Quick comment: sapply() / parSapply() can behaves "unexpectedly". To troubleshoot this, use parLapply() instead to see if you at least get the individual results you think you should get.
Henrik On Feb 2, 2017 08:03, "Art U" <art.tem...@gmail.com> wrote: > Hello, > > I have a data orig.raw that contains 8 predictors and 1 outcome variable. > I'm trying to run simulation (bootstrap) and create, let's say, 10 > confidence intervals for coefficients estimated by LASSO. I did it with > regular function replicate, but now I want to do it by using parallel > programming. Here is my code: > > cl <- makeCluster(detectCores()) > clusterEvalQ(cl,library(glmnet)) > clusterEvalQ(cl,library(MASS)) > clusterExport(cl,c("orig.raw")) > > pp=parSapply(cl,1:10,function(i,data=orig.raw,...){ > library(parallel) > cl <- makeCluster(detectCores()) > clusterEvalQ(cl,library(glmnet)) > clusterEvalQ(cl,library(MASS)) > clusterExport(cl,c("orig.raw")) > > repl=parSapply(cl=cl,1:10,function(i,data=orig.raw,...){ > s1=data[sample(nrow(data),size=500,replace=TRUE),] > cross=cv.glmnet(s1[,1:8],s1[,9]) > penalty <- cross$lambda.min > fit=glmnet(s1[,1:8],s1[,9],alpha=1,lambda=penalty) > coe=coef(fit) > m=as(coe, "matrix") > return(m) > }) > > stopCluster(cl) > > mr=t(matrix(repl,nrow = 9,ncol=10)) > means=colMeans(mr) > std=apply(mr, 2, sd) > lb=means-1.96*std; > ub=means+1.96*std; > ind=t(as.numeric({beta>lb & beta<ub})) > return(ind)}) > stopCluster(cl) > > And here is the error I'm getting > > Error in checkForRemoteErrors(val) : 8 nodes produced errors; first > error: comparison (6) is possible only for atomic and list types > > If I run only function repl - it works and I get the matrix that contains > coefficients from 10 runs. > > Can you please help me to solve the problem? > Regards, > Ariel > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.