Nanoscale Molecular Dynamics* Program (NAMD*)

A parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems

Performance Accelerated1 with the Intel® Xeon Phi™ Processor

Nanoscale Molecular Dynamics program (NAMD) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++* parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with Amber*, Charm++*, and X-PLOR*. 

Intel® Advanced Vector Extensions 512 (Intel® AVX 512) instructions are used heavily by the Assembler code, and source code performance tuning with intrinsics demonstrates MCDRAM and simultaneous multithreading advantages the Intel® Xeon Phi™ processor provides. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.

Performance results

NAMD Improves Performance

Figure 1 shows the Intel® Xeon Phi™ Processor can boost NAMD performance by up to 1.36X.

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More Information

Improved Energy Efficiency

Figure 2 shows the Intel® Xeon Phi™ Processor can boost NAMD performance-per-watt by up to 1.91X.

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Nanoscale Molecular Dynamics Program*

System Overview Intel® Xeon® processor E5-2697 v4  Intel® Xeon Phi™ processor 7250  Intel® Xeon Phi™ processor 7210
Processor Information Dual Socket Intel® Xeon® processor E5-2697 v4 2.3 GHz (Turbo OFF), 18 Cores/Socket, 36 Cores, 72 Threads (HT on) Intel® Xeon Phi™ processor 7250 68 core, 272 threads, 1400 MHz core freq. (Turbo ON), 1700 MHz uncore freq., MCDRAM 16 GB 7.2 GT/s Intel® Xeon Phi™ processor 7210 64 core, 256 threads, 1300 MHz core freq. (Turbo ON), 1600 MHz uncore freq., MCDRAM 16 GB 6.4 GT/s
Memory Configuration DDR4 128 GB, 2400 MHz DDR4 96GB 2400 MHz, MCDRAM flat memory mode DDR4 96 GB 2133 MHz, MCDRAM flat memory mode
BIOS Configuration   BIOS 09D10, quad cluster mode BIOS 09D10, quad cluster mode
Operating System Red Hat* 6.5 Red Hat* 6.7 (Santiago) Red Hat 6.7 (Santiago)

Nanoscale Molecular Dynamics Program* (perf./watt)

System Overview Intel® Xeon® processor E5-2697 v4  Intel® Xeon Phi™ processor 7250 
Motherboard Motherboard Wildcat Pass, BMC 1.33.9832, FRU/SDR package 1.09 Motherboard Adams Pass, Sleds per Chassis 1, BMC 12.951, FRU/SDR package 1.1
Processor Information Dual Socket Intel® Xeon® processor E5-2697 v4 2.3 GHz (Turbo OFF), 18 Cores/Socket, 36 Cores, 72 Threads (HT on),  Intel® Xeon Phi™ processor 7250 68 core, 272 threads, 1400 MHz core freq. (Turbo ON), 1700 MHz uncore freq.
Memory Configuration DDR4 8x16 GB 2400 MHz DDR4 6x16 GB 2400 MHz quadrant cluster mode, MCDRAM 16 GB 6.4 GT/s flat memory mode
BIOS Configuration BIOS 86B0271.R00 BIOS 10R00
HDD Specs System Disk 1 1.0 TB SATA drive WD1003FZEX-00MK2A0 System Disk 1 1.0 TB SATA drive WD1003FZEX-00MK2A0
Operating System Red Hat 7.2 kernel 3.10.0-327.el7.x86_64 Red Hat 7.2 kernel 3.10.0-327.el7.x86_64
Power Consumption Idle Power measurement 129W, energy usage to complete benchmark calculation in Joules: APOA1 – 4,565; STMV – 61,138 Idle Power measurement 89W, energy usage to complete benchmark calculation in Joules: APOA1 – 3,899; STMV – 43,218

Product and Performance Information

1

Benchmark results were obtained prior to implementation of recent software patches and firmware updates intended to address exploits referred to as "Spectre" and "Meltdown". Implementation of these updates may make these results inapplicable to your device or system.

Software and workloads used in performance tests may have been optimized for performance only on Intel® microprocessors. Performance tests, such as SYSmark* and MobileMark*, are measured using specific computer systems, components, software, operations and functions. Any change to any of those factors may cause the results to vary. You should consult other information and performance tests to assist you in fully evaluating your contemplated purchases, including the performance of that product when combined with other products. For more complete information visit https://www.intel.com/benchmarks.

Intel is a sponsor and member of the BenchmarkXPRT Development Community, and was the major developer of the XPRT family of benchmarks. Principled Technologies is the publisher of the XPRT family of benchmarks.