[Rd] Problem using F77_CALL(dgemm) in a package
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sun Feb 20 16:42:44 CET 2011
Look a close look at matprod in src/main/array in the R sources.
Hint: it is the other dimensions you have wrong.
And as BLAS is Fortran, counts do start at 1.
On Sat, 19 Feb 2011, Jason Rudy wrote:
> Dear R-devel,
>
> I've written a numerical solver for SOCPs (second order cone programs)
> in R, and now I want to move most of the solver code into C for speed.
> I've written combined R/C packages before, but in this case I need to
> do matrix operations in my C code. As I have never done that before,
> I'm trying to write some simple examples to make sure I understand the
> basics. I am stuck on the first one. I'm trying to write a function
> to multiply two matrices using the blas routine dgemm. The name of my
> example package is CMATRIX. My code is as follows.
>
> I have a file matrix.c in my src directory:
>
> #include <R.h>
> #include <R_ext/Utils.h>
> #include <R_ext/Lapack.h>
> #include <R_ext/BLAS.h>
>
> //Computes C = A*B
> void R_matrix_multiply(double * A, double * B, int * m, int *n, int *
> p, double * C){
> double one = 1.0;
> double zero = 0.0;
>
> //Just printing the input arguments
> Rprintf("m = %d, n = %d, p = %d\n",*m,*n,*p);
> int i;
> for(i=0;i<(*m**n);i++){
> Rprintf("%f ",A[i]);
> }
> Rprintf("\n");
> for(i=0;i<(*n**p);i++){
> Rprintf("%f ",B[i]);
> }
> Rprintf("\n");
> for(i=0;i<(*m**p);i++){
> Rprintf("%f ",C[i]);
> }
> Rprintf("\n");
>
>
> //Here is the actual multiplication
> F77_CALL(dgemm)("N","N",m,n,p,&one,A,m,B,n,&zero,C,m);
> }
>
> And the file C_matrix_multiply.R in my R directory:
>
> C_matrix_multiply = function(A,B){
> C <- matrix(0,nrow(A),ncol(B))
> cout <- .C("R_matrix_multiply",as.double(A),as.double(B),nrow(A),ncol(A),ncol(B),as.double(C))
> return(matrix(cout$C,nrowA,ncol(B)))
>
> }
>
> My namespace file is:
>
> export("C_matrix_multiply")
> useDynLib(CMATRIX.so,R_matrix_multiply)
>
> I'm not sure if it's necessary, but I've also included a Makevars.in
> file in my src directory:
>
> PKG_CPPFLAGS=@PKG_CPPFLAGS@
> PKG_CFLAGS=@PKG_CFLAGS@
> PKG_LIBS=@PKG_LIBS@ ${LAPACK_LIBS} ${BLAS_LIBS} ${FLIBS}
>
> which I simply copied from the diversitree package, which seems to use
> a lot of fortran. I have the same problem (which I am getting to)
> with or without this Makevars.in file.
>
> I install my package using:
>
> R CMD INSTALL CMATRIX
>
> Then I start up R and attempt to run the following code:
>
> #Make some random matrices
> A = matrix(rnorm(8),4,2)
> B = matrix(rnorm(6),2,3)
>
> #Load my package
> library(CMATRIX)
>
> #Print the matrices
> A
> B
>
> #Try to multiply them
> product = C_matrix_multiply(A,B)
>
> What I want, and what according to my understanding should happen, is
> for product to contain the same matrix as would result from A %*% B.
> Instead, I get the following:
>
>> A = matrix(rnorm(8),4,2)
>> B = matrix(rnorm(6),2,3)
>> library(CMATRIX)
>> A
> [,1] [,2]
> [1,] -0.4981664 -0.7243532
> [2,] 0.1428766 -1.5501623
> [3,] -2.0624701 1.5104507
> [4,] -0.5871962 0.3049442
>> B
> [,1] [,2] [,3]
> [1,] 0.02477964 0.5827084 1.8434375
> [2,] -0.20200104 1.7294264 0.9071397
>> C_matrix_multiply(A,B)
> m = 4, n = 2, p = 3
> -0.498166 0.142877 -2.062470 -0.587196 -0.724353 -1.550162 1.510451 0.304944
> 0.024780 -0.202001 0.582708 1.729426 1.843437 0.907140
> 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
> 0.000000 0.000000 0.000000 0.000000 0.000000
> Parameter 10 to routine DGEMM was incorrect
> Mac OS BLAS parameter error in DGEMM , parameter #0, (unavailable), is 0
>
> and R immediately dies. I know the arguments are being passed into
> the C code and everything up to my F77_CALL is functioning based on
> the printed output. The problem is definitely something to do with my
> F77_CALL(dgemm) line. My understanding is that parameter 10 should be
> the leading dimension of the matrix B, which in this case should be
> equal to 2, the number of rows in that matrix, which is what I am
> doing. I have also considered that parameter numbering starts at 0,
> in which case the incorrect parameter is &zero, but again that seems
> correct to me. All of my reading and research suggests I am doing
> everything correctly, so I am somewhat stumped. Perhaps I am missing
> something simple or obvious, as I have never done this before and am
> proceeding with only google and the R docs as my guide. I am
> wondering if anybody can see what I'm doing wrong here, or perhaps
> something I could do to try to fix it. Any assistance would be
> greatly appreciated.
>
> Best Regards,
>
> Jason Rudy
> Graduate Student
> Bioinformatics and Medical Informatics Program
> San Diego State University
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
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)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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