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
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.
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).
A suite of programs that allow users to carry out molecular dynamics simulations.
A versatile package used to perform molecular dynamics, using Newtonian equations of motion for systems with hundreds to millions of particles.
A parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
An integrated suite of open-source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
A computational chemistry software package that includes quantum chemical and molecular dynamics functionality.
|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 - 2.1.03.0386|
|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|
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.