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=BWA Benchmark=
=BWA Benchmark=
BWA is a tool for mapping reads against a genome. This is nice for doing a non-synthetic benchmark, as meaningful work is done, and IO, Memory and CPU is all used.
Using BWA from https://github.com/smikkelsendk/bwa-for-arm/tree/master/bin (with NEON)
==BWA Setup instructions==
*Install zlib devlopment libraries (dnf install zlib-devel, apt-get install zlib-dev, apt-get install zlib1g-dev)
*Retrieve https://files.subsecret.dk/bwa/bwa-0.6.2-simple.tar.gz (if this cannot compile due to the use of inline, this alternative version can be used https://files.subsecret.dk/bwa/bwa-0.6.2-simple-no-inline.tar.gz)
**Compile BWA with command: ./compile.sh


Dataset:
*Retrieve https://files.subsecret.dk/benchmark/GCF_000005845.2_ASM584v2_genomic.fna.gz
*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
*Retrieve (normal size benchmark) https://files.subsecret.dk/benchmark/ecolireads.fastq.gz
*Retrieve (small size benchmark) https://files.subsecret.dk/benchmark/ecolireads-small.fastq.gz
 
*Run ./bwa index GCF_000005845.2_ASM584v2_genomic.fna.gz
*Run ./bwa index GCF_000005845.2_ASM584v2_genomic.fna.gz
 
*1 thread benchmark
==Running Benchmark==
Benchmark command
*1 thread
**./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  
*4 threads benchmark
**./bwa aln -t4 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==
==Results (32 bit)==
{| class="wikitable sortable"
{| class="wikitable sortable"
!Device
!Device
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!GCC
!GCC
!1 thread walltime (sec.)
!1 thread walltime (sec.)
!4 thread walltime (sec.)
!4 threads walltime (sec.)
!8 thread walltime (sec.)
!MAX threads walltime (sec.)
!16 thread walltime (sec.)
|-
|-
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Revision as of 12:58, 6 August 2019

BWA Benchmark

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 ARCH Kernel OS GCC 1 thread walltime (sec.) 4 threads walltime (sec.) MAX threads walltime (sec.)