Hello Jim, thanks for the reply!
What I'm trying to do:
I have a small function that makes use of many other functions, such as the
one I called "estimate.NAC.structure.of()"
I'm trying to make run everything faster. Thus I'm using Rprof to perform a
line by line profiling to help me decide what lines of code I should
replace. Mostly it's this estimate.NACstructure.of function that requires
time. I could copy paste this function, but it has more than a 1000 lines
of code...
The line #33 and what's around is
rankCR=function(a, b, c) {
vvv=c(-1, -1, -1)
dens=.C("rankC", as.integer(sample.size), as.double(vvv),
as.double(a), as.double(b),as.double(c),
result=as.double(rep(-1, sample.size*3)), ties=as.double(rep(-1,
sample.size*3))) ################ line 33
return(list(matrix(dens[["result"]], ncol=3, nrow=sample.size, byrow=TRUE),
as.numeric(dens[["ties"]])))
}
This rankCR function is then used in a loop:
pre.r <- rankCR(pseudo.samples[[a]], pseudo.samples[[b]],
pseudo.samples[[c]])
where pseudo.samples[[whatever]] is just a vector.
And so the problem is that this rankCR function eats up more than 50% of
the execution time according to the first profiling (more precisely, line
33 is eating up more than 50% of the execution time), then does not even
show up in the top 30 in the second profiling... thus what I have to
improve to make the code run faster is getting not that clear.
On Wed, Jan 29, 2014 at 10:02 PM, jim holtman <jholt...@gmail.com> wrote:
> You should at least post the script so that we see what line 33 is.
> For example, was it an input statement so that on the second time you
> ran the data was cached in memory? Did you remove all the objects and
> do a gc() to clean up memory before trying again (maybe there was some
> data hanging around that helped out). It is not unknown to get
> different results if you are having to access, especially, external
> data.
>
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
> Tell me what you want to do, not how you want to do it.
>
>
> On Wed, Jan 29, 2014 at 8:29 AM, Nathan Uyttendaele <na.uyt...@gmail.com>
> wrote:
> > Hello,
> >
> > when I run this code in a brand new R session
> >
> > --------------------------------------------------
> > ### loading of libraries and other functions
> >
> > Rprof("profiling.out")
> > start.time=proc.time()[3]
> > for(i in 1:50) {
> > main.function()
> > }
> > end.time=proc.time()[3]
> > Rprof()
> > ---------------------------------------------------
> >
> > I get as result of the profiling
> >
> > estimateNACstructureof.R#33 56.6900000
> >
> > estimateNACstructureof.R#93 5.2200000
> >
> > estimateNACstructureof.R#87 4.9700000
> >
> > estimateNACstructureof.R#78 1.9400000
> >
> > oldFriedman.R#39 1.2600000
> >
> > estimateNACstructureof.R#81 1.2100000
> >
> > estimateNACstructureof.R#88 1.2000000
> >
> > estimateNACstructureof.R#657 0.9600000
> >
> > todecompose.R#34 0.6900000
> >
> > estimateNACstructureof.R#658 0.6600000
> >
> > estimateNACstructureof.R#264 0.6500000
> >
> > estimateNACstructureof.R#923 0.5900000
> >
> > aresameNACstructures.R#4 0.5600000
> >
> > estimateNACstructureof.R#1059 0.4800000
> >
> > estimateNACstructureof.R#1064 0.4700000
> >
> > estimateNACstructureof.R#22 0.4600000
> >
> > estimateNACstructureof.R#659 0.4500000
> >
> > nicenodenames.R#22 0.4400000
> >
> > estimateNACstructureof.R#1029 0.4200000
> >
> > todecompose.R#119 0.4200000
> >
> > estimateNACstructureof.R#1061 0.4000000
> >
> > estimateNACstructureof.R#654 0.3800000
> >
> > todecompose.R#12 0.3800000
> >
> > estimateNACstructureof.R#85 0.3700000
> >
> > estimateNACstructureof.R#89 0.3700000
> >
> > todecompose.R#19 0.3500000
> >
> > todecompose.R#160 0.3500000
> >
> > estimateNACstructureof.R#1060 0.3300000
> >
> > estimateNACstructureof.R#83 0.3100000
> >
> > todecompose.R#144 0.3100000
> >
> > sampling.time 207.1400000
> >
> > total.elapsed.time 235.9440000
> >
> > total.elapsed.time/samping.time*100 87.79202
> >
> >
> > Except for the 3 last rows, what we have is the self.pct value in
> > decreasing order, by line.
> >
> >
> > What I do not understand is that if am to run the same code all over
> again,
> > I now get
> >
> >
> > estimateNACstructureof.R#852 4.34000
> >
> > estimateNACstructureof.R#923 3.94000
> >
> > estimateNACstructureof.R#87 3.38000
> >
> > estimateNACstructureof.R#93 3.31000
> >
> > estimateNACstructureof.R#859 2.70000
> >
> > estimateNACstructureof.R#1029 2.27000
> >
> > estimateNACstructureof.R#657 1.65000
> >
> > estimateNACstructureof.R#933 1.51000
> >
> > estimateNACstructureof.R#78 1.49000
> >
> > estimateNACstructureof.R#721 1.49000
> >
> > todecompose.R#34 1.49000
> >
> > estimateNACstructureof.R#658 1.39000
> >
> > estimateNACstructureof.R#1064 1.26000
> >
> > estimateNACstructureof.R#1059 1.25000
> >
> > estimateNACstructureof.R#659 1.21000
> >
> > estimateNACstructureof.R#1061 1.20000
> >
> > aresameNACstructures.R#4 1.17000
> >
> > estimateNACstructureof.R#1060 1.09000
> >
> > todecompose.R#12 1.00000
> >
> > todecompose.R#145 0.98000
> >
> > estimateNACstructureof.R#723 0.97000
> >
> > getNACadjacencyof.R#10 0.97000
> >
> > estimateNACstructureof.R#709 0.96000
> >
> > oldFriedman.R#39 0.90000
> >
> > estimateNACstructureof.R#81 0.89000
> >
> > estimateNACstructureof.R#88 0.88000
> >
> > estimateNACstructureof.R#708 0.88000
> >
> > todecompose.R#119 0.86000
> >
> > todecompose.R#160 0.84000
> >
> > estimateNACstructureof.R#715 0.83000
> >
> > sampling.time 198.38000
> >
> > total.elapsed.time 203.56800
> >
> > total.elapsed.time /samping.time*100 97.45147
> >
> >
> >
> > And the line 33 of estimateNACstructureof, which previously was observed
> > 56.69% of the sampling time is now... gone ! If I profile he code in the
> > same R session again and again, line 33 of estimateNACstructureof seems
> > never to appear again.
> >
> >
> > In fact the line 33 of estimateNACstructureof appears only when Rprof is
> > run for the first time in the R session.
> >
> >
> > Note: this is maybe relevant, the line 33 of estimateNACstructureof
> refers
> > to C function.
> >
> >
> > Any thoughts of what I get this peculiar result?
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
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