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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 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==
==BWA Setup instructions==
*Retrieve https://sourceforge.net/projects/bio-bwa/files/bwa-0.6.2.tar.bz2/download
*Install zlib devlopment libraries (dnf install zlib-devel, apt-get install zlib-dev, apt-get install zlib1g-dev)
**Patch the Makefile:
*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)
***Add to DFLAGS: -std=gnu90 -D_NO_SSE2
**Compile BWA with command: ./compile.sh
**Compile BWA with command: make
 
*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


*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==
==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 ecolireads.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 ecolireads.fastq.gz > /dev/null
 


==Results==
==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.)
|-
|
|
|
|
|
|
|
|
|
|}


{| class="wikitable"
==Results (old data)==
These benchmarks are generated with a now unavailable dataset.
{| class="wikitable sortable"
!Device
!Device
!ARCH
!ARCH
Line 28: Line 49:
!OS
!OS
!GCC
!GCC
!1 thread walltime
!1 thread walltime (sec.)
!4 thread walltime
!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)
|PC (i7-6700k@4.5 GHz)
Line 36: Line 89:
|Fedora 24
|Fedora 24
|6.1.1
|6.1.1
| 144.221 sec
|144.221  
| 53.833 sec
|53.833  
|-
|-
|PC (i7-6700k@4.5 GHz)
|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
|x64
|4.6.4-301.fc24.x86_64
|4.6.4-301.fc24.x86_64
|Fedora 24
|Fedora 24
|6.1.1
|6.1.1
| 77.836 sec
|130.605
| 27.840 sec
|45.549
|-  
|-  
|ODROID U2
|ODROID U2
|armhf
|arm7l
|3.8.13.30
|3.8.13.30
|Ubuntu 14.04.4 LTS
|Ubuntu 14.04.4 LTS
|4.8.4
|4.8.4
|939.300 sec
|939.300
|
|266.262
|-
|-
|ODROID C2
|ODROID C2
|aarch64
|arm64
|
|3.14.65-73
|Ubuntu 16.04 LTS
|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 3
|Raspberry Pi 2
|aarch64
|armv7l
|
|4.4.13-v7+
|Fedora 24
|Raspbian Jessie
|
|4.9.2
|
|2009.622
|
|592.694
|}
|}

Latest revision as of 11:15, 14 September 2018

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

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.)

Results (old data)

These benchmarks are generated with a now unavailable dataset.

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
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