无法使用parLapply打开连接错误 [英] cannot open the connection error with parLapply

问题描述

我使用parLapply在4核计算机上成功处理了一些数据，如下所示:

I successfully processed some data on a 4 core computer using parLapply, using a code like below:

require("parallel")
setwd("C:/...")

file_summary<-read.table("file_summary",header=T,sep=" ",stringsAsFactors=F)
new_filename<-sub(".asc",".dat",file_summary$filename)

file_list<-list.files()

myfunction <- function(k) {

x<-M$x[k]
y<-M$y[k]

for (i in 1:length(file_summary[,1])) {
    if ( # logical condition on x and y ) {
    new_file<-new_filename[i]
    new_data<-read.table(new_file,header=T,sep=" ")
    eval<-matrix(,nrow=length(new_data$x),ncol=1)

      for (j in 1:length(new_data$x)) {
      eval[j]<-(new_data$x[j]-x)^2+(new_data$y[j]-y)^2
    }
    index<-which(eval == max(eval))
    out<-c(new_data$x[index],new_data$y[index],new_data$mean[index],new_data$S[index])
}
rm(eval)
gc()
}
return(out)
}

n_tasks <- length(M$x) 
n_cores <- 8

Cl = makeCluster(n_cores, type = "PSOCK") 
clusterExport(Cl, "M")
clusterExport(Cl, "file_summary")
clusterExport(Cl, "new_filename")
clusterExport(Cl, "file_list")

Results <- parLapply(Cl, c(1:n_tasks), myfunction)

stopCluster(Cl)

，现在使用完全相同的代码，相同的数据和目录结构(即路径)，我试图在8核计算机上运行分析以进一步加快分析速度.但是，在我第一次尝试时，出现以下错误:

and now using exactly the same code and the same data and directory structure (ie. paths), I am trying to run the analysis on a 8 core machine to speed it up further. However, at my first attempt I get the following error:

8 nodes produced errors; first error: cannot open the connection

我试图清除RAM(对于非R进程)，看是否有帮助，但没有.有什么建议吗?

I tried to clear the RAM a bit (for non R processes) to see if it helped, but it didnt. Any suggestions?

推荐答案

我在"myfunction"中看到的唯一可以生成无法打开连接"错误的操作是"read.table".您可能需要在调用read.table之前添加以下权限:

The only operation that I see in "myfunction" that can generate a "cannot open the connection" error is "read.table". You might want to add the following right before calling read.table:

if (! file.exists(new_file))
  stop(paste(new_file, "does not exist"))

检查工作人员是否具有读取文件的权限可能也很有用:

It might also be useful to check that the worker has permission to read the file:

if (file.access(new_file, mode=4) == -1)
  stop(paste("no read permission on", new_file))

排除这些问题似乎很值得.

It seems worthwhile to rule out these problems.

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