AN EVOLUTIONARY COMPUTATIONAL SYSTEM ARCHITECTURE BASED ON A SOFTWARE TRANSACTIONAL MEMORY
Keywords:
Software transactional memory, Python, Diffusion equation evolutionary programming simulated annealing method (DEEPSAM), Python software transactional memory (PSTM), Evolutionary programming (EP)Abstract
In the last decade software transactional memory has become a prominent programming paradigm, which aims to improve the execution performance of concurrent programs. However, most research in the field is done in programming languages such as C, C++ and JAVA. In this paper, we present a PSTM-based architecture of DEEPSAM, a computational chemistry program written in Python language. The PSTM-based architecture aims to improve execution performance of the original computational chemistry system architecture based on evolutionary programming and to provide transactional-memory-based means for its future optimizations. The metric analysis includes system execution time and problem size scalability. The experimental results show that the new PSTM-based version gained better execution time results relative to the original version. Likewise, the results did not reveal any architectural bottleneck of the new architecture.
References
(1) M. Herlihy, J. E. B. Moss: Transactional memory: Architectural support for lock-free data structures, Proc. of the 20th Annual International Symposium on Computer Architecture, pp. 289-300, ACM, New York, NY, USA (1993).
(2) T. Harris, J. R. Larus, R. Rajwar, Transactional Memory, 2nd edition, Morgan and Claypool, 2010.
(3) N. Shavit, D. Touitou: Software transactional memory, Proc. of the 14th Annual ACM Symposium on Principles of Distributed Computing, pp. 204-213,ACM, New York,NY, USA (1995).
(4.)M. Goldstein, E. Fredj, B. Gerber, A New Hybrid Algorithm for Finding the Lowest Minima of Potential Surfaces: Approach and Application to Peptides, Journal of Computational Chemistry, 32, pp. 1785-1800 (2011).
(5) M. Goldstein, DEEPSAM: A Hybrid Evolutionary Algorithm for the Prediction of Biomolecules Structure, Lect Notes in Comput Sc - Hybrid Metaheuristics, 9668, pp. 218–221 (2016).
(6) A. E. Eiben, J. E. Smith, Introduction to evolutionary computing, Springer,Berlin Heidelberg (2007).
(7) T. Back, D. B. Fogel, Z. Michalewicz, Evolutionary Computation 1: Basic Algorithms and Operations, IOP Publishing Ltd.,UK (2000).
(8) L. J. Fogel, A. J. Owens, M. J. Walsh, Artificial Intelligence through Simulated Evolution, Wiley, USA (1966).
(9) J. W. L. Ponder, TINKER Molecular Modelling Package (2003), https://dasher.wustl.edu/tinker/
(10) M. Popovic, B. Kordic: PSTM: Python software transactional memory, Proc. of the 22nd Telecomm. Forum, pp. 1106–1109 (2014).
(11) K. Guerraiche, M. Rahli, L. Dekhici, A. Zeblah, Optimal design of redundancy series-parallel electrical systems using metaheuristics, Revue roumaine des sciences techniques, 63, 1 , pp. 46-51 (2018).
(12) S. Ziane, A. Abdelghani, M. Abid, Power control of doubly fed induction generator using hybrid adaptive neural fuzzy sliding mode controller optimised by genetic algorithm, Revue Roumaine des sciences techniques, 63, 4, pp. 411–416 (2018).
(13) H. Labdelaoui, F. Boudjema, D. Boukhetala, Multiobjective optimal design of dual-input power system stabilizer using genetic algorithms, Revue roumaine des sciences techniques, 62, 1 , pp. 93–97 (2017).
(14) A. Boulayoune, C. Guerroudj, R. Saou, L. Moreau, M. E. Zaim, Optimization with particle swarm and genetic algorithm of flux reversal machine, Revue roumaine des sciences techniques, 62, 1 , pp. 19–24 (2017).
(15) F. Zyulkyarov, V. Gajinov, O. S. Unsal, A. Cristal, Atomic Quake: Using Transactional Memory in an Interactive Multiplayer Game Server, Proc. of the 14th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, pp. 25–34 (2009).
(16) V. Gajinov, F. Zyulkyarov, O. S. Unsal, A. Cristal, E. Ayguadé, T. L. Harris, M. Valero: QuakeTM: Parallelizing a Complex Sequential Application Using Transactional Memory, Proc. of the 23rd International Conference on Supercomputing, pp. 126–135 (2009).
(17) T. Nakaike, R. Odaira, T. Nakatani, M. M. Michael: Real Java Applications in Software Transactional Memory, Proc. of the IEEE International Symposium on Workload Characterization, pp. 1–10 (2010).
(18) O. S. Hofmann, D. E. Portere, E. Witchel, C. J. Rossbach, H. E. Ramadan, A. Bhandari, MetaTM/TxLinux: Transactional Memory for an Operating System, ACM SIGARCH Computer Architecture News, 35, 2 , pp. 92–103 (2007).
(19) H. A. Scheraga, J. Lee, J. Pillardy, Y. J. Ye, A. Liwo, D. Ripoll, Surmounting the Multiple-Minima Problem in Protein Folding, J Global Optim, 15, 3, pp. 235–260 (1999).
(20) A. Lamiable, P. Thevenet, J. Rey, M. Vavrusa, P. Derreumaux, P. Tuffery, PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex, Nucleic Acids Res, 44, pp. W449–W454 (2016).
(21) R.F. Alford, A. Leaver-Fay, J.R. Jeliazkov, et al., The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design, J. Chem. Theory Comput., 13, pp. 3031–3048 (2017).
(22) H. Kaur, A. Garg, G.P.S. Raghava, PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides, Protein Pept. Lett., 14, pp. 626-631 (2007).
(23) S. Singh, H. Singh, A. Tuknait, K. Chaudhary, B. Singh, S. Kumaran, G.P.S. Raghava, PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues, Biol. Direct., 10, pp. 73 (2015).
(24) J. Kostrowicki, H. A. Scheraga, Application of the Diffusion Equation Method for Global Optimization to Oligopeptides, J Phys Chem, 96, 18, pp. 7442–7449 (1992).
(25) T. Schlick, Molecular Modeling and Simulation – An Interdisciplinary Guide, Springer (2002).
(26) S. Kirkpatrick, C. D. Gelatt, M. P. Vecchi, Optimization by simulated annealing, Science, 220, 4598, pp. 671–80 (1983).
(27) Y. Sugita, Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chem Phys Lett, 314(1-2), pp. 141-151 (1999).
(28) D. C. Liu, J. Nocedal, On the Limited Memory BFGS Method for Large Scale Optimization, Math Program, 45, pp. 503–528 (1989).
(29) Y. Goldtzvik, M. Goldstein, R.B. Gerber, On the crystallographic accurace of structure prediction by implicit water models: Test for cyclic peptides, Chem Phys, 415, pp. 168–172 (2013).
(30) M. Amitay, M. Goldstein, Evaluating the peptide structure prediction capabilities of a purely ab-initio method, Protein Eng Des Sel, 30, 10, pp. 723–727 (2017).
(31) Y. Isogai, G. Nemethy, H.A. Scheraga, Enkephalin: Conformational analysis by means of empirical energy calculations, Proc Natl Acad Sci USA, 74, 2, pp. 414–418 (1977).
(32) H. Mohanram, S. Bhattacharjya, Cysteine deleted protegrin-1 (CDP-1): anti-bacterial activity, outer-membrane disruption and selectivity. Biochim Biophys Acta, 1840, 10, pp. 3006–3016 (2014).
(33) J. Neidigh, R. Fesinmeyer, N. Andersen, Designing a 20-residue protein. Nat Struct Mol Biol, 9, pp. 425–430 (2002).
(34) R. B. Yehezkael, M. Goldstein, D. Dayan, Sh. Mizrahi, Flexible Algorithms: Enabling Well-defined Order-Independent Execution with an Imperative Programming Style", Proc. of ECBS-EERC 2015, IEEE Press, pp 75–82 (2015).