[Rd] Interpretting R profiling output (was More efficient code?)
Duncan Murdoch
murdoch at stats.uwo.ca
Fri Jul 8 13:31:37 CEST 2005
Gavin Simpson wrote:
> On Wed, 2005-07-06 at 19:54 +0100, Gavin Simpson wrote:
>
>>Dear List,
>>
>
>
> I fixed up the code in coinertiaI to only return the bits I needed from
> La.svd() within the permutations - thus producing a 10% speed up. I am
> still a little unclear about the results from Rprof() (below).
>
> Do the timings under self time for .Call and .Fortran include the time
> spent actually running the called compiled code or are they the overhead
> of setting up the calls to the compiled code?
They include both. The profiler only sees R calls, it doesn't know what
goes on within functions. .Call() is an R call which internally calls
some C function, but the profiler just sees the call to .Call.
Duncan Murdoch
>
> Many thanks,
>
> Gav
>
>
>>summaryRprof(filename = "Rprof.out")
>>$by.self
>> self.time self.pct total.time total.pct
>>".Call" 50.40 59.6 50.40 59.6
>>"%*%" 10.50 12.4 10.50 12.4
>>".Fortran" 2.78 3.3 2.78 3.3
>>"La.svd" 2.52 3.0 57.98 68.6
>>"^" 2.48 2.9 2.48 2.9
>>"t.default" 2.30 2.7 2.30 2.7
>>"matrix" 1.92 2.3 1.98 2.3
>>"as.double" 1.78 2.1 2.70 3.2
>>"list" 0.88 1.0 0.88 1.0
>>"as.double.default" 0.86 1.0 0.86 1.0
>>"rep.default" 0.74 0.9 0.86 1.0
>>"sum" 0.72 0.9 2.58 3.1
>>"!" 0.50 0.6 0.50 0.6
>>"diag" 0.44 0.5 1.46 1.7
>>"qr.coef" 0.42 0.5 6.26 7.4
>>"permtest" 0.38 0.4 83.60 98.9
>>"is.finite" 0.38 0.4 0.38 0.4
>>"storage.mode<-" 0.36 0.4 3.26 3.9
>>"as.integer" 0.34 0.4 0.40 0.5
>>"t" 0.32 0.4 2.62 3.1
>>"$" 0.32 0.4 0.32 0.4
>>"paste" 0.28 0.3 0.54 0.6
>>"teststat" 0.24 0.3 83.10 98.3
>>"residualMatrix" 0.22 0.3 10.32 12.2
>>"qr" 0.20 0.2 1.24 1.5
>>...
>>
>>$by.total
>> total.time total.pct self.time self.pct
>>"predcoca.perm" 84.50 100.0 0.00 0.0
>>"permtest" 83.60 98.9 0.38 0.4
>>"teststat" 83.10 98.3 0.24 0.3
>>"coinertiaI" 73.24 86.7 0.18 0.2
>>"La.svd" 57.98 68.6 2.52 3.0
>>".Call" 50.40 59.6 50.40 59.6
>>"%*%" 10.50 12.4 10.50 12.4
>>"residualMatrix" 10.32 12.2 0.22 0.3
>>"qr.coef" 6.26 7.4 0.42 0.5
>>"storage.mode<-" 3.26 3.9 0.36 0.4
>>".Fortran" 2.78 3.3 2.78 3.3
>>"as.double" 2.70 3.2 1.78 2.1
>>"t" 2.62 3.1 0.32 0.4
>>"eval" 2.62 3.1 0.14 0.2
>>"sum" 2.58 3.1 0.72 0.9
>>...
>>
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