Groningen Machine for Chemical Simulations* (GROMACS*) 5.0 RC1

A versatile package used to perform molecular dynamics using Newtonian equations of motion for systems with hundreds to millions of particles.

Performance Per Watt Results Increased by Up to 1.45X1

In recent years, GROMACS* has become the most highly utilized molecular dynamics program. The number of publications utilizing GROMACS exceeds 15,000 and grows by nearly 2,000 annually. GROMACS is employed for true, enterprise-level science in socially important fields such as drug design and metabolic research. Consequently, porting and optimization for next-generation Intel® processor and Intel® Xeon Phi™ processor-based machines is expected to catalyze advances for today’s scientists and tomorrow’s industries.

This application provides users with a wide range of functionality for chemical simulations and highest out-of-the-box performance across all MD codes. GROMACS on the Intel® Xeon Phi™ processor outperforms Intel® Xeon® processors for simulating large biochemical systems due to enabling new Intel® Advanced Vector Extensions 512 (Intel® AVX-512) features and enabling enhanced parallelism.

Improved Performance

Optimized GROMACS 2016 code powered by an Intel® Xeon Phi™ processor 7250 achieved a performance increase of up to 1.22X2 over a 2S Intel® Xeon® processor E5-2697 v4 (Figure 1).

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Improved Energy Efficiency

Optimized GROMACS 2016 code powered by an Intel® Xeon Phi™ processor 7250 achieved a performance-per-watt increase of up to 1.45X3 (Figure 2).

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Configuration Table

System Overview Intel® Xeon® Processor E5-2697 v2 with Intel® Xeon Phi™ Coprocessor 7120A
Platform Intel® R2208GZ4GC platform, 2U chassis, hot-swap drives, 24 DIMMs, 1 750W redundant power supply
CPU/Stepping Intel® Xeon® processor E5-2697 v2, 2.7 GHz , 12 core, 8 GT/s dual Intel® QuickPath Interconnect (Intel® QPI) links, 130W, 3.5 GHz max turbo frequency, 768 kB instr L1 / 3072 kB L2 / 30 MB L3 cache
Coprocessor Intel® Xeon Phi™ coprocessor 7110 and 7120; 61 cores, 1.1 and 1.238 GHz, error-correcting code (ECC) enabled, Intel® Turbo Boost Technology disabled. Software details: Intel® Manycore Platform Software Stack (Intel® MPSS) version - 2.1.6720-13/16/19, Flash* version -
Memory Hynix HMT31GR7BFR-PB*, 64 GB total 8*8 GB 1600 MHZ Reg ECC DDR3
Chipset Rev 4.6, SE5C600.86B.99.99.x069.071520130923
BIOS BIOS configuration: Default except: Intel® Turbo Boost Technology enabled, Enhanced Intel SpeedStep® Technology enabled, surface-mount technology (SMT) enabled, non-uniform memory access (NUMA) enabled, memory speed 1600 MHz, Note: all prefetchers enabled (this is default)
GigE node adapter Intel® Ethernet Controller I350 (rev 01), 4 Gigabit network connections, only one connection in use
IB switch 36-port switch/rack Mellanox FDR* (model MSX6025F-1BFR), Firmware version: 9_2_4002
IB adapters 36-port switch/rack Mellanox FDR (model MSX6025F-1BFR), Firmware version: 9_2_4002
HDD specs Seagate ST9600205SS* (scsi), 1x600 GB SAS HDD 10kRPM
Operating system Red Hat Enterprise Linux* 6.4
Intel® Xeon® processor E5-2697 v4 Dual Socket Intel® Xeon® processor E5-2697 v4 2.3 GHz (Turbo ON), 18 Cores/Socket, 36 Cores, 72 Threads (HT on), Wildcat Pass, DDR4 128GB, 2400 MHz, BMC ver. 1.33.9832, Red Hat 7.2, BIOS 86B0271.R00, FRU/SDR Package 1.09, kernel 3.10.0-327.el7.x86_64, 1 1.0 TB SATA drive WD1003FZEX-00MK2A0, Idle Power measurement 89W
Intel® Xeon Phi™ processor 7250 Intel® Xeon Phi™ processor 7250 68 core, 272 threads, 1400 MHz core freq. 6 x 16 GB 2400 MHz DDR4, BMC ver. 12.951, Red Hat 7.2, BIOS 10R00, FRU/SDR Package 1.1, kernel 3.10.0-327.el7.x86_64, 1 1.0 TB SATA drive WD1003FZEX-00MK2A0, Idle Power measurement 125W




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