Parallel computing: Infectious Disease Modeling with OpenMP

Modeling the spread of infectious diseases with computer simulations is an important and useful step in learning how populations could respond to hypothetical treatments or predict pandemics. The focus of this assignment is a simplified model of an infectious disease spreading over a population. This assignment is inspired by the work of Eubank et al. [1]. The individ- uals are moving around in a random fashion over a graph that represents spatial locations. Spreading of the disease is possible whenever an infected and a healthy individual share the same location. Design and implement a parallel algorithm for the above simulation. Write code in C/C++ and use OpenMP for parallelization.

Implementation

Three versions of the source code where created:

1. Serial Naive: Undirected Acyclic Graph algorithm, utilizing map look-up tables, native C++ 11, using STD, STL and Boost Graph library[4].
2. Serial: Undirected Acyclic Graph algorithm, utilizing map look-up tables, native C++ 11, using STD, STL and Boost Graph library. Some algorithmic optimizations were applied:
   • Breaking an inner for-loop that was comparing if a susceptible individuals got infected individuals.
   • Skipping iteration loops for individuals that are already infected.
3. Parallel: Undirected Acyclic Graph algorithm, utlizing map look-up tables, native C++ 11, using STD, STL, Boost Graph library and OpenMP version 4.1 (most of the features). Also the optimizations mentioned above were applied.

Documentation

Documentation comparing the speed-up between the serial and parallel versions: https://onedrive.live.com/redir?resid=F3C315EB7F683B03!20269&authkey=!AG_HeLbTwupstY0&ithint=file%2cpdf

References

1. Eubank et al., Modelling disease outbreaks in realistic urban social networks, Nature 429, 180-184 (13 May 2004) - http://www.nature.com/nature/journal/v429/n6988/full/nature02541.html
2. 32 OpenMP Traps For C++ Developers - http://www.viva64.com/en/a/0054/
3. FIRSTPRIVATE Clause - https://computing.llnl.gov/tutorials/openMP/FIRSTPRIVATE
4. Exploring the Boost Graph Library - http://www.ibm.com/developerworks/aix/library/au-aix-boost-graph/
5. Learning the OpenMP framework with GCC - http://www.ibm.com/developerworks/aix/library/au-aix-openmp-framework/