[R-sig-Debian] 50% performance of custom R build compared to PPA R for a command

Scott Kostyshak skostysh at princeton.edu
Thu Apr 24 22:10:48 CEST 2014


I have R installed from the Ubuntu PPA and a local build of R (more
details below). I will refer to these as "R" and "R-devel",
respectively. I've reproduced the following on Ubuntu 13.10 and 14.04.
Below is an example (which requires the bootstrap package) that takes
10 seconds for me to run with R-devel and 5 seconds with R

theta <- function(ind) {
    easy <- lm(strength ~ E1+E2, data=tooth, subset=ind)
    diffi<- lm(strength ~ D1+D2, data=tooth, subset=ind)
    (sum(resid(easy)^2) - sum(resid(diffi)^2))/13   }
tooth.boot <- bootstrap(1:13, 2000, theta)

I'm wondering if this is due to different compiler flags. For R, when
installing the bootstrap package, I see
gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o
bootstrap.so boott.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR

For R-devel I see:
ccache gcc -shared -L/usr/local/lib -o bootstrap.so boott.o -lgfortran
-lm -lquadmath -L/usr/local/lib/R-devel/lib/R/lib -lR

My install script for the local build is based on Dirk's script [1].
In particular, my configure command is:

R_PAPERSIZE=letter R_BATCHSAVE="--no-save --no-restore"
R_BROWSER=xdg-open PAGER=/usr/bin/pager PERL=/usr/bin/perl
R_UNZIPCMD=/usr/bin/unzip R_ZIPCMD=/usr/bin/zip
R_PRINTCMD=/usr/bin/lpr LIBnn=lib AWK=/usr/bin/awk CC="gcc"
CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic" CXX="g++"
CXXFLAGS="-ggdb -pipe -Wall -pedantic" FC="gfortran" F77="gfortran"
MAKE="make -j$NJOBS" "${repoDir}/configure"
--prefix=/usr/local/lib/R-devel --enable-R-shlib --with-blas
--with-lapack --with-readline --without-recommended-packages >
../build-logs/configure 2>&1

I'm using R-devel updated to today's revision but I compiled a version
from a year ago and had the same performance so that is why I suspect
my installation script accounts for the differences.

Any advice would be appreciated and please let me know if any other
information would be helpful.




Scott Kostyshak
Economics PhD Candidate
Princeton University

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