R foreach：并行读取和操作多个文件

Question

我有 500 个 tar.xz 文件，其中包含 2000 个 csv 文件。我需要一次解压几个 tar 文件（因为磁盘空间），将它们处理成 data.table，从磁盘中删除 csv 文件，然后将结果保存为 RDS，然后再继续下几个 tar 文件。

我的函数在串行中运行良好，但在并行时它会在内核之间混淆文件。这是为什么呢？

一些样本数据：

    for(j in 1:5){
     for(i in 1:5){
      a<-df[sample(x = 1:nrow(df), size = 50, replace = TRUE),]
      write.csv(a,paste0("seed_",i,".csv"))
      lf<-list.files(pattern=".csv")
                  }
     tar(tarfile = paste0("seed_",j,".tar"),files = lf,compression = c("xz"), tar="tar")
                 }

foreach 示例代码

require(dplyr)
require(tidyr)
require(foreach)
require(doParallel)
require(magrittr)

#List all tar files in directory
list_of_files<-list.files(pattern = ".tar")

  packsINeed<-c("vroom","magrittr","dplyr","tidyr","doParallel")
    
  #Start for loop

myCluster<-makeCluster(6,type="PSOCK")
registerDoParallel(myCluster) 

  foreach(i= 1:NROW(list_of_files),.packages = packsINeed)%dopar%{

print(paste(list_of_files[i], "which is", i, "of", NROW(list_of_files) ))

print("2. Untar .csv files inside")
 untar(tarfile = list_of_files[i], exdir = "tempOutputFiles")



 print("#3. Read in files and add up two columns")
df<-vroom::vroom(list.files("tempOutputFiles/$.csv"), id="path")

df$A<-df$B+df$C

    print("#4. save RDS")

saveRDS(object = df, file = paste0(tools::file_path_sans_ext(list_of_files[i], compression = TRUE),".rds"))

 print("#5. Clean up files")

.files<-list.files("tempOutputFiles",pattern=".csv")

    file.remove(basename(.files))
}

使用 mclapply - 行为相同

require(dplyr)
require(tidyr)
require(foreach)
require(doParallel)
require(magrittr)

#List all tar files in directory
list_of_files<-list.files(pattern = ".tar")

myParFun

print(paste(filename))

print("2. Untar all .csv files inside")
 untar(tarfile = filename, exdir = "tempOutputFiles")



 print("#3. Read in files and add up two columns")
df<-vroom::vroom(list.files("tempOutputFiles/$.csv"), id="path")

df$A<-df$B+df$C

    print("#4. save RDS")

saveRDS(object = df, file = paste0(tools::file_path_sans_ext(filename, compression = TRUE),".rds"))

 print("#5. Clean up files")

   .files<-list.files("tempOutputFiles",pattern=".csv")

    file.remove(.files)
}

mclapply(FUN=myParFun, list_of_files, mc.cores=4)

根据 Waldi 的评论，我为 list_of_files 中的每个文件创建了一个目录，现在它可以正常工作了。但是有打鼾的方法吗？以 tempdir 为例？

Answer 1

按照 cmets 中的建议，下面的代码为每个进程 / tar 文件创建一个目录，解压缩，将 CSV 合并到 .rds 文件中并删除它们。
请注意，vroom 似乎需要 altrep = FALSE 参数来避免在删除时出现 permission denied error。

# Generate sample tars for test
write.csv(mtcars,'file1.csv')
write.csv(mtcars,'file2.csv')
write.csv(iris,'file3.csv')
write.csv(iris,'file4.csv')
tar('tar1.tar',files=c('file1.csv','file2.csv'),tar="tar")
tar('tar2.tar',files=c('file3.csv','file4.csv'),tar="tar")

require(dplyr)
require(tidyr)
require(foreach)
require(doParallel)
require(magrittr)

#List all tar files in directory
list_of_files<-list.files(pattern = "\\.tar")

packsINeed<-c("vroom","magrittr","dplyr","tidyr","doParallel")

#Start for loop

myCluster<-makeCluster(2,type="PSOCK")
registerDoParallel(myCluster) 

foreach(i= 1:NROW(list_of_files),.packages = packsINeed)%dopar%{
  print(paste(list_of_files[i], "which is", i, "of", NROW(list_of_files) ))
  
  print("2. Untar .csv files inside")
  fileout <- tools::file_path_sans_ext(list_of_files[i], compression = TRUE)
  exdir <- paste0("temp",fileout)
  untar(tarfile = list_of_files[i], exdir = exdir)
  
  print("#3. Read in files and add up two columns")
  df<-vroom::vroom(file.path(exdir,dir(exdir,"*.csv")),altrep = FALSE)
  
  # df$A<-df$B+df$C   # These columns don't exist in mtcars used as example
  
  print("#4. save RDS")
  
  saveRDS(object = df, file = file.path(exdir,paste0(fileout,".rds")))
  
  print("#5. Clean up files")
  
  .files<-list.files(exdir,pattern="\\.csv")
  
  file.remove(file.path(exdir,.files))
}

不确定 .rds 应该放在哪里，所以暂时留在临时文件夹中。