From gavin.simpson at ucl.ac.uk  Fri Jul  8 13:07:26 2005
From: gavin.simpson at ucl.ac.uk (Gavin Simpson)
Date: Fri, 08 Jul 2005 12:07:26 +0100
Subject: [Rd] Interpretting R profiling output (was More efficient code?)
In-Reply-To: <1120676089.6814.18.camel@gsimpson.geog.ucl.ac.uk>
References: <1120676089.6814.18.camel@gsimpson.geog.ucl.ac.uk>
Message-ID: <1120820846.10211.18.camel@gsimpson.geog.ucl.ac.uk>

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?

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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Gavin Simpson                     [T] +44 (0)20 7679 5522
ENSIS Research Fellow             [F] +44 (0)20 7679 7565
ENSIS Ltd. & ECRC                 [E] gavin.simpsonATNOSPAMucl.ac.uk
UCL Department of Geography       [W] http://www.ucl.ac.uk/~ucfagls/cv/
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[Rd] Interpretting R profiling output (was More efficient code?)
Gavin Simpson