seqParallelSetup: Setup/Get a Parallel Environment

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Setup/Get a Parallel Environment

Description

Setups a parallel environment in R for the current session.

Usage

seqParallelSetup(cluster=TRUE, verbose=TRUE)
seqGetParallel()
seqMulticoreSetup(num, type=c("psock", "fork"), verbose=TRUE)

Arguments

cluster	NULL or FALSE: serial processing; TRUE: parallel processing with the maximum number of cores minor one; a numeric value: the number of cores to be used; a cluster object for parallel processing, created by the functions in the package parallel, like makeCluster. See details
num	the maximum number of cores used for the user-defined multicore setting; FALSE, NA or any value less than 2, to disable the multicore cluster
type	either PSOCK or Fork cluster setup for the multicore setting, the resulting parallel cluster will be used if 'parallel' is a number greater than one in associated functions
verbose	if TRUE, show information

Details

When cl is TRUE or a numeric value, forking techniques are used to create a new child process as a copy of the current R process, see ?parallel::mcfork. However, forking is not available on Windows, so multiple processes created by makeCluster are used instead. The R environment option seqarray.parallel will be set according to the value of cluster. Using seqParallelSetup(FALSE) removes the registered cluster, as does stopping the registered cluster.

Value

seqParallelSetup() has no return, and seqGetParallel() returns getOption("seqarray.parallel", FALSE).

Author(s)

Xiuwen Zheng

See Also

seqParallel, seqApply

Examples

library(parallel)

seqParallelSetup(2L)

# the GDS file
(gds.fn <- seqExampleFileName("gds"))

# display
(f <- seqOpen(gds.fn))

# run in parallel
summary(seqMissing(f))

# close the GDS file
seqClose(f)

seqParallelSetup(FALSE)

zhengxwen/SeqArray documentation built on May 1, 2024, 6:26 p.m.