search for: checkforremoteerror

Hi all, I am trying to use snow package to do a parallel MCMC. I have read a few guides and articles, the following is that I came up with. When I run it I got the error message: Error in checkForRemoteErrors(lapply(cl, recvResult)) : 4 nodes produced errors; first error: could not find function "ui.Next" The data is a longitudinal data with few repeated readings on a number of individuals. However, the response is organised in a vector rather than a matrix. E.g. (y_11 , y_12 , y_13 , y_1...

...ob2 <- ob1 at lineobj } else if (class(ob1)=="SpatialLines") { ob2 <- ob1 } ob3 <- data.frame(length_m=sapply(1:length(ob2), function(l) gLength(ob2 [l, ]))) ..... } ..... } sfStop() The problem is that the code returns the error message: Error in checkForRemoteErrors(val) : one node produced an error: object 'ob2' not found >From the debugging function "sfCat", I also get these warning messages: Warning messages: 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, : Unknown option on command...

...luster,c(10:100),test.each.term,call=call.m) } stopCluster(cluster) The problem that I am having is that sometimes it will run for 50 iterations of this loop then crash. Sometimes 15 iterations, sometimes 2. When the crash happens, I receive the following error message every time: Error in checkForRemoteErrors(val) : one node produced an error: cannot open the connection Calls: clusterApplyLB -> dynamicClusterApply -> checkForRemoteErrors Execution halted Any ideas as to what might be going on? I have run this code successfully many times when I do not use the loop. I have a lot of data to...

...;,"localhost")) nrslaves = length(cl) CreateData= function(path){ ... } clusterApply(cl,c("bgcdata1.txt","bgcdata2.txt","bgcdata3.txt","bgcdata4.txt","bgcdata5.txt","bgcdata6.txt","bgcdata7.txt"),CreateData) Error in checkForRemoteErrors(val) : 7 nodes produced errors; first error: cannot open the connection -- View this message in context: http://r.789695.n4.nabble.com/Problems-in-snow-can-t-open-connection-with-nodes-tp2529692p2529692.html Sent from the R help mailing list archive at Nabble.com.

...ently modified something). Anyway, now when I make the call: parallel.model.results <- clusterApply(cl,processors.struct,MCexe) exactly as I used to do, where MCexe is my function and processors.struct is a list containing everything required by MCexe, I obtain the following error: Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: incorrect number of dimensions Please, do you have any clue about what could be the error? Best regards, Javier Garc?a-Pintado

...,Hess=T,rang=A3,skip=T) dif=sum((predict(regm1,Xcc)-Ycr)^2) return(dif) } somar=DEoptim(pred_regm1,c(1,0.00001,0.01), c(25,0.999,0.95), control = DEoptim.control(steptol=25,trace = FALSE,itermax=500,parallelType=1)) but implemented parallel process, i have next error: Error en checkForRemoteErrors(val) : 4 nodes produced errors; first error: could not find function "nnet" how I can solve my mistake? Thanks and kind regards -- David Zamora Ávila (I.C.) Estudiante de la Maestría en Hidrosistemas Pontificia Universidad Javeriana Bogota, Colombia Ed. José Gabriel Maldonado Tel....

...astList, function(v) mfv(v)[1]) ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred))) } testK = function() { k = seq(3, 25, 2) r = parSapply(cl, k, function(i) predR(x, i)) # r = sapply(k, function(i) predR(x, i)) } r = testK() stopCluster(cl) Here is the error: Error in checkForRemoteErrors(val) : 8 nodes produced errors; first error: could not find function "predR" Best regards, Kaiyin ZHONG ------------------------------ FMB, Erasmus MC k.zhong@erasmusmc.nl kindlychung@gmail.com [[alternative HTML version deleted]]

...1(y3)) } dat <- 1:5 f1(dat) f3('NY', dat) sapply(c("state1", 'state2', 'state3'), f3, dat) sfExportAll() sfClusterEval(ls()) sfSapply(c("s1", 's2', 's3'), f3, dat) sfStop() # sfSapply generates the following error # Error in checkForRemoteErrors(val) : # 2 nodes produced errors; first error: "dogg" is not a defined class === end ============= -- View this message in context: http://r.789695.n4.nabble.com/undefined-S4-class-in-parallel-computing-at-snowfall-tp4634757.html Sent from the R help mailing list archive at Nabble...

Hi, The following function use to work, but now it doesn't giving the error "> CallSnow(, 100) Using snow package, asking for 2 nodes 2 slaves are spawned successfully. 0 failed. Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: no applicable method for 'lapply' applied to an object of class "list" ". Where this is the problem line of code "yusum <- parLapply(cl, yu, sum)" The function is CallSnow <- function (Nnodes = 2, Nsamples =...

...odes. > noclusters<-2 > cl <- makeCluster(noclusters, type = "MPI") 2 slaves are spawned successfully. 0 failed. > foo<-clusterApply(cl,1:noclusters,function(noderank) {2+2}) > foo [[1]] [1] 4 [[2]] [1] 4 > clusterCall(cl,setwd("C:/")) Error in checkForRemoteErrors(lapply(cl, recvResult)) : 2 nodes produced errors; first error: variable "C:/" of mode "function" was not found > Any suggestions ? Thanks in advance, Tolga Generally, this communication is for informational purposes only and it is not intended as an offer or solic...

...iterature), I can't get the bootstrap to run. For example, using snow: cl <- makeCluster(8) clusterSetupRNG(cl) clusterEvalQ(cl,library(boot)) clusterEvalQ(cl,library(lme4)) boot.out<-clusterCall(cl,boot(dat.res,boot.fun, R = nboot)) stopCluster() returns the following error: Error in checkForRemoteErrors(lapply(cl, recvResult)) : 8 nodes produced errors; first error: could not find function "fun" I am stuck and at the limit of my programming knowledge and am punting to the R-help list. I need to run this process thousands of times, which is the reason to make it parallel. Any sugge...

...+ print(paste("loop.end = ",loop.end)) + + rr[[i]] <- sfClusterApplyLB(loop.start:loop.end,wrapper1,reps) + a<-rr[[i]] + save(a,file=paste("rr_",i,".RData",sep="")) + } + ) [1] "loop.start = 1" [1] "loop.end = 10" Error in checkForRemoteErrors(val) : 10 nodes produced errors; first error: cannot open the connection Timing stopped at: 0 0 0.06 ************** END OF OUTPUT AND ERROR MESSAGE ******************* ++++++++++++++++++++++++++++++++++ Edmond Ng, MSc CStat Lecturer in Medical Statistics Department of Health Services Research...

...and x parameters read in OK , ee gets calculated but not returned #now try to apply the function in parallel via SNOW cl <- makeCluster(3,type="SOCK") #make a cluster ll <- clusterMap(cl,fun=myfun, + a=mydat$a.in, + b=mydat$b.in, + x=mydat$x.in, + flow.dat=flow.dat) >Error in checkForRemoteErrors(val) : 10 nodes produced errors; first error: incorrect number of dimensions stopCluster(cl) _______________________________________________________ Here is system info > Sys.info() sysname release version...

...CPUs Detected: 4 Laplace's Demon is preparing environments for CPUs... ################################################## ################################################## Status messages are not displayed for parallel processing. Laplace's Demon is beginning parallelization... Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: incorrect number of dimensions Laplace's Demon has finished.

..."formula" "formula" "formula" "formula" Mode "call" "call" "call" "call" "call" And when I export summary.statistics, which is used inside my wrapper function, I get an error message: Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: could not find function "summary.statistics" Do I have to export the summary method that is provided by the ergm package to the cluster object? If so, how? The following code is a self-contained example. ########## library("ergm&...

...ture), I can't get the bootstrap to run. For example, using snow: cl <- makeCluster(8) clusterSetupRNG(cl) clusterEvalQ(cl,library(boot)) clusterEvalQ(cl,library(lme4)) m2.ph.rlm.boot<-clusterCall(cl,boot(m2.ph,m2.ph.fun, R = nboot)) stopCluster() returns the following error: Error in checkForRemoteErrors(lapply(cl, recvResult)) : 8 nodes produced errors; first error: could not find function "fun" I am stuck and at the limit of my programming knowledge and am punting to the R-help list. Any suggestions are much appreciated. Anthony -- Anthony Steven Dick, Ph.D. Assistant Professo...