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Benchmark command | Benchmark command | ||
*1 thread | *1 thread | ||
**bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /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.gz ecoli_ref-5m-trim.fastq.gz > /dev/null | **./bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna.gz ecoli_ref-5m-trim.fastq.gz > /dev/null | ||
Revision as of 20:41, 10 May 2017
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://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/000/005/845/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.) | 8 thread walltime (sec.) | 16 thread walltime (sec.) |
|---|---|---|---|---|---|---|---|---|
| PC (i5-750@2.67GHz) | x64 | 4.4.0-53-generic x86_64 | Ubuntu 16.04 | 5.4.0 | 162.644 | 54.980 | ||
| PC (R7 1700@3.8GHz) | x64 | 4.4.0-75-generic x86_64 | Ubuntu 16.04 | 97.116 | 32.375 | 21.908 | 18.246 | |
| PC (Xeon Gold 6148@2.4GHz) | x64 | 3.10.0-514.16.1.el7.x86_64 | CentOS 7 | 6.3.1 | 102.149 | 34.774 | 22.088 | 16.100 |
| 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 | arm7l | 3.8.13.30 | Ubuntu 14.04.4 LTS | 4.8.4 | 939.300 | 266.262 | ||
| ODROID C2 | arm64 | 3.14.65-73 | Ubuntu 16.04 LTS | 5.4.0 | 797.158 | 235.510 | ||
| Raspberry Pi 3 | armv7l | 4.4.13-v7+ | Raspbian Jessie | 4.9.2 | 1224.290 | 355.897 | ||
| Raspberry Pi 3 | arm64 | 4.9.26-v8 | Raspbian Jessie (Debian 64bit chroot) | 6.3.0 | 924.110 | 297.149 | ||
| Orange PI one | armv7l | 3.4.112 | Armbian Jessie | 4.9.2 | 1677.26 | 486.256 | ||
| Raspberry Pi zero | armv6l | 4.4.13+ | Raspbian Jessie | 4.9.2 | 2801.69 | 2812.427 | ||
| Raspberry Pi 1 | armv6l | 4.4.13+ | Raspbian Jessie | 4.9.2 | 4031.349 | 4072.279 | ||
| Raspberry Pi 2 | armv7l | 4.4.13-v7+ | Raspbian Jessie | 4.9.2 | 2009.622 | 592.694 |
