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=BWA Benchmark=
=BWA Benchmark (SBC)=
Using BWA from https://github.com/smikkelsendk/bwa-for-arm/tree/master/bin (with NEON)
Using BWA from https://github.com/smikkelsendk/bwa-for-arm/tree/master/bin (with NEON)


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**./bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecolireads.fastq.gz > /dev/null
**./bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecolireads.fastq.gz > /dev/null
*4 threads benchmark
*4 threads benchmark
**./bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecolireads.fastq.gz > /dev/null
**./bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna.gz ecolireads.fastq.gz > /dev/null
 
Run on Android:
*Enable USB Debugging on device (https://www.embarcadero.com/starthere/xe5/mobdevsetup/android/en/enabling_usb_debugging_on_an_android_device.html)
*On your PC: Download Android Platform tools: https://developer.android.com/studio/releases/platform-tools
*run (from your PC)
adb push BWA-EXECUTABLE /data/local/tmp
adb push GCF_000005845.2_ASM584v2_genomic.fna.gz /data/local/tmp
adb push ecolireads.fastq.gz /data/local/tmp
*then run
adb shell
 
You can now set bwa as executable (chmod a+x BWA-EXECUTABLE) and generate index and run bwa from directory /data/local/tmp


==Results (32 bit)==
==Results (32 bit)==
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|-
|-
|ODROID-C2
|ODROID-C2
|
|3.16.70-42
|
|Ubuntu 18.04.3 LTS
|
|748
|
|211
|
|211
|-
|-
|ODROID-N2
|ODROID-N2
Line 43: Line 55:
|-
|-
|RPI-4
|RPI-4
|4.19.58-v7l+
|Raspbian (Buster)
|459
|130
|130
|-
|a1.4xlarge (16 cores)
|5.0.0-1016-aws
|Ubuntu 19.04
|289
|75
|25
|-
|PC (i7-8700k@4.7GHz)
|5.2.15-200
|Fedora 30
|100
|27
|16
|-
|vkworld F1 (ARMv7 Processor rev 3 (v7l))
|3.10.72
|Android 5.1
|1233
|348
|348
|-
|Linksys WRT3200ACM
|4.14.131
|OpenWrt 18.06.4
|109
|
|
|57
|-
|Synology ds416j
|3.10.105
|Synology
|147
|
|
|
|77
|
|-
|
|PC eee1011px Atom N570 1.66GHz
|4.4.153-perf+
|Debian 7.8
|913
|369
|369
|}
 
==Results (64 bit)==
{| class="wikitable sortable"
!Device
!Kernel
!OS
!1 thread walltime (sec.)
!4 threads walltime (sec.)
!MAX threads walltime (sec.)
|-
|ODROID-C2 (Amlogic S905)
|3.16.70-42
|Ubuntu 18.04.3 LTS
|607
|178
|178
|-
|ODROID-N2 (Amlogic 922x)
|4.9.185-44
|Ubuntu 18.04.3 LTS
|344
|98
|88
|-
|Mi 9T Pro (Snapdragon 855)
|4.14.83
|Android 9
|165
|46
|34
|-
|LG G5 (Snapdragon 820)
|3.18.71
|Android 8
|348
|126
|126
|-
|a1.4xlarge (16 cores)
|5.0.0-1016-aws
|Ubuntu 19.04
|212
|56
|21
|-
|PC (i7-8700k@4.7GHz)
|5.2.15-200
|Fedora 30
|65
|18
|11
|-
|RPI-4
|5.3.0-1008
|Ubuntu 19.10
|350
|105
|105
|-
|Xiaomi Redmi Note 6 Pro
|4.4.153-perf+
|Android 9
|414
|101
|71
|}
|}

Latest revision as of 15:52, 26 October 2019

BWA Benchmark (SBC)

Using BWA from https://github.com/smikkelsendk/bwa-for-arm/tree/master/bin (with NEON)

Dataset:

  • Run ./bwa index GCF_000005845.2_ASM584v2_genomic.fna.gz
  • 1 thread benchmark
    • ./bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecolireads.fastq.gz > /dev/null
  • 4 threads benchmark
    • ./bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna.gz ecolireads.fastq.gz > /dev/null

Run on Android: 

adb push BWA-EXECUTABLE /data/local/tmp
adb push GCF_000005845.2_ASM584v2_genomic.fna.gz /data/local/tmp
adb push ecolireads.fastq.gz /data/local/tmp
  • then run
adb shell

You can now set bwa as executable (chmod a+x BWA-EXECUTABLE) and generate index and run bwa from directory /data/local/tmp

Results (32 bit)

Device Kernel OS 1 thread walltime (sec.) 4 threads walltime (sec.) MAX threads walltime (sec.)
ODROID-C2 3.16.70-42 Ubuntu 18.04.3 LTS 748 211 211
ODROID-N2 4.9.185-44 Ubuntu 18.04.3 LTS 435 120 97
RPI-3 4.19.58-v7+ Raspbian (Buster) 852 249 249
RPI-4 4.19.58-v7l+ Raspbian (Buster) 459 130 130
a1.4xlarge (16 cores) 5.0.0-1016-aws Ubuntu 19.04 289 75 25
PC (i7-8700k@4.7GHz) 5.2.15-200 Fedora 30 100 27 16
vkworld F1 (ARMv7 Processor rev 3 (v7l)) 3.10.72 Android 5.1 1233 348 348
Linksys WRT3200ACM 4.14.131 OpenWrt 18.06.4 109 57
Synology ds416j 3.10.105 Synology 147 77
PC eee1011px Atom N570 1.66GHz 4.4.153-perf+ Debian 7.8 913 369 369

Results (64 bit)

Device Kernel OS 1 thread walltime (sec.) 4 threads walltime (sec.) MAX threads walltime (sec.)
ODROID-C2 (Amlogic S905) 3.16.70-42 Ubuntu 18.04.3 LTS 607 178 178
ODROID-N2 (Amlogic 922x) 4.9.185-44 Ubuntu 18.04.3 LTS 344 98 88
Mi 9T Pro (Snapdragon 855) 4.14.83 Android 9 165 46 34
LG G5 (Snapdragon 820) 3.18.71 Android 8 348 126 126
a1.4xlarge (16 cores) 5.0.0-1016-aws Ubuntu 19.04 212 56 21
PC (i7-8700k@4.7GHz) 5.2.15-200 Fedora 30 65 18 11
RPI-4 5.3.0-1008 Ubuntu 19.10 350 105 105
Xiaomi Redmi Note 6 Pro 4.4.153-perf+ Android 9 414 101 71
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