similar to: MacOS parallel::makeCluster fails

Hi Thomas, thanks for your reply (and thanks for your patience...). I am now using the following minimal reprex: > library(parallel) > cl <- makeCluster(2L) I freshly started the machine and did not open any other app. Just R.app (3.6.1). After executing the second line of code, R seems to hang infinitely and does not respond. The R process itself uses almost no CPU. Unfortunately,

Hi Dominik, from the output, the master process could not "listen" on the port where it expects a connection from the worker. We need to find out why. I'd recommend first to create a minimal reproducible example (and one that does not use future, only parallel, and a minimal number of threads, ideally just 2). Then I'd recommend to check if the problem still exists with

(Bcc: CRAN) This is a proposal helping CRAN and alike as well as individual developers to avoid stray R processes being left behind that might be produced when an example or a package test fails to set up a parallel::makeCluster(). ISSUE If a package test sets up a PSOCK cluster and then the master process dies for one reason or the other, the PSOCK worker processes will remain running for 30

BACKGROUND: While troubleshooting random, occasionally occurring, errors from parallel::makePSOCKcluster("localhost", port = 11000); Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : cannot open the connection I had another look at parallel:::newPSOCKnode(), which is used internally to set up each background worker. It is designed to,

A solution is to have parallel:::.slaveRSOCK() attempt to connect multiple times before failing, e.g. makeSOCKmaster <- function(master, port, timeout, useXDR, maxTries = 10L, interval = 1.0) { port <- as.integer(port) for (i in seq_len(maxTries)) { con <- tryCatch({ socketConnection(master, port = port, blocking = TRUE,

Great. For the record of this thread, I've submitted patch PR17391 (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17391). I've patched it against the latest R-devel on the SVN, passes 'make check-all', and I've verified it works with the above tests. /Henrik On Fri, Mar 9, 2018 at 4:37 AM, <luke-tierney at uiowa.edu> wrote: > I'm happy to look at a

The problem causing the stray worker processes when the master fails to open a server socket to listen to connections from workers is not related to timeout in socketConnection(), because socketConnection() will fail right away. It is caused by a bug in checking the setup timeout (PR 17391). Fixed in 76275. Best Tomas On 3/18/19 2:23 AM, Henrik Bengtsson wrote: > (Bcc: CRAN) > >

On Mon, 31 Oct 2016, Henrik Bengtsson wrote: > Thank you for looking into this Luke. > > On Thu, Oct 27, 2016 at 9:26 AM, <luke-tierney at uiowa.edu> wrote: >> On unix, unless event polling is enabled Sys.sleep just waits in a >> select() call (with a SIGINT handler in place) so the elapsed time >> isn't checked until after the select call is complete.

I'm happy to look at a patch that does this. I'd start with a small interval and increase it by 50%, say, on each try wit a max retry time limit. This isn't eliminating the problem,only reducing the probability, but still worth it. I had considered doing something like this but it didn't seem necessary at the time. You don't want to retry indefinitely since the connection

Hello! Can I use DBM databases (as they are used in Perl) for the import of large datasets in R? Thanks in advance for your help, Petra Steiner - --------------------------------------------------- Petra Steiner Arbeitsbereich Linguistik Universitaet Muenster Huefferstrasse 27 48149 Muenster

I just noticed that parallel:::.slaveRSOCK() passes 'timeout' to socketConnection() as a character, i.e. there's a missing timeout <- as.integer(timeout), cf. port <- as.integer(port) and useXDR <- as.logical(value): > parallel:::.slaveRSOCK function () { makeSOCKmaster <- function(master, port, timeout, useXDR) { port <- as.integer(port) con

Dear experts, when trying to estimate an kernel density function with density(x) I get the following error message with imported data from either EXCEL or text files: Error in density(spr) : argument must be numeric. Other procedues such as truehist work. If I generate data within R density works fine. Does anybody have an idea? Yours -- Christoph Hanck Wissenschaftliche Hilfskraft

Platform: Windows Version: 1.6.2 When first called, socketConnection gives an error. On subsequent calls it performs correctly. Thus the first call has the effect of "priming" the connection. Eg > socketConnection(port=50) Error in socketConnection(port = 50) : unable to open connection In addition: Warning message: localhost:50 cannot be opened > MIM <-

Hi Henrik, Thanks for the detailed in fast reply! My guess would be that the confusion comes from the different use of nice and renice. The workraund you provided work fine! Thanks a lot. Best, Andreas Henrik Bengtsson <henrik.bengtsson at gmail.com> writes: > Looks like a bug to me due to wrong assumptions about 'nice' > arguments, but could be because a

I assume smaller types like <4 x i1> are getting zero extended to e.g., i8? Am 04.08.2017 um 15:58 schrieb Amara Emerson: > Actually for mask vectors of i1 values, you don't need to use reductions > at all(although for SVE this is what we'll do). You can instead bitcast > the vector value to an i8/i16/whatever and then compare against zero. > > Amara > > On

Dear Henrik, thank you, for the quick reply. Bizarrely enough, the problem vanished when I woke the computer from sleep (I had previously replicated the problem after several restarts of both R and the MacOS). I will follow-up if I can again replicate the problem. Florian On 2/10/18 4:39 PM, Henrik Bengtsson wrote: > A few quick comments: > > * You mention R --vanilla, but make sure

Hi there is it possible that pdfs generated using the pdf() function with default settings leads to loss of information? I was plotting copy number changes from Agilent 180k data in form of rectangles (rect()) while each rectangle represents one region of copy number change. When plotting into a pdf I noticed that some very small rectangles do not appear (even after extensive zooming) in the pdf

Dear list, I?m running a postfix (2.5.6) / Dovecot (1.1.11) on a Centos 5.2 box. I?ve written a small gui application to simply create Out of Office replys with sieve. The resulting code did work with maildrop without any problems. Now sieve fails when it meets any german umlauts like ? or ?. It just stops compiling the scripts and complains about the missing "};". A simple fix is

Hi all, I can't get the functionality of the package parallel to work. Specifically, makeCluster() hangs when I run it. I first noticed the problem when trying to run Rstan with multiple cores and the traced it back to the core package parallel. The following results in R hanging after the call to makeCluster. library(parallel) # Calculate the number of cores no_cores <-

Dear list, this may not be related to R but rather to my OS, but I do not understand the issue of compiling R packages deeply enough to figure out the exact cause of the problem. I am trying to install a R package from source as it is not yet available under Cran (Rssa, downloaded here: https://github.com/asl/rssa). Running sudo R CMD INSTALL asl-rssa-6f458e4.tar.gz from the console