Sunday, May 26, 2013

More bubble sort tuning

After last week's post bubble sort tuning I got an email from Berend Hasselman noting that my 'best' function did not protect against cases n<=2 and a speed improvement was possible. That made me realize that I should have been profiling the functions rather than just look for inspiration in the code. So, that's what I wanted to do this week. Unfortunately the examples were a bit too simple to see good power of profiling. So, after wring a too long post, removed a lot again.

Simple Improvements 

The first thing I did was compare Berend's code, bubble_sort6, with mine own, bubble_sort5. The difference is, I thought, in the indexing, the double [ ][ ].  And it was 10% to 20% faster.
library(microbenchmark)

bubble_sort5 = function(vec) {
  wm <- which.max(vec)
  vec <- c(vec[-wm],vec[wm])
  for (iend in ((length(vec)-1):2)) {
    wm <- which.max(vec[1:iend])
    vec <- c(vec[1:iend][-wm],vec[1:iend][wm],vec[(iend+1):length(vec)])
  }
  vec
}

bubble_sort6 = function(vec) {
  wm <- which.max(vec)
  vec <- c(vec[-wm],vec[wm])
  for (iend in ((length(vec)-1):2)) {
    tmp <- vec[1:iend]
    wm <- which.max(tmp)
    vec <- c(tmp[-wm],tmp[wm],vec[(iend+1):length(vec)])
  }
  vec
}
So how about removing more indices? I can copy the vector, push the maximum in the correct space and eliminate from the original vector.
bubble_sort7 = function(vec) {
  final <- vec
  for (iend in (length(vec):1)) {
    wm <- which.max(vec)
    final[iend] <- vec[wm]
    vec <- vec[-wm]
  }
  final
}
Why not eliminate the removal from the vector and place a low number there, so which.max skips those?
bubble_sort8 = function(vec) {
  final <- vec
  smallest <- min(vec)
  for (iend in (length(vec):1)) {
    wm <- which.max(vec)
    final[iend] <- vec[wm]
    vec[wm] <- smallest
  }
  final
}
The speed of number 7 and 8 are highest. Number 8 at vector_size = 1000. (To make the display compacted, the expression is slightly shortened).                                                                             
vector_size = 1000
mbm <- microbenchmark(bubble_sort5(sample(vector_size)),
    bubble_sort6(sample(vector_size)),
    bubble_sort7(sample(vector_size)),
    bubble_sort8(sample(vector_size)),
    sort(sample(vector_size)),
    sample(vector_size))  
su <- summary(mbm)
levels(su$expr) <- gsub('sample(vector_size)','',levels(su$expr),fixed=TRUE)
su

            expr       min         lq     median         uq        max neval
1 bubble_sort5() 58382.570 69967.8920 70629.8475 71088.0120  85883.413   100
2 bubble_sort6() 42090.254 43020.5110 54414.1360 55058.8650  74350.140   100
3 bubble_sort7() 27909.892 28862.5065 29183.9545 39707.0685 241396.777   100
4 bubble_sort8() 24635.301 25061.5775 25356.6345 36344.5100  40485.581   100
5         sort()   321.081   503.2475   522.6735   534.7695    641.430   100
6                   31.521    38.8525    48.3830    50.5815     53.514   100
but number 7 is fastest at vector.size=100. 
            expr      min       lq    median       uq       max neval
1 bubble_sort5() 1792.338 1836.322 1880.6720 1928.322  2313.546   100
2 bubble_sort6() 1392.819 1416.644 1454.7630 1536.499 28460.422   100
3 bubble_sort7() 1364.230 1408.579 1433.5045 1507.177  1894.967   100
4 bubble_sort8() 1724.896 1773.279 1808.8320 1881.038 26898.999   100
5         sort()  177.401  258.405  336.8425  364.332   599.645   100
6                   5.864    9.530   10.9960   13.562    20.526   100

Profiling

The classic way to profile is using rprof(). I checked R-bloggers and found improved R profiling summaries by Noam Ross, from which I concluded that the only improvements were on output. I will use the classic output. This seems to work best, maybe that's because I work from Eclipse, maybe because I still use R 2.15.3, but other summaries did not work so well. It also seems 17% of the time is consumed by which.max and 80% by processes which are not registered by the profiler. Not very informative, but that may be because the example is too simple.
Rprof("file.out",interval=.002)
for(i in 1:100) bubble_sort7(sample(1000))
Rprof(NULL)
summaryRprof("file.out")
$by.self
             self.time self.pct total.time total.pct
bubble_sort7     2.704    81.30      3.322     99.88
which.max        0.594    17.86      0.594     17.86
-                0.020     0.60      0.020      0.60
sample           0.004     0.12      0.004      0.12
$<-              0.002     0.06      0.002      0.06
parse            0.002     0.06      0.002      0.06

$by.total
             total.time total.pct self.time self.pct
<Anonymous>       3.326    100.00     0.000     0.00
bubble_sort7      3.322     99.88     2.704    81.30
eval              3.322     99.88     0.000     0.00
which.max         0.594     17.86     0.594    17.86
-                 0.020      0.60     0.020     0.60
sample            0.004      0.12     0.004     0.12
doTryCatch        0.004      0.12     0.000     0.00
tryCatchList      0.004      0.12     0.000     0.00
tryCatchOne       0.004      0.12     0.000     0.00
$<-               0.002      0.06     0.002     0.06
parse             0.002      0.06     0.002     0.06
srcfilecopy       0.002      0.06     0.000     0.00

$sample.interval
[1] 0.002

$sampling.time
[1] 3.326

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