similar to: snow, ssh, and socket connections

All, I'm attempting to run this: table.CAPM(series[,"Strat.Return",drop=FALSE],series[,"spy.Return",drop=FALSE]) and getting this error Error in as.vector(data[, i]) : subscript out of bounds I've searched around and cannot find a solution to the problem.  I've used this in the past without problem and I'm not sure what I did different this time. Other

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

I am trying to use rgenoud and snow with an external model and file I/O. Unlike the typical application of rgenoud and snow, I need to run an external executable and do pre- and post-processing of input and output files for each parameter set generated by genoud(). I'm hoping that someone can suggest improvements to my approach and a work-around for file I/O problems I've encountered when

When trying to create (a very simple) cluster using makeSOCKcluster or makeCluster I get the following error message: > library(snow) > cl <- makeSOCKcluster("localhost") Fatal error: kann Datei '~/R/i686-suse-linux-gnu-library/2.8/snow/RSOCKnode.R' nicht ?ffnen: Datei oder Verzeichnis nicht gefunden (translation: could not open file [...]: File or directory not

hello, I'm using R 1.8.1 with the lastest snow package on FreeBSD 4.9. However, when I try to using socket clusters, it's very unstable. Sometimes it dies half way when I run parSapply(), sometimes it dies when cluster connection is idle. I create a socket cluster by following cmd cl = makeCluster("foo", type = "SOCK", outfile="/tmp/rafanlog");

Dear Luke and others, I have many R versions on my machine and want to start a particular one when snow builds its cluster. (The same version I start snow from.) It seems that everything is set up correctly in defaultClusterOptions: > mget(ls(defaultClusterOptions), defaultClusterOptions) $homogeneous [1] TRUE $manual [1] FALSE $master nodename "maya.unil.ch" $outfile [1]

Dear "R-help"ers, using snow on socket connections, I ran into the following error > cl <- makeSOCKcluster(hosts) Error in socketConnection(port = port, server = TRUE, blocking = TRUE : all connections are in use with "showConnections(all=T)" showing 50 open connections. As - for administrative reasons - I would prefer to use snow's SOCK capabilities (instead

Hello All, I can run the "lower level" functions OK, but many of the higher level (eg. parSApply) functions are generating errors. When running the example (from the snow help docs) for parApply on MacOSX 10.5.5, I get the following error: cl <- makeSOCKcluster(c("localhost","localhost")) sum(parApply(cl, matrix(1:100,10), 1, sum)) Error in

Hello all; I'm trying to execute parallel jobs trough library snow on a cluster built through torque/PSB. I'm succesfully obtaining the cluster with: >system("cat $PBS_NODEFILE > cluster.txt") >mycluster <- scan(file="cluster.txt",what="character") >cl <- makeSOCKcluster(mycluster) The only problem, at the moment, is that if I use

I'm working with snow and created a local cluster. So far, the same code has always worked (please see below). However, now I receive a message that the connection with the nodes cannot be opened. I restarted my workstation but that didn't help. Is there a known solution for this problem? Thanks a lot for any help. bram foubert library(snow) cl =

Hi I try parallelising some code using the snow package and the following lines: cl <- makeSOCKcluster(8) pfunc <- function (x) (if(x <= (-th)) 1 else 0) ###correlation coefficient clusterExport(cl,c("pfunc","th")) cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc) The parApply results in the error message: > cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc) Error

Hi, if we have a file called Rscript.R that contains the following, for example: x <- 1:100 outfile = "Rscript.Rout" sink(outfile) print(x) and then we run >> source("Rscript.R") we get an output file called Rscript.Rout - great! Is there an internal variable, something like .Platform, that holds the script name when it is being executed? I would like to use

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 <-

Hi Greg, I don't know if this is related to your problem, but I get the same error (on both ubuntu and fedora linux, R 2.9) and just found a very curious behaviour - snowfall apply functions don't like the variable name "c". E.g.: c<-1 sfLapply(1:10, exp) issues the same error you had posted, while subsequent rm("c") sfLapply(1:10, exp) runs fine. Rainer

Hi Sayan, Just stumbled upon this email, three months old, since I was having the same problem, and noticed you hadn't been answered. I was able to solve this problem by noting that the "snow" library was not installed on the nodes--it has to be installed everywhere. So, you need to ssh to the "ip to another computer on the network ", then be sure the same version of R

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

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

Hello, After getting help to solve part of my problem and some delay on my part, I am posting a more refined version to see if someone can help me further. I am trying to autocalibrate a model in my subject area using the snow and rgenoud packages. I want to use the key function "fn" that is called by genoud() to finalize input, run the model executable, and compute the objective

Thanks to Luke Tiernay and some experimenting I found out some issues. I don't claim this infomation is complete, but it may be helpful for anyone experimenting with SNOW on Linux: - environment variables PATH and R_SNOW_LIB need to be set on master and slaves. (manually or permanent in ~/.bashrc (adjust your pathnames accordingly). Don't use ~ for home directory, instead specify

Hello, I was using snow to parallel-process some code in R-2.10 (32-bit windows. ). The code is as follows: require(foreach) require(doSNOW) cl <- makeCluster(6, type='SOCK') registerDoSNOW(cl) bl2 <- foreach(i=icount(length(unqmrno))) %dopar% { (some code here) } stopCluster(cl) When I run the same code in Windows R-2.11 (either 32-bit or 64-bit), R hangs at