View source for Distributed computing in R with Rmpi

__NOTOC__
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== Load modules and install Rmpi ==
Change to the new software stack and load required modules. Here we need MPI and R libraries.
 $ env2lmod
 $ module load gcc/8.2.0 openmpi/4.1.4 r/4.1.3
 $ R
 > install.packages("Rmpi")

== Request an interactive session ==
Rmpi assigns one processor to be the master and other processors to be workers. Here we would like to use 5 processors on 2 nodes for computation. Therefore, we request 6 processors

 $ bsub -n 6 -R "span[ptile=3]" -Is bash
 Generic job.
 Job <225427996> is submitted to queue <normal.4h>.
 <<Waiting for dispatch ...>>

== Use Rmpi ==
Create an R script called ''test_rmpi.R''
 # Load Rmpi which calls mpi.initialize()
 library(Rmpi)
 
 # Spawn R-slaves to the host. nslaves = requested number of processors - 1
 usize <- mpi_universe_size()
 ns <- usize - 1
 mpi.spawn.Rslaves(nslaves=ns)
 
 # Set up a variable array
 var = c(11.0, 22.0, 33.0, 44.0, 55.0)
 
 # Root sends state variables and parameters to other ranks
 mpi.bcast.data2slave(var, comm = 1, buffunit = 100)
 # Get the rank number of that processor
 mpi.bcast.cmd(id <- mpi.comm.rank())
 # Check if each rank can use its own value
 mpi.remote.exec(paste("The variable on rank ",id," is ", var[id]))
 
 # Root orders other ranks to calculate
 mpi.bcast.cmd(output <- var[id]*2)
 # Root orders other ranks to gather the output
 mpi.bcast.cmd(mpi.gather(output, 2, double(1)))
 
 # Root gathers the output from other ranks
 mpi.gather(double(1), 2, double(usize))
 
 # Close down and quit
 mpi.close.Rslaves(dellog = FALSE)
 mpi.quit()

Run the script with '''mpirun'''

 $ mpirun -np 1 Rscript test_rmpi.R
         5 slaves are spawned successfully. 0 failed.
 master (rank 0, comm 1) of size 6 is running on: eu-g1-016-2
 slave1 (rank 1, comm 1) of size 6 is running on: eu-g1-016-2
 slave2 (rank 2, comm 1) of size 6 is running on: eu-g1-016-2
 slave3 (rank 3, comm 1) of size 6 is running on: eu-g1-019-4
 slave4 (rank 4, comm 1) of size 6 is running on: eu-g1-019-4
 slave5 (rank 5, comm 1) of size 6 is running on: eu-g1-019-4
 $slave1
 [1] "The variable on rank  1  is  11"
 
 $slave2
 [1] "The variable on rank  2  is  22"
 
 $slave3
 [1] "The variable on rank  3  is  33"
 
 $slave4
 [1] "The variable on rank  4  is  44"
 
 $slave5
 [1] "The variable on rank  5  is  55"
 
 [1]   0  22  44  66  88 110
 [1] 1

<!--
== Exercises ==

# Try replacing mpi.scatter.Robj() instead of mpi.bcast.data2slave()
# Create an R script using Rmpi and submit a batch job through BSUB command line
# Create a BSUB job script and submit a batch job
-->

== Further reading ==
https://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf

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