sge.parApply: Method used to integrate apply, lapply, sapply fcuntionality...

Description Usage Arguments Details Value Author(s) Examples

Description

applies each row/column of a matrix or each element of a list to a function.

Usage

 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
  sge.apply   (X, MARGIN, FUN, ..., 
               join.method=cbind,
               njobs,batch.size=getOption('sge.block.size'),
               packages=NULL, global.savelist=NULL,function.savelist=NULL,
               cluster =getOption("sge.use.cluster"),
               trace=getOption("sge.trace"), debug=getOption("sge.debug"),
               file.prefix=getOption("sge.file.prefix"))
  sge.parRapply(X, FUN, ..., join.method=cbind, 
               njobs, batch.size=getOption('sge.block.size'),
               packages=NULL, global.savelist=NULL, function.savelist=NULL,
               cluster =getOption("sge.use.cluster"),
               trace=getOption("sge.trace"), debug=getOption("sge.debug"),
               file.prefix=getOption("sge.file.prefix"))
 
  sge.parCapply(X, FUN, ..., join.method=cbind, 
               njobs, batch.size=getOption('sge.block.size'),
               packages=NULL, global.savelist=NULL, function.savelist=NULL,
               cluster =getOption("sge.use.cluster"),
               trace=getOption("sge.trace"), debug=getOption("sge.debug"),
               file.prefix=getOption("sge.file.prefix"))
 
  sge.parLapply(X, FUN, ..., join.method=c, 
               njobs, batch.size=getOption('sge.block.size'),
               packages=NULL, global.savelist=NULL, function.savelist=NULL,
               cluster =getOption("sge.use.cluster"),
               trace=getOption("sge.trace"), debug=getOption("sge.debug"),
               file.prefix=getOption("sge.file.prefix")) 

  sge.parSapply(X, FUN, ...,  
                USE.NAMES=TRUE, simplify=TRUE,
                join.method=c, 
                njobs, batch.size=getOption('sge.block.size'),
                packages=NULL, global.savelist=NULL, function.savelist=NULL,
                cluster=getOption("sge.use.cluster"),
                trace=getOption("sge.trace"), debug=getOption("sge.debug"),
                file.prefix=getOption("sge.file.prefix"))
  sge.parParApply(X, FUN, ...,
               join.method=cbind,
               njobs,
               batch.size=getOption('sge.block.size'),
               trace=getOption("sge.trace"),
               packages=NULL,
               global.savelist=NULL, function.savelist=NULL,
               debug=getOption("sge.debug"),
               file.prefix=getOption('sge.file.prefix'),
               apply.method
              )

Arguments

X

Object to be applied to function (matrix, data.frame, list, array, or vector supported)

MARGIN

Used by sge.par to determime if (1) sge.Rapply or (2) sge.Capply should be called.

FUN

Function to be applied to object

...

Additional arguments to be applied to function

njobs

Number of parallel jobs to use

join.method

Function used to merge results from each job.

batch.size

Number of rows to include in parallel job if njobs is excluded.

global.savelist

Character vector giving the names of variables from the global environemnt that should be imported. If sge.save.global is set to TRUE, then this will clear the global environment. To set the global environment to be empty, use vector()

function.savelist

Character vector giving the variables to save from the local environment. <Passing a vector() will cause the local function to be empty, any value here will remove any non-listed values

packages

List of library packages to be loaded by each worker process before computation is started.

cluster

determines if the job should be submitted to the cluster or run locally (default:submit to cluster, TRUE)

trace

Prints some information about job submission. (TRUE|FALSE)

file.prefix

Prefix for the data files used to pass information between nodes

debug

Prints debug level info about jobs. (TRUE|FALSE)

USE.NAMES

Determines if the sapply use names functionality should be used

simplify

Detemines if the sapply simplify functionality should be used

apply.method

tells apply if it should apply as a list or matrix

Details

sge.parApply applies the function argument to either the rows, or elements of x. (depending on the value of apply.method)

The arguments packages and savelist can be used to properly initialize the worker processes.

sge.parCapply computes the transpose of X and uses it for the arguments of parRapply.

sge.parLapply and sge.parSapply use lapply, sge.parCapply, and sge.parRapply use apply (Margin=1)

Value

Returns an object whose type is determined by the join.method. This object should be equivalent to the object that would be returned by an equivalent call to apply, sapply, or lapply.

Author(s)

Dan Bode [email protected]

Examples

 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
## Not run:   
 # there are tons of examples (actually my crude unit tests)
 # in the tests directory of this package. These contain tons of 
 # examples of how to dop everything
 # I also recommend taking a look at the ENVIRONMENTS document, since 
 # the environment is being handled specially. 

 # basic lapply call
 sge.parLapply(c(1:10), function(x) x + 1)
 # run locally
 options(sge.use.cluster=FALSE)
 sge.parLapply(c(1:10), function(x) x + 1)
 options(sge.use.cluster=TRUE)
 #pass extra arguments
 sge.parLapply(c(1:10), function(x,y) x + y, 3) 

 # work with martices
 m2 <- array(1:20, dim=c(4,5))
 # apply rows, split into 3 jobs
 sge.parRapply(m2, function(x,y) x + y, 3, njobs=3)
 # bind results with c, since we are changing dimensions
 sge.parRapply(m2, mean, njobs=3, join.method=c)

 # working with GLOBAL variables
 GLOBAL1 = 1
 # rather this variable is saved by default depends on the value of sge.save.global
 sge.options(sge.save.global=TRUE)
 sge.parLapply(c(1:10), function(x) x + GLOBAL1)
 sge.options(sge.save.global=FALSE)
 sge.parLapply(c(1:10), function(x) x + GLOBAL1, global.savelist=c("GLOBAL1"))

## End(Not run)

mcvaneede/Rsge documentation built on May 21, 2019, 12:44 p.m.