Fabrice HARROUET - The TransProg library

TransProg is a set of facilities (multiplatform and writen in C language) for a programmer to harness the full potential of modern general purpose computers.

It was designed with individual-based simulations in mind, and consequently makes use of multiple cores and processors, as well as graphical processing units for both rendering and computing.

It is dedicated to interactive simulations of highly dynamic systems where entities can move, change, appear, disappear and interact with each other and the user at any time.

Experiments with various computers, operating systems and compilers yield very satisfying results in terms of performance and scalability relating to the number of CPUs used.

A dynamic load-balancing mechanism, taking into account the applicative affinity between entities ensures good data locality within cache memories.
              

Example: interactive simulation of millions of bacteria.
     The substrate is 1.783 cm wide and 1 cm thick.
     Made of 1 656 837 spatial cells organised as a 357x357 regular horizontal grid and 13 planes with a geometrical progression, it is responsible for glucose and lactate diffusion and pH computation.
     Bacteria are from two types, with different sets of parameters, but each individual consumes glucose, to grow and duplicate itself, and produces lactate which in turn limits growth and duplication.
     Moreover, each individual interacts with its nearest neighbours (around twenty) according to attraction/repulsion rules.
     The following pictures and video show 16 million bacteria but this simulation reaches memory exhaustion beyond 262 million bacteria on a dual Intel Xeon E5-2697 v2 computer with 16GB RAM.
                    (20 MB video)
     Layers of bacteria : 7 MB video

         

The source code (TransProg_2016m07d04.tgz) is released under the GNU LGPL license.

Publications

The following article describes the design of this library:

• Fabrice HARROUET,
  "Designing a Multicore and Multiprocessor Individual-Based Simulation Engine",
  IEEE Micro, vol. 32, no. 1, pp. 54-65, Jan./Feb. 2012
  doi: 10.1109/MM.2011.80
  url: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5989785&isnumber=6144277
  preprint version
  
  

The various works described in these articles make use of this library:

• Ignace TACK, Fabrice HARROUET, Gireg DESMEULLES, Philip LOGIST and Jan VAN IMPE,
  "Individual-Based Modelling of Microbial Colony Dynamics on Food Surfaces in a Parallel Simulator",
  Proceedings of FoodSim'2016, Ghent (Belgium), 3-7 April 2016, pp. 77-82
  preprint version
  simulation source code and data: Pattern_2016m07d04.tgz
  
  
• Fabrice HARROUET, Pascal REDOU, Gireg DESMEULLES and Laurent GAUBERT,
  "3D Individual Based Model for Bacteria Growth and Spatial Interactions: Application to the Case of Listeria Monocytogenes and Carnobacterium Piscicola",
  Proceedings of FoodSim'2016, Ghent (Belgium), 3-7 April 2016, pp. 92-96
  preprint version
  simulation source code and data: Misivi_2016m07d04.tgz
  
  
• Gireg DESMEULLES, Fabrice HARROUET, Dominique THUAULT, Véronique HUCHET, Pascal REDOU, Laurent GAUBERT, Guillaume LONGELIN PÉRON, Pascal BALLET and Vincent RODIN,
  "3D individual based model for simultaneous growth and interaction of L. Monocytogenes and lactic acid bacteria",
  Proceedings of 9th International Conference on Predictive Modelling in Food (ICPMF9), Rio de Janeiro, Brazil, 2015, abstract book pp. 11-12 [O03.02]
  preprint version
  
  
• Laurent CRÉPIN, Fabrice HARROUET, Sebastien KERDÉLO, Jacques TISSEAU and Pascal REDOU,
  "Computational Methods for the Parallel 3D Simulation of Biochemical Kinetics at the Microscopic Scale",
  Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA) 2013,
  Lecture Notes in Computer Science series, volume 7875, pp. 28-39
  doi: 10.1007/978-3-642-38036-5_7
  url: http://link.springer.com/content/pdf/10.1007%2F978-3-642-38036-5_7.pdf