On 25 April 2014 at 11:38, Scott Kostyshak wrote: | On Thu, Apr 24, 2014 at 4:32 PM, Dirk Eddelbuettel <[email protected]> wrote: | > | > Scott, | > | > My first quick hunches are a) 50% is too much for compiler switches, b) your | > examples shows R code, and c) are you sure you are using the same BLAS? | | Thanks for the quick reply Dirk and for the suggestions. | | As for BLAS, yes I believe I'm using the same BLAS. The output of the | following two commands is the same (except for the memory addresses of | course): | $ ldd /usr/local/lib/R-devel/lib/R/bin/exec/R | $ ldd /usr/lib/R/bin/exec/R | | And executing | $ lsof -p <PID> | grep 'blas\|lapack' | also returns the same output for both Rs: | R 13017 scott mem REG 8,1 9142768 2097161 | /usr/lib/atlas-base/atlas/liblapack.so.3.0 | R 13017 scott mem REG 8,1 3776592 2097162 | /usr/lib/atlas-base/atlas/libblas.so.3.0 | | I profiled and it seems that all of the R functions are slow (I can | post the output if anyone is interested). I rebuilt with -O3 in CFLAGS | and this improved things a lot. Time went down from 10 seconds to 5.7
That is surprisingly large. In my mail yesterday I basically bet against it. | or so. I reprofiled and again the R functions of R-devel seem just a | tad slower across the board (I can send output if interested). | | Below are some timings comparing the optimized R-devel to R. | | $ time R-devel CMD BATCH mwe.R | | real 0m5.755s | user 0m5.678s | sys 0m0.079s | | $ time R CMD BATCH mwe.R | | real 0m5.453s | user 0m5.371s | sys 0m0.054s | | Rerunning the above commands multiple times gives about the same output. | | There's still a .3 second difference and I'm curious to know why. Any ideas? Different code base? If you want _identical_ outcomes you need identical _input_: code, compiler, settings, hardware, ... Dirk -- Dirk Eddelbuettel | [email protected] | http://dirk.eddelbuettel.com _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
