CUDA-BLAST-2024

This repository is to compile NCBI BLAST with CUDA backend. The repo implements both k-mer filtering and Smith-Waterman Alignment processes.

CUDA-BLAST-2024 Installation

• Follow the below steps to clone this repo:

git clone https://github.com/Abhiram-kandiyana/CUDA-BLAST-2024.git
cd CUDA-BLAST-2024

Dependency Installation

• Install CUDA to your machine so you can compile the .cu files. Follow this guide for Linux and Windows.

Running CUDA-BLAST-2024

1. The SRC directory has all the source code (C, CUDA). Move to the SRC directory

cd SRC

2. It has both the CPU and GPU implementation of BLAST. The CPU implementation is not as fast the GPU implementation. If you are unfamiliar with CUDA, go through the CPU implementation first and then try to read through the GPU implementation.

• To run the CPU (C) CODE:

  cd CPU_codes
  
  g++ -std=c++17 -o kmer_cpu_final kmer_cpu_final.cpp -pthread
  
  ./kmer_cpu_final
  

• To run the GPU (CUDA) CODE:

  cd GPU_codes
  
  nvcc kmer_gpu_final.cu -o kmer_gpu_final
  
  ./kmer_gpu_final
  

Results

Method	K-mer Length	Duration (in seconds)	Throughput (queries/sec)
Multithreaded CPU	15	10.014	49.930
CUDA-BLAST-2024 (Ours)	15	2.682	186.428
NCBI BLAST	15	11.000	43.478
Multithreaded CPU	10	10.458	47.811
CUDA-BLAST-2024 (Ours)	10	2.909	171.880
NCBI BLAST	10	14.000	43.478

• The best results for each K-mer length are bolded.
• CUDA-BLAST-2024 achieves a 5x improvment in speed over NCBI-BLAST.