The closeness of a match is an important measure with a number of practical applications, including computational biology, signal processing and text retrieval. The approximate string matching (ASM) problem asks to find a substring of string Y of length n that is most similar to string X of length m. It is well-know that the ASM can be solved by dynamic programming technique by computing a table of size m×n. The main contribution of this work is to present a memory-access-efficient implementation for computing the ASM on a GPU. The proposed GPU implementation relies on warp shuffle instructions which are used to accelerate the communication between threads without resorting to shared memory access. Despite the fact that O(mn) memory access operations are necessary to access all elements of a table with size n×m, the proposed implementation performs only $O(rac{mn}{w})$ memory access operations, where w is the warp size. Experimental results carried out on a GeForce GTX 980 GPU show that the proposed implementation, called w-SCAN, provides speed-up of over two fold in computing the ASM as compared to another prominent alternative.

The volume of digital information is growing at an extremely fast pace which, in turn, exacerbates the need of efficient mechanisms to find the presence of a pattern in an input text or a set of input strings. Combining the processing power of Graphics Processing Unit (GPU) with matching algorithms seems a natural alternative to speedup the string-matching process. This work proposes a Parallel Rabin-Karp implementation (PRK) that encompasses a fast-parallel prefix-sums algorithm to maximize parallelization and accelerate the matching verification. Given an input text T of length n and p patterns of length m, the proposed implementation finds all occurrences of p in T in O(m+q+n/τ+nm/q) time, where q is a sufficiently large prime number and τ is the available number of threads. Sequential and parallel versions of the PRK have been implemented. Experiments have been executed on p≥1 patterns of length m comprising of m=10, 20, 30 characters which are compared against a text string of length n=227. The results show that the parallel implementation of the PRK algorithm on NVIDIA V100 GPU provides speedup surpassing 372 times when compared to the sequential implementation and speedup of 12.59 times against an OpenMP implementation running on a multi-core server with 128 threads. Compared to another prominent GPU implementation, the PRK implementation attained speedup surpassing 37 times.