From braunm at MIT.EDU  Fri Jan 25 17:55:46 2008
From: braunm at MIT.EDU (Michael Braun)
Date: Fri, 25 Jan 2008 11:55:46 -0500
Subject: [Rd] Problem building R with Intel MKL v10 BLAS
In-Reply-To: <479A03AE.4070107@cimr.cam.ac.uk>
References: <47993905.9000206@mit.edu> <479A03AE.4070107@cimr.cam.ac.uk>
Message-ID: <479A1492.1010901@mit.edu>

NO

Thanks for everyone's help.  Unfortunately, still no success.  So I took 
the alternate route suggested in section A.3.1.5 of R-admin, and just 
created a symbolic link from libRblas.so to .../libmkl_gf_lp64.so.  I 
can still multiply 2 matrices together in R, so it looks like this is 
working.  Can you propose any other test to be sure?

Should I make a similar link for LAPACK?

I'm still perplexed as to why configure couldn't find the MKL BLAS, but 
I suppose any solution that works is a good one.

Thanks again.

Michael




Hin-Tak Leung wrote:
> This part "-lmkl_gf_lp64.so -lmkl_gnu_thread.so -lmkl_core.so"
> looks wrong - it should be "-lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core"
> without the ".so" part.
>
> I don't know how BLAS_LIBS does it, but when I was linking against
> mkl 9, all I did which different from the usual build (diff from the
> two rpm spec file I wrote) was 3 changes:
>
> export LDFLAGS=...  -L/opt/intel/mkl/9.1/lib/em64t/
> export FFLAGS=... -ff2c
> ./configure ... --with-blas="-lmkl -lguide -lpthread"
>
> The FFLAGS ezport was needed because of difference between g77 and 
> gfortran.
>
>
> Michael Braun wrote:
>> NO
>>
>> Hi.  I'm not sure if this is an R-help or R-devel problem, so I'm 
>> starting here in the hope that someone can help (and willing to go to 
>> the other list if it's more appropriate).  I think I am following all 
>> of the instructions in the various manuals, but clearly I am missing 
>> something.
>>
>> I have an Intel EM64T Dell with 2 dual-core Xeon processors running 
>> Red Hat EL5.  I would like to build R 2.6.1 with lots of debugging 
>> and profiling options, and link it to the processor-specific Intel 
>> MKL blas. The problem is that after I compile R, and do R CMD config 
>> BLAS_LIBS, the response is
>> -L/usr/local/lib64/R/lib -lRblas.
>>
>> This tells me that R is not linked to the Intel BLAS at all.
>>
>> My config.site file for R is:
>>
>> #! /bin/sh
>>
>> R_PAPERSIZE=letter
>> CFLAGS="-g -O2 -p -pg"
>> CPPFLAGS="-I/opt/intel/mkl/10.0.1.014/include -I/usr/include 
>> -I/usr/local/include"
>> LIBnn=lib64
>> BLAS_LIBS="-L/opt/intel/mkl/10.0.1.014/lib/em64t -Wl,--start-group 
>> -lmkl_gf_lp64.so -lmkl_gnu_thread.so -lmkl_core.so -l -l -l -Wl, 
>> --end-group -lguide -lpthread -lm"
>>
>> I have set the CONFIG_SITE environment variable to the location of 
>> the config.site.file.
>> I am doing everything as superuser.
>>
>> The command I am using for configure is
>>
>> ./configure --disable-R-profiling --with-blas=no
>>
>> following the instructions in the R-admin file regarding enabling 
>> C-level profiling and linking to the external BLAS libraries 
>> referenced in the config.site file.
>>
>> The BLAS_LIBS files are different than in the R-admin manual because 
>> of changes in the Intel MKL for version 10.  These libraries, in this 
>> order, were taken from the Intel MKL for Linux User's Guide, chapter 5.
>>
>> So, still no luck linking to the optimized BLAS.  I'd appreciate any 
>> suggestions.
>>
>> Thanks,
>>
>> Michael
>>
>>
>>
>>
>>
>


-- 
Michael Braun
Assistant Professor of Marketing
MIT Sloan School of Management
One Amherst St., E40-169
Cambridge, MA 02142
USA

braunm at mit.edu
+1 (617) 253-3436



[Rd] Problem building R with Intel MKL v10 BLAS
Michael Braun