Dear R'ers, when I e.g. install the integrate2.2-2 package under R1.1.1 (debian2.2) atlas is linked into the library: Installing package `integrate' ... libs gcc -shared -lc -shared -o /usr/lib/R/library/integrate/libs/integrate.so adapt.o adapt_callback.o bsrl.o flfm.o nxprt.o symrl.o wht.o -L/usr/local/lib -lf77blas -lcblas -latlas -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.2 -lm R ...however, for R1.2.0 (snapshot ~3 days ago) it looks different: Installing package `integrate' ... libs gcc -shared -o integrate.so adapt.o adapt_callback.o bsrl.o flfm.o nxprt.o symrl.o wht.o -L/usr/local/lib -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.2 -lm R I ask because integrate behaves differently for both R-versions. Marcus -- +------------------------------------------------------- | Marcus Eger +-------------------------------------------------------- | E-Mail: eger.m at gmx.de (NEW) | marcus.eger at physik.uni-marburg.de (OLD) | WWW: http://neuro.physik.uni-marburg.de/~eger (NEW) +-------------------------------------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
atlas for R1.1.1 and R1.2 different?
7 messages · Marcus Eger, Douglas Bates, Peter Dalgaard +2 more
Marcus Eger <marcus.eger at physik.uni-marburg.de> writes:
when I e.g. install the integrate2.2-2 package under R1.1.1 (debian2.2) atlas is linked into the library: Installing package `integrate' ... libs gcc -shared -lc -shared -o /usr/lib/R/library/integrate/libs/integrate.so adapt.o adapt_callback.o bsrl.o flfm.o nxprt.o symrl.o wht.o -L/usr/local/lib -lf77blas -lcblas -latlas -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.2 -lm R ...however, for R1.2.0 (snapshot ~3 days ago) it looks different: Installing package `integrate' ... libs gcc -shared -o integrate.so adapt.o adapt_callback.o bsrl.o flfm.o nxprt.o symrl.o wht.o -L/usr/local/lib -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.2 -lm R I ask because integrate behaves differently for both R-versions.
I don't think the presence or absence of atlas should affect the results from integrate. The atlas library is an enhanced, faster version of the basic linear algebra subroutines (blas) and a few of the lapack subroutines. Unless the C code in integrate is calling these subroutines explicitly, atlas should not affect the results. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Douglas Bates wrote:
I don't think the presence or absence of atlas should affect the results from integrate. The atlas library is an enhanced, faster version of the basic linear algebra subroutines (blas) and a few of the lapack subroutines. Unless the C code in integrate is calling these subroutines explicitly, atlas should not affect the results.
An example for the different behaviour is the following: "prds" <- function (s,r,sn=1) 1/(pi*sqrt(1-s^2))/(sqrt(2*pi)*sn)*exp(-(r-s)^2/(2*sn^2)) UNDER R1.2: ===========
integrate(prds, -1,+1,minpts=100,maxpts=NULL,eps=0.01,r=0)
value relerr minpts lenwrk ifail 2.735080e-269 7.38275e-08 165 73 0
UNDER R.1.1: ============
integrate(prds, -1,+1,minpts=100,maxpts=NULL,eps=0.01,r=0)
value relerr minpts lenwrk ifail 0.3146147 0.009182386 1023 283 0 .... which makes more sense. I'm wondering why the same integrate package under R1.1.1 uses atlas, but under R1.2 it doesn't. Marcus -- +------------------------------------------------------- | Marcus Eger +-------------------------------------------------------- | E-Mail: eger.m at gmx.de (NEW) | marcus.eger at physik.uni-marburg.de (OLD) | WWW: http://neuro.physik.uni-marburg.de/~eger (NEW) +-------------------------------------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Marcus Eger <marcus.eger at physik.uni-marburg.de> writes:
Douglas Bates wrote:
I don't think the presence or absence of atlas should affect the results from integrate. The atlas library is an enhanced, faster version of the basic linear algebra subroutines (blas) and a few of the lapack subroutines. Unless the C code in integrate is calling these subroutines explicitly, atlas should not affect the results.
An example for the different behaviour is the following: "prds" <- function (s,r,sn=1) 1/(pi*sqrt(1-s^2))/(sqrt(2*pi)*sn)*exp(-(r-s)^2/(2*sn^2)) UNDER R1.2: ===========
integrate(prds, -1,+1,minpts=100,maxpts=NULL,eps=0.01,r=0)
value relerr minpts lenwrk ifail 2.735080e-269 7.38275e-08 165 73 0
UNDER R.1.1: ============
integrate(prds, -1,+1,minpts=100,maxpts=NULL,eps=0.01,r=0)
value relerr minpts lenwrk ifail 0.3146147 0.009182386 1023 283 0 .... which makes more sense. I'm wondering why the same integrate package under R1.1.1 uses atlas, but under R1.2 it doesn't.
On a Debian 2.2 system running yesterday's snapshot of R-1.2.0 I get
library(integrate) "prds" <- function (s,r,sn=1)
+ 1/(pi*sqrt(1-s^2))/(sqrt(2*pi)*sn)*exp(-(r-s)^2/(2*sn^2))
integrate(prds, -1,+1,minpts=100,maxpts=NULL,eps=0.01,r=0)
value relerr minpts lenwrk ifail 0.3146147 0.009182386 1023 283 0 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Douglas Bates <bates at stat.wisc.edu> writes:
On a Debian 2.2 system running yesterday's snapshot of R-1.2.0 I get
library(integrate) "prds" <- function (s,r,sn=1)
+ 1/(pi*sqrt(1-s^2))/(sqrt(2*pi)*sn)*exp(-(r-s)^2/(2*sn^2))
integrate(prds, -1,+1,minpts=100,maxpts=NULL,eps=0.01,r=0)
value relerr minpts lenwrk ifail 0.3146147 0.009182386 1023 283 0
Ditto with RH6.2 linked with gcc -shared -o integrate.so adapt.o adapt_callback.o bsrl.o flfm.o nxprt.o symrl.o wht.o -L/usr/local/lib -lg2c -lm -L/usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66 -L/usr/i386-redhat-linux/lib -lm [but I wonder how -L/usr/local/lib got into my LIBPATHS...]
O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Marcus Eger writes:
Douglas Bates wrote:
I don't think the presence or absence of atlas should affect the results from integrate. The atlas library is an enhanced, faster version of the basic linear algebra subroutines (blas) and a few of the lapack subroutines. Unless the C code in integrate is calling these subroutines explicitly, atlas should not affect the results.
An example for the different behaviour is the following:
... I'm wondering why the same integrate package under R1.1.1 uses atlas, but under R1.2 it doesn't.
The configure detection of fast BLAS libraries is different between these versions, but I don't think that this is the reason. I suspect that your R 1.1.1 is from a .deb file which requires package atlas2, and the R 1.2.0 is compiled from source but cannot find atlas (look at config.log) because package atlas2-dev is not installed. Bingo? -k -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On Tue, 14 Nov 2000, Marcus Eger wrote:
I'm wondering why the same integrate package under R1.1.1 uses atlas, but under R1.2 it doesn't.
The integrate package never uses atlas. The linker uses atlas under 1.1.1 because R does. This would allow integrate to use atlas if it wanted to. It doesn't. -thomas -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._