[R-SIG-Mac] source compile R -- emutls_get_address | libgomp.1.dylib

[Simon Urbanek]

On Jul 7, 2011, at 9:41 PM, Benton, Paul wrote:

> Dear R mac people,
> 
> I have some code that I would like to run as fast as possible. After reading some blogs I decided that I should try and install R from source again.

The CRAN binary is pretty much as fast at it gets, even with additional flags and/or compilers you won't squeeze much more out of it. The biggest difference is BLAS and you can switch to either of the two that we supply with R or others such as ATLAS or MKL (see the archives of this list). If you have any evidence otherwise, I'd be happy to see it.


> I have a what seems like a very odd error, to me at least. I've followed the installation guide at http://r.research.att.com/building.html. I googled the link file 'libgomp.1.dylib' that seems to be causing the error and got stuff about openMPI. I reinstalled openMPI to check if this did anything, which it didn't. I've also tried using the configure parameter --disable-openmp also with no luck. :(
> 
> Any ideas?
> 

It seem you have some really nasty stuff in /usr/local  - possibly from some 3rd party compilers. Under normal circumstances there should be no libgomp in /usr/local. In addition, check your DYLD_LIBRARY_PATH - it should be empty, if it's not, you're asking for trouble.
Either way, you are using non-standard compilers and/or have such in /usr/local. I suspect that is your main problem, but you'd have to tell us more about it.

My suggestion would be for you to rename /usr/local so it doesn't get in the way - I bet R will compile that way (assuming you are using Fortran merged into Xcode). The real fix is to sort out your /usr/local to put it in a more usable state ...

Cheers,
Simon


> Cheers,
> 
> Paul
> 
>> ./configure SHELL='/bin/bash' r_arch=x86_64 CC="gcc -arch x86_64 -std=gnu99" CXX="g++ -arch x86_64" OBJC="gcc -arch x86_64" F77="gfortran -arch x86_64" FC="gfortran -arch x86_64" --with-system-zlib --with-blas='-framework vecLib' --with-lapack --with-tcltk --with-readline --enable-R-profiling --with-system-bzlib R_BROWSER='/Applications/Firefox.app/Contents/MacOS/firefox' R_PDFVIEWER='/Applications/Preview.app/Contents/MacOS/Preview' && \
> make -j4
> ....
> ....
> R is now configured for x86_64-apple-darwin10.7.0
> 
>  Source directory:          .
>  Installation directory:    /Library/Frameworks
> 
>  C compiler:                gcc -arch x86_64 -std=gnu99  -g -O2
>  Fortran 77 compiler:       gfortran -arch x86_64  -g -O2
> 
>  C++ compiler:              g++ -arch x86_64  -g -O2
>  Fortran 90/95 compiler:    gfortran -arch x86_64 -g -O2
>  Obj-C compiler:     gcc -arch x86_64 -g -O2
> 
>  Interfaces supported:      X11, aqua, tcltk
>  External libraries:        readline, BLAS(vecLib), LAPACK(in blas), ICU
>  Additional capabilities:   PNG, JPEG, NLS, cairo
>  Options enabled:           framework, R profiling, Java
> 
>  Recommended packages:      yes
> ....
> ....
> make[3]: `libunix.a' is up to date.
> gcc -arch x86_64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2 -DR_HOME='"/Users/pbenton//R/R-2.13.0"' -o Rscript \
> ./Rscript.c
> make[3]: `Makedeps' is up to date.
> /Users/pbenton/R/R-2.13.0/lib/x86_64/libR.dylib is unchanged
> /Users/pbenton/R/R-2.13.0/bin/exec/x86_64/R is unchanged
> make[4]: `Makedeps' is up to date.
> make[4]: `internet.so' is up to date.
> make[4]: `Makedeps' is up to date.
> make[4]: `lapack.so' is up to date.
> make[4]: `Makedeps' is up to date.
> make[4]: `vfonts.so' is up to date.
> make[4]: `Makedeps' is up to date.
> make[4]: `R_X11.so' is up to date.
> building system startup profile
> building package 'base'
> all.R is unchanged
> ../../../library/base/R/base is unchanged
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>  Referenced from: /usr/local/lib/libgomp.1.dylib
>  Expected in: /usr/local/lib/libgcc_s.1.dylib
> 
> dyld: Symbol not found: ___emutls_get_address
>  Referenced from: /usr/local/lib/libgomp.1.dylib
>  Expected in: /usr/local/lib/libgcc_s.1.dylib
> 
> /bin/bash: line 1: 92017 Done                    cat ./makebasedb.R
>     92018 Trace/BPT trap          | R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../../bin/R --vanilla --slave > /dev/null
> make[3]: *** [all] Error 133
> make[2]: *** [R] Error 1
> make[1]: *** [R] Error 1
> make: *** [R] Error 1
> 
> 
> H. Paul Benton
> Graduate Student
> 
> 
> 
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