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Title: A hybrid parallel framework for the cellular Potts model simulations

Abstract

The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).

Authors:
 [1];  [2];  [2]
  1. Los Alamos National Laboratory
  2. SOUTH CHINA UNIV
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
956541
Report Number(s):
LA-UR-09-00386; LA-UR-09-386
TRN: US201014%%1910
DOE Contract Number:  
AC52-06NA25396
Resource Type:
Conference
Resource Relation:
Conference: CC Grid 2009 ; May 18, 2009 ; Shanghai, China
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICAL METHODS AND COMPUTING; ACCURACY; CELL DIVISION; GROWTH; HYBRIDIZATION; INTERFACES; NEOPLASMS; PERFORMANCE; SIMULATION

Citation Formats

Jiang, Yi, He, Kejing, and Dong, Shoubin. A hybrid parallel framework for the cellular Potts model simulations. United States: N. p., 2009. Web.
Jiang, Yi, He, Kejing, & Dong, Shoubin. A hybrid parallel framework for the cellular Potts model simulations. United States.
Jiang, Yi, He, Kejing, and Dong, Shoubin. Thu . "A hybrid parallel framework for the cellular Potts model simulations". United States. https://www.osti.gov/servlets/purl/956541.
@article{osti_956541,
title = {A hybrid parallel framework for the cellular Potts model simulations},
author = {Jiang, Yi and He, Kejing and Dong, Shoubin},
abstractNote = {The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2009},
month = {1}
}

Conference:
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