Yet Another Blog in Statistical Computing

I can calculate the motion of heavenly bodies but not the madness of people. -Isaac Newton

Test Drive of Parallel Computing with R

Today, I did a test run of parallel computing with snow and multicore packages in R and compared the parallelism with the single-thread lapply() function.

In the test code below, a data.frame with 20M rows is simulated in a Ubuntu VM with 8-core CPU and 10-G memory. As the baseline, lapply() function is employed to calculate the aggregation by groups. For the comparison purpose, parLapply() function in snow package and mclapply() in multicore package are also used to generate the identical aggregated data.

n <- 20000000
df <- data.frame(id = sample(20, n, replace = TRUE), x = rnorm(n), y = runif(n), z = rpois(n, 1))

benchmark(replications = 5, order = "user.self",
  LAPPLY = {
  df1 <- data.frame(lapply(split(df[-1], df[1]), colMeans))
  SNOW = {
  cl <- makeCluster(8, type = "SOCK")
  df2 <- data.frame(parLapply(cl, split(df[-1], df[1]), colMeans))
  df3 <- data.frame(mclapply(split(df[-1], df[1]), colMeans, mc.cores = 8))

all.equal(df1, df2)
all.equal(df1, df3)

Below is the benchmark output. As shown, the parallel solution, e.g. SNOW or MULTICORE, is 3 times more efficient than the baseline solution, e.g. LAPPLY, in terms of user time.

       test replications elapsed relative user.self sys.self user.child
3 MULTICORE            5 101.075    1.000    48.587    6.620    310.771
2      SNOW            5 127.715    1.264    53.192   13.685      0.012
1    LAPPLY            5 184.738    1.828   179.855    4.880      0.000
3     7.764
2     0.740
1     0.000

Attaching package: ‘compare’

The following object is masked from ‘package:base’:


[1] TRUE
[1] TRUE

In order to illustrate the CPU usage, multiple screenshots have also been taken to show the difference between parallelism and single-thread.

In the first screenshot, it is shown that only 1 out of 8 CPUs is used at 100% with lapply() function and the rest 7 are idle.
Screenshot from 2013-05-25 22:14:18

In the second screenshot, it is shown that all 8 CPUs are used at 100% with parLapply() function in the snow package.
Screenshot from 2013-05-25 22:16:47

In the third screenshot, it is also shown that all 8 CPUs are used at 100% with mulapply() function in the multicore package.
Screenshot from 2013-05-25 22:18:40


Written by statcompute

May 25, 2013 at 11:40 pm

Posted in S+/R