Time and Energy Benefits of Using Automatic Optimization Compilers for NPDP Tasks
Open Access
- 24 August 2023
- journal article
- research article
- Published by MDPI AG in Electronics
- Vol. 12 (17) , 3579
Abstract
In this article, we analyze the program codes generated automatically using three advanced optimizers: Pluto, Traco, and Dapt, which are specifically tailored for the NPDP benchmark set. This benchmark set comprises ten program loops, predominantly from the field of bioinformatics. The codes exemplify dynamic programming, a challenging task for well-known tools used in program loop optimization. Given the intricacy involved, we opted for three automatic compilers based on the polyhedral model and various loop-tiling strategies. During our evaluation of the code’s performance, we meticulously considered locality and concurrency to accurately estimate time and energy efficiency. Notably, we dedicated significant attention to the latest Dapt compiler, which applies space–time loop tiling to generate highly efficient code for the NPDP benchmark suite loops. By employing the aforementioned optimizers and conducting an in-depth analysis, we aim to demonstrate the effectiveness and potential of automatic transformation techniques in enhancing the performance and energy efficiency of dynamic programming codes.Keywords
This publication has 27 references indexed in Scilit:
- An improved Four-Russians method and sparsified Four-Russians algorithm for RNA foldingAlgorithms for Molecular Biology, 2016
- Multicore and GPU algorithms for Nussinov RNA foldingBMC Bioinformatics, 2014
- Compiling affine loop nests for distributed-memory parallel architectures2013
- Improved RNA secondary structure prediction by maximizing expected pair accuracyRNA, 2009
- A practical automatic polyhedral parallelizer and locality optimizerACM SIGPLAN Notices, 2008
- The equilibrium partition function and base pair binding probabilities for RNA secondary structureBiopolymers, 1990
- A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins1989
- Optimal computer folding of large RNA sequences using thermodynamics and auxiliary informationNucleic Acids Research, 1981
- Algorithms for Loop MatchingsSIAM Journal on Applied Mathematics, 1978
- Optimum binary search treesActa Informatica, 1971