R: Difference between revisions

For more on submitting jobs, see the [[Running jobs]] page.

====Usage====

You must register the backend by feeding it the nodes name multiplied by the desired number of processes. For instance, with two nodes (node1 and node2) and two processes, we would create a cluster composed of : <tt>node1 node1 node2 node2</tt> hosts. The ''PSOCK'' cluster type will run commands through SSH connections into the nodes.

1. Place your R code in a script file, in this case the file is called <tt>test_makecluster.R</tt>.

{{File

library(doParallel)

# Create an array from the NODESLIST environnement variable

nodeslist = unlist(strsplit(Sys.getenv("NODESLIST"), split=" "))

# Create the cluster with the nodes name. One process per count of node name.

# nodeslist = node1 node1 node2 node2, means we are starting 2 processes on node1, likewise on node2.

registerDoParallel(cl)

# Compute (Source : https://cran.r-project.org/web/packages/doParallel/vignettes/gettingstartedParallel.pdf)

x <- iris[which(iris[,5] != "setosa"), c(1,5)]

ptime[3]

# Don't forget to release resources

stopCluster(cl)

}}

2. Copy the following content in a job submission script called <tt>job_makecluster.sh</tt>:

{{File

#SBATCH --time=00:05:00        # time (HH:MM:SS)

module load r/3.5.0

# Export the nodes names.  

# If all processes are allocated on the same node, NODESLIST contains : node1 node1 node1 node1

}}

3. Submit the job with:

{{Command|sbatch job_makecluster.sh}}

For more information on submitting jobs, see the [[Running jobs]] page.

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