A No BS Guide to the Basics of Parallelization in R

March 15, 2012
By

(This article was first published on librestats » R, and kindly contributed to R-bloggers)

What is parallelization?
Parallelization is using multiple processing cores to, hopefully, make your programs run faster than serial code, which is the use of just one processing core.

Parallel code is not always faster than its serial counterpart (but if you're doing it right and you're careful about what you parallelize, it will be --- remember, that's your goal here).  Don't rush to parallelize something just because you can.  Look for the serious bottlenecks in your code.

Think of your code like the checkout line at a supermarket.  The shoppers are the "component jobs" of the code and the cashier is the processor.  Usually (universally?), each customer gets one cashier.  But imagine suddenly you can chop up your shopping cart into 4 pieces and pass them along to 4 cashiers.  If you're only buying 7 things and they're all easy to ring up, this is probably dumb, because in the end the cashiers are going to have to coordinate and tally for final billing (an inherent sunken time cost to this approach).  On the other hand, if you're buying half of the entire store and the items are slow to ring up (like clothing), this kind of cashier scheme might seriously speed things up for you.  My point is that for some people it makes sense to send to multiple cashiers, and for some it really doesn't make sense to do this.  The same is true of your code.

If you are a computer science nerd who wants to write a 100,000 word dissertation about why this is not an appropriate metaphor, please send your submissions to [email protected].

Ok, so that's (kind of) how it works.  So why should you even bother to learn how to parallelize your code?  Because:

  1. Computers aren't really getting faster, just stuffed full of more cores
  2. Other people care about parallel code (i.e., looks good on a resume)
  3. R is slow
  4. Easy way to speed up your code (in my opinion, MUCH easier than Rcpp and, usually, vectorization)

Just remember to try basic optimization before you jump to parallelization.  Slow serial code produces slow parallel code.

 

How does parallelization work in R?

There are some things in R which usualy parallelize very naturally.  These are:

  1. lapply() calls
  2. probably most other "ply" functions
  3. for loops

As hinted at above, don't necessarily just go hog wild and replace every for loop with a parallel implementation (especially if you're on Windows, which has issues).  Good candidates for easy parallelization usually involve many independent calculations (e.g., checking many models at once and ranking by AIC/BIC/etc, bootstrapping, cross-validation, monte carlo simulation, ...).  Bad candidates for parallelization include things that couldn't possibly be bottlenecking anything, so just leave them alone.  Additionally, some things are, as far as I'm concerned, immune to parallelization; but I'm dumb, so that's probably wrong.

As of R version 2.14, your parallel tools are in the parallel package.  This comes with R, so you don't even have to install it, assuming R is installed (if you don't have R installed and you are still reading this, you have some odd priorities in your life).  Just load it up by calling 'library(parallel)' in R.  This package basically merges the old multicore and snow packages, so that you get mclapply() from multicore and the clusterApply family from snow.  You can also use the foreach package for parallelization, but I personally don't.  Experiment for yourself and come to your own conclusions, but for the remainder, I'm not going to talk about it.

Thankfully, parallelization in R is fairly straight forward.  There are just a few functions you have to become familiar with, and then you let your operating system do most of the magic behind the scenes.  The main workhorses for parallelization in R via library(parallel) are:

  1. mclapply() --- relies on system forking.  Works on any POSIX-like operating system (Linux, Mac OS X, etc---basically all but Windows).  Usually reasonably fast.
  2. clusterApply(), clusterApplyLB(), etc --- relies on voodoo.  Necessary if you're working on Windows.  Will work on POSIX OS's too if you're lazy, but mclapply() is pretty much guaranteed to be faster.  Often slower than serial implementations (which is rare for mclapply()).
  3. The detectCores() function determines the number of cores available to R, which can be very handy, if only for setting defaults.

These functions that facilitate parallelization, mclapply() and the clusterApply functions, all behave kind of like lapply().  In fact, mclapply() is kind of giving the game away by its name, as it is the multiple core lapply.  If you're familiar with lapply(), then you're already halfway there.

 

Stop typing things no one wants to read and give me an example

We're going to simulate 1,000,000 runs of the Monty Hall game (switching every time) to see if we've been lied to all these years about the probability of winning with this switching strategy really being 2/3.  The serial (one core) implementation might look like this:

system.time({
	doors <- 1:3
	runs <- 1e6
	game.outputs <- numeric(runs)
	for (run in 1:runs){
		prize.door <- sample(doors, size=1)
		choice <- sample(doors, size=1)

		if (choice!=prize.door) game.outputs[run] <- 1 # Always switch
	}
	avg <- mean(game.outputs)
})[3]

When we do this, after 7.354 seconds we get a winning average of 0.666297, or approximately 0.666.  Clearly this result shows that Bayes' Theorem is the work of Satan.  From Satan to voodoo, let's run the simulation on multiple cores. Using the code below (Edit:  Correction thanks to Owe Jessen)

#########################################
# ---------------------------------------
# Functions
# ---------------------------------------
#########################################

# One simulation of the Monty Hall game
onerun <- function(.){ # Function of no arguments
	doors <- 1:3
	prize.door <- sample(doors, size=1)
	choice <- sample(doors, size=1)

	if (choice==prize.door) return(0) else return(1) # Always switch
}

# Many simulations of Monty Hall games
MontyHall <- function(runs, cores=detectCores()){
	require(parallel)
	# clusterApply() for Windows
	if (Sys.info()[1] == "Windows"){
		cl <- makeCluster(cores)
		runtime <- system.time({
			avg <- mean(unlist(clusterApply(cl=cl, x=1:runs, fun=onerun)))
		})[3]
		stopCluster(cl) # Don't forget to do this--I frequently do

	# mclapply() for everybody else
	} else {
		runtime <- system.time({
			avg <- mean(unlist(mclapply(X=1:runs, FUN=onerun, mc.cores=cores)))
		})[3]
	}
	return(list(avg=avg, runtime=runtime))
}

#########################################
# ---------------------------------------
# Outputs
# ---------------------------------------
#########################################

run1 <- rbind(c(MontyHall(1e6, cores=1), "cores"=1))
run2 <- rbind(c(MontyHall(1e6, cores=4), "cores"=4))
run3 <- rbind(c(MontyHall(1e6, cores=8), "cores"=8))
rbind(run1, run2, run3)

we get

avg      runtime cores
[1,] 0.666452 8.395   1
[2,] 0.665846 2.876   4
[3,] 0.666336 2.553   8

So for us, there was some pretty good speedup in going from 1 to 4 cores (but a little slow down in going from an ordinary serial implementation to mclapply() with mc.cores=1).  Notice that the one core time here is roughly 3 times the 4 core time.  In an ideal world of perfect magical rainbows, the 4 core time would be 4 times as fast as the 1 core time.  The closer you can get to this kind of optimal scaling, the better, but getting anything close to this ideal is rare.  The kind of scaling we are seeing here is fairly typical and, frankly, not too bad.

Ok, so why the small jump from 4 to "8" cores?  Well, I don't have 8 cores; this computer only has 4.  So what's the deal?  You can set the "number of cores" argument in these functions to a higher value than what you actually have, and sometimes you can get some interesting speedup.  Slightly more on this is discussed below in point 5.

Now, if you're on Windows, I'm not sure that this will be faster in parallel than in serial.  The clusterApply family of functions have, in my experience, very odd behavior on Linux, and I can only assume that this odd behavior also exists on Windows.  What I'm trying to say is that your mileage/kilometerage(?) may vary.

UPDATE:  It strikes me that because of the fat startup costs of the clusterApply family, that this kind of scheme, while great for mclapply() (my primary tool), is inappropriate.  So what you might do instead is something like


runs <- 1e6
manyruns <- function(n) mean(unlist(lapply(X=1:(runs/4), FUN=onerun)))

library(parallel)
cores <- 4
cl <- makeCluster(cores)

# Send function to workers
tobeignored <- clusterEvalQ(cl, {
	onerun <- function(.){ # Function of no arguments
		doors <- 1:3
		prize.door <- sample(doors, size=1)
		choice <- sample(doors, size=1)
		if (choice==prize.door) return(0) else return(1) # Always switch
	}
; NULL
})

# Send runs to the workers
tobeignored <- clusterEvalQ(cl, {runs <- 1e6; NULL})
runtime <- system.time({
	avg <- mean(unlist(clusterApply(cl=cl, x=rep(runs, 4), fun=manyruns)))
})[3]
stopCluster(cl)

cbind(avg, runtime)

with output

> cbind(avg, runtime)
             avg runtime
elapsed 0.666466   3.644

So what we are doing here is chopping up the work so that, with 4 cores, each one of the 4 cores is initialized to do 1/4 of the work all at once.  It seems the title of this entry should be changed...whoopsies.

 

Other thoughts

  1. RTFM.  See 'library(help="parallel")' in R
  2. Check out the book Parallel R by McCallum and Weston, O'Reilly publishing.  I've only thumbed it, but I liked what I saw, and it's cheap.
  3. Practice and experiment!
  4. The "parallel functions" all assume you have just one input.  If you have multiple inputs you want to feed in parallel (i.e., multiple things you want to vary), this problem can easily be remedied by dumping everything into strings with separater characters, then inside the function that gets fed to mclapply/clusterApply, unpack the single input into its multiple component inputs.
  5. When using mclapply(), mc.cores is the number of forks you wish to spawn, not necessarily the exact number of physical cores you want to use (or even have).  The way cores get utilized in dealing with the forks is (thankfully) handled by the operating system.  However, as a result of this, if you experiment with different values of mc.cores, you may sometimes find non-trivial speedup by setting it to a value higher than detectCores().  Speaking from practice (not theory), the returns quickly diminish when increasing the cores beyond what your computer physically has.  This may also work for the clusterApply family, but it might not; don't know as I tend not to use those functions.

To close, even though I (jokingly) discouraged it at the top of the article, all comments are certainly welcome.

To leave a comment for the author, please follow the link and comment on his blog: librestats » R.

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