View source for 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, 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==
{| class="wikitable sortable"
!Device
!ARCH
!Kernel
!OS
!GCC
!1 thread walltime (sec.)
!4 thread walltime (sec.)
!8 thread walltime (sec.)
!16 thread walltime (sec.)
|-
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|}

==Results (old data)==
These benchmarks are generated with a now unavailable dataset.
{| class="wikitable sortable"
!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
|-
|ASUS Tinker Board
|armv7l
|4.4.16
|Debian 4.9.2-10
|4.9.2
|786.833
|239.936
|-
|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
|}