[R-SIG-Mac] using optimized BLAS [Was: problem installing rjags package]

Simon Urbanek simon.urbanek at r-project.org
Tue Oct 12 17:44:02 CEST 2010 

On Oct 12, 2010, at 11:19 AM, Michael Braun wrote:

> Thanks, Simon:
> 
> I do have a Nehalem Mac Pro, and I've found MKL to be much faster than vecLib.

Yes, because vecLib has a serious bug and doesn't spawn threads on Nehalem, but ATLAS is faster than MKL on Nehalem Mac Pro  -- here are the tcrossprod timings (on 2.66GHz Mac Pro):

vecLib           6.43
ATLAS serial     4.80
MKL serial       4.30
MKL parallel     0.90
ATLAS parallel   0.71


>  I saw in one of the manuals that one could point R to another BLAS.  But I wasn't sure what to do with MKL because of their "layering" approach to linking.  So if I point libRblas to something else, how to I tell the link which of the multiple libraries I need?
> 

MKL is picking them at run time so you don't have to point it to the machine-specific libraries. You can simply create one library (ld -dylib) re-exporting exactly what you would have done when linking it in R (i.e. use -reexport-l instead of -l).

For ATLAS it's much easier since you can compile it statically with PIC and create one library -- e.g. see
http://r.research.att.com/libatlas-MacPro.dylib
(Note that one is 10.6 only but includes both 32-bit and 64-bit ATLAS 3.9.25)

Cheers,
Simon
	

> And since we are now straying away from the original topic about JAGS, let me know if you prefer that I start another thread.  I do try to follow the posting guide as best I can.
> 
> Michael
> 
> 
> 
> 
> 
> On Oct 12, 2010, at 9:10 AM, Simon Urbanek wrote:
> 
>> Michael,
>> 
>> On Oct 9, 2010, at 5:56 PM, Michael Braun wrote:
>> 
>>> Hi!
>>> 
>>> I am trying to install rjags on my Mac Pro running OSX 10.6.4, and R 2.11.1 (which I compiled myself so I could link to the Intel MKL blas, which I prefer to other options).  
>> 
>> 
>> Just FWIW: CRAN R comes with shared BLAS option enabled and allows easy plug-in of MKL BLAS without the need to re-compile (just use the libRblas.dylib symlink). Note that MKL BLAS is often slower than ATLAS so if your main goal is speed I suggest using ATLAS (or vecLib unless you have Nehalem-type Mac Pro) - it is also easier to handle (both from technical and licensing point of view).
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> I was successfully able to install JAGS 2.1.0 through both the binary installer, and compiling from source (I get the same problem either way).
>>> 
>>> But I would like to use the rjags package. When I do 
>>> 
>>> install.packages("rjags")
>>> 
>>> 
>>> I get the folliowing output:
>>> 
>>> * installing *source* package ‘rjags’ ...
>>> checking for prefix by checking for jags... /usr/local/bin/jags
>>> checking for g++... g++
>>> checking for C++ compiler default output file name... a.out
>>> checking whether the C++ compiler works... yes
>>> checking whether we are cross compiling... no
>>> checking for suffix of executables... 
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether g++ accepts -g... yes
>>> checking how to run the C++ preprocessor... g++ -E
>>> checking for grep that handles long lines and -e... /usr/bin/grep
>>> checking for egrep... /usr/bin/grep -E
>>> checking for ANSI C header files... yes
>>> checking for sys/types.h... yes
>>> checking for sys/stat.h... yes
>>> checking for stdlib.h... yes
>>> checking for string.h... yes
>>> checking for memory.h... yes
>>> checking for strings.h... yes
>>> checking for inttypes.h... yes
>>> checking for stdint.h... yes
>>> checking for unistd.h... yes
>>> checking Console.h usability... yes
>>> checking Console.h presence... yes
>>> checking for Console.h... yes
>>> checking for gcc... gcc
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking for jags_version in -ljags... yes
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> config.status: creating R/unix/zzz.R
>>> ** libs
>>> *** arch - x86_64
>>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include/JAGS -I/opt/intel/Compiler/11.1/089/Frameworks/mkl/Headers -I/Install_Files/MKL_gfortran_interface/include/em64t/lp64    -fPIC  -m64 -msse4.2 -g -O2 -c jags.cc -o jags.o
>>> g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/intel/Compiler/11.1/089/Frameworks/mkl/Libraries/em64t -L/Users/braunm/Install_Files/MKL_gfortran_interface/lib/em64t -o rjags.so jags.o -lgsl -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>>> installing to /Users/braunm/.R/Library/rjags/libs/x86_64
>>> ** R
>>> ** data
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices ...
>>> Error : .onLoad failed in loadNamespace() for 'rjags', details:
>>> call: dyn.load(file, DLLpath = DLLpath, ...)
>>> error: unable to load shared library '/Users/braunm/.R/Library/rjags/libs/x86_64/rjags.so':
>>> dlopen(/Users/braunm/.R/Library/rjags/libs/x86_64/rjags.so, 10): Symbol not found: _JAGS_NA
>>> Referenced from: /Users/braunm/.R/Library/rjags/libs/x86_64/rjags.so
>>> Expected in: flat namespace
>>> in /Users/braunm/.R/Library/rjags/libs/x86_64/rjags.so
>>> ERROR: installing package indices failed
>>> * removing ‘/Users/braunm/.R/Library/rjags’
>>> 
>>> 
>>> However, when I go to look at the symbols in the jags library, I see
>>> 
>>> braunm4: /usr/local/lib $ nm libjags.dylib |grep JAGS
>>> 0000000000098650 S _JAGS_NA
>>> 0000000000110338 S _JAGS_NAN
>>> 0000000000110348 S _JAGS_NEGINF
>>> 0000000000110340 S _JAGS_POSINF
>>> 000000000000133c t __GLOBAL__I_JAGS_NA
>>> 
>>> and when I try
>>> 
>>> braunm4: /usr/local/lib $ nm libjags.a |grep JAGS
>>>               U _JAGS_NA
>>>               U _JAGS_NEGINF
>>>               U _JAGS_NA
>>>               U _JAGS_NA
>>> 0000000000000060 S _JAGS_NA
>>> 00000000000000b8 B _JAGS_NAN
>>> 00000000000000c8 B _JAGS_NEGINF
>>> 00000000000000c0 B _JAGS_POSINF
>>>               U _JAGS_NA
>>>               U _JAGS_NEGINF
>>>               U _JAGS_POSINF
>>>               U _JAGS_NEGINF
>>>               U _JAGS_POSINF
>>>               U _JAGS_NEGINF
>>>               U _JAGS_NA
>>>               U _JAGS_NEGINF
>>>               U _JAGS_NEGINF
>>>               U _JAGS_NA
>>>               U _JAGS_NEGINF
>>>               U _JAGS_POSINF
>>> 
>>> 
>>> So the jags libraries (both static and dynamic) are in the standard place, and it looks like the symbols rjags.so needs are there as well.  So I'm not sure what the rjags installer is looking for.  Is there perhaps an environment variable that I am missing?
>>> 
>>> Here is my sessionInfo():
>>> 
>>>> sessionInfo()
>>> R version 2.11.1 (2010-05-31) 
>>> x86_64-apple-darwin10.4.2 
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats     grDevices datasets  graphics  utils     methods   base     
>>> 
>>> other attached packages:
>>> [1] xtable_1.5-6     doMC_1.2.1       multicore_0.1-3  foreach_1.3.0    codetools_0.2-2  iterators_1.0.3  coda_0.13-5      matrixcalc_1.0-1 lattice_0.18-8   reshape_0.8.3    plyr_1.2.1      
>>> [12] mvtnorm_0.9-92  
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] grid_2.11.1  tcltk_2.11.1 tools_2.11.1
>>> 
>>> 
>>> Thanks in advance for your help.
>>> 
>>> Michael
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> -------------------------------------------
>>> Michael Braun
>>> Homer A. Burnell (1928) Career Development Professor, 
>>> 	and Assistant Professor of Management Science (Marketing Group)
>>> MIT Sloan School of Management
>>> 100 Main St.., E62-535
>>> Cambridge, MA 02139
>>> 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 (1928) Career Development Professor, 
> 	and Assistant Professor of Management Science (Marketing Group)
> MIT Sloan School of Management
> 100 Main St.., E62-535
> Cambridge, MA 02139
> braunm at mit.edu
> 617-253-3436
> 
> 
>

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