BWA Benchmark (ODROID C2,RPI3)

BWA Benchmark

BWA is a tool for mapping reads against a genome. This is nice for doing a non-synthetic benchmark, as meaningful work is done, and IO, Memory and CPU is all used.

BWA Setup instructions

• Install zlib devlopment libraries (dnf install zlib-devel, apt-get install zlib-dev)
• Retrieve https://sourceforge.net/projects/bio-bwa/files/bwa-0.6.2.tar.bz2/download
  • Patch the Makefile:
    • Add to DFLAGS: -std=gnu90 -D_NO_SSE2
  • Compile BWA with command: make

• Retrieve ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
• Retrieve https://s3.amazonaws.com/public.ged.msu.edu/ecoli_ref-5m-trim.fastq.gz
• Run bwa index GCF_000005845.2_ASM584v2_genomic.fna.gz

Running Benchmark

Benchmark command

• 1 thread
  • bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null
• 4 threads
  • bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null

Results

Device	ARCH	Kernel	OS	GCC	1 thread walltime (sec.)	4 thread walltime (sec.)
PC (i7-6700k@4.5 GHz)	x86	4.6.4-301.fc24.x86_64	Fedora 24	6.1.1	144.221	53.833
PC (i7-6700k@4.5 GHz)	x64	4.6.4-301.fc24.x86_64	Fedora 24	6.1.1	77.836	27.840
PC (i7-980x@4.0 GHz)	x64	4.6.4-301.fc24.x86_64	Fedora 24	6.1.1	130.605	45.549
ODROID U2	armhf	3.8.13.30	Ubuntu 14.04.4 LTS	4.8.4	939.300	266.262
ODROID C2	aarch64	3.14.65-73	Ubuntu 16.04 LTS	5.4.0	797.158	235.510
Raspberry Pi 3	aarch64	4.6.4-1-main	Fedora 24	6.1.1	1521.175	486.585
Raspberry Pi 3	armhf	4.6.4-1-main	Fedora 24	6.1.1	2172.660	649.805
Raspberry Pi 3	armhf	4.4.13-v7+	Raspbian Jessie	4.9.2	1224.290	355.897
Orange PI one	armhf	3.4.112	armbian jessie desktop	4.9.2	1677.26	486.256