Inconsistent results between first run of Rprof and next runs of Rprof
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.uytten at 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?
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