[DEPRECATED] A Docker container with base R + several parallel/asynchronous packages
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2019-03-25: Please use https://hub.docker.com/r/rocker/r-parallel instead. This repository is now deprecated and will no longer be maintained.
This is a Docker-based Linux container that consists of the base R installation, by extending the rocker/r-base container, together with several system libraries and R packages useful for parallel/asynchronous processing.
To build the container locally, do:
$ docker build . --tag henrikbengtsson/r-parallel
Sending build context to Docker daemon 56.32kB
Step 1/17 : FROM rocker/r-base
latest: Pulling from rocker/r-base
28507814f909: Pull complete
8205b68cfb04: Pull complete
bbf1b2b5c36c: Pull complete
6fc27852fced: Pull complete
8cdff7e970c4: Pull complete
e81d795a3e2b: Downloading ...
[...]
$
To pull it down from Docker Hub, do:
$ docker pull henrikbengtsson/r-parallel
Using default tag: latest
latest: Pulling from henrikbengtsson/r-parallel
[...]
$
To launch R by itself, do:
$ docker run -ti henrikbengtsson/r-parallel
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> y <- sapply(1:3, FUN = function(x) sqrt(x))
> y
[1] 1.000000 1.414214 1.732051
> library(parallel)
> y <- mclapply(1:3, FUN = function(x) sqrt(x))
> y <- Reduce(c, y)
> y
[1] 1.000000 1.414214 1.732051
> cl <- makeCluster(future::availableCores())
> y <- parSapply(cl, X = 1:3, FUN = function(x) sqrt(x))
> y
[1] 1.000000 1.414214 1.732051
> stopCluster(cl)
> library(future.apply)
> plan(multiprocess)
> y <- future_sapply(1:3, FUN = function(x) sqrt(x))
> y
[1] 1.000000 1.414214 1.732051
> library(foreach)
> doFuture::registerDoFuture()
> y <- foreach(x = 1:3, .combine = c) %dopar% sqrt(x)
> y
[1] 1.000000 1.414214 1.732051
> quit("no")
$
To launch a parallel cluster consisting of two R workers that are running in their own Docker container, from the R installation installed on the host system, do:
$ R --quiet
> library(parallel)
> cl <- future::makeClusterPSOCK(rep("localhost", times = 2L), rscript = c(
"docker", "run", "--net=host", "henrikbengtsson/r-parallel", "Rscript"
))
> print(cl)
socket cluster with 2 nodes on host ‘localhost’
> y <- parSapply(cl, 1:3, function(x) sqrt(x))
> y
[1] 1.000000 1.414214 1.732051
> stopCluster(cl)
To do the same using Singularity, do:
> library(parallel)
> cl <- future::makeClusterPSOCK(rep("localhost", times = 2L), rscript = c(
"singularity", "exec", "docker://henrikbengtsson/r-parallel", "Rscript"
))
> print(cl)
socket cluster with 2 nodes on host ‘localhost’
> y <- parSapply(cl, 1:3, function(x) sqrt(x))
> y
[1] 1.000000 1.414214 1.732051
> stopCluster(cl)
Content type
Image
Digest
Size
420.4 MB
Last updated
over 7 years ago
docker pull henrikbengtsson/r-parallel