similar to: network connectivity is *not* symmetric -- library(parallel)

Dear list, I observed two problems that I suppose are generic. First, using 'Rprof' to profile a parallel (based on the package 'parallel') code caused .... Error in unserialize(node$con) : error reading from connection.... Second, on a multicore desktop, I concurrently opened two terminals and ran two separate R sessions, both running (actually identical) parallel code (which

Dear list, i have some problems using the snow package to create a SOCK cluster. The errors just occour irregularly but it seems to me that they occour when I try to create more than one cluster on the same machine via different R instances started via submitting LSF jobs to a cluster. Does anyone have an idea how to solve this or where to start digging for solutions? The error messages

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) > >

I feel like I've tried the works on something that should be obvious but I'm stuck. Package snowfall used to run just great under debian etch (amd-64, 2x quad-core). After upgrading to lenny (debian 5, reinstalled from scratch), I haven't been able to get snowfall running again. Password-less ssh works fine to localhost, its IP, or zero- config name. But when calling sfInit I

Dear All, I am trying to create socket clusters (using snow and snowfall) with a Windows OS. I am running Windows inside VirtualBox and VMware player (i.e., Windows is guest) from a Debian Linux host system (I've tried in two different Linux systems, an AMD x86-64 workstation and an Intel i686 laptop). However, almost always seting up the cluster fails: either R will hang forever or I will

(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

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

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

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

Hi, I am attempting to implement a mixed (windows/linux) snow sockets parallelism in R, but am running into difficulties similar to a post made Aug 31, 2006 under the same subject heading. I feel like I may be one or two non-obvious steps away from getting it all working, but I'm stuck. If anyone can shed some light on this (I believe Prof. Tierney stated that he has successfully run a

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,

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

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. i'm building a package using autotools. to propagate the package version number from configure.ac to DESCRIPTION, i'm using a DESCRIPTION.in file. both of these files are "shar"'d below. i need to distribute the DESCRIPTION.in file, as ./configure will need it. but, "R CMD check" wants to look at DESCRIPTION, so i've let that also come into the package

Hi all, The call parallel::makeCluster(1L) hangs infinitely on my MacOS machine which seems to be already reported by some people (e.g., https://stat.ethz.ch/pipermail/r-devel/2018-February/075565.html). However, the solutions posted on SO, GH or R-devel do not work in my case. So far, I unsuccessfully tested ? 1. Couple of reboots 2. Adding 192.0.0.1 to /etc/hosts 3. Using R.app

Hi. I have some problems trying to make cluster via "snow" package and haven't found a solution for my problem in archives and relative topics. I installed ssh server using cygwin and set a password-less SSH Login. In R session after starting ssh service: > system("ssh 10.10.5.15 date") Tue Nov 22 16:22:36 AST 2011 But when I make connection: > con <-

Hello, I am using function makePSOCKcluster to make parallel computation on 3 EC2 Amazon machines. I have a passwordless between machines and ssh is correct. In the R 2.15.1 release this function works correctly. Installing R 3.0.1 on my EC2 machines makePSOCKcluster does not produce the cluster. If I run the function with outfile="" option, I obtain this message Error in

Running with Samba 3.5.4, the Samba3x packages from CentOS 5.6 with added gpfs and tsmsm VFS modules against a GPFS 3.4.0.6 file system. Unix extensions are turned off because otherwise OS X 10.5 messes with group ownership and permissions and shares for "groups" don't work as required. Unfortunately being at a University I don't get to control the environment tightly, unless

People of R(th), I have been ramming my head against this problem, and I wondered if anyone could lend a hand. I want to parallelize a bootstrap of a linear model on my 8-core mac. Below is the process that I want to parallelize (namely, the m2.ph.rlm.boot<-boot(m2.ph,m2.ph.fun, R = nboot) command). This is an extension of the bootstrapping linear models example in Venables and Ripley to