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Revision as of 18:27, 1 August 2016
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
- 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
- Patch the Makefile:
- 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 gunzip GCF_000005845.2_ASM584v2_genomic.fna.gz
- Run gunzip ecoli_ref-5m-trim.fastq.gz
- Run bwa index GCF_000005845.2_ASM584v2_genomic.fna
Running Benchmark
Benchmark command
- 1 thread
- bwa aln GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null
- 4 threads
- bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null
Results
| Device | ARCH | Kernel | OS | GCC | 1 thread walltime | 4 thread walltime | |
|---|---|---|---|---|---|---|---|
| PC (i7-6700k@4.5 GHz) | x86 | 4.6.4-301.fc24.x86_64 | Fedora 24 | 6.1.1 | 144.221 sec | 53.833 sec | |
| PC (i7-6700k@4.5 GHz) | x64 | 4.6.4-301.fc24.x86_64 | Fedora 24 | 6.1.1 | 77.836 sec | 27.840 sec | |
| ODROID U2 | armhf | 3.8.13.30 | Ubuntu 14.04.4 LTS | 4.8.4 | 939.300 sec | 266.262 sec | |
| ODROID C2 | aarch64 | Ubuntu 16.04 LTS | |||||
| Raspberry Pi 3 | aarch64 | 4.6.4-1-main | Fedora 24 | 6.1.1 | 1521.175 sec | 486.585 sec | |
| Raspberry Pi 3 | armhf | 4.6.4-1-main | Fedora 24 | 6.1.1 | |||
| Raspberry Pi 3 | armhf | Rasbian |
