Migrating CUDA to oneAPI: A Smith-Waterman Case Study

• Published in: Bioinformatics and Biomedical Engineering Vol. 13347; pp. 103 - 116
• Main Authors: Costanzo, Manuel, Rucci, Enzo, García-Sánchez, Carlos, Naiouf, Marcelo, Prieto-Matías, Manuel
• Format: Book Chapter
• Language: English
• Published: Switzerland Springer International Publishing AG 2022; Springer International Publishing
• Series: Lecture Notes in Computer Science
• Subjects: Bioinformatics; CUDA; GPU; oneAPI; SYCL
• ISBN: 3031078012; 9783031078019
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-031-07802-6_9

In order to tackle the programming challenges related to heterogeneous computing, Intel recently introduced oneAPI, which is a new programming environment that allows code developed in the Data Parallel C++ (DPC++) language to be run on different devices such as CPUs, GPUs, and FPGAs, among others. To handle CUDA-based legacy codes, oneAPI provides a compatibility tool (dpct) that facilitates the migration to DPC++. In view of the large amount of existing CUDA-based software in the bioinformatics context, this paper presents our experiences porting SW#db, a well-known sequence alignment tool, to DPC++ using dpct. From the experimental work, it was possible to prove the usefulness of dpct for SW#db code migration and the cross-vendor GPU, cross-architecture portability of the migrated DPC++ code. In addition, the performance results showed that the migrated DPC++ code reports similar efficiency rates to its CUDA-native counterpart, or even better in some tests (by approximately 5%).