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*Retrieve ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz | *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 | *Retrieve https://s3.amazonaws.com/public.ged.msu.edu/ecoli_ref-5m-trim.fastq.gz | ||
*Run | *Run bwa index GCF_000005845.2_ASM584v2_genomic.fna.gz | ||
==Running Benchmark== | ==Running Benchmark== | ||
Benchmark command | Benchmark command | ||
*1 thread | *1 thread | ||
**bwa aln GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null | **bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null | ||
*4 threads | *4 threads | ||
**bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null | **bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null | ||
Revision as of 13:23, 4 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 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 |
| 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 |
