Neighbor search algorithm for lattice-free simulations with short-range forces
| Autor: | Roberto Chignola, Federico Dogo, Edoardo Milotti, Sabrina Stella |
|---|---|
| Rok vydání: | 2014 |
| Předmět: |
Neighbor search
Multi-core processor Computer science Biological system modeling Computational modeling Parallel computing Time step Quantitative Biology::Cell Behavior Computational science Computer architecture General Processing on GPU Tumors Lattice (order) Graphics Algorithm Fermi Gamma-ray Space Telescope |
| Zdroj: | HPCS |
| DOI: | 10.1109/hpcsim.2014.6903745 |
| Popis: | We have recently developed a lattice-free simulation program in computational cell biology which needs the introduction and management of the biomechanical interactions of cells. These interactions are associated with short range forces which act on nearest-neighbors only. The forces act in the rearrangement of cells due to proliferation and cell growth and this requires a recalculation of the proximity relations at each time step. Here we describe the implementation of an algorithm to efficiently compute the proximity relations and designed to run on Graphics Processing Units (GPUs). The results of the first test runs on an NVidia Fermi GPU are encouraging: the algorithm has the potential to significantly boost the simulation program and to map the disordered lattice also on other multicore machines with hypercubic connectivity. |
| Databáze: | OpenAIRE |
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