Paper Info
Title
Parallel implementation of inverse adding-doubling and Monte Carlo multi-layered programs for high performance computing systems with shared and distributed memory.
Abstract
Parallel implementation of two numerical tools popular in optical studies of biological materials–Inverse Adding-Doubling (IAD) program and Monte Carlo Multi-Layered (MCML) program–was developed and tested in this study. The implementation was based on Message Passing Interface (MPI) and standard C-language. Parallel versions of IAD and MCML programs were compared to their sequential counterparts in validation and performance tests. Additionally, the portability of the programs was tested using a local high performance computing (HPC) cluster, Penguin-On-Demand HPC cluster, and Amazon EC2 cluster. Parallel IAD was tested with up to 150 parallel cores using 1223 input datasets. It demonstrated linear scalability and the speedup was proportional to the number of parallel cores (up to 150x). Parallel MCML was tested with up to 1001 parallel cores using problem sizes of 104–109 photon packets. It demonstrated classical performance curves featuring communication overhead and performance saturation point. Optimal performance curve was derived for parallel MCML as a function of problem size. Typical speedup achieved for parallel MCML (up to 326x) demonstrated linear increase with problem size. Precision of MCML results was estimated in a series of tests — problem size of 106 photon packets was found optimal for calculations of total optical response and 108 photon packets for spatially-resolved results. The presented parallel versions of MCML and IAD programs are portable on multiple computing platforms. The parallel programs could significantly speed up the simulation for scientists and be utilized to their full potential in computing systems that are readily available without additional costs.
Year
DOI
Venue
2015
10.1016/j.cpc.2015.02.029
Computer Physics Communications
Keywords
Field
DocType
Parallel computing,Monte Carlo,Simulation,Inverse Adding-Doubling,Tissue,Photon
Supercomputer,Computer science,Parallel computing,Distributed memory,Unix,Compiler,Message Passing Interface,Test data,Scalability,Speedup
Journal
Volume
ISSN
Citations 
194
0010-4655
1
PageRank 
References 
Authors
0.40
3
2
Name
Order
Citations
PageRank
Svyatoslav Chugunov131.29
Changying Li25610.72