[R-SIG-Mac] Building R-devel from Source on Snow Leopard

Simon Urbanek simon.urbanek at r-project.org
Sun Sep 6 04:05:46 CEST 2009 

On Sep 5, 2009, at 7:10 PM, Adam D. I. Kramer wrote:

> Hi Simon, Tony, and anybode else who attempts to complie 2.9.2 for
> themselves on Snow Leopard,
>

I would strong suggest *against* what you're doing, your configuration  
is far from any normal SL system. You're clearly free to use it for  
yourself but is not something any R-SIG-Mac users should follow. The  
setup is incompatible with CRAN and anything we build. (There are many  
reasons - stating with disabling aqua, using 3rd party BLAS (which is  
not a good idea if you want speed since vecLib is highly optimized)  
and mixing in fink (again, a really bad idea for any normal user)).

I see that the most common mistake here is to use Leopard Xcode 3.1  
fortran which is NOT meant to be used with SL and Xcode 3.2. To if you  
upgrade from Leopard and Xcode 3.1, make sure you delete the Xcode 3.1  
fortran as Xcode 3.2 is NOT able to upgrade it. Use the gfortran 4.2.3  
from CRAN instead - it works just fine and no special flags are  
necessary for SL (except for the mandatory -arch).

Cheers,
Simon


> The configure line which eventually led to R configuring, building,  
> and
> running was this:
>
> ./configure --prefix=/usr/local --with-x --disable-R-framework -- 
> enable-threads=posix --without-aqua --with-lapack=" /usr/local/lib/ 
> liblapack.a /usr/local/lib/libptf77blas.a /usr/local/lib/ 
> libptcblas.a -lpthread /usr/local/lib/libatlas.a " --with-blas=" / 
> usr/local/lib/liblapack.a /usr/local/lib/libptf77blas.a /usr/local/ 
> lib/libptcblas.a -lpthread /usr/local/lib/libatlas.a " CFLAGS="-O3 - 
> fopenmp -mtune=native -m64" CXXFLAGS="-O3 -fopenmp -mtune=native - 
> m64" FFLAGS="-O3 -fopenmp -mtune=native -m64" LDFLAGS="-m64 -L/sw/ 
> lib -L/usr/X11R6/lib -L/usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64 - 
> lgfortran" F77="gfortran -arch x86_64" CPPFLAGS="-I/sw/include"  
> FC="gfortran -arch x86_64" FCFLAGS="-O3 -fopenmp -mtune=native -m64"
>
> ...dropping the --with-blas and --with-lapack items also lets R  
> compile fine
> (but see benchmarks below). Note also that I have libreadline and  
> libiconv
> installed in the /sw tree using 64-bit Fink for Snow  
> Leopard...you'll need
> 64bit versions of readline and iconv to compile R; check out
> /Developer/SDKs/MacOSX10.6.sdk/usr/lib maybe.
>
> The one oddity is that when I pass
>
> --with-blas="-L/usr/local/lib -llapack -lptf77blas -lptcblas - 
> lpthread -latlas"
> (and --with-lapack the same, or one and not the other)
>
> ...the build fails in the manner described in my last message  
> (lapack.so,
> compiled by R, ends up not containing the functions it should),  
> while if I
> explicitly list the libraries:
>
> --with-blas=" /usr/local/lib/liblapack.a /usr/local/lib/ 
> libptf77blas.a /usr/local/lib/libptcblas.a -lpthread /usr/local/lib/ 
> libatlas.a
>
> ...it builds successfully. Not sure what this portends.
>
> Also, I have done some benchmarking to see how much faster R is (on  
> my Mac
> Pro, dual quad-core Xeon @ 2.8GHz, 6G RAM) when I go through all this
> trouble:
>
> (benchmarked using http://r.research.att.com/benchmarks/R-benchmark-25.R 
> )
>
> nightly build
> (http://r.research.att.com/R-2.9-branch-leopard-universal.tar.gz,  
> built Sept
> 5 2009, run with --arch x86_64):
> Overall mean (sum of I, II and III trimmed means/3)_ (sec):   
> 0.835276859437347
>
> my build, no BLAS or LAPACK:
> Overall mean (sum of I, II and III trimmed means/3)_ (sec):   
> 1.83643467491601 (This build did consistently better on non-matrix  
> math, FAR worse on the matrix math)
>
> my build, BLAS, no LAPACK:
> Overall mean (sum of I, II and III trimmed means/3)_ (sec):   
> 0.760949143043198 (outperforms nightly on most metrics,  
> underperforms on none, outperforms no-blas on all)
>
> my build, LAPACK & BLAS:
> Overall mean (sum of I, II and III trimmed means/3)_ (sec):   
> 0.70660451743888 (outperforms everything else on most metrics,  
> underperforms on none)
>
> So it seems that letting ATLAS compile your BLAS and LAPACK (Atlas  
> 3.9.14
> does this), plus adding optimization flags, leads to a 15%  
> improvement over
> the nightly build (when using this specific benchmarking system, ymmv
> depending on what functions you actually use R for).
>
> --Adam
>
> On Fri, 4 Sep 2009, Adam D. I. Kramer wrote:
>
>> Simon,
>>
>> 	Thanks for your comments; responses below.
>>
>> On Fri, 4 Sep 2009, Simon Urbanek wrote:
>>
>>> Adam,
>>> On Sep 4, 2009, at 5:52 PM, Adam D. I. Kramer wrote:
>>>> Hi Tony and Simon,
>>>>
>>>> 	I was having this trouble today/yesterday and have been following
>>>> along on this thread. The solution I found was to add this to my
>>>> ./configure:
>>>> LDFLAGS="-m64 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64 - 
>>>> lgfortran"
>>>> and
>>>> F77="gfortran -arch x86_64"
>>> You should not touch LDFLAGS and besides F77 you'll also need to  
>>> set FC.
>>
>>> From configure --help:
>> LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
>>             nonstandard directory <lib dir>
>>
>> ...the gfortran library lives in a nonstandard directory, which is  
>> why I put
>> the -L there... so I then moved -lgfortran to LIBS='-lgfortran' and  
>> things
>> broke in the same way, as did moving the -L...-lgfortran there.   
>> Both of
>> these need to be passed to the linker when mixing C/Fortran code.
>>
>> It also throws the error "Maybe check LDFLAGS for paths to Fortran
>> libraries?" which is what tipped me off to the fact that I should  
>> provide a
>> link to the Fortran libraries in LDFLAGS.  If this is incorrect,  
>> please let
>> me know where to put them instead (and consider updating the  
>> configure
>> script).
>>
>>>> ...this gets me through the "can't make mixed C/Fortran code"  
>>>> errors. However, through one hoop of fire and I'm confronted by  
>>>> another:
>>>> checking for iconv.h... yes
>>>> checking for iconv... no
>>>> checking for iconvlist... no
>>>> configure: error: --with-iconv=yes (default) and a suitable iconv  
>>>> is not
>>>> available
>>>> ...this strikes me as odd. The relevant lines from the config.log  
>>>> file are:
>>>> configure:39212: gcc -std=gnu99 -o conftest -O3 -fopenmp - 
>>>> mtune=native -m64 -m64 -L/usr/lib/gcc/i686-apple-darwin9/4.2.1/ 
>>>> x86_64 -lgfortran conftest.c -lm >&5
>>>> conftest.c: In function 'main':
>>>> conftest.c:189: warning: passing argument 1 of 'libiconvlist' from
>>>> incompatible pointer type
>>>> Undefined symbols:
>>>> "_libiconvlist", referenced from:
>>>>    _main in cc2XgkAg.o
>>>> ld: symbol(s) not found
>>>> collect2: ld returned 1 exit status
>>>> However:
>>>> swiss:R-2.9.2$ nm /usr/lib/libiconv.dylib | grep _libiconvlist
>>>> 00008807 T _libiconvlist
>>>> ...I'm not sure where else configure could be trying to find  
>>>> libiconv,
>>> check /usr/local/lib that is the most common problem area ...
>>
>> I had, and there was no libiconv there.
>>
>> I eventually solved this problem by upgrading fink to the 64bit  
>> version and
>> installing libiconv and adding CPPFLAGS="-I/sw/include" and adding - 
>> L/sw/lib
>> to LDFLAGS, forcing it to link against the new library. It seems  
>> like the
>> Apple libraries should serve the purpose, but for whatever reason  
>> they did
>> not.
>>
>> My current problem is that, during make, R complains about the  
>> lapack.so
>> file it has compiled from my lapack libraries (I configured with
>> --with-lapack="-L/usr/local -llapack -lptf77blas -lcblas -lpthread - 
>> latlas"
>> and a similar --with-blas):
>>
>> Warning in solve.default(rgb) :
>> unable to load shared library '/Volumes/Tubby2/nobackup/R-2.9.2/ 
>> modules//lapack.so':
>> dlopen(/Volumes/Tubby2/nobackup/R-2.9.2/modules//lapack.so, 6):  
>> Symbol not found: _cblas_cdotc_sub
>> Referenced from: /Volumes/Tubby2/nobackup/R-2.9.2/modules//lapack.so
>> Expected in: flat namespace
>> in /Volumes/Tubby2/nobackup/R-2.9.2/modules//lapack.so
>> Error in solve.default(rgb) : lapack routines cannot be loaded
>> Error: unable to load R code in package 'grDevices'
>> Execution halted
>>
>> ...that said, I understand that --with-lapack is "not recommended"  
>> in the
>> admin manual, so I'm pretty much on my own here, but I'd be  
>> interested if
>> you have an idea or two about what might be going on.  
>> _cblas_cdotc_sub is
>> indeed in my lapack.a file (but not the lapack.so file R refers  
>> to), and I
>> can use _cblas_cdotc if I write some simple c code and link it  
>> against
>> lapack using the same flags as noted above.
>>
>> My interest, really, is in whether ATLAS's LAPACK-tuning system  
>> (which is
>> pretty new) actually leads to speed improvements in R.  So, I don't
>> desperately need to use it, but am still concerned that a compile  
>> that used
>> to run smoothly no longer does.
>>
>> --Adam
>>
>>> Cheers,
>>> Simon
>>>> but
>>>> running "locate libiconv" shows versions in
>>>> /Developer/SDKs/MacOSX10.6.sdk/usr/lib/ also, which also show  
>>>> _libiconvlist
>>>> when I nm them.
>>>> Any suggestions? I'm not sure how to further debug this...the  
>>>> symbols are
>>>> there.
>>>> Cordially,
>>>> Adam
>>>>> Hi Simon,
>>>>> I think that you might have resolved my issue. I did not specify  
>>>>> the arch,
>>>>> so I will try that and let everyone know if that works.
>>>>> Cheers,
>>>>> --Tony
>>>>> On Thu, Sep 3, 2009 at 4:11 PM, Simon Urbanek
>>>>> <simon.urbanek at r-project.org>wrote:
>>>>>> Tony,
>>>>>> On Sep 3, 2009, at 6:14 PM, Tony Chiang wrote:
>>>>>> So I am trying to configure and build the latest of R-devel on  
>>>>>> one of the
>>>>>>> new Macbook Pro's running Snow leopard. I have installed the  
>>>>>>> latest
>>>>>>> X-Code
>>>>>>> tools (downloaded from the Apple Site) and have gcc installed:
>>>>>>> gcc --versioni686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple  
>>>>>>> Inc. build
>>>>>>> 5646)
>>>>>>> So as I am trying to configure, I get this error message:
>>>>>> What is the exact configure command you're running? I suspect  
>>>>>> that your
>>>>>> problem is a 32-bit vs 64-bit mismatch, because SL changed the  
>>>>>> gcc default
>>>>>> to 64-bit whereas the gfortran default is 32-bit, so you have  
>>>>>> to make sure
>>>>>> your archs match (depending on which you actually want to  
>>>>>> build) - ideally
>>>>>> you should specify -arch for all compilers (as the CRAN binary  
>>>>>> does - also
>>>>>> see the FAQ).
>>>>>> Cheers,
>>>>>> Simon
>>>>>> ...cut...
>>>>>>> checking for Fortran 77 libraries of gfortran...  -L/usr/local/ 
>>>>>>> lib
>>>>>>>> -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3
>>>>>>>> -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../.. - 
>>>>>>>> lgfortranbegin
>>>>>>>> -lgfortran
>>>>>>>> checking how to get verbose linking output from gcc - 
>>>>>>>> std=gnu99... -v
>>>>>>>> checking for C libraries of gcc -std=gnu99...  -lcrt1.10.6.o
>>>>>>>> -L/usr/local/lib -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/ 
>>>>>>>> x86_64
>>>>>>>> -L/usr/lib/i686-apple-darwin10/4.2.1
>>>>>>>> -L/usr/lib/gcc/i686-apple-darwin10/4.2.1
>>>>>>>>
>>>>>>>> -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/../../../i686-apple- 
>>>>>>>> darwin10/4.2.1
>>>>>>>> -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/../../.. -lSystem
>>>>>>>> checking for dummy main to link with Fortran 77 libraries...  
>>>>>>>> rm:
>>>>>>>> conftest.dSYM: is a directory
>>>>>>>> none
>>>>>>>> checking for Fortran 77 name-mangling scheme... rm:  
>>>>>>>> conftest.dSYM: is a
>>>>>>>> directory
>>>>>>>> unknown
>>>>>>>> configure: WARNING: unknown Fortran name-mangling scheme
>>>>>>>> checking whether gfortran appends underscores to external  
>>>>>>>> names...
>>>>>>>> unknown
>>>>>>>> configure: error: cannot use Fortran
>>>>>>> I have not seen any messages quite like this on the mailing  
>>>>>>> list. What is
>>>>>>> pretty strange is the conftest.dSYM needs to be removed (?)  
>>>>>>> for some
>>>>>>> reason
>>>>>>> but is a directory. Any ideas or suggestions on how to resolve  
>>>>>>> this?
>>>>>>> Best,
>>>>>>> --Tony
>>>>>>>
>>>>>>>     [[alternative HTML version deleted]]
>>>>>>> _______________________________________________
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