A Lock Free Approach To Parallelize The Cellular Potts Model: Application To Ductal Carcinoma In Situ
| Autor: | Alberto Salguero, Antonio J. Tomeu |
|---|---|
| Přispěvatelé: | Ingeniería Informática |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Speedup
Java DCIS Computer science Breast Neoplasms Parallel computing Cellular Automata 03 medical and health sciences 0302 clinical medicine parallel Non-blocking algorithm Humans Computer Simulation Cellular Potts Model 030304 developmental biology computer.programming_language 0303 health sciences Multi-core processor cellular automata speedup Cellular Potts model multicore Transactional memory Computational Biology General Medicine software transactional memory Cellular automaton cellular potts model Carcinoma Intraductal Noninfiltrating dcis 030220 oncology & carcinogenesis Software transactional memory computer TP248.13-248.65 Research Article Biotechnology |
| Zdroj: | Journal of Integrative Bioinformatics, Vol 17, Iss 1, Pp 730-45 (2020) Journal of Integrative Bioinformatics Journal of Integrative Bioinformatics. 2020; 20190070 RODIN. Repositorio de Objetos de Docencia e Investigación de la Universidad de Cádiz Agencia Estatal de Meteorología (AEMET) RODIN: Repositorio de Objetos de Docencia e Investigación de la Universidad de Cádiz Universidad de Cádiz |
| ISSN: | 1613-4516 |
| Popis: | In the field of computational biology, in order to simulate multiscale biological systems, the Cellular Potts Model (CPM) has been used, which determines the actions that simulated cells can perform by determining a hamiltonian of energy that takes into account the influence that neighboring cells exert, under a wide range of parameters. There are some proposals in the literature that parallelize the CPM; in all cases, either lock-based techniques or other techniques that require large amounts of information to be disseminated among parallel tasks are used to preserve data coherence. In both cases, computational performance is limited. This work proposes an alternative approach for the parallelization of the model that uses transactional memory to maintain the coherence of the information. A Java implementation has been applied to the simulation of the ductal adenocarcinoma of breast in situ (DCIS). Times and speedups of the simulated execution of the model on the cluster of our university are analyzed. The results show a good speedup. |
| Databáze: | OpenAIRE |
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