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DTSTAMP:20260422T143138Z
LOCATION:B301
DTSTART;TZID=America/New_York:20241117T102000
DTEND;TZID=America/New_York:20241117T102500
UID:submissions.supercomputing.org_SC24_sess729_ws_eduhpca102@linklings.co
 m
SUMMARY:DNA sequence alignment: An assignment for OpenMP, MPI, and CUDA/Op
 enCL
DESCRIPTION:Arturo Gonzalez-Escribano (University of Valladolid, Spain) an
 d Diego García-Álvarez and Jesús Cámara (Universidad de Valladolid, Spain)
 \n\nWe present an assignment for a full Parallel Computing course. Since 2
 017/2018, we have proposed a different problem each academic year to illus
 trate various methodologies for approaching the same computational problem
  using different parallel programming models. They are designed to be para
 llelized using shared-memory programming with OpenMP, distributed-memory p
 rogramming with MPI, and GPU programming with CUDA or OpenCL. The problem 
 chosen for this year implements a brute-force solution for exact DNA seque
 nce alignment of multiple patterns. The program searches for exact coincid
 ences of multiple nucleotide strings in a long DNA sequence. The sequentia
 l implementation is designed to be clear and understandable to students wh
 ile offering many opportunities for parallelization and optimization.\n\nT
 his assignment addresses key basic concepts that many students find diffic
 ult to apply in practical scenarios: race conditions, reductions, collecti
 ve operations, and point-to-point communications. It also covers the probl
 em of parallel generation of pseudo-random sequences and strategies to not
 ify and stop speculative computations when matches are found. This assignm
 ent serves as an exercise that reinforces basic knowledge and prepares stu
 dents for more complex parallel computing concepts and structures. It has 
 been successfully implemented as a practical assignment in a third-year Pa
 rallel Computing course of a Computer Engineering degree program. Supporti
 ng materials for previous assignments in this series are available at http
 s://gamuva.infor.uva.es/peachy-assignments/\n\nTag: Broader Engagement, Ed
 ucation, Inclusivity\n\nRegistration Category: Workshop Reg Pass\n\nSessio
 n Chairs: David P. Bunde (Knox College); Sushil K. Prasad (University of T
 exas at San Antonio); Erik Saule (University of North Carolina at Charlott
 e); and George K. Thiruvathukal (Loyola University, Chicago; Argonne Natio
 nal Laboratory (ANL))\n\n
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