From subsecret
Jump to: navigation, search
Line 10: Line 10:
 
**./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
  
 
==Results (32 bit)==
 
==Results (32 bit)==

Revision as of 21:08, 6 August 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

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

Results (64 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 607 178 178
ODROID-N2 4.9.185-44 Ubuntu 18.04.3 LTS 344 98 88