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Revision as of 09:30, 4 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 5.1 1233 348 348
PC eee1011px Atom N570 1.66GHz 4.4.153-perf+ 9 913 369 369

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