Migrating CUDA to oneAPI: A Smith-Waterman Case Study

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%).