Fast byte-wise replace if

Question

I have a function that copies binary data from one area to another, but only if the bytes are different from a specific value. Here is a code sample:

void copy_if(char* src, char* dest, size_t size, char ignore)
{
  for (size_t i = 0; i < size; ++i)
  {
    if (src[i] != ignore)
      dest[i] = src[i];
  }
}

The problem is that this is too slow for my current need. Is there a way to obtain the same result in a faster way?

Update: Based on answers I tried two new implementations:

void copy_if_vectorized(const uint8_t* src, uint8_t* dest, size_t size, char ignore)
{
    for (size_t i = 0; i < size; ++i)
    {
        char temps = src[i];
        char tempd = dest[i];
        dest[i] = temps == ignore ? tempd : temps;
    }
}

void copy_if_SSE(const uint8_t* src, uint8_t* dest, size_t size, uint8_t ignore)
{
    const __m128i vignore = _mm_set1_epi8(ignore);

    size_t i;

    for (i = 0; i + 16 <= size; i += 16)
    {
        __m128i v = _mm_loadu_si128((__m128i *)&src[i]);
        __m128i vmask = _mm_cmpeq_epi8(v, vignore);
        vmask = _mm_xor_si128(vmask, _mm_set1_epi8(-1));
        _mm_maskmoveu_si128(v, vmask, (char *)&dest[i]);
    }
    for (; i < size; ++i)
    {
        if (src[i] != ignore)
            dest[i] = src[i];
    }

}

And I got the following results:

Naive: 
Duration: 2.04844s
Vectorized: 
Pass: PASS
Duration: 3.18553s
SIMD: 
Pass: PASS
Duration: 0.481888s

I guess my compiler failed to vectorized (last MSVC), but the SIMD solution is good enough, thanks!

Update (bis) I managed to vectorized it using some pragma instructions for my compile (MSVC) and indeed it is actually faster that SIMD, here is the final code:

void copy_if_vectorized(const uint8_t* src, uint8_t* dest, size_t size, char ignore)
{

#pragma loop(hint_parallel(0))
#pragma loop(ivdep)

for (int i = 0; i < size; ++i) // Sadly no parallelization if i is unsigned, but more than 2Go of data is very unlikely
{
    char temps = src[i];
    char tempd = dest[i];
    dest[i] = temps == ignore ? tempd : temps;
}
}

Answer 1

gcc vectorizes the following code:

#include <stddef.h>
void copy_if(char* src, char* dest, size_t size, char ignore)
{
  for (size_t i = 0; i < size; ++i)
  {
    char temps = src[i];
    char tempd = dest[i];
    dest[i] = temps == ignore ? tempd : temps;
  }
}

Note that both the load from- and the assignment to dest[i] are unconditional, so the compiler is not restricted by the prohibition against inventing stores in a multi-threaded program.

Edit for a less ancient compiler and processor, and godbolt links:

x86-64 gcc 11.1 compiles the code to the following with -O3 -mavx512f -mavx512bw, producing an aligned loop processing 64 bytes at a time:

.L5:
        vmovdqu8        (%rdi,%rax), %zmm2
        vpcmpb  $4, %zmm0, %zmm2, %k1
        vmovdqu8        %zmm2, (%rsi,%rax){%k1}
        addq    $64, %rax
        cmpq    %rax, %r8
        jne     .L5

This compiler also does well for gcc -std=gnu11 -O3 -mavx2, processing 32 bytes at a time:

.L5:
        vpcmpeqb        (%rdi,%rax), %ymm1, %ymm0
        vmovdqu (%rdi,%rax), %ymm2
        vpblendvb       %ymm0, (%rsi,%rax), %ymm2, %ymm0
        vmovdqu %ymm0, (%rsi,%rax)
        addq    $32, %rax
        cmpq    %rax, %r8
        jne     .L5

In general, modern compilers do well for any processor architecture with a vector unit.

Old compiler (gcc 4.8.4), old processor (no AVX512), old answer:

For -march=core-avx2, the generated assembly contains this vectorized loop, working on 32 bytes at a time:

.L9:
    vmovdqu (%rdi,%rcx), %ymm1
    addq    $1, %r10
    vmovdqu (%rsi,%rcx), %ymm2
    vpcmpeqb    %ymm0, %ymm1, %ymm3
    vpblendvb   %ymm3, %ymm2, %ymm1, %ymm1
    vmovdqu %ymm1, (%rsi,%rcx)
    addq    $32, %rcx
    cmpq    %r10, %r8
    ja  .L9

For generic x86-64, the generated assembly contains this vectorized loop, working on 16 bytes at a time:

.L9:
    movdqu  (%rdi,%r8), %xmm3
    addq    $1, %r10
    movdqa  %xmm3, %xmm1
    movdqu  (%rsi,%r8), %xmm2
    pcmpeqb %xmm0, %xmm1
    pand    %xmm1, %xmm2
    pandn   %xmm3, %xmm1
    por %xmm2, %xmm1
    movdqu  %xmm1, (%rsi,%r8)
    addq    $16, %r8
    cmpq    %r9, %r10
    jb  .L9

For armv7l-neon, clang-3.7 generates the following loop, working on 16 bytes at a time:

.LBB0_9:                                @ %vector.body
                                        @ =>This Inner Loop Header: Depth=1
        vld1.8  {d18, d19}, [r5]!
        subs.w  lr, lr, #16
        vceq.i8 q10, q9, q8
        vld1.8  {d22, d23}, [r4]
        vbsl    q10, q11, q9
        vst1.8  {d20, d21}, [r4]!
        bne     .LBB0_9

So, the code is not only more readable than assembly or intrinsics, it's also portable to multiple architectures and compilers. New architectures and instruction-set extensions can easily be utilized by recompilation.

Answer 2

Here is an example using SSE2 instrinsics to exploit the maskmovdqu instruction. The SIMD version seems to run at around 2x the speed of the original version on a Haswell CPU (code compiled with clang):

    #include <stdio.h>
    #include <string.h>
    #include <emmintrin.h>  // SSE2
    #include <sys/time.h>   // gettimeofday

    void copy_if_ref(const uint8_t* src, uint8_t* dest, size_t size, uint8_t ignore)
    {
        for (size_t i = 0; i < size; ++i)
        {
            if (src[i] != ignore)
                dest[i] = src[i];
        }
    }

    void copy_if_SSE(const uint8_t* src, uint8_t* dest, size_t size, uint8_t ignore)
    {
        const __m128i vignore = _mm_set1_epi8(ignore);

        size_t i;

        for (i = 0; i + 16 <= size; i += 16)
        {
            __m128i v = _mm_loadu_si128((__m128i *)&src[i]);
            __m128i vmask = _mm_cmpeq_epi8(v, vignore);
            vmask = _mm_xor_si128(vmask, _mm_set1_epi8(-1));
            _mm_maskmoveu_si128 (v, vmask, (char *)&dest[i]);
        }
        for ( ; i < size; ++i)
        {
            if (src[i] != ignore)
                dest[i] = src[i];
        }
    }

    #define TIME_IT(init, copy_if, src, dest, size, ignore) \
    do { \
        const int kLoops = 1000; \
        struct timeval t0, t1; \
        double t_ms = 0.0; \
     \
        for (int i = 0; i < kLoops; ++i) \
        { \
            init; \
            gettimeofday(&t0, NULL); \
            copy_if(src, dest, size, ignore); \
            gettimeofday(&t1, NULL); \
            t_ms += ((double)(t1.tv_sec - t0.tv_sec) + (double)(t1.tv_usec - t0.tv_usec) * 1.0e-6) * 1.0e3; \
        } \
        printf("%s: %.3g ns / element\n", #copy_if, t_ms * 1.0e6 / (double)(kLoops * size)); \
    } while (0)

    int main()
    {
        const size_t N = 10000000;

        uint8_t *src = malloc(N);
        uint8_t *dest_ref = malloc(N);
        uint8_t *dest_init = malloc(N);
        uint8_t *dest_test = malloc(N);

        for (size_t i = 0; i < N; ++i)
        {
            src[i] = (uint8_t)rand();
            dest_init[i] = (uint8_t)rand();
        }

        memcpy(dest_ref, dest_init, N);
        copy_if_ref(src, dest_ref, N, 0x42);

        memcpy(dest_test, dest_init, N);
        copy_if_SSE(src, dest_test, N, 0x42);
        printf("copy_if_SSE: %s\n", memcmp(dest_ref, dest_test, N) == 0 ? "PASS" : "FAIL");

        TIME_IT(memcpy(dest_test, dest_init, N), copy_if_ref, src, dest_ref, N, 0x42);
        TIME_IT(memcpy(dest_test, dest_init, N), copy_if_SSE, src, dest_test, N, 0x42);

        return 0;
    }

Compile and test:

$ gcc -Wall -msse2 -O3 copy_if.c && ./a.out 
copy_if_SSE: PASS
copy_if_ref: 0.416 ns / element
copy_if_SSE: 0.239 ns / element

(Note: earlier version of this answer had a stray factor of 16 in the timing code, so earlier numbers were 16x higher than they should have been.)

---

UPDATE

Inspired by @EOF's solution and compiler-generated code I tried a different approach with SSE4, and got much better results:

#include <stdio.h>
#include <string.h>
#include <smmintrin.h>  // SSE4
#include <sys/time.h>   // gettimeofday

void copy_if_ref(const uint8_t* src, uint8_t* dest, size_t size, uint8_t ignore)
{
    for (size_t i = 0; i < size; ++i)
    {
        if (src[i] != ignore)
            dest[i] = src[i];
    }
}

void copy_if_EOF(const uint8_t* src, uint8_t* dest, size_t size, uint8_t ignore)
{
    for (size_t i = 0; i < size; ++i)
    {
        char temps = src[i];
        char tempd = dest[i];
        dest[i] = temps == ignore ? tempd : temps;
    }
}

void copy_if_SSE(const uint8_t* src, uint8_t* dest, size_t size, uint8_t ignore)
{
    const __m128i vignore = _mm_set1_epi8(ignore);

    size_t i;

    for (i = 0; i + 16 <= size; i += 16)
    {
        __m128i vsrc = _mm_loadu_si128((__m128i *)&src[i]);
        __m128i vdest = _mm_loadu_si128((__m128i *)&dest[i]);
        __m128i vmask = _mm_cmpeq_epi8(vsrc, vignore);
        vdest = _mm_blendv_epi8(vsrc, vdest, vmask);
        _mm_storeu_si128 ((__m128i *)&dest[i], vdest);
    }
    for ( ; i < size; ++i)
    {
        if (src[i] != ignore)
            dest[i] = src[i];
    }
}

#define TIME_IT(init, copy_if, src, dest, size, ignore) \
do { \
    const int kLoops = 1000; \
    struct timeval t0, t1; \
    double t_ms = 0.0; \
 \
    for (int i = 0; i < kLoops; ++i) \
    { \
        init; \
        gettimeofday(&t0, NULL); \
        copy_if(src, dest, size, ignore); \
        gettimeofday(&t1, NULL); \
        t_ms += ((double)(t1.tv_sec - t0.tv_sec) + (double)(t1.tv_usec - t0.tv_usec) * 1.0e-6) * 1.0e3; \
    } \
    printf("%s: %.3g ns / element\n", #copy_if, t_ms * 1.0e6 / (double)(kLoops * size)); \
} while (0)

int main()
{
    const size_t N = 10000000;

    uint8_t *src = malloc(N);
    uint8_t *dest_ref = malloc(N);
    uint8_t *dest_init = malloc(N);
    uint8_t *dest_test = malloc(N);

    for (size_t i = 0; i < N; ++i)
    {
        src[i] = (uint8_t)rand();
        dest_init[i] = (uint8_t)rand();
    }

    memcpy(dest_ref, dest_init, N);
    copy_if_ref(src, dest_ref, N, 0x42);

    memcpy(dest_test, dest_init, N);
    copy_if_EOF(src, dest_test, N, 0x42);
    printf("copy_if_EOF: %s\n", memcmp(dest_ref, dest_test, N) == 0 ? "PASS" : "FAIL");

    memcpy(dest_test, dest_init, N);
    copy_if_SSE(src, dest_test, N, 0x42);
    printf("copy_if_SSE: %s\n", memcmp(dest_ref, dest_test, N) == 0 ? "PASS" : "FAIL");

    TIME_IT(memcpy(dest_test, dest_init, N), copy_if_ref, src, dest_ref, N, 0x42);
    TIME_IT(memcpy(dest_test, dest_init, N), copy_if_EOF, src, dest_test, N, 0x42);
    TIME_IT(memcpy(dest_test, dest_init, N), copy_if_SSE, src, dest_test, N, 0x42);

    return 0;
}

Compile and test:

$ gcc -Wall -msse4 -O3 copy_if_2.c && ./a.out 
copy_if_EOF: PASS
copy_if_SSE: PASS
copy_if_ref: 0.419 ns / element
copy_if_EOF: 0.114 ns / element
copy_if_SSE: 0.114 ns / element

---

Conclusion: while _mm_maskmoveu_si128 seems like a good solution for this problem from a functionality perspective, it doesn't seem to be as efficient as using explicit loads, masking and stores. Furthermore, compiler-generated code (see @EOF's answer) seems to be just as fast as explicitly coded SIMD in this instance.

Answer 3

If the freq of ignore isnt to high a memcpy code like below might help.

size_t copy_if(char* src, char* dest, size_t size, char ignore)
{
    size_t i=0, count =0 , res= 0;
    while (count < size)
    {
    while (*src != ignore){
        count++;
        if (count > size)
             break;
        src++;
        i++;
        res++;
    }
    count++;
    if (i> 0){
        memcpy(dest,src-i, i);
        dest += i;
    }
    i = 0;
    src++;
  }
return res;
}

Answer 4

The following would be an improvement, though compilers could devise this themselves.

void copy_if(char* src, char* dest, size_t size, char ignore)
{
  while (size--)
  {
    if (*src != ignore)
      *dest = *src;
    src++; dest++;
  }
}