I would like to thank you Ernest for your answer.
I guess that this is gonna be faster as right now R only sees one core. In my work there is a system with 64 cores and you can see only one working.
If I understand it right a [m,n][n,k] matrix multiplication can be split into rows (from first matrice) and columns (from the second matrice) and then combine all the local results of each cpu together.

Would that be too weird for mclapply to handle?

B.R
Alex



________________________________
 From: Ernest Adrogué <nfdisco@gmail.com>
To: r-help@r-project.org 
Sent: Tuesday, February 7, 2012 11:02 AM
Subject: Re: [R] using mclapply (multi core apply) to do matrix multiplication

7-02-2012, 00:29 (-0800); Alaios escriu:
> Dear all, I am trying to multiply three different matrices and each
> matrice is of size 16384,16384 the normal %*% multiplciation
> operator has not finished one day now. As I am running a system with
> many cores (and it seems that R is using only one of those) I would
> like to write fast a brief function that converts the typical for
> loops of a matrix multiplication to a set of lapply sets (mclapply
> uses the lapply syntax but it applies the work to many cores).
>
> If my thinking is correct , in the sense that this will speed up
> things a lot, I want you to help me covert the first matrix in rows
> the second in columns and convert those in  a format that lapply
> would like to work with.

If I understand correctly, R uses a specialized library called BLAS to
do matrix multiplications. I doubt re-implementing the matrix
multiplication code at R-level would be any faster. What you can try
is replace BLAS with a multicore version of BLAS although it's not
easy if you have to compile it yourself.

Also, you may try to re-think the problem you're trying to solve.
Maybe there's a different approach that is less computation-intensive.

-- 
Cheers,
Ernest

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