R devel - Sep 2009 - calling Lapack and BLAS routines from C

Hi,

I am working on a UNIX machine and I am interfacing R and C with the .C
function. I am trying to call LAPACK and BLAS routines, but am running
into a problem where, while I am able to run the BLAS routines, I cannot
run the LAPACK routines.

I compile my .c file (at end of email) in the following way:

[mhitczen at jlogin2 ~/Cstuff]$ R CMD SHLIB testmore.c

gcc -std=gnu99 -I/home/mhitczen/R-2.9.0/include  -I/usr/local/include   
-fpic  -g -O2 -c testmore.c -o testmore.o
gcc -std=gnu99 -shared -L/usr/local/lib -o testmore.so testmore.o

However, I get the following error in R:
> dyn.load("testmore.so")
Error in dyn.load("testmore.so") :
  unable to load shared library '/home/mhitczen/Cstuff/testmore.so':
/home/mhitczen/Cstuff/testmore.so: undefined symbol: dpotrf_

This error goes away and everything works when I simply call the BLAS
routine (In the testmore.c file I simply remove funct2, leaving funct
which calls the routine "dgemm" found in the BLAS.h file).

I read the "Writing R Extensions" and created a file:
/R-2.9.0/src/Makevars that contains the line:
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

What am I doing wrong? Thanks for your time and effort.

My testmore.c file is:

#include <Rinternals.h>
#include <Rmath.h>
#include <R.h>
#include <R_ext/Applic.h>
#include <R_ext/Lapack.h>
#include <R_ext/BLAS.h>
#include <R_ext/RS.h>

// FUNCTION CALLING BLAS
void funct(double *x, int *dim, double *y, double *result){

  double one=1.0; double zero =0.0;
  char *transa="N"; char *transb="N";

  F77_CALL(dgemm)
(transa,transb,dim,dim,dim,&one,x,dim,y,dim,&zero,result,dim);
}

// FUNCTION CALLING LAPACK
void funct4(double *x, int *dim, double *result){

  char *UorL="L";
  int info=0;

  F77_CALL(dpotrf)(UorL,dim,x,dim, &info);
}



Best,

Marcin Hitczenko

On Fri, 4 Sep 2009, Marcin Hitczenko wrote:
> Hi,
>
> I am working on a UNIX machine and I am interfacing R and C with the .C
> function. I am trying to call LAPACK and BLAS routines, but am running
> into a problem where, while I am able to run the BLAS routines, I cannot
> run the LAPACK routines.
>
> I compile my .c file (at end of email) in the following way:
>
> [mhitczen at jlogin2 ~/Cstuff]$ R CMD SHLIB testmore.c
>
> gcc -std=gnu99 -I/home/mhitczen/R-2.9.0/include  -I/usr/local/include
> -fpic  -g -O2 -c testmore.c -o testmore.o
> gcc -std=gnu99 -shared -L/usr/local/lib -o testmore.so testmore.o
>
> However, I get the following error in R:
>
>> dyn.load("testmore.so")
> Error in dyn.load("testmore.so") :
>  unable to load shared library '/home/mhitczen/Cstuff/testmore.so':
> /home/mhitczen/Cstuff/testmore.so: undefined symbol: dpotrf_
>
> This error goes away and everything works when I simply call the BLAS
> routine (In the testmore.c file I simply remove funct2, leaving funct
> which calls the routine "dgemm" found in the BLAS.h file).
>
> I read the "Writing R Extensions" and created a file:
> /R-2.9.0/src/Makevars that contains the line:
> PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
That is not where it tells you to put the file.  It needs to be in the 
direcctory where you run the compile (normally the 'src' directory of 
a package), and in your case that seems to be ~/Cstuff.

That BLAS works is fortuitous, depending on the way you built R.

[...]

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
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