Dear list,

According to this presentation (
http://www.rinfinance.com/agenda/2010/MarkSeligman_Tutorial.pdf), gpuHclust
in the gputools package should be about 20x faster than clust, but after
some testing, I find it actually 4x slower. Here is the code:

test.data <- function(dim, num, seed=17) {
    set.seed(seed)
    matrix(rnorm(dim * num), nrow=num)
}
m <- test.data(1920, 9500)
library(gputools)
d <- gpuDist(m)                # Euclidean distance

system.time(gpuHclust(d))
   user  system elapsed
 28.230  41.283  69.727
system.time(hclust(d))
   user  system elapsed
  6.517   0.260   6.790

The gpu on my machine is Telsa C5020 from NVIDIA.


Best regards,

Kaiyin ZHONG
------------------------------
FMB, Erasmus MC
k.zhong@erasmusmc.nl
kindlychung@gmail.com

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