From subsecret
No edit summary |
|||
| (43 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
=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) | ||
| Line 8: | Line 8: | ||
*Run ./bwa index GCF_000005845.2_ASM584v2_genomic.fna.gz | *Run ./bwa index GCF_000005845.2_ASM584v2_genomic.fna.gz | ||
*1 thread benchmark | *1 thread benchmark | ||
**./bwa aln GCF_000005845.2_ASM584v2_genomic.fna.gz ecolireads.fastq.gz | **./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 | **./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)== | ||
| Line 24: | Line 34: | ||
|- | |- | ||
|ODROID-C2 | |ODROID-C2 | ||
| | |3.16.70-42 | ||
| | |Ubuntu 18.04.3 LTS | ||
| | |748 | ||
| | |211 | ||
| | |211 | ||
|- | |- | ||
|ODROID-N2 | |ODROID-N2 | ||
|4.9.185-44 | |4.9.185-44 | ||
| | |Ubuntu 18.04.3 LTS | ||
| | |435 | ||
| | |120 | ||
| | |97 | ||
|- | |- | ||
|RPI-3 | |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)== | |||
{| 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 | |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:
- 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
- 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:
- 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)
| 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 |
