Thanks, Simon:
I do have a Nehalem Mac Pro, and I've found MKL to be much faster than vecLib.
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?
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
>> bra...@mit.edu
>> 617-253-3436
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac@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
bra...@mit.edu
617-253-3436
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