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export R_LIBS=~/local/R_libs/ | export R_LIBS=~/local/R_libs/ | ||
R CMD BATCH --no-save --no-restore test_foreach.R | R CMD BATCH --no-save --no-restore test_foreach.R | ||
}} | |||
<!--T:44--> | |||
3. Submit the job with: | |||
<!--T:45--> | |||
<source lang="bash"> | |||
sbatch job_foreach.sh | |||
</source> | |||
<!--T:47--> | |||
For more on submitting jobs, see the [[Running jobs]] page. | |||
=== doParallel and makeCluster === | |||
====Running==== <!--T:40--> | |||
1. Place your R code in a script file, in this case the file is called <tt>test_makecluser.R</tt>. | |||
<!--T:41--> | |||
{{File | |||
|name=test_makecluster.R | |||
|lang="r" | |||
|contents= | |||
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. | |||
cl = makeCluster(nodeslist, type = "PSOCK") | |||
registerDoParallel(cl) | |||
# Compute | |||
x <- iris[which(iris[,5] != "setosa"), c(1,5)] | |||
trials <- 10000 | |||
ptime <- system.time({ | |||
foreach(icount(trials), .combine=cbind) %dopar% | |||
{ | |||
ind <- sample(100, 100, replace=TRUE) | |||
result1 <- glm(x[ind,2]~x[ind,1], family=binomial(logit)) | |||
coefficients(result1) | |||
} | |||
}) | |||
ptime[3] | |||
# Don't forget to release resources | |||
stopCluster(cl) | |||
}} | |||
2. Copy the following content in a job submission script called ''job_makecluser.sh'': | |||
{{File | |||
|name=job_foreach.sh | |||
|lang="bash" | |||
|contents= | |||
#!/bin/bash | |||
#SBATCH --account=def-someacct # replace this with your own account | |||
#SBATCH --ntasks=4 # number of processes | |||
#SBATCH --mem-per-cpu=512M # memory; default unit is megabytes | |||
#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 | |||
export NODESLIST=$(echo $(srun hostname)) | |||
R -f test_makecluster.R | |||
}} | }} | ||