BarraCUDA

Introduction

BarraCUDA is a GPU-accelerated sequence mapping software. BarraCUDA’s code and sample data are open source and available at sourceforge. BarraCUDA’s FAQ page provides useful instructions for installing and running benchmarks.

We study BarraCUDA 0.7.107h, using the Saccharomyces_cerevisiae.SGD1.01.50.dna_rm.toplevel.fa sample data.

Profiling

The input we used elapses for a short time so that we can profile it directly using the gvprof script.

# prepare
./bin/barracuda index sample_data/Saccharomyces_cerevisiae.SGD1.01.50.dna_rm.toplevel.fa

# data_flow
gvprof -e data_flow ./bin/barracuda aln sample_data/Saccharomyces_cerevisiae.SGD1.01.50.dna_rm.toplevel.fa sample_data/sample_reads.fastq > quicktest.sai

# value_pattern
gvprof -e value_pattern -cfg ./bin/barracuda aln sample_data/Saccharomyces_cerevisiae.SGD1.01.50.dna_rm.toplevel.fa sample_data/sample_reads.fastq > quicktest.sai

Optimizations

• data_flow - redundant values

barracuda.cu: 398. In this function, cuda memory apis called after Line 440 are not necessary when number_of_sequences=0. In that case, zero data are transferred between CPUs and GPUs such that arrays remain the same values, but still triggering API invocation cost.

• value_pattern - frequent values

cuda2.cuh: 865. This line copies all the elements from a local array to a global array, regardless of their values. While CPU’s memcpy is fast for contiguous copy, GPU’s memcpy is not. We observe that this copy operation involes many zeros. Therefore, we can create a hits array to record which positions have been updated, then only copy values at these positions.