Difference between revisions of "R MPI Example"
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− | [[Category:Software]] | + | [[Category:Software]][[Category:Compiler]] |
[[R|back to the main R page]] | [[R|back to the main R page]] | ||
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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 $SLURM_CPUS_PER_TASK cores." | ||
− | module purge; module load | + | module purge; module load gcc openmpi rmpi |
− | + | srun --mpi=${HPC_PMIX} Rscript /data/training/SLURM/rmpi_test.R | |
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− | |||
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− | srun --mpi= | ||
date | date | ||
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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 |
Latest revision as of 16:08, 14 June 2024
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 $SLURM_CPUS_PER_TASK cores." module purge; module load gcc openmpi rmpi srun --mpi=${HPC_PMIX} 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