Hi David and list,
I'm a little puzzled to see these results below. Since, "apply" is basically a for loop, I was expecting "foreach" uses about same amount of time as apply, whereas foreach after registering 2-cores runs much faster. However, the results show apply is the fastest. Also could you please explain the error message (i.e. Error in ipcTaskSetEnvironment(taskq, envir) : ...) in the second run? The results were recorded on REvolution R 3.2 and I observed the same on regular R2.11.0. Many thanks! ...Tao > library(doSMP) Loading required package: foreach Loading required package: iterators Loading required package: codetools foreach: simple, scalable parallel programming from REvolution Computing Use REvolution R for scalability, fault tolerance and more. http://www.revolution-computing.com Loading required package: revoIPC > > m <- matrix(rnorm(100000), 10000, 10) > > system.time(tmp <- t(apply(m, 1, function(x) x/mean(x)))) user system elapsed 0.21 0.00 0.21 > system.time(tmp1 <- foreach(i=1:nrow(m), .combine=rbind) %dopar% (m[i,] / > mean(m[i,]))) user system elapsed 5.50 0.00 5.53 Warning message: executing %dopar% sequentially: no parallel backend registered > > > w <- startWorkers(2) Warning messages: 1: In startWorkers(2) : there is an existing doSMP session using doSMP1 2: In startWorkers(2) : there is an existing doSMP session using doSMP2 > registerDoSMP(w) > system.time(tmp1 <- foreach(i=1:nrow(m), .combine=rbind) %dopar% (m[i,] / > mean(m[i,]))) user system elapsed 6.02 0.03 7.84 > stopWorkers(w) > > ## second run > system.time(tmp <- t(apply(m, 1, function(x) x/mean(x)))) user system elapsed 0.22 0.02 0.23 > system.time(tmp1 <- foreach(i=1:nrow(m), .combine=rbind) %dopar% (m[i,] / > mean(m[i,]))) Error in ipcTaskSetEnvironment(taskq, envir) : The task queue has been freed. Timing stopped at: 0.03 0.02 0.04 > > > w <- startWorkers(2) Warning messages: 1: In startWorkers(2) : there is an existing doSMP session using doSMP1 2: In startWorkers(2) : there is an existing doSMP session using doSMP2 > registerDoSMP(w) > system.time(tmp1 <- foreach(i=1:nrow(m), .combine=rbind) %dopar% (m[i,] / > mean(m[i,]))) user system elapsed 6.11 0.01 7.62 > stopWorkers(w) > dim(m) [1] 10000 10 > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-intel32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] doSMP_1.0-1 revoIPC_1.0-2 foreach_1.3.0 codetools_0.2-2 iterators_1.0.3 Revobase_3.2.0 > _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. N:WL:en-US:WM_HMP:042010_3 ______________________________________________ R-help@r-project.org mailing list 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.
