Burrows-Wheeler Aligner* (BWA*)

A popular software package for mapping low-divergent sequences against a large-reference genome, such as the human genome.

BWA-ALN* 0.5.10

The BWA* project focused on how running the optimized code on an Intel® Xeon® processor and adding an Intel® Xeon Phi™ coprocessor improves modular performance1 and supports symmetric running models on hybrid Intel® Xeon® processors and Intel® Xeon Phi™ coprocessor nodes.

Performance Results

The Intel® Xeon® processor E5-2697 v2 and the Intel® Xeon Phi™ coprocessor symmetric process demonstrated up to 1.86X improved performance over the baseline Intel Xeon processor E5-2697 v2.

Workload is korean_female (read file 3.5 GB, 3.0 GB reference data base).

Download the code ›

Reproduce these results with this optimization recipe ›

Related content

Related Content

The Removing Load Imbalance in Burrows-Wheeler Sequence Alignment* (BWA-ALN* 0.7.5) white paper focuses on how the use of tools such as Pintools, Intel® VTune™, and Intel® Cilk™ assisted in the optimization of BWA-ALN 0.7.5a.  With minimal programming effort, load imbalances were removed and scaling improved, achieving up to a 2X performance improvement.

Read the white paper

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 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

Informações de produto e desempenho


Os resultados de benchmark foram obtidos antes da implementação de patches de software e atualizações de firmware destinadas a solucionar violações referentes a "Spectre" e "Meltdown". A implementação dessas atualizações pode tornar estes resultados inaplicáveis para seu dispositivo ou sistema.

O desempenho varia de acordo com o uso, a configuração e outros fatores. Saiba mais em www.Intel.com.br/PerformanceIndex.