[R-SIG-Mac] profiling C shared libraries loaded into R

[Simon Urbanek]

On Jun 13, 2009, at 5:58 PM, Michael Braun wrote:

> Simon:
>
> Sorry, please disregard my last email.  Shark was crashing because  
> some of something with Shark, not R.  But unfortunately, the Unknown  
> Libraries remain.
>
> Here is how I compiled R.  In the config.site file, I set:
>
> R_PAPERSIZE=letter
> R_BATCHSAVE=--no-save
> CC='gcc-4.2 -arch x86_64 -m64 -march=core2 -msse3 -g -pg -O2'
> OBJC='gcc-4.2 -arch x86_64 -m64 -march=core2 -msse3 -g -pg -O2'
> DEFS=-DHAVE_INLINE
> F77='gfortran -arch x86_64 -g -pg -O2'
> LIBnn=lib
> CXX='g++-4.2 -arch x86_64 -march=core2 -p -pg -O2'
> FC='gfortran -arch x86_64 -m64 -march=core2 -g -pg -O2'
> TCLTK_LIBS=/usr/lib
>
> To configure, I ran the following script
>
> #!/bin/bash
>
> ./configure \
> SHELL='/bin/bash' \
> r_arch=x86_64 \
> --with-system-zlib \
> --with-blas='-framework vecLib' --with-lapack='-framework vecLib' \
> --with-ICU \
> --with-aqua \
> --enable-R-framework \
> --enable-BLAS-shlib \
> --with-x \
> --with-readline=/usr/local \
> --with-tcltk \
> --with-iconv=no \
> --with-cairo \
> --disable-R-profiling \
> --with-recommended-packages=no
>
>
> Any idea what I did wrong?
>

You didn't set -pg for link-time* which is the crucial one (adding -pg  
to compile flags is not strictly necessary unless you want to profile  
R itself).

Also you may want to tweak the flags (CFLAGS et al.) instead of the  
compilers since they have higher precedence (also you have a typo in  
CXX). [And why the DEFS?]

Always check the output when your library is actually compiled - you  
may find your flags being overridden by others.

Cheers,
Simon


* you can use LDFLAGS or LIBS but in this instance MAIN_LDFLAGS may be  
more interesting, but I didn't test it.


> Thanks,
>
> Michael
>
>
>
> On Jun 12, 2009, at 7:27 PM, Simon Urbanek wrote:
>
>> Michael,
>>
>> On Jun 12, 2009, at 4:20 PM, Michael Braun wrote:
>>
>>> Hi.  I have a shared library that I would like to profile.  I see  
>>> that this issue has been touched on in some previous posts, but I  
>>> am still having trouble, and I am hoping someone here can help.
>>>
>>> First things first...  I am running R 2.8.0 patched on OS X  
>>> 10.5.7, on a dual quad-core Mac Pro.   It is the 64-bit binary  
>>> build for Leopard, as downloaded from CRAN.
>>>
>>> I am compiling my code using gcc-4.2, and I am including the -g -p  
>>> -pg flags.
>>
>> The -p -pg part (they are mutually-exclusive aren't they? so you  
>> get just -pg) won't really help unless you also compile R that way  
>> since the gprof initialization happens in the executable, not in  
>> the library (and don't forget it at link time).
>>
>>
>>> Optimization is turned off (-O0).
>>
>> Just to make sure - using PKG_CFLAGS doesn't have the desired  
>> effect, because R's -O2 will override it, so better be sure that  
>> the optimization is off. If you run the steps manually, make sure  
>> you have -g (and -pg if you wish) everywhere.
>>
>>
>>> I AM able to debug the code using gdb (called as R -d gdb).  I  
>>> always run R from the command line.
>>>
>>> I have tried profiling using Shark, which recognizes functions in  
>>> libR.dylib, but none of the functions in mylib.so.  For each  
>>> function call, Shark refers to "Unknown Library", and after the  
>>> function address, there is an indicator of [unknown].  Also, when  
>>> I use Shark, it appears to want to profile the entire R session.   
>>> All I care about is my library.
>>>
>>
>> I'm unable to replicate that. Shark correctly recognizes the  
>> function and the loaded library for me. Try using default flags -  
>> they do include -g -O2 (which worked for me).
>>
>>
>>> I am also open to using gprof instead, but I cannot find the  
>>> requisite gmon.out file.
>>>
>>
>> See above - you won't find it unless you compile R with -pg since  
>> the gprof init code must be in the executable (more precisely you  
>> don't have to re-compile the entire R with that, it should be  
>> sufficient to use -pg in the link step for exec/R).
>>
>> Cheers,
>> Simon
>>
>>
>>> Thanks in advance for any suggestions.
>>>
>>> Michael
>>>
>>>
>>>
>>> -------------------------------------------
>>> Michael Braun
>>> Homer A. Burnell Career Development Professor, and
>>> 	Assistant Professor of Management Science (Marketing Group)
>>> MIT Sloan School of Management
>>> One Amherst St., E40-169
>>> Cambridge, MA 02142
>>> braunm at mit.edu
>>> 617-253-3436
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>
>
> -------------------------------------------
> Michael Braun
> Homer A. Burnell Career Development Professor, and
> 	Assistant Professor of Management Science (Marketing Group)
> MIT Sloan School of Management
> One Amherst St., E40-169
> Cambridge, MA 02142
> braunm at mit.edu
> 617-253-3436
>
>
>
>
>