raster (version 2.0-41)

cluster: Use a multi-core cluster

Description

beginCluster creates, and endCluster deletes a 'snow' cluster object. This object can be used for multi-core computing with those 'raster' functions that support it. beginCluster determines the number of nodes (cores) that are available and uses all of them (unless the argument n is used). NOTE: beginCluster may fail when the package 'nws' is installed. You can fix that by removing the 'nws' package, or by setting the cluster type manually, e.g. beginCluster(type="SOCK") endCluster closes the cluster and removes the object. The use of the cluster is automatic in these functions: projectRaster, resample and in extract when using polygons. clusterR is a flexible interface for using cluster with other functions. This function only works with functions that have a Raster* object as first argument and that operate on a cell by cell basis (i.e., there is no effect of neigboring cells) and return an object with the same number of cells as the input raster object. The first argument of the function called must be a Raster* object. There can only be one Raster* object argument. For example, it works with calc but not with overlay. This function is particularly useful to speed up computations in functions like predict, interpolate and perhaps calc. Among other functions, it does _not_ work with merge, crop, mosaic, (dis)aggregate, resample, projectRaster, focal, distance, buffer, direction. But not that projectRaster has a build in capacity for clustering that is automatically used if beginCluster() has been run.

Usage

beginCluster(n, type='SOCK', nice, exclude)
endCluster()
clusterR(x, fun, args=NULL, filename='', cl=NULL, m=2, ...)

Arguments

n

Integer. The number of nodes to be used (optional)

type

Character. The cluster type to be used

nice

Integer. To set the prioirty for the workers, between -20 and 20 (UNIX like platforms only)

exclude

Character. Packages to exclude from loading on the nodes (because they may fail there) but are required/loaded on the master

x

Raster* object

fun

function that takes x as its first argument

args

list with the arguments for the function (excluding x, which should always be the first argument

filename

character. Output filename (optional)

cl

cluster object (do not use it if beginCluster() has been called

m

tuning parameter to determine how many blocks should be used. The number is rounded and multiplied with the number of nodes.

...

additional arguments as for writeRaster

Value

• beginCluster and endCluster: None. The side effect is to create or delete a cluster object. clusterR: as for the function called with argument fun

Examples

beginCluster()

r <- raster()
r[] <- 1:ncell(r)

x <- clusterR(r, sqrt, verbose=T)

f1 <- function(x) calc(x, sqrt)
y <- clusterR(r, f1)

s <- stack(r, r*2, r*3)
f2 <- function(x) calc(x, range)
z <- clusterR(s, f2)

pts <- matrix(c(0,0, 45,45), ncol=2, byrow=T)
d <- clusterR(r, distanceFromPoints, args=list(xy=pts))

values(r) <- runif(ncell(r))
m <- c(0, 0.25, 1,  0.25, 0.5, 2,  0.5, 1, 3)
m <- matrix(m, ncol=3, byrow=TRUE)
rc1 <- clusterR(r, reclassify, args=list(rcl=m, right=FALSE), 
               filename='rcltest.grd', datatype='INT2S', overwrite=TRUE)

# equivalent to:
rc2 <- reclassify(r, rcl=m, right=FALSE, filename='rcltest.grd', datatype='INT2S', overwrite=TRUE)
			   
endCluster()