Burrows-Wheeler Aligner* (BWA*)
A popular software package for mapping low-divergent sequences against a large-reference genome, such as the human genome.
Burrows-Wheeler Aligner* (BWA-ALN*)
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).
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.
Genomics Codes
BWA-ALN* 0.5.10
A popular software package for mapping low-divergent sequences against a large-reference genome, such as the human genome.
MPI-HMMER* v2.3
An open-source implementation of the HMMER* protein sequence analysis suite.
BLASTn*/BLASTp*
An algorithm for comparing primary biological sequence information.
GATK*
A software package developed at the Broad Institute to analyze next-generation sequencing data.
QIAGEN
QIAGEN Bioinformatics* solutions deliver faster time to insight by combining powerful analytics that are able to interpret complex biological processes.
Halvade*
Halvade* is a MapReduce implementation of the best-practice DNA sequencing pipeline as recommended by Broad Institute.
ABySS*
ABySS* is an open-source de novo genome assembler for short paired-end reads.
DIDA*
DIDA* performs large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes.
elPrep*
elPrep* is a high-performance tool for preparing SAM/BAM/CRAM files for variant calling in genomic sequencing pipelines.
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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 - 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 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 |
Informacje o produktach i wydajności
1
Wyniki testów uzyskano przed instalacją najnowszych poprawek oprogramowania i aktualizacji oprogramowania sprzętowego, które służą do likwidacji luk w zabezpieczeniach określanych mianem „Spectre” i „Meltdown”. Po zainstalowaniu tych aktualizacji wyniki te mogą nie mieć zastosowania do posiadanego urządzenia lub systemu.
Oprogramowanie i obciążenia wykorzystane w testach wydajności mogły zostać zoptymalizowane pod kątem wydajnego działania tylko na mikroprocesorach Intel®. Testy wydajności, takie jak SYSmark* i MobileMark*, mierzą wydajność określonych systemów komputerowych, komponentów, oprogramowania, operacji i funkcji. Jakakolwiek zmiana wyżej wymienionych czynników może spowodować uzyskanie innych wyników. Aby wszechstronnie ocenić planowany zakup, w tym wydajność danego produktu w porównaniu z konkurencyjnymi, należy zapoznać się z informacjami z innych źródeł oraz innymi testami wydajności. Więcej informacji można znaleźć na stronie http://www.intel.pl/benchmarks.