Using inline assembly to speed up Matrix multiplication

Question

I have been trying to speed up matrix-matrix multiplication C <- C + alpha * A * B via register blocking, SSE2 vectorization and L1 cache blocking (note that I have specially chosen the transpose setting op(A)=A and op(B)=B). After some effort my written code is still about 50% slower than GotoBLAS in single thread mode .

The following is my code for the "kernel" square matrix-matrix multiplication on L1 cache, called "DGEBB" (general block-block operation) in Goto's work, that multiplies two NB*NB square matrices (NB restricted to be a multiple of 4). I have examined its assembly output under GCC 4.8, realizing that the compiler is not doing a good job in scheduling the unrolled innermost loop: kk-loop. What I hope is that the compiler optimizes register allocation to attain register reuse, and schedules the computation interleaving multiplication, addition and memory operation for pipelining; however, the compiler failed to do this. For this reason, I would like to replace the innermost loop by some inline assembly .

I am completely new to x86 assembly. Though having read around for GCC's extended asm for hours, I am still not sure how to do it properly. I have attached a stupid version I could write at my best, yet knowing it is wrong. This version is modified from the compiler's original assembly output for the kk-loop. As I know how to allocate register using "movl", "movapd", etc, I have re-arranged the computation in the order I fancy. But It does not work yet. 1) It seems to me that registers %eax, %ebx, %ecx are used both inside and outside the assembly which is nasty. 2) Also, the way I pass the input and output operands does not work. 3) Finally, I really want a version that the whole kk-loop can be inlined. Thanks if someone could helps me out!

The C code for DGEBB (called DGEBB_SSE2_x86, as my laptop is 32-bit x86 machine, with SSE2 - SSE4.1 support):

#include <stdint.h>  /* type define of "uintptr_t" */
#include <emmintrin.h>  /* double precision computation support since SSE2 */
#include <R.h>  /* use R's error handling error() */

void DGEBB_SSE2_x86 (int *NB, double *ALPHA, double *A, double *B, double *C) {
/* check "nb", must be a multiple of 4 */
int TWO=2, FOUR=4, nb=*NB; if (nb%FOUR) error("error in DGEBB_SSE2_x86: nb is not a multiple of 4!\n");
/* check memory alignment of A, B, C, 16 Byte alignment is mandatory (as XMM registers are 128-bit in length) */
uintptr_t sixteen_bytes=0xF;
if ((uintptr_t)A & sixteen_bytes) error("error in DGEBB_SSE2_x86: A is not 16 Bytes aligned in memory!");
if ((uintptr_t)B & sixteen_bytes) error("error in DGEBB_SSE2_x86: B is not 16 Bytes aligned in memory!");
if ((uintptr_t)C & sixteen_bytes) error("error in DGEBB_SSE2_x86: C is not 16 Bytes aligned in memory!");
/* define vector variables */
__m128d C1_vec_reg=_mm_setzero_pd(), C2_vec_reg=C1_vec_reg, C3_vec_reg=C1_vec_reg, C4_vec_reg=C1_vec_reg,A1_vec_reg, A2_vec_reg, B_vec_reg, U_vec_reg;
/* define scalar variables */
int jj, kk, ii, nb2=nb+nb, nb_half=nb/TWO;
double *B1_copy, *B1, *C1, *a, *b, *c, *c0;
/* start triple loop nest */
C1=C;B1=B;  /* initial column tile of C and B */
jj=nb_half;
while (jj--) {
  c=C1;B1_copy=B1;C1+=nb2;B1+=nb2;b=B1_copy;
  for (ii=0; ii<nb; ii+=FOUR) {
    a=A+ii;b=B1_copy;
    kk=nb_half;
    while (kk--) {
    /* [kernel] amortize pointer arithmetic! */
    A1_vec_reg=_mm_load_pd(a);  /* [fetch] */
    B_vec_reg=_mm_load1_pd(b);  /* [fetch] */
    U_vec_reg=_mm_mul_pd(A1_vec_reg,B_vec_reg);C1_vec_reg=_mm_add_pd(C1_vec_reg,U_vec_reg);  /* [daxpy] */
    A2_vec_reg=_mm_load_pd(a+TWO);a+=nb;  /* [fetch] */
    U_vec_reg=_mm_mul_pd(A2_vec_reg,B_vec_reg);C2_vec_reg=_mm_add_pd(C2_vec_reg,U_vec_reg);  /* [daxpy] */
    B_vec_reg=_mm_load1_pd(b+nb);b++;  /* [fetch] */
    U_vec_reg=_mm_mul_pd(A1_vec_reg,B_vec_reg);C3_vec_reg=_mm_add_pd(C3_vec_reg,U_vec_reg);  /* [daxpy] */
    A1_vec_reg=_mm_load_pd(a);  /* [fetch] */
    U_vec_reg=_mm_mul_pd(A2_vec_reg,B_vec_reg);C4_vec_reg=_mm_add_pd(C4_vec_reg,U_vec_reg);  /* [daxpy]*/
    B_vec_reg=_mm_load1_pd(b);  /* [fetch] */
    U_vec_reg=_mm_mul_pd(A1_vec_reg,B_vec_reg);C1_vec_reg=_mm_add_pd(C1_vec_reg,U_vec_reg);  /* [daxpy] */
    A2_vec_reg=_mm_load_pd(a+TWO);a+=nb;  /* [fetch] */
    U_vec_reg=_mm_mul_pd(A2_vec_reg,B_vec_reg);C2_vec_reg=_mm_add_pd(C2_vec_reg,U_vec_reg);  /* [daxpy] */
    B_vec_reg=_mm_load1_pd(b+nb);b++;  /* [fetch] */
    U_vec_reg=_mm_mul_pd(A1_vec_reg,B_vec_reg);C3_vec_reg=_mm_add_pd(C3_vec_reg,U_vec_reg);  /* [daxpy] */
    U_vec_reg=_mm_mul_pd(A2_vec_reg,B_vec_reg);C4_vec_reg=_mm_add_pd(C4_vec_reg,U_vec_reg);  /* [daxpy] */
    }  /* [end of kk-loop] */
  /* [write-back] amortize pointer arithmetic! */
  A2_vec_reg=_mm_load1_pd(ALPHA);
  U_vec_reg=_mm_load_pd(c);c0=c+nb;C1_vec_reg=_mm_mul_pd(C1_vec_reg,A2_vec_reg);  /* [fetch] */
  A1_vec_reg=U_vec_reg;C1_vec_reg=_mm_add_pd(C1_vec_reg,A1_vec_reg);U_vec_reg=_mm_load_pd(c0);  /* [fetch] */
  C3_vec_reg=_mm_mul_pd(C3_vec_reg,A2_vec_reg);_mm_store_pd(c,C1_vec_reg);c+=TWO;  /* [store] */
  A1_vec_reg=U_vec_reg;C3_vec_reg=_mm_add_pd(C3_vec_reg,A1_vec_reg);U_vec_reg=_mm_load_pd(c);  /* [fetch] */
  C2_vec_reg=_mm_mul_pd(C2_vec_reg,A2_vec_reg);_mm_store_pd(c0,C3_vec_reg);c0+=TWO;  /* [store] */
  A1_vec_reg=U_vec_reg;C2_vec_reg=_mm_add_pd(C2_vec_reg,A1_vec_reg);U_vec_reg=_mm_load_pd(c0);  /* [fetch] */
  C4_vec_reg=_mm_mul_pd(C4_vec_reg,A2_vec_reg);_mm_store_pd(c,C2_vec_reg);c+=TWO;  /* [store] */
  C4_vec_reg=_mm_add_pd(C4_vec_reg,U_vec_reg);_mm_store_pd(c0,C4_vec_reg);  /* [store] */
  C1_vec_reg=_mm_setzero_pd();C3_vec_reg=C1_vec_reg;C2_vec_reg=C1_vec_reg;C4_vec_reg=C1_vec_reg;
  }  /* [end of ii-loop] */
}  /* [end of jj-loop] */
}

My stupid version of inline assembly for the kk-loop is here:

      while (kk--) {
    asm("movapd %0, %%xmm3\n\t"     /* C1_vec_reg -> xmm3 */
        "movapd %1, %%xmm1\n\t"     /* C2_vec_reg -> xmm1 */
        "movapd %2, %%xmm2\n\t"     /* C3_vec_reg -> xmm2 */
        "movapd %3, %%xmm0\n\t"     /* C4_vec_reg -> xmm0 */
        "movl %4, %%eax\n\t"    /* pointer a -> %eax */
        "movl %5, %%edx\n\t"    /* pointer b -> %edx */
        "movl %6, %%ecx\n\t"    /* block size nb -> %ecx */
        "movapd (%%eax), %%xmm5\n\t"   /* A1_vec_reg -> xmm5 */
    "movsd (%%edx), %%xmm4\n\t"        /* B_vec_reg -> xmm4 */
    "unpcklpd %%xmm4, %%xmm4\n\t"
        "movapd %%xmm5, %%xmm6\n\t"        /* xmm5 -> xmm6 */
        "mulpd %%xmm4, %%xmm6\n\t"        /* xmm6 *= xmm4 */
    "addpd %%xmm6, %%xmm3\n\t"        /* xmm3 += xmm6 */
        "movapd 16(%%eax), %%xmm7\n\t"        /* A2_vec_reg -> xmm7 */
        "movapd %%xmm7, %%xmm6\n\t"        /* xmm7 -> xmm6 */
        "mulpd %%xmm4, %%xmm6\n\t"        /* xmm6 *= xmm4 */
    "addpd %%xmm6, %%xmm1\n\t"        /* xmm1 += xmm6 */
    "movsd (%%edx,%%ecx), %%xmm4\n\t"        /* B_vec_reg -> xmm4 */
    "addl $8, %%edx\n\t"          /* b++ */
    "movsd (%%edx), %%xmm4\n\t"       /* B_vec_reg -> xmm4 */
    "unpcklpd %%xmm4, %%xmm4\n\t"
        "movapd %%xmm5, %%xmm6\n\t"        /* xmm5 -> xmm6 */
        "mulpd %%xmm4, %%xmm6\n\t"        /* xmm6 *= xmm4 */
    "addpd %%xmm6, %%xmm2\n\t"        /* xmm2 += xmm6 */
    "addl %%ecx, %%eax\n\t"          /* a+=nb */
    "movapd (%%eax), %%xmm5\n\t"        /* A1_vec_reg -> xmm5 */
        "movapd %%xmm7, %%xmm6\n\t"        /* xmm7 -> xmm6 */
        "mulpd %%xmm4, %%xmm6\n\t"        /* xmm6 *= xmm4 */
    "addpd %%xmm6, %%xmm0\n\t"      /* xmm0 += xmm6 */
    "movsd (%%edx), %%xmm4\n\t"        /* B_vec_reg -> xmm4 */
    "unpcklpd %%xmm4, %%xmm4\n\t"
        "movapd %%xmm5, %%xmm6\n\t"        /* xmm5 -> xmm6 */
        "mulpd %%xmm4, %%xmm6\n\t"        /* xmm6 *= xmm4 */
        "addpd %%xmm6, %%xmm3\n\t"        /* xmm3 += xmm6 */
        "movapd 16(%%eax), %%xmm7\n\t"        /* A2_vec_reg -> xmm7 */
        "movapd %%xmm7, %%xmm6\n\t"        /* xmm7 -> xmm6 */
        "mulpd %%xmm4, %%xmm6\n\t"        /* xmm6 *= xmm4 */
    "addpd %%xmm6, %%xmm1\n\t"        /* xmm1 += xmm6 */
    "movsd (%%edx,%%ecx), %%xmm4\n\t"        /* B_vec_reg -> xmm4 */
    "addl $8, %%edx\n\t"          /* b++ */
    "movsd (%%edx), %%xmm4\n\t"       /* B_vec_reg -> xmm4 */
    "unpcklpd %%xmm4, %%xmm4\n\t"
        "movapd %%xmm5, %%xmm6\n\t"        /* xmm5 -> xmm6 */
        "mulpd %%xmm4, %%xmm6\n\t"        /* xmm6 *= xmm4 */
    "addpd %%xmm6, %%xmm2\n\t"        /* xmm2 += xmm6 */
        "movapd %%xmm7, %%xmm6\n\t"        /* xmm7 -> xmm6 */
        "mulpd %%xmm4, %%xmm6\n\t"        /* xmm6 *= xmm4 */
    "addpd %%xmm6, %%xmm0\n\t"      /* xmm0 += xmm6 */
    "addl %%ecx, %%eax"
        : "+x"(C1_vec_reg), "+x"(C2_vec_reg), "+x"(C3_vec_reg), "+x"(C4_vec_reg), "+m"(a), "+m"(b)
        : "x"(C1_vec_reg), "x"(C2_vec_reg), "x"(C3_vec_reg), "x"(C4_vec_reg), "4"(a), "5"(b), "rm"(nb)); 
}

Here is some explanation of the code:

Unrolling out loops to expose a micro "dger" kernel for register resue:
 (c11 c12) += (a1) * (b1 b2)
 (c21 c22)    (a2)
 (c31 c32)    (a3)
 (c41 c42)    (a4)
This can be implemented as 4 vectorized "daxpy":
 (c11) += (a1) * (b1)  ,  (c31) += (a3) * (b1)  ,  (c12) += (a1) * (b2)  ,  (c32) += (a3) * (b2)  .
 (c21)    (a2)   (b1)     (c41)    (a4)   (b1)     (c22)    (a2)   (b2)     (c42)    (a4)   (b2)
4 micor C-vectors are held constantly in XMM registers named C1_vec_reg, C2_vec_reg, C3_vec_reg, C4_vec_reg.
2 micro A-vectors are loaded into XMM registers named A1_vec_reg, A2_vec_reg.
2 micro B-vectors can reuse a single XMM register named B_vec_reg.
1 additional XMM register, U_vec_reg, will store temporary values.
The above scheduling exploits all 8 XMM registers on x84 architectures with SIMD unit, and each XMM is used twice after loaded.

PS: I am an R user from stats group. The header file enables the use of R's error handling functionality error(). This will just terminate C program rather than the whole R process. If you do not use R, delete this line and corresponding lines in the code.

Answer 1

This is an old problem back to the early phase of development of my HPC Cholesky factorization routine. The C code is outdated, and the assembly is naively incorrect. Later posts follow this thread.

(inline assembly in C) Assembler messages: Error: unknown pseudo-op: gives a correct implementation of inline assembly.

How to ask GCC to completely unroll this loop (ie, peel this loop)? gives better C code.

When writing GCC inline assembly, cares need to paid to potential changes of status flag. (inline assembly in C) Funny memory segmentation fault is a lesson for me.

Vectorization is key to HPC. SSE instruction MOVSD (extended: floating point scalar & vector operations on x86, x86-64) contains some discussion on Intel SSE2/3, while FMA instruction _mm256_fmadd_pd(): "132", "231" and "213"? has some information on Intel AVX's FMA instruction.

Surely all these are only related to computational kernels. There are a lot of other work related to how everything are wrapped up for a final high performance Cholesky factorization routine. The performance of the first release of my routine is in Why can't my CPU maintain peak performance in HPC .

Currently I am upgrading the kernel routine for even higher performance. Possibly there will be further posts on this thread. Thanks to stack overflow community, especially Z boson , Peter Cordes and nominal animal for answering various my questions. I learnt a lot and feel really happy in this process. [Surely at the same time, I learnt to be a better SO member.]