Abstract
We implemented a parallel version (hereafter referred as “msPar”) of the coalescent simulation program ms, providing the same functionality and output, parallelized using a Master-Worker scheme with on-demand scheduling and MPI to run on an HPC cluster. To our knowledge this is the first time such parallelization has been applied to ms, and shown to be effective in using all computational resources of an HPC cluster, performing up to 42 times faster than original ms when using 72 logical processors. We propose msPar as an alternative to ms and other simulators using approximations to the standard coalescent approach. Source code is available at https://github.com/cmontemuino/mspar
Chapter PDF
Similar content being viewed by others
Keywords
References
Hudson, R.: Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7, 1–44 (1990)
Carvajal-Rodríguez, A.: Simulation of Genomes: A Review. Current Genomics 9, 155–159 (2008)
Schaffner, S., Foo, C., Gabriel, S., Reich, D., Daly, M., Altshuler, D.: Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 15, 1576–1583 (2005)
Carvajal-Rodríguez, A.: Simulation of Genes and Genomes Forward in Time. Current Genomics 11, 58–61 (2010)
Kim, Y., Thomas, W.: Simulation of DNA sequence evolution under models of recent directional selection. Brief. Bioinform. 10(1), 84–96 (2009)
Liang, L., Zöllner, S., Abecasis, G.: GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 23(12), 1565–1567 (2007)
Peng, B., Chen, H.-S., Mechanic, L., Racine, B., Clarke, J., Clarke, L., Gillanders, E., Feuer, E.: Genetic Simulation Resources: a website for the registration and discovery of genetic data simulators. Bioinformatics, 1–2 (2013)
Peng, B., Kimmel, M.: simuPOP: a forward-time population genetics simulation environment. Bioinformatics 21(18), 3686–3687 (2005)
Guillaume, F., Rougemont, J.: Nemo: an evolutionary and population genetics programming framework. Bioinformatics 22, 2556–2557 (2006)
Sanford, J., Baumgardner, J., Brewer, W., Gibson, P., Remine, W.: Mendel’s Accountant: A biologically realistic forward-time population genetics program. SCPE 8(2), 147–165 (2007)
Hudson, R.: Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18(2), 337–338 (2002)
Hoban, S., Bertorelle, G., Gaggiotti, O.: Computer simulations: tools for population and evolutionary genetics. Nature Reviews Genetics 13, 110–122 (2012)
Ewing, G., Hermisson, J.: MSMS: a coalescent simulation program including recombination, demographic structure, and selection at a single locus. Bioinformatics 26(16), 2064–2065 (2010)
Sanford, J., Nelson, C.: Studies in Population Genetics, pp. 117–135 (August 2012)
Peng, B., Kimmel, M.: Simulations Provide Support for the Common Disease–Common Variant Hypothesis. Genetics 175(2), 763–776 (2007)
Chen, G., Marjoram, P., Wall, J.: Fast and flexible simulation of DNA sequence data. Genome Res. 19, 136–142 (2009)
Excoffier, L., Foll, M.: fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27(9), 1332–1334 (2011)
Grünwald, N., Goss, E.: Evolution and population genetics of exotic and re-emergin pathogns: novel tools and appoaches. Annual Review of Phytopathol. 49, 249–267 (2011)
Ramos-Onsins, S., Mitchell-Olds, T.: Mlcoalsims: multilocus coalescent simulations. Evol. Bioinform. Online 3, 41–44 (2007)
Yuan, X., Miller, D., Zhang, J., Hirrington, D., Wang, Y.: An Overview of Population Genetic Data Simulation. J. Comput. Biol. 19(1), 42–54 (2012)
Dongarra, J., Foster, I., Fox, G., Gropp, W., Kennedy, K., Torczon, L., White, A.: Source book of parallel computing. Morgan Kaufmann (2003)
Breshears, C.: The art of concurrency: a thread monkey’s guide to writing parallel applications. O’Reilly Media (2009)
Mattson, T., Sanders, B., Massingil, B.: Patterns for parallel programming. Addison-Wesley Professional (2004)
Shao, G.: Adaptive scheduling of master/worker applications on distributed computational resources. PhD thesis, University of California at San Diego (2001)
Basney, J., Raman, R., Livny, M.: High throughput Monte Carlo. In: Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific Computing (1999)
Pacheco, P.: Parallel programming with MPI. Morgan Kaufmann (1996)
Open MPI: open source high performance MPI
Beaumont, M., Zhang, W., Balding, D.: Approximate bayesian computation in population genetics. Genetics 162, 2025–2035 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Montemuiño, C., Espinosa, A., Moure, JC., Vera-Rodríguez, G., Ramos-Onsins, S., Budé, P.H. (2014). msPar: A Parallel Coalescent Simulator . In: an Mey, D., et al. Euro-Par 2013: Parallel Processing Workshops. Euro-Par 2013. Lecture Notes in Computer Science, vol 8374. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-54420-0_32
Download citation
DOI: https://doi.org/10.1007/978-3-642-54420-0_32
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-54419-4
Online ISBN: 978-3-642-54420-0
eBook Packages: Computer ScienceComputer Science (R0)