added readr.read_csv, data.tables.fread to experiments

bench/test_fread.R

@@ -0,0 +1,55 @@
+#!/usr/bin/env Rscript
+#
+# test_fread.R in.csv out.json
+#
+# Loads the file in.csv into an R data frame with fread, sums its numeric
+# columns, and outputs the run times and memory usage to the JSON file
+# out.json.
+
+require("data.table", quietly=TRUE)
+require("rjson", quietly=TRUE)
+
+"OlsonNames" = function () 
+{
+    if (.Platform$OS.type == "windows") 
+        tzdir <- Sys.getenv("TZDIR", file.path(R.home("share"), 
+            "zoneinfo"))
+    else {
+        tzdirs <- c(Sys.getenv("TZDIR"), file.path(R.home("share"), 
+            "zoneinfo"), "/usr/share/zoneinfo", "/usr/share/lib/zoneinfo", 
+            "/usr/lib/zoneinfo", "/usr/local/etc/zoneinfo", "/etc/zoneinfo", 
+            "/usr/etc/zoneinfo")
+        tzdirs <- tzdirs[file.exists(tzdirs)]
+        if (!length(tzdirs)) {
+            warning("no Olson database found")
+            return(character())
+        }
+        else tzdir <- tzdirs[1]
+    }
+    x <- list.files(tzdir, recursive = TRUE)
+    grep("^[ABCDEFGHIJKLMNOPQRSTUVWXYZ]", x, value = TRUE)
+}
+
+memory_usage <- function(){
+ return(strtoi(system(paste("ps -o rss ", Sys.getpid(), "| tail -1"), intern=TRUE))*1024)
+}
+
+args <- commandArgs(TRUE)
+filename <- args[1]
+result_filename <- args[2]
+load_tic <- Sys.time()
+df = fread(filename)
+load_toc <- Sys.time()
+load_time <- as.double(difftime(load_toc, load_tic, units="secs"))
+
+mem <- memory_usage()
+
+sum_tic <- Sys.time()
+s <- colSums(Filter(is.numeric, df))
+s <- s + apply(Filter(function(x){!is.numeric(x)}, df), 2, function(x){sum(nchar(x))})
+sum_toc <- Sys.time()
+sum_time <- as.double(difftime(sum_toc, sum_tic, units="secs"))
+
+results = list(cmd = "R-fread", load_time = load_time, mem = mem, sum_time = sum_time)
+json = rjson::toJSON(results)
+write(json, result_filename)

bench/test_readcsv.R

@@ -0,0 +1,33 @@
+#!/usr/bin/env Rscript
+#
+# test_readcsv.R in.csv out.json
+#
+# Loads the file in.csv into an R data frame. Sums its numeric
+# columns. Outputs the run times and memory usage to the JSON file
+# out.json.
+
+require("rjson", quietly=TRUE)
+
+memory_usage <- function(){
+ return(strtoi(system(paste("ps -o rss ", Sys.getpid(), "| tail -1"), intern=TRUE))*1024)
+}
+
+args <- commandArgs(TRUE)
+filename <- args[1]
+result_filename <- args[2]
+load_tic <- Sys.time()
+df = read.csv(filename)
+load_toc <- Sys.time()
+load_time <- as.double(difftime(load_toc, load_tic, units="secs"))
+
+mem <- memory_usage()
+
+sum_tic <- Sys.time()
+s <- colSums(Filter(is.numeric, df))
+s2 <- apply(Filter(function(x){!is.numeric(x)}, df), 2, function(x){sum(nchar(x))})
+sum_toc <- Sys.time()
+sum_time <- as.double(difftime(sum_toc, sum_tic, units="secs"))
+
+results = list(cmd = "R-readcsv", load_time = load_time, mem = mem, sum_time = sum_time)
+json = rjson::toJSON(results)
+write(json, result_filename)

bench/test_readr.R

@@ -0,0 +1,54 @@
+#!/usr/bin/env Rscript
+#
+# test_datatable.R in.csv out.json
+#
+# Loads the file in.csv into an R data frame with fread, sums its numeric
+# columns, and outputs the run times and memory usage to the JSON file
+# out.json.
+
+require("readr", quietly=TRUE)
+
+"OlsonNames" = function () 
+{
+    if (.Platform$OS.type == "windows") 
+        tzdir <- Sys.getenv("TZDIR", file.path(R.home("share"), 
+            "zoneinfo"))
+    else {
+        tzdirs <- c(Sys.getenv("TZDIR"), file.path(R.home("share"), 
+            "zoneinfo"), "/usr/share/zoneinfo", "/usr/share/lib/zoneinfo", 
+            "/usr/lib/zoneinfo", "/usr/local/etc/zoneinfo", "/etc/zoneinfo", 
+            "/usr/etc/zoneinfo")
+        tzdirs <- tzdirs[file.exists(tzdirs)]
+        if (!length(tzdirs)) {
+            warning("no Olson database found")
+            return(character())
+        }
+        else tzdir <- tzdirs[1]
+    }
+    x <- list.files(tzdir, recursive = TRUE)
+    grep("^[ABCDEFGHIJKLMNOPQRSTUVWXYZ]", x, value = TRUE)
+}
+
+memory_usage <- function(){
+ return(strtoi(system(paste("ps -o rss ", Sys.getpid(), "| tail -1"), intern=TRUE))*1024)
+}
+
+args <- commandArgs(TRUE)
+filename <- args[1]
+result_filename <- args[2]
+load_tic <- Sys.time()
+df = read_csv(filename)
+load_toc <- Sys.time()
+load_time <- as.double(difftime(load_toc, load_tic, units="secs"))
+
+mem <- memory_usage()
+
+sum_tic <- Sys.time()
+s <- colSums(Filter(is.numeric, df))
+s2 <- apply(Filter(function(x){!is.numeric(x)}, df), 2, function(x){sum(nchar(x))})
+sum_toc <- Sys.time()
+sum_time <- as.double(difftime(sum_toc, sum_tic, units="secs"))
+
+results = list(cmd = "R-readr", load_time = load_time, mem = mem, sum_time = sum_time)
+json = rjson::toJSON(results)
+write(json, result_filename)