similar to: segfault and RunSnowWorker: not found

A new version of the 'snow' package for parallel computing in R is available at http://www.stat.uiowa.edu/~luke/R/cluster/snow_0.3-3.tar.gz This substantially revises the way in which worker processes are started to allow snow to be used on Windows and Mac/Windows/Linux combinations. I have successfully used the SOCK version on a standalone Windows machine and combinations of

Hi Simon, I'm having trouble with nested parallel workers, specifically, forking inside socket connections. When mclapply is called inside a SOCK, PSOCK or FORK worker I get an error in unserialize(). cl <- makeCluster(1, "SOCK") fun = function(i) { library(parallel) mclapply(1:2, sqrt) } Failure occurs after multiple calls to clusterApply: > clusterApply(cl, 1,

On 03/25/2015 07:48 PM, Simon Urbanek wrote: > On Mar 25, 2015, at 3:46 PM, Valerie Obenchain <vobencha at fredhutch.org> wrote: > >> Hi Simon, >> >> I'm having trouble with nested parallel workers, specifically, forking inside socket connections. >> > > You simply can't by definition - when you fork *all* the workers share the same connection

Hi all, With the help of Tomas, I was able to track the issue down: Prior to R v3.6.0 the parallel package passes an uninitialized variable as the file descriptor argument to the close system call. In my particular R session this uninitialized variable (reproducibly) was holding the value 7, which corresponded to the file descriptor of the write end of the pipe the second child would use to

Hi all, With the help of Tomas, I was able to track the issue down: Prior to R v3.6.0 the parallel package passes an uninitialized variable as the file descriptor argument to the close system call. In my particular R session this uninitialized variable (reproducibly) was holding the value 7, which corresponded to the file descriptor of the write end of the pipe the second child would use to

Thanks Jeremy, i'm analyzing this with the application team, we'll see what we can find. > I was hoping to find a way for the samba4 server to behave like samba3 (as > in ignoring bad characters and replacing them with an underscore > character), which in the end resulted in the best compromise. In the meantime, do you have any idea why there is difference between the two

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

Hi Andreas, thank you very much, good job finding it was EBADF. Now the question is why the pipe has been closed prematurely; it could be accidentally by R (a race condition in the cleanup code in fork.c) or possibly by some other code running in the same process (maybe the R program itself or some other code it runs). Maybe we can take this off the list and come back when we know the cause

Dear All, Since upgrading to 3.6.0, I've been getting a strange error messages from the child process when using mcparallel/mccollect. Before filing a report in the Bugzilla, I want to figure out whether I had been doing something wrong all this time and R 3.6.0 has exposed it, or whether something else is going on. # Background # Ultimately, what I want to do is to be able to set a time

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

Hi, I am a newbie to R and trying to implement parallelism in R. I am currently using R-2.3.1, and Cygwin to run R on Windows xp. ssh and all are working fine, When I try to create a socket connection as makeSOCKcluster(c("localhost","localhost")), it just waits for the other prcess on localhost to get created and respond. But this other process is

Hello list, probably a known issue (but I haven't found a link yet): I'm using 3.0.2a with 'unix charset = ISO8859-15' and get the following then a file with ticks is created: - desired: "???????`'??" - displayed: "???????`'??" ^^^ The euro sign is created correctly in a file name. The filename will be displayed in the filesystem

Running the example in the documentation causes R to crash. dario at bioinfo:~$ R R version 3.0.3 (2014-03-06) -- "Warm Puppy" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or

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

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

Dear list, in R under wheezy the following error occurs: > library(cairoDevice) > Cairo() Error in Cairo() : Graphics API version mismatch It seems to be Debian-specific, as I tried the same under OpenSUSE 11.3 and it worked. I tried installing cairoDevice via `apt-get install r-cran-cairodevice' and with `install.packages("cairoDevice")' in R (without any

Hi, after a lengthy but unsuccessfull search I couldn't come up with a solution to the following problem: I would like to have a "comma" instead of a "point" as the decimal point in my graphics, i.e. postscript and pdf files, for I write my thesis in German. My system is: OS: Debian Unstable R-Version: 2.0.1 System locale: de_DE at euro Could someone, please, help

With newest R devel #sessionInfo() R Under development (unstable) (2012-01-10 r58085) Platform: amd64-portbld-freebsd10.0 (64-bit) locale: [1] de_DE.ISO8859-15/de_DE.ISO8859-15/de_DE.ISO8859-15/C/de_DE.ISO8859-15/de_DE.ISO8859-15 attached base packages: [1] stats graphics grDevices utils datasets methods base I get the following error when I try to build and install lubridate from

Hello, is there any function in the package snow to check for a really running cluster? The function checkCluster only checks the variable cl. And the variable is still available after stopping the cluster! ( a simple solution would be deleting the cluster variable cl in the function stopCluster) > library(snow) > cl <- makeCluster(5) 5 slaves are spawned successfully. 0