Thread-cooperative, bit-parallel computation of Levenshtein distance on GPU

Approximate string matching is a very important problem in computational biology; it requires the fast computation of string distance as one of its essential components. Myers' bit-parallel algorithm improves the classical dynamic programming approach to Levenshtein distance computation, and offers competitive performance on CPUs. The main challenge when designing an efficient GPU implementation is to expose enough SIMD parallelism while at the same time keeping a relatively small working set for each thread. In this work we implement and optimise a CUDA version of Myers' algorithm suitable to be used as a building block for DNA sequence alignment. We achieve high efficiency by means of a cooperative parallelisation strategy for (1) very-long integer addition and shift operations, and (2) several simultaneous pattern matching tasks. In addition, we explore the performance impact obtained when using features specific to the Kepler architecture. Our results show an overall performance of the order of tera cells updates per second using a single high-end Nvidia GPU, and factor speedups in excess of 20 with respect to a sixteen-core, non-vectorised CPU implementation

Activity recognition from videos with parallel hypergraph matching on GPUs

In this paper, we propose a method for activity recognition from videos based on sparse local features and hypergraph matching. We benefit from special properties of the temporal domain in the data to derive a sequential and fast graph matching algorithm for GPUs. Traditionally, graphs and hypergraphs are frequently used to recognize complex and often non-rigid patterns in computer vision, either through graph matching or point-set matching with graphs. Most formulations resort to the minimization of a difficult discrete energy function mixing geometric or structural terms with data attached terms involving appearance features. Traditional methods solve this minimization problem approximately, for instance with spectral techniques. In this work, instead of solving the problem approximatively, the exact solution for the optimal assignment is calculated in parallel on GPUs. The graphical structure is simplified and regularized, which allows to derive an efficient recursive minimization algorithm. The algorithm distributes subproblems over the calculation units of a GPU, which solves them in parallel, allowing the system to run faster than real-time on medium-end GPUs

Accelerating edit-distance sequence alignment on GPU using the wavefront algorithm

Sequence alignment remains a fundamental problem with practical applications ranging from pattern recognition to computational biology. Traditional algorithms based on dynamic programming are hard to parallelize, require significant amounts of memory, and fail to scale for large inputs. This work presents eWFA-GPU, a GPU (graphics processing unit)-accelerated tool to compute the exact edit-distance sequence alignment based on the wavefront alignment algorithm (WFA). This approach exploits the similarities between the input sequences to accelerate the alignment process while requiring less memory than other algorithms. Our implementation takes full advantage of the massive parallel capabilities of modern GPUs to accelerate the alignment process. In addition, we propose a succinct representation of the alignment data that successfully reduces the overall amount of memory required, allowing the exploitation of the fast shared memory of a GPU. Our results show that our GPU implementation outperforms by 3- 9× the baseline edit-distance WFA implementation running on a 20 core machine. As a result, eWFA-GPU is up to 265 times faster than state-of-the-art CPU implementation, and up to 56 times faster than state-of-the-art GPU implementations.This work was supported in part by the European Unions’s Horizon 2020 Framework Program through the DeepHealth Project under Grant 825111; in part by the European Union Regional Development Fund within the Framework of the European Regional Development Fund (ERDF) Operational Program of Catalonia 2014–2020 with a Grant of 50% of Total Cost Eligible through the Designing RISC-V-based Accelerators for next-generation Computers Project under Grant 001-P-001723; in part by the Ministerio de Ciencia e Innovacion (MCIN) Agencia Estatal de Investigación (AEI)/10.13039/501100011033 under Contract PID2020-113614RB-C21 and Contract TIN2015-65316-P; and in part by the Generalitat de Catalunya (GenCat)-Departament de Recerca i Universitats (DIUiE) (GRR) under Contract 2017-SGR-313, Contract 2017-SGR-1328, and Contract 2017-SGR-1414. The work of Miquel Moreto was supported in part by the Spanish Ministry of Economy, Industry and Competitiveness under Ramon y Cajal Fellowship under Grant RYC-2016-21104.Peer ReviewedPostprint (published version

A New Multi-threaded and Interleaving Approach to Enhance String Matching for Intrusion Detection Systems

String matching algorithms are computationally intensive operations in computer science. The algorithms find the occurrences of one or more strings patterns in a larger string or text. String matching algorithms are important for network security, biomedical applications, Web search, and social networks. Nowadays, the high network speeds and large storage capacity put a high requirement on string matching methods to perform the task in a short time. Traditionally, Aho-Corasick algorithm, which is used to find the string matches, is executed sequentially. In this paper, a new multi-threaded and interleaving approach of Aho-Corasick using graphics processing units (GPUs) is designed and implemented to achieve high-speed string matching. Compute Unified Device Architecture (CUDA) programming language is used to implement the proposed parallel version. Experimental results show that our approach achieves more than 5X speedup over the sequential and other parallel implementations. Hence, a wide range of applications can benefit from our solution to perform string matching faster than ever before

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing