search for: parapply

I'm using /parApply/() function in "snow" package for parallel computing (boostrapping repeating calculation), as the follows: MyBoostrapping <- function( i ){ ..... } cl <- makeCluster( ncluster, type = "SOCK") i.circle <- as.matrix( 1:128, , 1) parApply( cl, i.circle, 1, FUN = MyB...

I've started to use the parallel package and it works very well speeding things up. Thank you for making this easy to do. Should I have expected that parCapply would return a vector when parApply returns a matrix? library(parallel) x <- matrix(rnorm(8), nc = 2) apply(x, 2, function(y) y) [,1] [,2] [1,] -0.9649685 0.91339851 [2,] -1.4313140 0.13457671 [3,] 1.0499248 1.58967879 [4,] -1.8974411 0.03639876 cl <- makeCluster(getOption("cl.cores", detectCore...

Hi I try parallelising some code using the snow package and the following lines: cl <- makeSOCKcluster(8) pfunc <- function (x) (if(x <= (-th)) 1 else 0) ###correlation coefficient clusterExport(cl,c("pfunc","th")) cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc) The parApply results in the error message: > cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc) Error in do.call("fun", lapply(args, enquote)) : could not find function "fun". Any ideas? Best wishes Kristian ________________________________ Helmh...

Hello All, I can run the "lower level" functions OK, but many of the higher level (eg. parSApply) functions are generating errors. When running the example (from the snow help docs) for parApply on MacOSX 10.5.5, I get the following error: cl <- makeSOCKcluster(c("localhost","localhost")) sum(parApply(cl, matrix(1:100,10), 1, sum)) Error in do.call("fun", lapply(args, enquote)) : could not find function "fun" Any ideas? Do I possibly need...

I've been using parApply() in snow package for parallel computing with the following lines in R 2.8.1: library(snow) nNodes <- 4 cl <- makeCluster(nNodes, type = "SOCK") fm <- parApply(cl, myData, c(1,2), func1, ...) Since I have a Mac OS X (version 10.4.11) with two dual-core processors, I tho...

...) runs fine. Rainer On Wed, 31 Dec 2008, Greg Riddick wrote: > Hello All, > > I can run the "lower level" functions OK, but many of the higher level > (eg. parSApply) functions are generating errors. > > When running the example (from the snow help docs) for parApply on > MacOSX 10.5.5, I get the > following error: > > > cl <- makeSOCKcluster(c("localhost","localhost")) > sum(parApply(cl, matrix(1:100,10), 1, sum)) > > Error in do.call("fun", lapply(args, enquote)) : > could not find function...

...er(2)) > parLapply(X=1:2, fun=function(...) {}) Error in cut.default(i, breaks) : invalid number of intervals This is because in parLapply length(cl) is determined before defaultCluster(cl) is called. By inspection, this appears to be true of other high-level functions, but ironically not of parApply. In defaultCluster, t would also be helpful to check that the detected cluster, user-supplied or other, is a valid cluster. diff attached. Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1...

...1]]' and 'clusterApply' has no 'seq' arg. There are a few other occurences of mistake (c) in the \details and \value section, for clusterApply() and clusterApplyLB(). Omissions --------- o X: A vector (atomic or list) for ?parLapply? and ?parSapply?, an array for ?parApply?. ==> Nothing is said for the 'X' argument of parLapplyLB() and parSapplyLB(). Inconsistencies --------------- The only function in that man page with a 'seq' argument is clusterSplit(), which is a questionable choice since split() (and strsplit()) use 'x'...

...tex mpi.get.sourcetag text html latex mpi.info text html latex mpi.init.sprng text html latex mpi.intercomm.merge text html latex mpi.parSim text html latex mpi.parapply text html latex example mpi.probe text html latex mpi.realloc text html latex mpi.reduce text html latex mpi.remote.exec text html latex example mp...

...cl <- makeCluster(3,type="PVM") R complains that tid<0 and I cannot go further even thoug R goes on working. Case 2) One of the 2 fbsd boxes as master and the others as slaves: R and snow seem to work; I can makeCluster but R freezes as soon as I try to execute a cluster order like parApply, clusterCall, etc. What should I check? Vittorio

Hello, The problem I'm working now requires to operate on big matrices. I've noticed that there are some packages that allows to run some commands in parallel. I've tried snow and NetWorkSpaces, without much success (they are far more slower that the normal functions) My problem is very simple, it doesn't require any communication between parallel tasks; only that it divides

Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to make the changes to support Open MPI. I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi) under R 2.6.0 but I cannot convince myself yet whether it works or not. Simple tests work. E.g. on my Debian testing box, with Rmpi installed directly using Open Mpi 1.2.3-2 (from Debian) and using 'r' from

...tex mpi.get.sourcetag text html latex mpi.info text html latex mpi.init.sprng text html latex mpi.intercomm.merge text html latex mpi.parSim text html latex mpi.parapply text html latex example mpi.probe text html latex mpi.realloc text html latex mpi.reduce text html latex mpi.remote.exec text html latex example mp...

Dear R users, we are trying to do some parallel computing using library(snow). In particular we have a cluster with 3 nodes >cl <- makeCluster(3, type = "MPI") 3 slaves are spawned successfully. 0 failed. and we want to compute the function op_mat (see below) first with the master and then with the cluster using system.time for checking the computational performance.

...tex mpi.get.sourcetag text html latex mpi.info text html latex mpi.init.sprng text html latex mpi.intercomm.merge text html latex mpi.parSim text html latex mpi.parapply text html latex example mpi.probe text html latex mpi.realloc text html latex mpi.reduce text html latex mpi.remote.exec text html latex example mp...