Difference between revisions of "R MPI Example"

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echo "Running example Rmpi script. Using $SLURM_JOB_NUM_NODES nodes with $SLURM_NTASKS  
 
echo "Running example Rmpi script. Using $SLURM_JOB_NUM_NODES nodes with $SLURM_NTASKS  
 
tasks, each with $SLURM_CPUS_PER_TASK cores."
 
tasks, each with $SLURM_CPUS_PER_TASK cores."
module purge; module load intel/2018 openmpi/3.1.2 Rmpi/3.5.1
+
module purge; module load gcc/9 openmpi rmpi
 
 
# Use '-np 1' since Rmpi does its own task management
 
# Make sure the mpi.spawn.Rslaves(nslaves=X) code spawns X slaves
 
# where X is one less than the total number of MPI ranks
 
  
 
srun --mpi=pmi2 Rscript /data/training/SLURM/rmpi_test.R
 
srun --mpi=pmi2 Rscript /data/training/SLURM/rmpi_test.R
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For rmpi/4.0 module the following command will work
 
For rmpi/4.0 module the following command will work
  
mpiexec -n ${SLURM_NTASKS} Rscript rmpi_test.R
+
mpiexec -n ${SLURM_NTASKS} Rscript rmpi_test.R
  
  
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<pre>
 
<pre>
ln -s Link the /apps/rmpi/conf/Rprofile .Rprofile
+
ln -s /apps/rmpi/conf/Rprofile .Rprofile
 
</pre>
 
</pre>

Latest revision as of 13:54, 30 September 2020

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Example, of using the parallel module to run MPI jobs under SLURM with Rmpi library.

# Load the R MPI package if it is not already loaded.
if (!is.loaded("mpi_initialize")) {
    library("Rmpi")
    }

ns <- mpi.universe.size() - 1
mpi.spawn.Rslaves(nslaves=ns)
#
# In case R exits unexpectedly, have it automatically clean up
# resources taken up by Rmpi (slaves, memory, etc...)
.Last <- function(){
       if (is.loaded("mpi_initialize")){
           if (mpi.comm.size(1) > 0){
               print("Please use mpi.close.Rslaves() to close slaves.")
               mpi.close.Rslaves()
           }
           print("Please use mpi.quit() to quit R")
           .Call("mpi_finalize")
       }
}
# Tell all slaves to return a message identifying themselves
mpi.bcast.cmd( id <- mpi.comm.rank() )
mpi.bcast.cmd( ns <- mpi.comm.size() )
mpi.bcast.cmd( host <- mpi.get.processor.name() )
mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))

# Test computations
x <- 5
x <- mpi.remote.exec(rnorm, x)
length(x)
x

# Tell all slaves to close down, and exit the program
mpi.close.Rslaves(dellog = FALSE)
mpi.quit()


Example job script using rmpi_test.R script.

#!/bin/sh
#SBATCH --job-name=mpi_job_test # Job name
#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=ENTER_YOUR_EMAIL_HERE # Where to send mail	
#SBATCH --cpus-per-task=1 # Number of cores per MPI rank 
#SBATCH --nodes=2 #Number of nodes
#SBATCH --ntasks=8 # Number of MPI ranks
#SBATCH --ntasks-per-node=4 #How many tasks on each node
#SBATCH --ntasks-per-socket=2 #How many tasks on each CPU or socket
#SBATCH --distribution=cyclic:cyclic #Distribute tasks cyclically on nodes and sockets
#SBATCH --mem-per-cpu=1gb # Memory per processor
#SBATCH --time=00:05:00 # Time limit hrs:min:sec
#SBATCH --output=mpi_test_%j.out # Standard output and error log
pwd; hostname; date

echo "Running example Rmpi script. Using $SLURM_JOB_NUM_NODES nodes with $SLURM_NTASKS 
tasks, each with $SLURM_CPUS_PER_TASK cores."
module purge; module load gcc/9 openmpi rmpi

srun --mpi=pmi2 Rscript /data/training/SLURM/rmpi_test.R

date

For rmpi/4.0 module the following command will work

mpiexec -n ${SLURM_NTASKS} Rscript rmpi_test.R


Link the /apps/rmpi/conf/Rprofile as .Rprofile in the current directory configuration file that must be placed in the working directory if the rmpi module doesn't add a symlink automatically.

ln -s /apps/rmpi/conf/Rprofile .Rprofile