BWA Benchmark (SBC)

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

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	100	27	16