-
Notifications
You must be signed in to change notification settings - Fork 12
/
seqParallelSetup.Rd
71 lines (62 loc) · 2.19 KB
/
seqParallelSetup.Rd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
\name{seqParallelSetup}
\alias{seqParallelSetup}
\alias{seqGetParallel}
\alias{seqMulticoreSetup}
\title{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{
\item{cluster}{\code{NULL} or \code{FALSE}: serial processing; \code{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 \code{\link{parallel}}, like \code{\link{makeCluster}}.
See details}
\item{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}
\item{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}
\item{verbose}{if \code{TRUE}, show information}
}
\details{
When \code{cl} is \code{TRUE} or a numeric value, forking techniques are
used to create a new child process as a copy of the current R process, see
\code{?parallel::mcfork}. However, forking is not available on Windows, so
multiple processes created by \code{\link{makeCluster}} are used instead.
The R environment option \code{seqarray.parallel} will be set according
to the value of \code{cluster}.
Using \code{seqParallelSetup(FALSE)} removes the registered cluster, as
does stopping the registered cluster.
}
\value{
\code{seqParallelSetup()} has no return, and \code{seqGetParallel()} returns
\code{getOption("seqarray.parallel", FALSE)}.
}
\author{Xiuwen Zheng}
\seealso{
\code{\link{seqParallel}}, \code{\link{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)
}
\keyword{gds}
\keyword{sequencing}
\keyword{genetics}