Package 'pbmcapply'

Tracking mclapply with progress bar

Description

pbmclapply is a wrapper around the mclapply function. It adds a progress bar to mclapply function.

Parallelization (mc.core > 1) works only on *nix (Linux, Unix such as macOS) system due to the lack of fork() functionality, which is essential for mcapply, on Windows.

Usage

pbmclapply(X, FUN, ...,
           mc.style = "ETA", mc.substyle = NA,
           mc.cores = getOption("mc.cores", 2L),
           ignore.interactive = getOption("ignore.interactive", F),
           mc.preschedule = TRUE, mc.set.seed = TRUE,
           mc.cleanup = TRUE, mc.allow.recursive = TRUE)

Arguments

X	a vector (atomic or list) or an expressions vector. Other objects (including classed objects) will be coerced by 'as.list'.
FUN	the function to be applied to.
...	optional arguments to FUN.
mc.cores	see mclapply.
mc.style, mc.substyle	style of the progress bar. See progressBar.
ignore.interactive	whether the interactive() is ignored. If set to TRUE, the progress bar will be printed even in a non-interactive environment (e.g. called by Rscript). Can be set as an option "ignore.interactive".
mc.preschedule, mc.set.seed, mc.cleanup, mc.allow.recursive	See mclapply.

Examples

# A lazy sqrt function which doesn't care about efficiency
lazySqrt <- function(num) {
  # Sleep randomly between 0 to 0.5 second
  Sys.sleep(runif(1, 0, 0.5))
  return(sqrt(num))
}

# On Windows, set cores to be 1
if (.Platform$OS.type == "windows") {
  cores = 1
} else {
  cores = 2
}

# A lazy and chatty sqrt function.
# An example of passing arguments to pbmclapply.
lazyChattySqrt <- function(num, name) {
  # Sleep randomly between 0 to 0.5 second
  Sys.sleep(runif(1, 0, 0.5))
  return(sprintf("Hello %s, the sqrt of %f is %f.", toString(name), num, sqrt(num)))
}

# Get the sqrt of 1-3 in parallel
result <- pbmclapply(1:3, lazySqrt, mc.cores = cores)
chattyResult <- pbmclapply(1:3, lazyChattySqrt, "Bob", mc.cores = cores)

---

Tracking mcmapply with progress bar

Description

pbmcmapply is a wrapper around the mcmapply function. It adds a progress bar to mcmapply function.

Parallelization (mc.core > 1) works only on *nix (Linux, Unix such as macOS) system due to the lack of fork() functionality, which is essential for mcapply, on Windows.

Usage

pbmcmapply(FUN, ..., MoreArgs = NULL,
           mc.style = "ETA", mc.substyle = NA,
           mc.cores = getOption("mc.cores", 2L),
           ignore.interactive = getOption("ignore.interactive", F),
           mc.preschedule = TRUE, mc.set.seed = TRUE,
           mc.cleanup = TRUE)

Arguments

FUN	the function to be applied in parallel to ...
...	arguments to vectorize over (vectors or lists of strictly positive length, or all of zero length).
MoreArgs	a list of other arguments to FUN.
mc.cores	see mcmapply.
mc.style, mc.substyle	style of the progress bar. See progressBar.
ignore.interactive	whether the interactive() is ignored. If set to TRUE, the progress bar will be printed even in a non-interactive environment (e.g. called by Rscript). Can be set as an option "ignore.interactive".
mc.preschedule, mc.set.seed, mc.cleanup	See mcmapply.

Examples

# A lazy sqrt function which doesn't care about efficiency
lazySqrt <- function(num) {
  # Sleep randomly between 0 to 0.5 second
  Sys.sleep(runif(1, 0, 0.5))
  return(sqrt(num))
}

# On Windows, set cores to be 1
if (.Platform$OS.type == "windows") {
  cores = 1
} else {
  cores = 2
}

# A lazy and chatty sqrt function.
# An example of passing arguments to pbmcmapply.
lazyChattySqrt <- function(num, name) {
  # Sleep randomly between 0 to 0.5 second
  Sys.sleep(runif(1, 0, 0.5))
  return(sprintf("Hello %s, the sqrt of %f is %f.", toString(name), num, sqrt(num)))
}

# Get the sqrt of 1-3 in parallel
result <- pbmcmapply(lazySqrt, 1:3, mc.cores = cores)
chattyResult <- pbmcmapply(lazyChattySqrt, 1:3, MoreArgs = list("Bob"), mc.cores = cores)

---

Progress bar with the estimated time to completion (ETA).

Description

This is an extended version of the txtProgressBar function with the estimated time to completion (ETA). Please refer to that for documentation (help(utils::txtProgressBar)). The original utils::setTxtProgressBar can be used to update the bar. Use help(setTxtProgressBar, "utils") to get help about the original function.

Usage

progressBar(min = 0, max = 1, initial = 0, style = "ETA", substyle = NA,
            char = "=", width = NA, file = "")

Arguments

min, max, initial	see txtProgressBar.
style	style of the progress bar - see 'Details'.
substyle	substyle of the progress bar - only needed when style is set to certain value (see 'Details').
char, width, file	see txtProgressBar.

Details

When style = "txt", it performs exactly the same as the original txtProgressBar. In this case, substyle shall be treated as the style in the original txtProgressBar. Please refer to the 'Detail' of txtProgressBar for the meanings of substyles.

When style = "ETA", it shows a progress bar with the estimated time to completion (ETA). Substyle is not used in this case. However, when running in a terminal and the width of the terminal windows is smaller than 40 characters, the progress bar will not be displayed.

Value

An object of class "txtProgressBar".

Note

Code derived from library pbarETA (https://github.com/franapoli/pbarETA) by Francesco Napolitano [email protected].

See Also

txtProgressBar

Examples

# Test function
testit <- function(x, ...)
{
    pb <- progressBar(...)
    for(i in c(0, x, 1)) {
      setTxtProgressBar(pb, i)
    }
    close(pb)
}

# Txt progress bar
testit(sort(runif(10)), style = "txt", substyle = 3)

# ETA progress bar
testit(sort(runif(10)), style = "ETA")

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