search for: makesockcluster

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 fil...

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 not created. To debug, I put print statements in the "snow " file in library\snow\r of R after every statement that comes unde...

...st had problems. I hope this is clear. I am intent on solving this problem, so feel free to ask questions if you have feedback but my description is not clear. I really appreciate any help! Yours, Michael Janis UCLA Bioinformatics *****transcript from original post entitles "makeSOCKcluster" follows***** makeSOCKcluster Click to flag this post by Hrishikesh Rajpathak Aug 31, 2006; 10:39pm :: Rate this Message: - Use ratings to moderate (?) Reply | Reply to Author | View Threaded | Show Only this Message Hi, I am a newbie to R and trying to implement paralle...

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

Hi, While I suspect that this is an issue peculiar to my machine (Debian squeeze amd64, R version 3.0.1, up-to-date packages), I'm hoping that somebody on this list may be able to give me suggestions on how to troubleshoot and fix the following: > library (snow) > cl <- makeSOCKcluster(c("localhost","localhost")) sh: 1: RunSnowWorker: not found I presume/hope that this may be related to an (even more pressing) issue I have with mclapply (package 'parallel'). While > example (mclapply) works as expected, any of my longer parallel jobs result in s...

...39;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 processors in nodes other that the one in which I'm running R, the communication is extremely slow. If all processor are in the "master" computer there not seems ti be any problem. Has anyone got any experience with this a...

...r, 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 = makeSOCKcluster(c("localhost","localhost","localhost","localhost","localhost","localhost","localhost")) nrslaves = length(cl) CreateData= function(path){ ... } clusterApply(cl,c("bgcdata1.txt","bgcdata2.txt","bgcdata3...

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 do.call("fun", lapply(args, enquote)) : could not find function "fun" Any ideas? Do I possibly need MPI or PVM to run the "Apply" functions? Thanks, -- Gregory...

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 of MPI and the like), I w...

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 in do.ca...

...n idea how to solve this or where to start digging for solutions? The error messages are: library(snow) cl <- makeCluster(8, type = "SOCK") Error in socketConnection(port = port, server = TRUE, blocking = TRUE, : cannot open the connection Calls: run.call ... makeCluster -> makeSOCKcluster -> newSOCKnode -> socketConnection In addition: Warning message: In socketConnection(port = port, server = TRUE, blocking = TRUE, : port 10187 cannot be opened R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC...

...ttler: edd at ron:~> orterun -np 3 r -e 'library(Rmpi); print(mpi.comm.rank(0))' [1] 0 [1] 1 [1] 2 edd at ron:~> but I basically cannot get anything more complicated to work yet. R / Rmpi just seem to hang, in particular snow and and getMPIcluster() just sit there: > cl <- makeSOCKcluster(c("localhost", "localhost")) > stopCluster(cl) > library(Rmpi) > cl <- makeMPIcluster(n=3) Error in makeMPIcluster(n = 3) : no nodes available. > I may be overlooking something simple here, in particular...

...gt; 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 do.call("fun", lapply(args, enquote)) : > could not find function "fun" > > > > Any ideas? Do I possibly need MPI or PVM to run the "Ap...

...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 <- makeSOCKcluster(rep('10.10.5.15',2), port = 22, master = '10.10.5.15') Error in socketConnection(port = port, server = TRUE, blocking = TRUE, : cannot open the connection In addition: Warning message: In socketConnection(port = port, server = TRUE, blocking = TRUE, : port 22 cannot be opened...

I'm trying to setup a snow grid using sockets (Windows 7).  On the test grid (my computer and another) I have an SSHD server up and running, can connect OK via public key authentication.  Running "makeSOCKcluster" on just my local machine works OK.  Running it to the other computer fails.  My SSH logs show the connection accepted, authenticated and then dropped.   I added "manual=TRUE" to get the command line for the remote machine.  Running what is printed on that machine from the console is...

Hello R experts, I've been searching for weeks a way to use my quad core xeon to increase speed of a very-very computer-intensive simulation I must do for my works. It seems that most purpose-made packages for R : Snow, Rmpi, snowfall,... are designed for Linux based OS. I do not have access to Linux due to professionnal reasons ... so I must work with windows XP. Do somebody know a way to

Hi I am trying to utilize my dual core processor (and later a High-performance clusters (HPC) ) by using the Rmpi, snow, snowfall, ... packages, but I am struggling at the beginning, i.e. to initialise the "cluster" on my dual core computer. Whenever I try to initialize it (via sfInit(parallel=TRUE, cpus=2) or mpi.spawn.Rslaves(nslaves=2) ), I get an error message: >

I am interested in running R commands asynchronously. My first choice is in the same R session that I am currently in. Here, the goal would be to run something like RunAsynchSameSession(myfunction(), "outputname.rda") Once RunAsynchSameSession had started myfunction(), RunAsynchSameSession would complete immediately. myfunction would keep going. It is OK if execution of the

...text html latex ** building package indices ... * DONE (Rmpi) The downloaded packages are in /tmp/RtmpdX6zlZ/downloaded_packages > > > Dirk Eddelbuettel > (https://stat.ethz.ch/pipermail/r-devel/2008-September/050665.html) > suggested that snow's makeSOCKcluster is an easier starting point for > single computer 'clusters' or other configurations where significant > system administration is not desired -- these should work without > additional software on most systems, even if more limiting in the long > term (in my opinion). See, e.g.,...