This is my job submission script for the raster extraction.
#!/bin/bash -l #PBS -l walltime=48:00:00,nodes=1:ppn=24,mem=61gb #PBS -m abe #PBS -M myaddress@email.com module load gdal/2.0.1 module load proj module load R module load ompi module load udunits module load geos export OMP_NUM_THREADS=1 mpirun -v -hostfile $PBS_NODEFILE -np 1 R --slave CMD BATCH ./extract.R /dev/stdout
This is the R script.
library(raster)
library(rgdal)
library(Rmpi)
library(sf)
all <- stack("all.tif")
forest <- st_read(dsn="./forest",layer="forest_simple")
beginCluster(n=23,type="MPI")
raster_cells <- extract(all,forest)
endCluster()
save(raster_cells,file="raster_vals.RData")