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README.md

DOI

fbseqOpenMP

The fbseqOpenMP package is an internal backend of the fbseq package that runs the Markov chain Monte Carlo (MCMC) procedure behind the scenes. It should install on most machines that have OpenMP, but it is slow for large datasets. For a faster backend, which uses parallel computing via CUDA-capable general-purpose graphics processing units (GPUs), use the fbseqCUDA package.

System requirements

The required R version and R packages listed in the "Depends", "Imports", and "Suggests" fields of the "package's DESCRIPTION file.

Installation

Option 1: install a stable release (recommended).

Navigate to a list of stable releases on the project's GitHub page. Download the desired tar.gz bundle, then install it either with install.packages(..., repos = NULL, type="source") from within R R CMD INSTALL from the Unix/Linux command line.

Option 2: use install_github to install the development version.

For this option, you need the devtools package, available from CRAN or GitHub. Open R and run

library(devtools)
install_github("wlandau/fbseqOpenMP")

Option 3: build the development version from the source.

Open a command line program such as Terminal in Mac/Linux and enter the following commands.

git clone git@github.com:wlandau/fbseqOpenMP.git
R CMD build fbseqOpenMP
R CMD INSTALL ...

where ... is replaced by the name of the tarball produced by R CMD build.

Check OpenMP

To check if OpenMP is correctly enabled for the package, run fbseqOpenMP::check_OpenMP().

About

Light backend of the fbseq package. Makes use of parallelism through OpenMP if R is compiled with OpenMP support.

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