From subsecret
(Created page with "=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 u...") |
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=BWA Benchmark= | =BWA Benchmark= | ||
BWA | 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 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 | ||
*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 | |||
**./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 | !4 threads walltime (sec.) | ||
! | !MAX threads walltime (sec.) | ||
|- | |- | ||
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Revision as of 11:58, 6 August 2019
BWA Benchmark
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
Results (32 bit)
| Device | ARCH | Kernel | OS | GCC | 1 thread walltime (sec.) | 4 threads walltime (sec.) | MAX threads walltime (sec.) |
|---|---|---|---|---|---|---|---|
