPS - Intel Device 1bce Ubuntu 23.10 - 6.5.0-17-generic - GCC 13.2.0 |
3 Systems - 177 Benchmark Results |
Intel Xeon E E-2488 - Supermicro Super Server X13SCL-F v0123456789 - Intel Device 7a27 Ubuntu 22.04 - 6.2.0-26-generic - GNOME Shell 42.9 |
2 Systems - 52 Benchmark Results |
2 x INTEL XEON PLATINUM 8592+ - Quanta Cloud QuantaGrid D54Q-2U S6Q-MB-MPS - Intel Device 1bce Ubuntu 23.10 - 6.6.0-060600-generic - GCC 13.2.0 |
3 Systems - 125 Benchmark Results |
2 x INTEL XEON PLATINUM 8592+ - Quanta Cloud QuantaGrid D54Q-2U S6Q-MB-MPS - Intel Device 1bce Ubuntu 23.10 - 6.5.0-17-generic - GCC 13.2.0 |
76 Systems - 921 Benchmark Results |
Intel Core i9-14900K - ASUS PRIME Z790-P - Intel Device 7a27 SystemRescue 10.01 - 6.1.30-1-lts - X Server 1.21.1.8 |
2 Systems - 85 Benchmark Results |
2 x AMD EPYC 9684X 96-Core - AMD Titanite_4G - AMD Device 14a4 Ubuntu 24.04 - 6.8.0-11-generic - GNOME Shell 45.3 |
3 Systems - 50 Benchmark Results |
AMD Ryzen 7 PRO 6850U - LENOVO ThinkPad X13 Gen 3 21CM0001US - AMD 17h-19h PCIe Root Complex Fedora Linux 39 - 6.5.7-300.fc39.x86_64 - GNOME Shell 45.0 |
2 Systems - 46 Benchmark Results |
AMD Ryzen Threadripper 7980X 64-Cores - System76 Thelio Major - AMD Device 14a4 Pop 22.04 - 6.7.0-060700daily20240120-generic - GNOME Shell 42.5 |
3 Systems - 7 Benchmark Results |
AMD Ryzen 5 8500G - ASRock B650 Pro RS - AMD Device 14e8 Ubuntu 23.10 - 6.7.3-060703-generic - GNOME Shell 45.2 |
3 Systems - 24 Benchmark Results |
AMD Ryzen Threadripper 3970X 32-Core - ASUS ROG ZENITH II EXTREME - AMD Starship Ubuntu 22.04 - 6.2.0-39-generic - GNOME Shell 42.2 |
5 Systems - 6 Benchmark Results |
AMD Ryzen 7 3800XT 8-Core - MSI X370 XPOWER GAMING TITANIUM - AMD Starship Debian 12 - 6.1.0-18-amd64 - X Server 1.20.11 |
Featured Processor Comparison |
AMD Ryzen 5 8500G - ASRock B650 Pro RS - AMD Device 14e8 Ubuntu 23.10 - 6.7.3-060703-generic - GNOME Shell 45.2 |
3 Systems - 79 Benchmark Results |
Intel Core i7-1185G7 - Dell XPS 13 9310 0DXP1F - Intel Tiger Lake-LP Ubuntu 23.10 - 6.7.0-060700rc5-generic - GNOME Shell 45.1 |