Hi John, Thank you for the reply. In fact my original list has 122^2 elements in it (I simplified the code here), and parLapply behaves in a similar way still. Can it be something else?
Yan On Dec 11, 2015, at 1:51 PM, John Magnotti <[email protected]<mailto:[email protected]>> wrote: Hello Yan, I think parLapply is just assigning a core for every item in the list, G, you supplied. Because you have more cores than items in the list, some of the cores won't receive any work. John On Fri, Dec 11, 2015 at 4:00 AM, ALPEROVYCH Yan <[email protected]<mailto:[email protected]>> wrote: Hello, I have a piece of code that needs parallelization and it used to work just fine before (about 6 months ago). However, I had to rerun it yesterday and found out that my code is now behaving in a weird way - not all worker processes are charged with the computation. I created a little code that allows reproducing the issue. Here is a snapshot of the top command: PID COMMAND %CPU TIME 872 R 97.7 00:02.45 871 R 0.0 00:00.03 870 R 98.2 00:02.93 869 R 0.0 00:00.03 868 R 97.7 00:02.46 867 R 0.0 00:00.03 866 R 94.4 00:02.36 862 R 1.0 00:04.64 Interestingly, the mclapply command seems to correctly charge all workers instantly. So is this an intended behavior? Example that reproduces the issue on my machine: # rm(list = ls()) library(parallel) set.seed(123) # expr <- expression(pnorm(b0 + b1*x1 + b2*x2 + b3*x3)) G <- list( D(D(expr, "x2"), "b0"), D(D(expr, "x2"), "b1"), D(D(expr, "x2"), "b2"), D(D(expr, "x2"), "b3")) # b0 <- 1.2 b1 <- 0.4 b2 <- 0.2 b3 <- -0.6 x1 <- rnorm(10^7) x2 <- rnorm(10^7) x3 <- rnorm(10^7) # nc <- detectCores() - 1 cl <- makeCluster(nc, type = "FORK") grad_g <- parLapply(cl, G, function(Z) lapply(Z, function(x) mean(eval(x)))) stopCluster(cl) # sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.2 (El Capitan) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base ---- Ce message electronique et tous les fichiers attaches qu'il contient sont confidentiels et destines exclusivement à l'usage de la personne à laquelle ils sont adresses. Si vous avez reçu ce message par erreur, merci de le retourner à son metteur. Les idees et opinions presentees dans ce message sont celles de son auteur, et ne representent pas necessairement celles de l'institution ou entite affiliee dont l'auteur est l'employe. La publication, l'usage, la distribution, l'impression ou la copie non autorisee de ce message et des attachements qu'il contient sont strictement interdits. This email and any files transmitted with it are confide...{{dropped:10}} _______________________________________________ R-SIG-Mac mailing list [email protected]<mailto:[email protected]> https://stat.ethz.ch/mailman/listinfo/r-sig-mac ---- Ce message electronique et tous les fichiers attaches qu'il contient sont confidentiels et destines exclusivement à l'usage de la personne à laquelle ils sont adresses. Si vous avez reçu ce message par erreur, merci de le retourner à son metteur. Les idees et opinions presentees dans ce message sont celles de son auteur, et ne representent pas necessairement celles de l'institution ou entite affiliee dont l'auteur est l'employe. La publication, l'usage, la distribution, l'impression ou la copie non autorisee de ce message et des attachements qu'il contient sont strictement interdits. This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please return it to the sender. The ideas and views expressed in this email are solely those of its author, and do not necessarily represent the views of the institution or company of which the author is an employee. Unauthorized publication, use, distribution, printing or copying of this e-mail or any attached files is strictly forbidden. _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
