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

Sun Jun 14 18:46:49 CEST 2009

Simon:

Now I'm having trouble getting R to compile at all.  I now set up my  
config.site file to something "bare bones."

CC='gcc-4.2 -arch x86_64'
OBJC='gcc-4.2 -arch x86_64'
F77='gfortran -arch x86_64'
CXX='g++-4.2 -arch x86_64'
FC='gfortran -arch x86_64'

I then use the same configure script as before.  I can compile, but  
then 'make check' fails with

BRAUNM2: ~/Downloads/R-2.9.0 $ make check

Collecting examples for package ‘base’
Running examples in package ‘base’
/Users/braunm/Downloads/R-2.9.0/bin/BATCH: line 59: 22777 Segmentation  
fault      ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > $ 
{out} 2>&1
Error: testing 'base' failed
Execution halted

Regardless, I did a sudo make install, and can still launch R, and  
load my shared libraries (no profiling, obviously).

Next, as suggested, I added a single line to config.site:

LDFLAGS='-g -pg'

'make' fails at the line

gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,- 
headerpad_max_install_names  -undefined dynamic_lookup -single_module - 
multiply_defined suppress -g -pg -install_name libR.dylib - 
compatibility_version 2.9.0  -current_version 2.9.0  - 
headerpad_max_install_names -o libR.dylib CConverters.o  
CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o apse.o  
arithmetic.o array.o attrib.o base.o bind.o builtin.o character.o  
coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o  
datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o  
dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o  
fourier.o gevents.o gram.o gram-ex.o gramRd.o graphics.o identical.o  
inspect.o inlined.o internet.o iosupport.o lapack.o list.o  
localecharset.o logic.o main.o mapply.o match.o memory.o model.o  
names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o  
platform.o plot.o plot3d.o plotmath.o print.o printarray.o  
printvector.o printutils.o qsort.o random.o regex.o registration.o  
relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o  
source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o  
summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o   ../ 
unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/ 
libnmath.a  ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a ../extra/ 
intl/libintl.a -L../../lib/x86_64 -lRblas -lgcrt1.o -L/usr/local/lib/ 
gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/ 
local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib -lgfortran    - 
Wl,-framework -Wl,CoreFoundation -lreadline  -lz -licucore -lm

ld: duplicate symbol dyld_stub_binding_helper in /usr/lib/gcrt1.o and / 
usr/lib/dylib1.10.5.o
collect2: ld returned 1 exit status

The same thing happens if I put the -g -pg flags in MAIN_LDFLAGS

As you can probably tell, I'm new to working with C, and I'm still  
learning the finer points of compilers and linkers.  Thanks again for  
helping me figure out what's going on here.

Michael

On Jun 14, 2009, at 10:22 AM, Simon Urbanek wrote:

>
> 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
>>
>>
>>
>>
>>
>

-------------------------------------------
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