R help - Jan 2002 - linking R against MKL

Dear R-help,

Has anyone tried linking R against the Intel Math Kernel Library on
(obviously) Intel architecture?  Since MKL claimed to provide optimized BLAS
and Lapack, I thought it might be possible to compile R against it w/o too
much trouble.

My first naive try under Linux (Mandrake 7.1), using R-patched dated Jan. 4,
2002:

./configure --with-blas=/usr/local/intel/mkl/LIB/libmkli32_p3.a

Unfortunately, life does not turn out to be that simple.  In config.log, I
get:

configure:8183: checking for dgemm_ in -lmkl32_p3
configure:8202: gcc -o conftest -g -O2 -I/usr/local/include  conftest.c
-lmkl32_p3 -L/usr/lib  -lg2c -lm
-L/usr/lib/gcc-lib/i586-mandrake-linux/2.95.3 -L/usr/i586-mandrake-linux/lib
-lm -ldl -lncurses -lm -L/usr/local/lib 1>&5
/usr/lib/libmkl32_p3.a(smp.o): In function `smp_setnprocessors':
smp.o(.text+0x2ce): undefined reference to `pthread_cancel'
/usr/lib/libmkl32_p3.a(smp.o): In function `smp_init':
smp.o(.text+0x462): undefined reference to `pthread_create'
collect2: ld returned 1 exit status
configure: failed program was:
#line 8191 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error.  */
/* We use char because int might match the return type of a gcc2
    builtin and then its argument prototype would still apply.  */
char dgemm_();
 
int main() {
dgemm_()
; return 0; }                    

Does anyone have any idea where to go from here?

Also, has anyone compared MKL with ATLAS?  Maybe it's not worth the effort
fooling with MKL?

Any hints/comments much appreciated!

Andy
Andy I. Liaw, PhD
Biometrics Research          Phone: (732) 594-0820
Merck & Co., Inc.              Fax: (732) 594-1565
P.O. Box 2000, RY70-38            Rahway, NJ 07065
mailto:andy_liaw at merck.com



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On Fri, 11 Jan 2002, Liaw, Andy wrote:
> Also, has anyone compared MKL with ATLAS?  Maybe it's not worth the
effort
> fooling with MKL?
There's some discusssion on the math-atlas-results list at the ATLAS
sourceforge page.  It looks as though it probably isn't worth the effort
at least for double precision reals. YMMV.

Another thing to note is that ATLAS is reporting substantial slowdowns
with gcc 3 especially on Athlons but even on Intel chips.

	-thomas

Thomas Lumley			Asst. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

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