r - Fastest way to read in 100,000 .dat.gz files

Question

I have a few hundred thousand very small .dat.gz files that I want to read into R in the most efficient way possible. I read in the file and then immediately aggregate and discard the data, so I am not worried about managing memory as I get near the end of the process. I just really want to speed up the bottleneck, which happens to be unzipping and reading in the data.

Each dataset consists of 366 rows and 17 columns. Here is a reproducible example of what I am doing so far:

Building reproducible data:

require(data.table)

# Make dir
system("mkdir practice")

# Function to create data
create_write_data <- function(file.nm) {
  dt <- data.table(Day=0:365)
  dt[, (paste0("V", 1:17)) := lapply(1:17, function(x) rnorm(n=366))]
  write.table(dt, paste0("./practice/",file.nm), row.names=FALSE, sep="", quote=FALSE)
  system(paste0("gzip ./practice/", file.nm))    
}

And here is code applying:

# Apply function to create 10 fake zipped data.frames (550 kb on disk)
tmp <- lapply(paste0("dt", 1:10,".dat"), function(x) create_write_data(x))

And here is my most efficient code so far to read in the data:

# Function to read in files as fast as possible
read_Fast <- function(path.gz) {
  system(paste0("gzip -d ", path.gz)) # Unzip file
  path.dat <- gsub(".gz", "", path.gz)
  dat_run <- fread(path.dat)
}

# Apply above function
dat.files <- list.files(path="./practice", full.names = TRUE)
system.time(dat.list <- rbindlist(lapply(dat.files, read_Fast), fill=TRUE))
dat.list

I have bottled this up in a function and applied it in parallel, but it is still much much too slow for what I need this for.

I have already tried the h2o.importFolder from the wonderful h2o package, but it is actually much much slower compared to using plain R with data.table. Maybe there is a way to speed up the unzipping of files, but I am unsure. From the few times that I have run this, I have noticed that the unzipping of the files usually takes about 2/3rd of the function time.

Answer 1

I'm sort of surprised that this actually worked. Hopefully it works for your case. I'm quite curious to know how speed compares to reading in compressed data from disk directly from R (albeit with a penalty for non-vectorization) instead.

tblNames = fread('cat *dat.gz | gunzip | head -n 1')[, colnames(.SD)]
tbl = fread('cat *dat.gz | gunzip | grep -v "^Day"')
setnames(tbl, tblNames)
tbl