Parallelized Trie library (PTrie)

Project Description

This project implements a parallelized Trie library, PTrie, on CUDA to search for DNA patterns in a given text file. The program supports both parallel (GPU-based) and sequential (CPU-based) implementations to evaluate the speedup (CPU Time / GPU Time)

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How to Compile the code

1. Ensure having CUDA installed on the system
2. To compile the program, run:

   make
   

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How to run the code

• After compiling, run the program with the following command:

  ./main <mode> <text_filename> <pattern_filename> <blockSize>
  

• Commend-line arguments
  1. <mode>:
     • 0: Run the parallel implementation (PTrie library) on the GPU
     • 1: Run the sequential implementation on the CPU
  2. <text_filename>:
     • Path the the file containing the DNA text sequence
     • Example: DNA_text_100000000.txt
  3. <pattern_filename>:
     • Path to the file containing DNA patterns to search for
     • Example: Patterns_3bp_10.txt
  4. <blockSize>:
     • Only for parallel mode; this value does not affect the sequential code (mode 0)
     • The size of each CUDA block, which determines GPU thread grouping
     • Example: 256