Matrix and vector multiplication optimization algorithm - c

Question

Assume that the dimensions are very large (up to 1 billion elements in a matrix). How would I implement a cache oblivious algorithm for matrix-vector product? Based on wikipedia I will need to recursively divide and conquer however I feel like there would be a lot of overhead.. Would it be efficient to do so?
Follow up question and answer: OpenMP with matrices and vectors

Answer 1

So the answer to the question, "how do I make this basic linear algebra operation fast", is always and everywhere to find and link to a tuned BLAS library for your platform. Eg, GotoBLAS (whose work is being continued in OpenBLAS), or the slower autotuned ATLAS, or commercial packages like Intel's MKL. Linear algebra is so fundamental to so many other operations that enormous amounts of effort goes into optimizing these packages for various platforms, and there's just no chance you're going to come up with something in a few afternoon's work that will compete. The particular subroutine calls you're looking for for general dense matrix-vector multiplicaiton is SGEMV/DGEMV/CGEMV/ZGEMV.
Cache-oblivious algorithms, or autotuning, are for when you can't be bothered tuning for the specific cache architecture of your system - which might be fine, normally, but since people are willing to do that for BLAS routines, and then make the tuned results available, means that you're best off just using those routines.
The memory access pattern for GEMV is straightforward enough that you don't really need divide and conquer (same for the standard case of matrix transpose) - you just find the cache blocking size and use it. In GEMV (y = Ax), you still have to scan through the entire matrix once, so there's nothing to be done for reuse (and thus effective cache use) there, but you can try reuse x as much as possible so you load it once instead of (number of rows) times - and you still want access to A to be cache friendly. So the obvious cache blocking thing to do is to break along blocks:
A x -> [ A11 | A12 ] | x1 | = | A11 x1 + A12 x2 |
[ A21 | A22 ] | x2 | | A21 x1 + A22 x2 |
And you can certainly do that recursively. But doing a naive implementation, it's slower than the simple double-loop, and way slower than a proper SGEMV library call:
$ ./gemv
Testing for N=4096
Double Loop: time = 0.024995, error = 0.000000
Divide and conquer: time = 0.299945, error = 0.000000
SGEMV: time = 0.013998, error = 0.000000
The code follows:
#include <stdio.h>
#include <stdlib.h>
#include <sys/time.h>
#include "mkl.h"
float **alloc2d(int n, int m) {
float *data = malloc(n*m*sizeof(float));
float **array = malloc(n*sizeof(float *));
for (int i=0; i<n; i++)
array[i] = &(data[i*m]);
return array;
}
void tick(struct timeval *t) {
gettimeofday(t, NULL);
}
/* returns time in seconds from now to time described by t */
double tock(struct timeval *t) {
struct timeval now;
gettimeofday(&now, NULL);
return (double)(now.tv_sec - t->tv_sec) + ((double)(now.tv_usec - t->tv_usec)/1000000.);
}
float checkans(float *y, int n) {
float err = 0.;
for (int i=0; i<n; i++)
err += (y[i] - 1.*i)*(y[i] - 1.*i);
return err;
}
/* assume square matrix */
void divConquerGEMV(float **a, float *x, float *y, int n,
int startr, int endr, int startc, int endc) {
int nr = endr - startr + 1;
int nc = endc - startc + 1;
if (nr == 1 && nc == 1) {
y[startc] += a[startr][startc] * x[startr];
} else {
int midr = (endr + startr+1)/2;
int midc = (endc + startc+1)/2;
divConquerGEMV(a, x, y, n, startr, midr-1, startc, midc-1);
divConquerGEMV(a, x, y, n, midr, endr, startc, midc-1);
divConquerGEMV(a, x, y, n, startr, midr-1, midc, endc);
divConquerGEMV(a, x, y, n, midr, endr, midc, endc);
}
}
int main(int argc, char **argv) {
const int n=4096;
float **a = alloc2d(n,n);
float *x = malloc(n*sizeof(float));
float *y = malloc(n*sizeof(float));
struct timeval clock;
double eltime;
printf("Testing for N=%d\n", n);
for (int i=0; i<n; i++) {
x[i] = 1.*i;
for (int j=0; j<n; j++)
a[i][j] = 0.;
a[i][i] = 1.;
}
/* naive double loop */
tick(&clock);
for (int i=0; i<n; i++) {
y[i] = 0.;
for (int j=0; j<n; j++) {
y[i] += a[i][j]*x[j];
}
}
eltime = tock(&clock);
printf("Double Loop: time = %lf, error = %f\n", eltime, checkans(y,n));
for (int i=0; i<n; i++) y[i] = 0.;
/* naive divide and conquer */
tick(&clock);
divConquerGEMV(a, x, y, n, 0, n-1, 0, n-1);
eltime = tock(&clock);
printf("Divide and conquer: time = %lf, error = %f\n", eltime, checkans(y,n));
/* decent GEMV implementation */
tick(&clock);
float alpha = 1.;
float beta = 0.;
int incrx=1;
int incry=1;
char trans='N';
sgemv(&trans,&n,&n,&alpha,&(a[0][0]),&n,x,&incrx,&beta,y,&incry);
eltime = tock(&clock);
printf("SGEMV: time = %lf, error = %f\n", eltime, checkans(y,n));
return 0;
}