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

[Dirk Eddelbuettel]

On 25 April 2014 at 11:38, Scott Kostyshak wrote:
| On Thu, Apr 24, 2014 at 4:32 PM, Dirk Eddelbuettel <edd at debian.org> 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 | edd at debian.org | http://dirk.eddelbuettel.com