BWA Benchmark (SBC)

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, apt-get install zlib1g-dev)
• Retrieve https://files.subsecret.dk/bwa/bwa-0.6.2-simple.tar.gz (if this cannot compile due to the use of inline, this alternative version can be used https://files.subsecret.dk/bwa/bwa-0.6.2-simple-no-inline.tar.gz)
  • Compile BWA with command: ./compile.sh

• Retrieve https://files.subsecret.dk/benchmark/GCF_000005845.2_ASM584v2_genomic.fna.gz
• Retrieve (normal size benchmark) https://files.subsecret.dk/benchmark/ecolireads.fastq.gz
• Retrieve (small size benchmark) https://files.subsecret.dk/benchmark/ecolireads-small.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 ecolireads.fastq.gz > /dev/null
• 4 threads
  • ./bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna.gz ecolireads.fastq.gz > /dev/null

Results

Device	ARCH	Kernel	OS	GCC	1 thread walltime (sec.)	4 thread walltime (sec.)	8 thread walltime (sec.)	16 thread walltime (sec.)