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d5d01df Jul 30, 2014
4101 lines (3370 sloc) 105 KB
#include <unistd.h>
#include <math.h>
#include <time.h>
#include <stdlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include <stdint.h>
#include <limits.h>
#include "axml.h"
#include <stdint.h>
#include <xmmintrin.h>
#include <pmmintrin.h>
#include <immintrin.h>
#ifdef _FMA
#include <x86intrin.h>
#define FMAMACC(a,b,c) _mm256_fmadd_pd(b,c,a)
#endif
extern const unsigned int mask32[32];
const union __attribute__ ((aligned (BYTE_ALIGNMENT)))
{
uint64_t i[4];
__m256d m;
} absMask_AVX = {{0x7fffffffffffffffULL, 0x7fffffffffffffffULL, 0x7fffffffffffffffULL, 0x7fffffffffffffffULL}};
static inline __m256d hadd4(__m256d v, __m256d u)
{
__m256d
a, b;
v = _mm256_hadd_pd(v, v);
a = _mm256_permute2f128_pd(v, v, 1);
v = _mm256_add_pd(a, v);
u = _mm256_hadd_pd(u, u);
b = _mm256_permute2f128_pd(u, u, 1);
u = _mm256_add_pd(b, u);
v = _mm256_mul_pd(v, u);
return v;
}
static inline __m256d hadd3(__m256d v)
{
__m256d
a;
v = _mm256_hadd_pd(v, v);
a = _mm256_permute2f128_pd(v, v, 1);
v = _mm256_add_pd(a, v);
return v;
}
void newviewGTRGAMMA_AVX(int tipCase,
double *x1, double *x2, double *x3,
double *extEV, double *tipVector,
int *ex3, unsigned char *tipX1, unsigned char *tipX2,
const int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling,
const unsigned int x1_presenceMap,
const unsigned int x2_presenceMap
)
{
int
i,
k,
scale,
addScale = 0;
__m256d
minlikelihood_avx = _mm256_set1_pd( minlikelihood ),
twoto = _mm256_set1_pd(twotothe256);
switch(tipCase)
{
case TIP_TIP:
{
double
*uX1,
umpX1[1024] __attribute__ ((aligned (BYTE_ALIGNMENT))),
*uX2,
umpX2[1024] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for (i = 1; i < 16; i++)
{
__m256d
tv = _mm256_load_pd(&(tipVector[i * 4]));
int
j;
if(mask32[i] & x1_presenceMap)
{
for (j = 0; j < 4; j++)
for (k = 0; k < 4; k++)
{
__m256d
left1 = _mm256_load_pd(&left[j * 16 + k * 4]);
left1 = _mm256_mul_pd(left1, tv);
left1 = hadd3(left1);
_mm256_store_pd(&umpX1[i * 64 + j * 16 + k * 4], left1);
}
}
if(mask32[i] & x2_presenceMap)
{
for (j = 0; j < 4; j++)
for (k = 0; k < 4; k++)
{
__m256d
left1 = _mm256_load_pd(&right[j * 16 + k * 4]);
left1 = _mm256_mul_pd(left1, tv);
left1 = hadd3(left1);
_mm256_store_pd(&umpX2[i * 64 + j * 16 + k * 4], left1);
}
}
}
for(i = 0; i < n; i++)
{
uX1 = &umpX1[64 * tipX1[i]];
uX2 = &umpX2[64 * tipX2[i]];
for(k = 0; k < 4; k++)
{
__m256d
xv = _mm256_setzero_pd();
int
l;
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(&uX1[k * 16 + l * 4]), _mm256_load_pd(&uX2[k * 16 + l * 4]));
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
#ifdef _FMA
xv = FMAMACC(xv,x1v,evv);
#else
xv = _mm256_add_pd(xv, _mm256_mul_pd(x1v, evv));
#endif
}
_mm256_store_pd(&x3[16 * i + 4 * k], xv);
}
}
}
break;
case TIP_INNER:
{
double
*uX1,
umpX1[1024] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for (i = 1; i < 16; i++)
{
if(mask32[i] & x1_presenceMap)
{
__m256d
tv = _mm256_load_pd(&(tipVector[i*4]));
int
j;
for (j = 0; j < 4; j++)
for (k = 0; k < 4; k++)
{
__m256d
left1 = _mm256_load_pd(&left[j * 16 + k * 4]);
left1 = _mm256_mul_pd(left1, tv);
left1 = hadd3(left1);
_mm256_store_pd(&umpX1[i * 64 + j * 16 + k * 4], left1);
}
}
}
for(i = 0; i < n; i++)
{
__m256d
xv[4];
scale = 1;
uX1 = &umpX1[64 * tipX1[i]];
for(k = 0; k < 4; k++)
{
__m256d
xvr = _mm256_load_pd(&(x2[i * 16 + k * 4]));
int
l;
xv[k] = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_load_pd(&uX1[k * 16 + l * 4]),
x2v = _mm256_mul_pd(xvr, _mm256_load_pd(&right[k * 16 + l * 4]));
x2v = hadd3(x2v);
x1v = _mm256_mul_pd(x1v, x2v);
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
#ifdef _FMA
xv[k] = FMAMACC(xv[k],x1v,evv);
#else
xv[k] = _mm256_add_pd(xv[k], _mm256_mul_pd(x1v, evv));
#endif
}
if(scale)
{
__m256d
v1 = _mm256_and_pd(xv[k], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
}
if(scale)
{
xv[0] = _mm256_mul_pd(xv[0], twoto);
xv[1] = _mm256_mul_pd(xv[1], twoto);
xv[2] = _mm256_mul_pd(xv[2], twoto);
xv[3] = _mm256_mul_pd(xv[3], twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&x3[16 * i], xv[0]);
_mm256_store_pd(&x3[16 * i + 4], xv[1]);
_mm256_store_pd(&x3[16 * i + 8], xv[2]);
_mm256_store_pd(&x3[16 * i + 12], xv[3]);
}
}
break;
case INNER_INNER:
{
for(i = 0; i < n; i++)
{
__m256d
xv[4];
scale = 1;
for(k = 0; k < 4; k++)
{
__m256d
xvl = _mm256_load_pd(&(x1[i * 16 + k * 4])),
xvr = _mm256_load_pd(&(x2[i * 16 + k * 4]));
int
l;
xv[k] = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(xvl, _mm256_load_pd(&left[k * 16 + l * 4])),
x2v = _mm256_mul_pd(xvr, _mm256_load_pd(&right[k * 16 + l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
xv[k] = _mm256_add_pd(xv[k], _mm256_mul_pd(x1v, evv));
}
if(scale)
{
__m256d
v1 = _mm256_and_pd(xv[k], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
}
if(scale)
{
xv[0] = _mm256_mul_pd(xv[0], twoto);
xv[1] = _mm256_mul_pd(xv[1], twoto);
xv[2] = _mm256_mul_pd(xv[2], twoto);
xv[3] = _mm256_mul_pd(xv[3], twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&x3[16 * i], xv[0]);
_mm256_store_pd(&x3[16 * i + 4], xv[1]);
_mm256_store_pd(&x3[16 * i + 8], xv[2]);
_mm256_store_pd(&x3[16 * i + 12], xv[3]);
}
}
break;
default:
assert(0);
}
if(useFastScaling)
*scalerIncrement = addScale;
}
void newviewGTRGAMMA_AVX_GAPPED_SAVE(int tipCase,
double *x1_start, double *x2_start, double *x3_start,
double *extEV, double *tipVector,
int *ex3, unsigned char *tipX1, unsigned char *tipX2,
const int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling,
unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap,
double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn,
const unsigned int x1_presenceMap,
const unsigned int x2_presenceMap)
{
int
i,
k,
scale,
scaleGap,
addScale = 0;
__m256d
minlikelihood_avx = _mm256_set1_pd( minlikelihood ),
twoto = _mm256_set1_pd(twotothe256);
double
*x1,
*x2,
*x3,
*x1_ptr = x1_start,
*x2_ptr = x2_start;
switch(tipCase)
{
case TIP_TIP:
{
double
*uX1,
umpX1[1024] __attribute__ ((aligned (BYTE_ALIGNMENT))),
*uX2,
umpX2[1024] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for (i = 1; i < 16; i++)
{
__m256d
tv = _mm256_load_pd(&(tipVector[i * 4]));
int
j;
if((mask32[i] & x1_presenceMap) || i == 15)
{
for (j = 0; j < 4; j++)
for (k = 0; k < 4; k++)
{
__m256d
left1 = _mm256_load_pd(&left[j * 16 + k * 4]);
left1 = _mm256_mul_pd(left1, tv);
left1 = hadd3(left1);
_mm256_store_pd(&umpX1[i * 64 + j * 16 + k * 4], left1);
}
}
if((mask32[i] & x2_presenceMap) || i == 15)
{
for (j = 0; j < 4; j++)
for (k = 0; k < 4; k++)
{
__m256d
left1 = _mm256_load_pd(&right[j * 16 + k * 4]);
left1 = _mm256_mul_pd(left1, tv);
left1 = hadd3(left1);
_mm256_store_pd(&umpX2[i * 64 + j * 16 + k * 4], left1);
}
}
}
x3 = x3_gapColumn;
{
uX1 = &umpX1[960];
uX2 = &umpX2[960];
for(k = 0; k < 4; k++)
{
__m256d
xv = _mm256_setzero_pd();
int
l;
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(&uX1[k * 16 + l * 4]), _mm256_load_pd(&uX2[k * 16 + l * 4]));
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
#ifdef _FMA
xv = FMAMACC(xv,x1v,evv);
#else
xv = _mm256_add_pd(xv, _mm256_mul_pd(x1v, evv));
#endif
}
_mm256_store_pd(&x3[4 * k], xv);
}
}
x3 = x3_start;
for(i = 0; i < n; i++)
{
if(!(x3_gap[i / 32] & mask32[i % 32]))
{
uX1 = &umpX1[64 * tipX1[i]];
uX2 = &umpX2[64 * tipX2[i]];
for(k = 0; k < 4; k++)
{
__m256d
xv = _mm256_setzero_pd();
int
l;
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(&uX1[k * 16 + l * 4]), _mm256_load_pd(&uX2[k * 16 + l * 4]));
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
#ifdef _FMA
xv = FMAMACC(xv,x1v,evv);
#else
xv = _mm256_add_pd(xv, _mm256_mul_pd(x1v, evv));
#endif
}
_mm256_store_pd(&x3[4 * k], xv);
}
x3 += 16;
}
}
}
break;
case TIP_INNER:
{
double
*uX1,
umpX1[1024] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for (i = 1; i < 16; i++)
{
__m256d
tv = _mm256_load_pd(&(tipVector[i*4]));
int
j;
if((mask32[i] & x1_presenceMap) || i == 15)
{
for (j = 0; j < 4; j++)
for (k = 0; k < 4; k++)
{
__m256d
left1 = _mm256_load_pd(&left[j * 16 + k * 4]);
left1 = _mm256_mul_pd(left1, tv);
left1 = hadd3(left1);
_mm256_store_pd(&umpX1[i * 64 + j * 16 + k * 4], left1);
}
}
}
{
__m256d
xv[4];
scaleGap = 1;
uX1 = &umpX1[960];
x2 = x2_gapColumn;
x3 = x3_gapColumn;
for(k = 0; k < 4; k++)
{
__m256d
xvr = _mm256_load_pd(&(x2[k * 4]));
int
l;
xv[k] = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_load_pd(&uX1[k * 16 + l * 4]),
x2v = _mm256_mul_pd(xvr, _mm256_load_pd(&right[k * 16 + l * 4]));
x2v = hadd3(x2v);
x1v = _mm256_mul_pd(x1v, x2v);
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
#ifdef _FMA
xv[k] = FMAMACC(xv[k],x1v,evv);
#else
xv[k] = _mm256_add_pd(xv[k], _mm256_mul_pd(x1v, evv));
#endif
}
if(scaleGap)
{
__m256d
v1 = _mm256_and_pd(xv[k], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scaleGap = 0;
}
}
if(scaleGap)
{
xv[0] = _mm256_mul_pd(xv[0], twoto);
xv[1] = _mm256_mul_pd(xv[1], twoto);
xv[2] = _mm256_mul_pd(xv[2], twoto);
xv[3] = _mm256_mul_pd(xv[3], twoto);
}
_mm256_store_pd(&x3[0], xv[0]);
_mm256_store_pd(&x3[4], xv[1]);
_mm256_store_pd(&x3[8], xv[2]);
_mm256_store_pd(&x3[12], xv[3]);
}
x3 = x3_start;
for(i = 0; i < n; i++)
{
if((x3_gap[i / 32] & mask32[i % 32]))
{
if(scaleGap)
{
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
else
{
if(x2_gap[i / 32] & mask32[i % 32])
x2 = x2_gapColumn;
else
{
x2 = x2_ptr;
x2_ptr += 16;
}
__m256d
xv[4];
scale = 1;
uX1 = &umpX1[64 * tipX1[i]];
for(k = 0; k < 4; k++)
{
__m256d
xvr = _mm256_load_pd(&(x2[k * 4]));
int
l;
xv[k] = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_load_pd(&uX1[k * 16 + l * 4]),
x2v = _mm256_mul_pd(xvr, _mm256_load_pd(&right[k * 16 + l * 4]));
x2v = hadd3(x2v);
x1v = _mm256_mul_pd(x1v, x2v);
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
#ifdef _FMA
xv[k] = FMAMACC(xv[k],x1v,evv);
#else
xv[k] = _mm256_add_pd(xv[k], _mm256_mul_pd(x1v, evv));
#endif
}
if(scale)
{
__m256d
v1 = _mm256_and_pd(xv[k], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
}
if(scale)
{
xv[0] = _mm256_mul_pd(xv[0], twoto);
xv[1] = _mm256_mul_pd(xv[1], twoto);
xv[2] = _mm256_mul_pd(xv[2], twoto);
xv[3] = _mm256_mul_pd(xv[3], twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&x3[0], xv[0]);
_mm256_store_pd(&x3[4], xv[1]);
_mm256_store_pd(&x3[8], xv[2]);
_mm256_store_pd(&x3[12], xv[3]);
x3 += 16;
}
}
}
break;
case INNER_INNER:
{
{
x1 = x1_gapColumn;
x2 = x2_gapColumn;
x3 = x3_gapColumn;
__m256d
xv[4];
scaleGap = 1;
for(k = 0; k < 4; k++)
{
__m256d
xvl = _mm256_load_pd(&(x1[k * 4])),
xvr = _mm256_load_pd(&(x2[k * 4]));
int
l;
xv[k] = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(xvl, _mm256_load_pd(&left[k * 16 + l * 4])),
x2v = _mm256_mul_pd(xvr, _mm256_load_pd(&right[k * 16 + l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
xv[k] = _mm256_add_pd(xv[k], _mm256_mul_pd(x1v, evv));
}
if(scaleGap)
{
__m256d
v1 = _mm256_and_pd(xv[k], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scaleGap = 0;
}
}
if(scaleGap)
{
xv[0] = _mm256_mul_pd(xv[0], twoto);
xv[1] = _mm256_mul_pd(xv[1], twoto);
xv[2] = _mm256_mul_pd(xv[2], twoto);
xv[3] = _mm256_mul_pd(xv[3], twoto);
}
_mm256_store_pd(&x3[0], xv[0]);
_mm256_store_pd(&x3[4], xv[1]);
_mm256_store_pd(&x3[8], xv[2]);
_mm256_store_pd(&x3[12], xv[3]);
}
x3 = x3_start;
for(i = 0; i < n; i++)
{
if(x3_gap[i / 32] & mask32[i % 32])
{
if(scaleGap)
{
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
else
{
if(x1_gap[i / 32] & mask32[i % 32])
x1 = x1_gapColumn;
else
{
x1 = x1_ptr;
x1_ptr += 16;
}
if(x2_gap[i / 32] & mask32[i % 32])
x2 = x2_gapColumn;
else
{
x2 = x2_ptr;
x2_ptr += 16;
}
__m256d
xv[4];
scale = 1;
for(k = 0; k < 4; k++)
{
__m256d
xvl = _mm256_load_pd(&(x1[k * 4])),
xvr = _mm256_load_pd(&(x2[k * 4]));
int
l;
xv[k] = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(xvl, _mm256_load_pd(&left[k * 16 + l * 4])),
x2v = _mm256_mul_pd(xvr, _mm256_load_pd(&right[k * 16 + l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&extEV[l * 4]);
xv[k] = _mm256_add_pd(xv[k], _mm256_mul_pd(x1v, evv));
}
if(scale)
{
__m256d
v1 = _mm256_and_pd(xv[k], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
}
if(scale)
{
xv[0] = _mm256_mul_pd(xv[0], twoto);
xv[1] = _mm256_mul_pd(xv[1], twoto);
xv[2] = _mm256_mul_pd(xv[2], twoto);
xv[3] = _mm256_mul_pd(xv[3], twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&x3[0], xv[0]);
_mm256_store_pd(&x3[4], xv[1]);
_mm256_store_pd(&x3[8], xv[2]);
_mm256_store_pd(&x3[12], xv[3]);
x3 += 16;
}
}
}
break;
default:
assert(0);
}
if(useFastScaling)
*scalerIncrement = addScale;
}
void newviewGTRCAT_AVX(int tipCase, double *EV, int *cptr,
double *x1_start, double *x2_start, double *x3_start, double *tipVector,
int *ex3, unsigned char *tipX1, unsigned char *tipX2,
int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling)
{
double
*le,
*ri,
*x1,
*x2;
int
i,
addScale = 0;
__m256d
minlikelihood_avx = _mm256_set1_pd( minlikelihood ),
twoto = _mm256_set1_pd(twotothe256);
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
int
l;
le = &left[cptr[i] * 16];
ri = &right[cptr[i] * 16];
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &(tipVector[4 * tipX2[i]]);
__m256d
vv = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(x1), _mm256_load_pd(&le[l * 4])),
x2v = _mm256_mul_pd(_mm256_load_pd(x2), _mm256_load_pd(&ri[l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&EV[l * 4]);
#ifdef _FMA
vv = FMAMACC(vv,x1v,evv);
#else
vv = _mm256_add_pd(vv, _mm256_mul_pd(x1v, evv));
#endif
}
_mm256_store_pd(&x3_start[4 * i], vv);
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
int
l;
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &x2_start[4 * i];
le = &left[cptr[i] * 16];
ri = &right[cptr[i] * 16];
__m256d
vv = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(x1), _mm256_load_pd(&le[l * 4])),
x2v = _mm256_mul_pd(_mm256_load_pd(x2), _mm256_load_pd(&ri[l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&EV[l * 4]);
#ifdef _FMA
vv = FMAMACC(vv,x1v,evv);
#else
vv = _mm256_add_pd(vv, _mm256_mul_pd(x1v, evv));
#endif
}
__m256d
v1 = _mm256_and_pd(vv, absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) == 15)
{
vv = _mm256_mul_pd(vv, twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&x3_start[4 * i], vv);
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
int
l;
x1 = &x1_start[4 * i];
x2 = &x2_start[4 * i];
le = &left[cptr[i] * 16];
ri = &right[cptr[i] * 16];
__m256d
vv = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(x1), _mm256_load_pd(&le[l * 4])),
x2v = _mm256_mul_pd(_mm256_load_pd(x2), _mm256_load_pd(&ri[l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&EV[l * 4]);
#ifdef _FMA
vv = FMAMACC(vv,x1v,evv);
#else
vv = _mm256_add_pd(vv, _mm256_mul_pd(x1v, evv));
#endif
}
__m256d
v1 = _mm256_and_pd(vv, absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) == 15)
{
vv = _mm256_mul_pd(vv, twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&x3_start[4 * i], vv);
}
break;
default:
assert(0);
}
if(useFastScaling)
*scalerIncrement = addScale;
}
void newviewGTRCAT_AVX_GAPPED_SAVE(int tipCase, double *EV, int *cptr,
double *x1_start, double *x2_start, double *x3_start, double *tipVector,
int *ex3, unsigned char *tipX1, unsigned char *tipX2,
int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling,
unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap,
double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn, const int maxCats)
{
double
*le,
*ri,
*x1,
*x2,
*x3,
*x1_ptr = x1_start,
*x2_ptr = x2_start,
*x3_ptr = x3_start;
int
i,
scaleGap = 0,
addScale = 0;
__m256d
minlikelihood_avx = _mm256_set1_pd( minlikelihood ),
twoto = _mm256_set1_pd(twotothe256);
{
int
l;
x1 = x1_gapColumn;
x2 = x2_gapColumn;
x3 = x3_gapColumn;
le = &left[maxCats * 16];
ri = &right[maxCats * 16];
__m256d
vv = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(x1), _mm256_load_pd(&le[l * 4])),
x2v = _mm256_mul_pd(_mm256_load_pd(x2), _mm256_load_pd(&ri[l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&EV[l * 4]);
#ifdef _FMA
vv = FMAMACC(vv,x1v,evv);
#else
vv = _mm256_add_pd(vv, _mm256_mul_pd(x1v, evv));
#endif
}
if(tipCase != TIP_TIP)
{
__m256d
v1 = _mm256_and_pd(vv, absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) == 15)
{
vv = _mm256_mul_pd(vv, twoto);
scaleGap = 1;
}
}
_mm256_store_pd(x3, vv);
}
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
if(noGap(x3_gap, i))
{
int
l;
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &(tipVector[4 * tipX2[i]]);
x3 = x3_ptr;
if(isGap(x1_gap, i))
le = &left[maxCats * 16];
else
le = &left[cptr[i] * 16];
if(isGap(x2_gap, i))
ri = &right[maxCats * 16];
else
ri = &right[cptr[i] * 16];
__m256d
vv = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(x1), _mm256_load_pd(&le[l * 4])),
x2v = _mm256_mul_pd(_mm256_load_pd(x2), _mm256_load_pd(&ri[l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&EV[l * 4]);
#ifdef _FMA
vv = FMAMACC(vv,x1v,evv);
#else
vv = _mm256_add_pd(vv, _mm256_mul_pd(x1v, evv));
#endif
}
_mm256_store_pd(x3, vv);
x3_ptr += 4;
}
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
if(isGap(x3_gap, i))
{
if(scaleGap)
{
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
else
{
int
l;
x1 = &(tipVector[4 * tipX1[i]]);
x3 = x3_ptr;
if(isGap(x1_gap, i))
le = &left[maxCats * 16];
else
le = &left[cptr[i] * 16];
if(isGap(x2_gap, i))
{
ri = &right[maxCats * 16];
x2 = x2_gapColumn;
}
else
{
ri = &right[cptr[i] * 16];
x2 = x2_ptr;
x2_ptr += 4;
}
__m256d
vv = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(x1), _mm256_load_pd(&le[l * 4])),
x2v = _mm256_mul_pd(_mm256_load_pd(x2), _mm256_load_pd(&ri[l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&EV[l * 4]);
#ifdef _FMA
vv = FMAMACC(vv,x1v,evv);
#else
vv = _mm256_add_pd(vv, _mm256_mul_pd(x1v, evv));
#endif
}
__m256d
v1 = _mm256_and_pd(vv, absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) == 15)
{
vv = _mm256_mul_pd(vv, twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(x3, vv);
x3_ptr += 4;
}
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
if(isGap(x3_gap, i))
{
if(scaleGap)
{
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
else
{
int
l;
x3 = x3_ptr;
if(isGap(x1_gap, i))
{
x1 = x1_gapColumn;
le = &left[maxCats * 16];
}
else
{
le = &left[cptr[i] * 16];
x1 = x1_ptr;
x1_ptr += 4;
}
if(isGap(x2_gap, i))
{
x2 = x2_gapColumn;
ri = &right[maxCats * 16];
}
else
{
ri = &right[cptr[i] * 16];
x2 = x2_ptr;
x2_ptr += 4;
}
__m256d
vv = _mm256_setzero_pd();
for(l = 0; l < 4; l++)
{
__m256d
x1v = _mm256_mul_pd(_mm256_load_pd(x1), _mm256_load_pd(&le[l * 4])),
x2v = _mm256_mul_pd(_mm256_load_pd(x2), _mm256_load_pd(&ri[l * 4]));
x1v = hadd4(x1v, x2v);
__m256d
evv = _mm256_load_pd(&EV[l * 4]);
#ifdef _FMA
vv = FMAMACC(vv,x1v,evv);
#else
vv = _mm256_add_pd(vv, _mm256_mul_pd(x1v, evv));
#endif
}
__m256d
v1 = _mm256_and_pd(vv, absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) == 15)
{
vv = _mm256_mul_pd(vv, twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(x3, vv);
x3_ptr += 4;
}
}
break;
default:
assert(0);
}
if(useFastScaling)
*scalerIncrement = addScale;
}
void newviewGTRCATPROT_AVX(int tipCase, double *extEV,
int *cptr,
double *x1, double *x2, double *x3, double *tipVector,
int *ex3, unsigned char *tipX1, unsigned char *tipX2,
int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling)
{
double
*le, *ri, *v, *vl, *vr;
int i, l, scale, addScale = 0;
#ifdef _FMA
int k;
#endif
switch(tipCase)
{
case TIP_TIP:
{
for (i = 0; i < n; i++)
{
le = &left[cptr[i] * 400];
ri = &right[cptr[i] * 400];
vl = &(tipVector[20 * tipX1[i]]);
vr = &(tipVector[20 * tipX2[i]]);
v = &x3[20 * i];
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d
x1v = _mm256_setzero_pd(),
x2v = _mm256_setzero_pd();
double
*ev = &extEV[l * 20],
*lv = &le[l * 20],
*rv = &ri[l * 20];
#ifdef _FMA
for(k = 0; k < 20; k += 4)
{
__m256d vlv = _mm256_load_pd(&vl[k]);
__m256d lvv = _mm256_load_pd(&lv[k]);
x1v = FMAMACC(x1v,vlv,lvv);
__m256d vrv = _mm256_load_pd(&vr[k]);
__m256d rvv = _mm256_load_pd(&rv[k]);
x2v = FMAMACC(x2v,vrv,rvv);
}
#else
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[0]), _mm256_load_pd(&lv[0])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[4]), _mm256_load_pd(&lv[4])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[8]), _mm256_load_pd(&lv[8])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[12]), _mm256_load_pd(&lv[12])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[16]), _mm256_load_pd(&lv[16])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[0]), _mm256_load_pd(&rv[0])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[4]), _mm256_load_pd(&rv[4])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[8]), _mm256_load_pd(&rv[8])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[12]), _mm256_load_pd(&rv[12])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[16]), _mm256_load_pd(&rv[16])));
#endif
x1v = hadd4(x1v, x2v);
#ifdef _FMA
for(k = 0; k < 5; k++)
{
__m256d evv = _mm256_load_pd(&ev[k*4]);
vv[k] = FMAMACC(vv[k],x1v,evv);
}
#else
__m256d
evv[5];
evv[0] = _mm256_load_pd(&ev[0]);
evv[1] = _mm256_load_pd(&ev[4]);
evv[2] = _mm256_load_pd(&ev[8]);
evv[3] = _mm256_load_pd(&ev[12]);
evv[4] = _mm256_load_pd(&ev[16]);
vv[0] = _mm256_add_pd(vv[0], _mm256_mul_pd(x1v, evv[0]));
vv[1] = _mm256_add_pd(vv[1], _mm256_mul_pd(x1v, evv[1]));
vv[2] = _mm256_add_pd(vv[2], _mm256_mul_pd(x1v, evv[2]));
vv[3] = _mm256_add_pd(vv[3], _mm256_mul_pd(x1v, evv[3]));
vv[4] = _mm256_add_pd(vv[4], _mm256_mul_pd(x1v, evv[4]));
#endif
}
_mm256_store_pd(&v[0], vv[0]);
_mm256_store_pd(&v[4], vv[1]);
_mm256_store_pd(&v[8], vv[2]);
_mm256_store_pd(&v[12], vv[3]);
_mm256_store_pd(&v[16], vv[4]);
}
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
le = &left[cptr[i] * 400];
ri = &right[cptr[i] * 400];
vl = &(tipVector[20 * tipX1[i]]);
vr = &x2[20 * i];
v = &x3[20 * i];
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d
x1v = _mm256_setzero_pd(),
x2v = _mm256_setzero_pd();
double
*ev = &extEV[l * 20],
*lv = &le[l * 20],
*rv = &ri[l * 20];
#ifdef _FMA
for(k = 0; k < 20; k += 4)
{
__m256d vlv = _mm256_load_pd(&vl[k]);
__m256d lvv = _mm256_load_pd(&lv[k]);
x1v = FMAMACC(x1v,vlv,lvv);
__m256d vrv = _mm256_load_pd(&vr[k]);
__m256d rvv = _mm256_load_pd(&rv[k]);
x2v = FMAMACC(x2v,vrv,rvv);
}
#else
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[0]), _mm256_load_pd(&lv[0])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[4]), _mm256_load_pd(&lv[4])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[8]), _mm256_load_pd(&lv[8])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[12]), _mm256_load_pd(&lv[12])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[16]), _mm256_load_pd(&lv[16])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[0]), _mm256_load_pd(&rv[0])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[4]), _mm256_load_pd(&rv[4])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[8]), _mm256_load_pd(&rv[8])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[12]), _mm256_load_pd(&rv[12])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[16]), _mm256_load_pd(&rv[16])));
#endif
x1v = hadd4(x1v, x2v);
__m256d
evv[5];
evv[0] = _mm256_load_pd(&ev[0]);
evv[1] = _mm256_load_pd(&ev[4]);
evv[2] = _mm256_load_pd(&ev[8]);
evv[3] = _mm256_load_pd(&ev[12]);
evv[4] = _mm256_load_pd(&ev[16]);
#ifdef _FMA
for(k = 0; k < 5; k++)
vv[k] = FMAMACC(vv[k],x1v,evv[k]);
#else
vv[0] = _mm256_add_pd(vv[0], _mm256_mul_pd(x1v, evv[0]));
vv[1] = _mm256_add_pd(vv[1], _mm256_mul_pd(x1v, evv[1]));
vv[2] = _mm256_add_pd(vv[2], _mm256_mul_pd(x1v, evv[2]));
vv[3] = _mm256_add_pd(vv[3], _mm256_mul_pd(x1v, evv[3]));
vv[4] = _mm256_add_pd(vv[4], _mm256_mul_pd(x1v, evv[4]));
#endif
}
__m256d minlikelihood_avx = _mm256_set1_pd( minlikelihood );
scale = 1;
for(l = 0; scale && (l < 20); l += 4)
{
__m256d
v1 = _mm256_and_pd(vv[l / 4], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
if(scale)
{
__m256d
twoto = _mm256_set1_pd(twotothe256);
for(l = 0; l < 20; l += 4)
vv[l / 4] = _mm256_mul_pd(vv[l / 4] , twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&v[0], vv[0]);
_mm256_store_pd(&v[4], vv[1]);
_mm256_store_pd(&v[8], vv[2]);
_mm256_store_pd(&v[12], vv[3]);
_mm256_store_pd(&v[16], vv[4]);
}
break;
case INNER_INNER:
for(i = 0; i < n; i++)
{
le = &left[cptr[i] * 400];
ri = &right[cptr[i] * 400];
vl = &x1[20 * i];
vr = &x2[20 * i];
v = &x3[20 * i];
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d
x1v = _mm256_setzero_pd(),
x2v = _mm256_setzero_pd();
double
*ev = &extEV[l * 20],
*lv = &le[l * 20],
*rv = &ri[l * 20];
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[0]), _mm256_load_pd(&lv[0])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[4]), _mm256_load_pd(&lv[4])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[8]), _mm256_load_pd(&lv[8])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[12]), _mm256_load_pd(&lv[12])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[16]), _mm256_load_pd(&lv[16])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[0]), _mm256_load_pd(&rv[0])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[4]), _mm256_load_pd(&rv[4])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[8]), _mm256_load_pd(&rv[8])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[12]), _mm256_load_pd(&rv[12])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[16]), _mm256_load_pd(&rv[16])));
x1v = hadd4(x1v, x2v);
#ifdef _FMA
for(k = 0; k < 5; k++)
{
__m256d evv = _mm256_load_pd(&ev[k*4]);
vv[k] = FMAMACC(vv[k],x1v,evv);
}
#else
__m256d
evv[5];
evv[0] = _mm256_load_pd(&ev[0]);
evv[1] = _mm256_load_pd(&ev[4]);
evv[2] = _mm256_load_pd(&ev[8]);
evv[3] = _mm256_load_pd(&ev[12]);
evv[4] = _mm256_load_pd(&ev[16]);
vv[0] = _mm256_add_pd(vv[0], _mm256_mul_pd(x1v, evv[0]));
vv[1] = _mm256_add_pd(vv[1], _mm256_mul_pd(x1v, evv[1]));
vv[2] = _mm256_add_pd(vv[2], _mm256_mul_pd(x1v, evv[2]));
vv[3] = _mm256_add_pd(vv[3], _mm256_mul_pd(x1v, evv[3]));
vv[4] = _mm256_add_pd(vv[4], _mm256_mul_pd(x1v, evv[4]));
#endif
}
__m256d minlikelihood_avx = _mm256_set1_pd( minlikelihood );
scale = 1;
for(l = 0; scale && (l < 20); l += 4)
{
__m256d
v1 = _mm256_and_pd(vv[l / 4], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
if(scale)
{
__m256d
twoto = _mm256_set1_pd(twotothe256);
for(l = 0; l < 20; l += 4)
vv[l / 4] = _mm256_mul_pd(vv[l / 4] , twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&v[0], vv[0]);
_mm256_store_pd(&v[4], vv[1]);
_mm256_store_pd(&v[8], vv[2]);
_mm256_store_pd(&v[12], vv[3]);
_mm256_store_pd(&v[16], vv[4]);
}
break;
default:
assert(0);
}
if(useFastScaling)
*scalerIncrement = addScale;
}
void newviewGTRCATPROT_AVX_GAPPED_SAVE(int tipCase, double *extEV,
int *cptr,
double *x1, double *x2, double *x3, double *tipVector,
int *ex3, unsigned char *tipX1, unsigned char *tipX2,
int n, double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling,
unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap,
double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn, const int maxCats)
{
double
*le,
*ri,
*v,
*vl,
*vr,
*x1_ptr = x1,
*x2_ptr = x2,
*x3_ptr = x3;
int
i,
l,
scale,
addScale = 0,
scaleGap = 0;
#ifdef _FMA
int k;
#endif
{
le = &left[maxCats * 400];
ri = &right[maxCats * 400];
vl = x1_gapColumn;
vr = x2_gapColumn;
v = x3_gapColumn;
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d
x1v = _mm256_setzero_pd(),
x2v = _mm256_setzero_pd();
double
*ev = &extEV[l * 20],
*lv = &le[l * 20],
*rv = &ri[l * 20];
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[0]), _mm256_load_pd(&lv[0])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[4]), _mm256_load_pd(&lv[4])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[8]), _mm256_load_pd(&lv[8])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[12]), _mm256_load_pd(&lv[12])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[16]), _mm256_load_pd(&lv[16])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[0]), _mm256_load_pd(&rv[0])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[4]), _mm256_load_pd(&rv[4])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[8]), _mm256_load_pd(&rv[8])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[12]), _mm256_load_pd(&rv[12])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[16]), _mm256_load_pd(&rv[16])));
x1v = hadd4(x1v, x2v);
#ifdef _FMA
for(k = 0; k < 5; k++)
{
__m256d evv = _mm256_load_pd(&ev[k*4]);
vv[k] = FMAMACC(vv[k],x1v,evv);
}
#else
__m256d
evv[5];
evv[0] = _mm256_load_pd(&ev[0]);
evv[1] = _mm256_load_pd(&ev[4]);
evv[2] = _mm256_load_pd(&ev[8]);
evv[3] = _mm256_load_pd(&ev[12]);
evv[4] = _mm256_load_pd(&ev[16]);
vv[0] = _mm256_add_pd(vv[0], _mm256_mul_pd(x1v, evv[0]));
vv[1] = _mm256_add_pd(vv[1], _mm256_mul_pd(x1v, evv[1]));
vv[2] = _mm256_add_pd(vv[2], _mm256_mul_pd(x1v, evv[2]));
vv[3] = _mm256_add_pd(vv[3], _mm256_mul_pd(x1v, evv[3]));
vv[4] = _mm256_add_pd(vv[4], _mm256_mul_pd(x1v, evv[4]));
#endif
}
if(tipCase != TIP_TIP)
{
__m256d minlikelihood_avx = _mm256_set1_pd( minlikelihood );
scale = 1;
for(l = 0; scale && (l < 20); l += 4)
{
__m256d
v1 = _mm256_and_pd(vv[l / 4], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
if(scale)
{
__m256d
twoto = _mm256_set1_pd(twotothe256);
for(l = 0; l < 20; l += 4)
vv[l / 4] = _mm256_mul_pd(vv[l / 4] , twoto);
scaleGap = 1;
}
}
_mm256_store_pd(&v[0], vv[0]);
_mm256_store_pd(&v[4], vv[1]);
_mm256_store_pd(&v[8], vv[2]);
_mm256_store_pd(&v[12], vv[3]);
_mm256_store_pd(&v[16], vv[4]);
}
switch(tipCase)
{
case TIP_TIP:
{
for (i = 0; i < n; i++)
{
if(noGap(x3_gap, i))
{
vl = &(tipVector[20 * tipX1[i]]);
vr = &(tipVector[20 * tipX2[i]]);
v = x3_ptr;
if(isGap(x1_gap, i))
le = &left[maxCats * 400];
else
le = &left[cptr[i] * 400];
if(isGap(x2_gap, i))
ri = &right[maxCats * 400];
else
ri = &right[cptr[i] * 400];
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d
x1v = _mm256_setzero_pd(),
x2v = _mm256_setzero_pd();
double
*ev = &extEV[l * 20],
*lv = &le[l * 20],
*rv = &ri[l * 20];
#ifdef _FMA
for(k = 0; k < 20; k += 4)
{
__m256d vlv = _mm256_load_pd(&vl[k]);
__m256d lvv = _mm256_load_pd(&lv[k]);
x1v = FMAMACC(x1v,vlv,lvv);
__m256d vrv = _mm256_load_pd(&vr[k]);
__m256d rvv = _mm256_load_pd(&rv[k]);
x2v = FMAMACC(x2v,vrv,rvv);
}
#else
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[0]), _mm256_load_pd(&lv[0])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[4]), _mm256_load_pd(&lv[4])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[8]), _mm256_load_pd(&lv[8])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[12]), _mm256_load_pd(&lv[12])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[16]), _mm256_load_pd(&lv[16])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[0]), _mm256_load_pd(&rv[0])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[4]), _mm256_load_pd(&rv[4])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[8]), _mm256_load_pd(&rv[8])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[12]), _mm256_load_pd(&rv[12])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[16]), _mm256_load_pd(&rv[16])));
#endif
x1v = hadd4(x1v, x2v);
#ifdef _FMA
for(k = 0; k < 5; k++)
{
__m256d evv = _mm256_load_pd(&ev[k*4]);
vv[k] = FMAMACC(vv[k],x1v,evv);
}
#else
__m256d
evv[5];
evv[0] = _mm256_load_pd(&ev[0]);
evv[1] = _mm256_load_pd(&ev[4]);
evv[2] = _mm256_load_pd(&ev[8]);
evv[3] = _mm256_load_pd(&ev[12]);
evv[4] = _mm256_load_pd(&ev[16]);
vv[0] = _mm256_add_pd(vv[0], _mm256_mul_pd(x1v, evv[0]));
vv[1] = _mm256_add_pd(vv[1], _mm256_mul_pd(x1v, evv[1]));
vv[2] = _mm256_add_pd(vv[2], _mm256_mul_pd(x1v, evv[2]));
vv[3] = _mm256_add_pd(vv[3], _mm256_mul_pd(x1v, evv[3]));
vv[4] = _mm256_add_pd(vv[4], _mm256_mul_pd(x1v, evv[4]));
#endif
}
_mm256_store_pd(&v[0], vv[0]);
_mm256_store_pd(&v[4], vv[1]);
_mm256_store_pd(&v[8], vv[2]);
_mm256_store_pd(&v[12], vv[3]);
_mm256_store_pd(&v[16], vv[4]);
x3_ptr += 20;
}
}
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
if(isGap(x3_gap, i))
{
if(scaleGap)
{
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
else
{
vl = &(tipVector[20 * tipX1[i]]);
vr = x2_ptr;
v = x3_ptr;
if(isGap(x1_gap, i))
le = &left[maxCats * 400];
else
le = &left[cptr[i] * 400];
if(isGap(x2_gap, i))
{
ri = &right[maxCats * 400];
vr = x2_gapColumn;
}
else
{
ri = &right[cptr[i] * 400];
vr = x2_ptr;
x2_ptr += 20;
}
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d
x1v = _mm256_setzero_pd(),
x2v = _mm256_setzero_pd();
double
*ev = &extEV[l * 20],
*lv = &le[l * 20],
*rv = &ri[l * 20];
#ifdef _FMA
for(k = 0; k < 20; k += 4)
{
__m256d vlv = _mm256_load_pd(&vl[k]);
__m256d lvv = _mm256_load_pd(&lv[k]);
x1v = FMAMACC(x1v,vlv,lvv);
__m256d vrv = _mm256_load_pd(&vr[k]);
__m256d rvv = _mm256_load_pd(&rv[k]);
x2v = FMAMACC(x2v,vrv,rvv);
}
#else
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[0]), _mm256_load_pd(&lv[0])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[4]), _mm256_load_pd(&lv[4])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[8]), _mm256_load_pd(&lv[8])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[12]), _mm256_load_pd(&lv[12])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[16]), _mm256_load_pd(&lv[16])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[0]), _mm256_load_pd(&rv[0])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[4]), _mm256_load_pd(&rv[4])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[8]), _mm256_load_pd(&rv[8])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[12]), _mm256_load_pd(&rv[12])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[16]), _mm256_load_pd(&rv[16])));
#endif
x1v = hadd4(x1v, x2v);
__m256d
evv[5];
evv[0] = _mm256_load_pd(&ev[0]);
evv[1] = _mm256_load_pd(&ev[4]);
evv[2] = _mm256_load_pd(&ev[8]);
evv[3] = _mm256_load_pd(&ev[12]);
evv[4] = _mm256_load_pd(&ev[16]);
#ifdef _FMA
for(k = 0; k < 5; k++)
vv[k] = FMAMACC(vv[k],x1v,evv[k]);
#else
vv[0] = _mm256_add_pd(vv[0], _mm256_mul_pd(x1v, evv[0]));
vv[1] = _mm256_add_pd(vv[1], _mm256_mul_pd(x1v, evv[1]));
vv[2] = _mm256_add_pd(vv[2], _mm256_mul_pd(x1v, evv[2]));
vv[3] = _mm256_add_pd(vv[3], _mm256_mul_pd(x1v, evv[3]));
vv[4] = _mm256_add_pd(vv[4], _mm256_mul_pd(x1v, evv[4]));
#endif
}
__m256d minlikelihood_avx = _mm256_set1_pd( minlikelihood );
scale = 1;
for(l = 0; scale && (l < 20); l += 4)
{
__m256d
v1 = _mm256_and_pd(vv[l / 4], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
if(scale)
{
__m256d
twoto = _mm256_set1_pd(twotothe256);
for(l = 0; l < 20; l += 4)
vv[l / 4] = _mm256_mul_pd(vv[l / 4] , twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&v[0], vv[0]);
_mm256_store_pd(&v[4], vv[1]);
_mm256_store_pd(&v[8], vv[2]);
_mm256_store_pd(&v[12], vv[3]);
_mm256_store_pd(&v[16], vv[4]);
x3_ptr += 20;
}
}
break;
case INNER_INNER:
for(i = 0; i < n; i++)
{
if(isGap(x3_gap, i))
{
if(scaleGap)
{
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
else
{
v = x3_ptr;
if(isGap(x1_gap, i))
{
vl = x1_gapColumn;
le = &left[maxCats * 400];
}
else
{
le = &left[cptr[i] * 400];
vl = x1_ptr;
x1_ptr += 20;
}
if(isGap(x2_gap, i))
{
vr = x2_gapColumn;
ri = &right[maxCats * 400];
}
else
{
ri = &right[cptr[i] * 400];
vr = x2_ptr;
x2_ptr += 20;
}
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d
x1v = _mm256_setzero_pd(),
x2v = _mm256_setzero_pd();
double
*ev = &extEV[l * 20],
*lv = &le[l * 20],
*rv = &ri[l * 20];
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[0]), _mm256_load_pd(&lv[0])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[4]), _mm256_load_pd(&lv[4])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[8]), _mm256_load_pd(&lv[8])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[12]), _mm256_load_pd(&lv[12])));
x1v = _mm256_add_pd(x1v, _mm256_mul_pd(_mm256_load_pd(&vl[16]), _mm256_load_pd(&lv[16])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[0]), _mm256_load_pd(&rv[0])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[4]), _mm256_load_pd(&rv[4])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[8]), _mm256_load_pd(&rv[8])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[12]), _mm256_load_pd(&rv[12])));
x2v = _mm256_add_pd(x2v, _mm256_mul_pd(_mm256_load_pd(&vr[16]), _mm256_load_pd(&rv[16])));
x1v = hadd4(x1v, x2v);
#ifdef _FMA
for(k = 0; k < 5; k++)
{
__m256d evv = _mm256_load_pd(&ev[k*4]);
vv[k] = FMAMACC(vv[k],x1v,evv);
}
#else
__m256d
evv[5];
evv[0] = _mm256_load_pd(&ev[0]);
evv[1] = _mm256_load_pd(&ev[4]);
evv[2] = _mm256_load_pd(&ev[8]);
evv[3] = _mm256_load_pd(&ev[12]);
evv[4] = _mm256_load_pd(&ev[16]);
vv[0] = _mm256_add_pd(vv[0], _mm256_mul_pd(x1v, evv[0]));
vv[1] = _mm256_add_pd(vv[1], _mm256_mul_pd(x1v, evv[1]));
vv[2] = _mm256_add_pd(vv[2], _mm256_mul_pd(x1v, evv[2]));
vv[3] = _mm256_add_pd(vv[3], _mm256_mul_pd(x1v, evv[3]));
vv[4] = _mm256_add_pd(vv[4], _mm256_mul_pd(x1v, evv[4]));
#endif
}
__m256d minlikelihood_avx = _mm256_set1_pd( minlikelihood );
scale = 1;
for(l = 0; scale && (l < 20); l += 4)
{
__m256d
v1 = _mm256_and_pd(vv[l / 4], absMask_AVX.m);
v1 = _mm256_cmp_pd(v1, minlikelihood_avx, _CMP_LT_OS);
if(_mm256_movemask_pd( v1 ) != 15)
scale = 0;
}
if(scale)
{
__m256d
twoto = _mm256_set1_pd(twotothe256);
for(l = 0; l < 20; l += 4)
vv[l / 4] = _mm256_mul_pd(vv[l / 4] , twoto);
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
_mm256_store_pd(&v[0], vv[0]);
_mm256_store_pd(&v[4], vv[1]);
_mm256_store_pd(&v[8], vv[2]);
_mm256_store_pd(&v[12], vv[3]);
_mm256_store_pd(&v[16], vv[4]);
x3_ptr += 20;
}
}
break;
default:
assert(0);
}
if(useFastScaling)
*scalerIncrement = addScale;
}
void newviewGTRGAMMAPROT_AVX(int tipCase,
double *x1, double *x2, double *x3, double *extEV, double *tipVector,
int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n,
double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling)
{
double
*uX1,
*uX2,
*v,
x1px2,
*vl,
*vr;
int
i,
j,
l,
k,
scale,
addScale = 0;
#ifndef GCC_VERSION
#define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#endif
#if GCC_VERSION < 40500
__m256d
bitmask = _mm256_set_pd(0,0,0,-1);
#else
__m256i
bitmask = _mm256_set_epi32(0, 0, 0, 0, 0, 0, -1, -1);
#endif
switch(tipCase)
{
case TIP_TIP:
{
double
umpX1[1840] __attribute__ ((aligned (BYTE_ALIGNMENT))),
umpX2[1840] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for(i = 0; i < 23; i++)
{
v = &(tipVector[20 * i]);
for(k = 0; k < 80; k++)
{
double
*ll = &left[k * 20],
*rr = &right[k * 20];
__m256d
umpX1v = _mm256_setzero_pd(),
umpX2v = _mm256_setzero_pd();
for(l = 0; l < 20; l+=4)
{
__m256d vv = _mm256_load_pd(&v[l]);
#ifdef _FMA
__m256d llv = _mm256_load_pd(&ll[l]);
umpX1v = FMAMACC(umpX1v,vv,llv);
__m256d rrv = _mm256_load_pd(&rr[l]);
umpX2v = FMAMACC(umpX2v,vv,rrv);
#else
umpX1v = _mm256_add_pd(umpX1v,_mm256_mul_pd(vv,_mm256_load_pd(&ll[l])));
umpX2v = _mm256_add_pd(umpX2v,_mm256_mul_pd(vv,_mm256_load_pd(&rr[l])));
#endif
}
umpX1v = hadd3(umpX1v);
umpX2v = hadd3(umpX2v);
_mm256_maskstore_pd(&umpX1[80 * i + k], bitmask, umpX1v);
_mm256_maskstore_pd(&umpX2[80 * i + k], bitmask, umpX2v);
}
}
for(i = 0; i < n; i++)
{
uX1 = &umpX1[80 * tipX1[i]];
uX2 = &umpX2[80 * tipX2[i]];
for(j = 0; j < 4; j++)
{
__m256d vv[5];
v = &x3[i * 80 + j * 20];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(k = 0; k < 20; k++)
{
x1px2 = uX1[j * 20 + k] * uX2[j * 20 + k];
__m256d x1px2v = _mm256_set1_pd(x1px2);
__m256d extEvv = _mm256_load_pd(&extEV[20 * k]);
#ifdef _FMA
vv[0] = FMAMACC(vv[0],x1px2v,extEvv);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[0],vv[0]);
extEvv = _mm256_load_pd(&extEV[20 * k + 4]);
#ifdef _FMA
vv[1] = FMAMACC(vv[1],x1px2v,extEvv);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[4],vv[1]);
extEvv = _mm256_load_pd(&extEV[20 * k + 8]);
#ifdef _FMA
vv[2] = FMAMACC(vv[2],x1px2v,extEvv);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[8],vv[2]);
extEvv = _mm256_load_pd(&extEV[20 * k + 12]);
#ifdef _FMA
vv[3] = FMAMACC(vv[3],x1px2v,extEvv);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[12],vv[3]);
extEvv = _mm256_load_pd(&extEV[20 * k + 16]);
#ifdef _FMA
vv[4] = FMAMACC(vv[4],x1px2v,extEvv);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
}
}
break;
case TIP_INNER:
{
double
umpX1[1840] __attribute__ ((aligned (BYTE_ALIGNMENT))),
ump_x2[20] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for(i = 0; i < 23; i++)
{
v = &(tipVector[20 * i]);
for(k = 0; k < 80; k++)
{
__m256d umpX1v = _mm256_setzero_pd();
for(l = 0; l < 20; l+=4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d leftv = _mm256_load_pd(&left[k * 20 + l]);
#ifdef _FMA
umpX1v = FMAMACC(umpX1v, vv, leftv);
#else
umpX1v = _mm256_add_pd(umpX1v, _mm256_mul_pd(vv, leftv));
#endif
}
umpX1v = hadd3(umpX1v);
_mm256_maskstore_pd(&umpX1[80 * i + k], bitmask, umpX1v);
}
}
for (i = 0; i < n; i++)
{
uX1 = &umpX1[80 * tipX1[i]];
for(k = 0; k < 4; k++)
{
v = &(x2[80 * i + k * 20]);
for(l = 0; l < 20; l++)
{
__m256d ump_x2v = _mm256_setzero_pd();
__m256d vv = _mm256_load_pd(&v[0]);
__m256d rightv = _mm256_load_pd(&right[k*400+l*20+0]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[4]);
rightv = _mm256_load_pd(&right[k*400+l*20+4]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[8]);
rightv = _mm256_load_pd(&right[k*400+l*20+8]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[12]);
rightv = _mm256_load_pd(&right[k*400+l*20+12]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[16]);
rightv = _mm256_load_pd(&right[k*400+l*20+16]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
ump_x2v = hadd3(ump_x2v);
_mm256_maskstore_pd(&ump_x2[l], bitmask, ump_x2v);
}
v = &(x3[80 * i + 20 * k]);
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
x1px2 = uX1[k * 20 + l] * ump_x2[l];
__m256d x1px2v = _mm256_set1_pd(x1px2);
#ifdef _FMA
__m256d ev = _mm256_load_pd(&extEV[l * 20 + 0]);
vv[0] = FMAMACC(vv[0],x1px2v, ev);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 0])));
#endif
_mm256_store_pd(&v[0],vv[0]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 4]);
vv[1] = FMAMACC(vv[1],x1px2v, ev);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 4])));
#endif
_mm256_store_pd(&v[4],vv[1]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 8]);
vv[2] = FMAMACC(vv[2],x1px2v, ev);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 8])));
#endif
_mm256_store_pd(&v[8],vv[2]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 12]);
vv[3] = FMAMACC(vv[3],x1px2v, ev);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 12])));
#endif
_mm256_store_pd(&v[12],vv[3]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 16]);
vv[4] = FMAMACC(vv[4],x1px2v, ev);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 16])));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
v = &x3[80 * i];
__m256d minlikelihood_avx = _mm256_set1_pd(minlikelihood);
scale = 1;
for(l = 0; scale && (l < 80); l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d vv_abs = _mm256_and_pd(vv,absMask_AVX.m);
vv_abs = _mm256_cmp_pd(vv_abs,minlikelihood_avx,_CMP_LT_OS);
if(_mm256_movemask_pd(vv_abs) != 15)
scale = 0;
}
if(scale)
{
__m256d twotothe256v = _mm256_set_pd(twotothe256,twotothe256,twotothe256,twotothe256);
for(l = 0; l < 80; l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
_mm256_store_pd(&v[l],_mm256_mul_pd(vv,twotothe256v));
}
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
}
break;
case INNER_INNER:
for(i = 0; i < n; i++)
{
scale = 1;
for(k = 0; k < 4; k++)
{
vl = &(x1[80 * i + 20 * k]);
vr = &(x2[80 * i + 20 * k]);
v = &(x3[80 * i + 20 * k]);
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d al = _mm256_setzero_pd();
__m256d ar = _mm256_setzero_pd();
__m256d leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 0]);
__m256d rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 0]);
__m256d vlv = _mm256_load_pd(&vl[0]);
__m256d vrv = _mm256_load_pd(&vr[0]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 4]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 4]);
vlv = _mm256_load_pd(&vl[4]);
vrv = _mm256_load_pd(&vr[4]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 8]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 8]);
vlv = _mm256_load_pd(&vl[8]);
vrv = _mm256_load_pd(&vr[8]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 12]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 12]);
vlv = _mm256_load_pd(&vl[12]);
vrv = _mm256_load_pd(&vr[12]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 16]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 16]);
vlv = _mm256_load_pd(&vl[16]);
vrv = _mm256_load_pd(&vr[16]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
/**************************************************************************************************************/
al = hadd3(al);
ar = hadd3(ar);
al = _mm256_mul_pd(ar,al);
/************************************************************************************************************/
#ifdef _FMA
__m256d ev = _mm256_load_pd(&extEV[20 * l + 0]);
vv[0] = FMAMACC(vv[0], al, ev);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 0])));
#endif
_mm256_store_pd(&v[0],vv[0]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[20 * l + 4]);
vv[1] = FMAMACC(vv[1], al, ev);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 4])));
#endif
_mm256_store_pd(&v[4],vv[1]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[20 * l + 8]);
vv[2] = FMAMACC(vv[2], al, ev);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 8])));
#endif
_mm256_store_pd(&v[8],vv[2]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[20 * l + 12]);
vv[3] = FMAMACC(vv[3], al, ev);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 12])));
#endif
_mm256_store_pd(&v[12],vv[3]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[20 * l + 16]);
vv[4] = FMAMACC(vv[4], al, ev);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 16])));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
v = &(x3[80 * i]);
scale = 1;
__m256d minlikelihood_avx = _mm256_set1_pd(minlikelihood);
for(l = 0; scale && (l < 80); l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d vv_abs = _mm256_and_pd(vv,absMask_AVX.m);
vv_abs = _mm256_cmp_pd(vv_abs,minlikelihood_avx,_CMP_LT_OS);
if(_mm256_movemask_pd(vv_abs) != 15)
scale = 0;
}
if(scale)
{
__m256d twotothe256v = _mm256_set_pd(twotothe256,twotothe256,twotothe256,twotothe256);
for(l = 0; l < 80; l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
_mm256_store_pd(&v[l],_mm256_mul_pd(vv,twotothe256v));
}
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
break;
default:
assert(0);
}
if(useFastScaling)
*scalerIncrement = addScale;
}
void newviewGTRGAMMAPROT_AVX_LG4(int tipCase,
double *x1, double *x2, double *x3, double *extEV[4], double *tipVector[4],
int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n,
double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling)
{
double
*uX1,
*uX2,
*v,
x1px2,
*vl,
*vr;
int
i,
j,
l,
k,
scale,
addScale = 0;
#ifndef GCC_VERSION
#define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#endif
#if GCC_VERSION < 40500
__m256d
bitmask = _mm256_set_pd(0,0,0,-1);
#else
__m256i
bitmask = _mm256_set_epi32(0, 0, 0, 0, 0, 0, -1, -1);
#endif
switch(tipCase)
{
case TIP_TIP:
{
double
umpX1[1840] __attribute__ ((aligned (BYTE_ALIGNMENT))),
umpX2[1840] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for(i = 0; i < 23; i++)
{
for(k = 0; k < 80; k++)
{
double
*ll = &left[k * 20],
*rr = &right[k * 20];
__m256d
umpX1v = _mm256_setzero_pd(),
umpX2v = _mm256_setzero_pd();
v = &(tipVector[k / 20][20 * i]);
for(l = 0; l < 20; l+=4)
{
__m256d vv = _mm256_load_pd(&v[l]);
#ifdef _FMA
__m256d llv = _mm256_load_pd(&ll[l]);
umpX1v = FMAMACC(umpX1v,vv,llv);
__m256d rrv = _mm256_load_pd(&rr[l]);
umpX2v = FMAMACC(umpX2v,vv,rrv);
#else
umpX1v = _mm256_add_pd(umpX1v,_mm256_mul_pd(vv,_mm256_load_pd(&ll[l])));
umpX2v = _mm256_add_pd(umpX2v,_mm256_mul_pd(vv,_mm256_load_pd(&rr[l])));
#endif
}
umpX1v = hadd3(umpX1v);
umpX2v = hadd3(umpX2v);
_mm256_maskstore_pd(&umpX1[80 * i + k], bitmask, umpX1v);
_mm256_maskstore_pd(&umpX2[80 * i + k], bitmask, umpX2v);
}
}
for(i = 0; i < n; i++)
{
uX1 = &umpX1[80 * tipX1[i]];
uX2 = &umpX2[80 * tipX2[i]];
for(j = 0; j < 4; j++)
{
__m256d vv[5];
v = &x3[i * 80 + j * 20];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(k = 0; k < 20; k++)
{
x1px2 = uX1[j * 20 + k] * uX2[j * 20 + k];
__m256d x1px2v = _mm256_set1_pd(x1px2);
__m256d extEvv = _mm256_load_pd(&extEV[j][20 * k]);
#ifdef _FMA
vv[0] = FMAMACC(vv[0],x1px2v,extEvv);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[0],vv[0]);
extEvv = _mm256_load_pd(&extEV[j][20 * k + 4]);
#ifdef _FMA
vv[1] = FMAMACC(vv[1],x1px2v,extEvv);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[4],vv[1]);
extEvv = _mm256_load_pd(&extEV[j][20 * k + 8]);
#ifdef _FMA
vv[2] = FMAMACC(vv[2],x1px2v,extEvv);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[8],vv[2]);
extEvv = _mm256_load_pd(&extEV[j][20 * k + 12]);
#ifdef _FMA
vv[3] = FMAMACC(vv[3],x1px2v,extEvv);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[12],vv[3]);
extEvv = _mm256_load_pd(&extEV[j][20 * k + 16]);
#ifdef _FMA
vv[4] = FMAMACC(vv[4],x1px2v,extEvv);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
}
}
break;
case TIP_INNER:
{
double
umpX1[1840] __attribute__ ((aligned (BYTE_ALIGNMENT))),
ump_x2[20] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for(i = 0; i < 23; i++)
{
for(k = 0; k < 80; k++)
{
__m256d umpX1v = _mm256_setzero_pd();
v = &(tipVector[k / 20][20 * i]);
for(l = 0; l < 20; l+=4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d leftv = _mm256_load_pd(&left[k * 20 + l]);
#ifdef _FMA
umpX1v = FMAMACC(umpX1v, vv, leftv);
#else
umpX1v = _mm256_add_pd(umpX1v, _mm256_mul_pd(vv, leftv));
#endif
}
umpX1v = hadd3(umpX1v);
_mm256_maskstore_pd(&umpX1[80 * i + k], bitmask, umpX1v);
}
}
for (i = 0; i < n; i++)
{
uX1 = &umpX1[80 * tipX1[i]];
for(k = 0; k < 4; k++)
{
v = &(x2[80 * i + k * 20]);
for(l = 0; l < 20; l++)
{
__m256d ump_x2v = _mm256_setzero_pd();
__m256d vv = _mm256_load_pd(&v[0]);
__m256d rightv = _mm256_load_pd(&right[k*400+l*20+0]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[4]);
rightv = _mm256_load_pd(&right[k*400+l*20+4]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[8]);
rightv = _mm256_load_pd(&right[k*400+l*20+8]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[12]);
rightv = _mm256_load_pd(&right[k*400+l*20+12]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[16]);
rightv = _mm256_load_pd(&right[k*400+l*20+16]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
ump_x2v = hadd3(ump_x2v);
_mm256_maskstore_pd(&ump_x2[l], bitmask, ump_x2v);
}
v = &(x3[80 * i + 20 * k]);
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
x1px2 = uX1[k * 20 + l] * ump_x2[l];
__m256d x1px2v = _mm256_set1_pd(x1px2);
#ifdef _FMA
__m256d ev = _mm256_load_pd(&extEV[k][l * 20 + 0]);
vv[0] = FMAMACC(vv[0],x1px2v, ev);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[k][l * 20 + 0])));
#endif
_mm256_store_pd(&v[0],vv[0]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[k][l * 20 + 4]);
vv[1] = FMAMACC(vv[1],x1px2v, ev);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[k][l * 20 + 4])));
#endif
_mm256_store_pd(&v[4],vv[1]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[k][l * 20 + 8]);
vv[2] = FMAMACC(vv[2],x1px2v, ev);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[k][l * 20 + 8])));
#endif
_mm256_store_pd(&v[8],vv[2]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[k][l * 20 + 12]);
vv[3] = FMAMACC(vv[3],x1px2v, ev);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[k][l * 20 + 12])));
#endif
_mm256_store_pd(&v[12],vv[3]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[k][l * 20 + 16]);
vv[4] = FMAMACC(vv[4],x1px2v, ev);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[k][l * 20 + 16])));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
v = &x3[80 * i];
__m256d minlikelihood_avx = _mm256_set1_pd(minlikelihood);
scale = 1;
for(l = 0; scale && (l < 80); l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d vv_abs = _mm256_and_pd(vv,absMask_AVX.m);
vv_abs = _mm256_cmp_pd(vv_abs,minlikelihood_avx,_CMP_LT_OS);
if(_mm256_movemask_pd(vv_abs) != 15)
scale = 0;
}
if(scale)
{
__m256d twotothe256v = _mm256_set_pd(twotothe256,twotothe256,twotothe256,twotothe256);
for(l = 0; l < 80; l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
_mm256_store_pd(&v[l],_mm256_mul_pd(vv,twotothe256v));
}
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
}
break;
case INNER_INNER:
for(i = 0; i < n; i++)
{
scale = 1;
for(k = 0; k < 4; k++)
{
vl = &(x1[80 * i + 20 * k]);
vr = &(x2[80 * i + 20 * k]);
v = &(x3[80 * i + 20 * k]);
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d al = _mm256_setzero_pd();
__m256d ar = _mm256_setzero_pd();
__m256d leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 0]);
__m256d rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 0]);
__m256d vlv = _mm256_load_pd(&vl[0]);
__m256d vrv = _mm256_load_pd(&vr[0]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 4]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 4]);
vlv = _mm256_load_pd(&vl[4]);
vrv = _mm256_load_pd(&vr[4]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 8]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 8]);
vlv = _mm256_load_pd(&vl[8]);
vrv = _mm256_load_pd(&vr[8]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 12]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 12]);
vlv = _mm256_load_pd(&vl[12]);
vrv = _mm256_load_pd(&vr[12]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 16]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 16]);
vlv = _mm256_load_pd(&vl[16]);
vrv = _mm256_load_pd(&vr[16]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
/**************************************************************************************************************/
al = hadd3(al);
ar = hadd3(ar);
al = _mm256_mul_pd(ar,al);
/************************************************************************************************************/
#ifdef _FMA
__m256d ev = _mm256_load_pd(&extEV[k][20 * l + 0]);
vv[0] = FMAMACC(vv[0], al, ev);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(al, _mm256_load_pd(&extEV[k][20 * l + 0])));
#endif
_mm256_store_pd(&v[0],vv[0]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[k][20 * l + 4]);
vv[1] = FMAMACC(vv[1], al, ev);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(al, _mm256_load_pd(&extEV[k][20 * l + 4])));
#endif
_mm256_store_pd(&v[4],vv[1]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[k][20 * l + 8]);
vv[2] = FMAMACC(vv[2], al, ev);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(al, _mm256_load_pd(&extEV[k][20 * l + 8])));
#endif
_mm256_store_pd(&v[8],vv[2]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[k][20 * l + 12]);
vv[3] = FMAMACC(vv[3], al, ev);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(al, _mm256_load_pd(&extEV[k][20 * l + 12])));
#endif
_mm256_store_pd(&v[12],vv[3]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[k][20 * l + 16]);
vv[4] = FMAMACC(vv[4], al, ev);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(al, _mm256_load_pd(&extEV[k][20 * l + 16])));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
v = &(x3[80 * i]);
scale = 1;
__m256d minlikelihood_avx = _mm256_set1_pd(minlikelihood);
for(l = 0; scale && (l < 80); l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d vv_abs = _mm256_and_pd(vv,absMask_AVX.m);
vv_abs = _mm256_cmp_pd(vv_abs,minlikelihood_avx,_CMP_LT_OS);
if(_mm256_movemask_pd(vv_abs) != 15)
scale = 0;
}
if(scale)
{
__m256d twotothe256v = _mm256_set_pd(twotothe256,twotothe256,twotothe256,twotothe256);
for(l = 0; l < 80; l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
_mm256_store_pd(&v[l],_mm256_mul_pd(vv,twotothe256v));
}
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
break;
default:
assert(0);
}
if(useFastScaling)
*scalerIncrement = addScale;
}
void newviewGTRGAMMAPROT_AVX_GAPPED_SAVE(int tipCase,
double *x1_start, double *x2_start, double *x3_start, double *extEV, double *tipVector,
int *ex3, unsigned char *tipX1, unsigned char *tipX2, int n,
double *left, double *right, int *wgt, int *scalerIncrement, const boolean useFastScaling,
unsigned int *x1_gap, unsigned int *x2_gap, unsigned int *x3_gap,
double *x1_gapColumn, double *x2_gapColumn, double *x3_gapColumn)
{
double
*x1 = x1_start,
*x2 = x2_start,
*x3_ptr = x3_start,
*x2_ptr = x2_start,
*x1_ptr = x1_start,
*uX1,
*uX2,
*v,
x1px2,
*vl,
*vr;
int
i,
j,
l,
k,
gapScaling = 0,
scale,
addScale = 0;
#ifndef GCC_VERSION
#define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#endif
#if GCC_VERSION < 40500
__m256d
bitmask = _mm256_set_pd(0,0,0,-1);
#else
__m256i
bitmask = _mm256_set_epi32(0, 0, 0, 0, 0, 0, -1, -1);
#endif
switch(tipCase)
{
case TIP_TIP:
{
double
umpX1[1840] __attribute__ ((aligned (BYTE_ALIGNMENT))),
umpX2[1840] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for(i = 0; i < 23; i++)
{
v = &(tipVector[20 * i]);
for(k = 0; k < 80; k++)
{
double
*ll = &left[k * 20],
*rr = &right[k * 20];
__m256d
umpX1v = _mm256_setzero_pd(),
umpX2v = _mm256_setzero_pd();
for(l = 0; l < 20; l+=4)
{
__m256d vv = _mm256_load_pd(&v[l]);
#ifdef _FMA
__m256d llv = _mm256_load_pd(&ll[l]);
umpX1v = FMAMACC(umpX1v,vv,llv);
__m256d rrv = _mm256_load_pd(&rr[l]);
umpX2v = FMAMACC(umpX2v,vv,rrv);
#else
umpX1v = _mm256_add_pd(umpX1v,_mm256_mul_pd(vv,_mm256_load_pd(&ll[l])));
umpX2v = _mm256_add_pd(umpX2v,_mm256_mul_pd(vv,_mm256_load_pd(&rr[l])));
#endif
}
umpX1v = hadd3(umpX1v);
umpX2v = hadd3(umpX2v);
_mm256_maskstore_pd(&umpX1[80 * i + k], bitmask, umpX1v);
_mm256_maskstore_pd(&umpX2[80 * i + k], bitmask, umpX2v);
}
}
{
uX1 = &umpX1[1760];
uX2 = &umpX2[1760];
for(j = 0; j < 4; j++)
{
__m256d vv[5];
v = &x3_gapColumn[j * 20];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(k = 0; k < 20; k++)
{
x1px2 = uX1[j * 20 + k] * uX2[j * 20 + k];
__m256d x1px2v = _mm256_set1_pd(x1px2);
__m256d extEvv = _mm256_load_pd(&extEV[20 * k]);
#ifdef _FMA
vv[0] = FMAMACC(vv[0],x1px2v,extEvv);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[0],vv[0]);
extEvv = _mm256_load_pd(&extEV[20 * k + 4]);
#ifdef _FMA
vv[1] = FMAMACC(vv[1],x1px2v,extEvv);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[4],vv[1]);
extEvv = _mm256_load_pd(&extEV[20 * k + 8]);
#ifdef _FMA
vv[2] = FMAMACC(vv[2],x1px2v,extEvv);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[8],vv[2]);
extEvv = _mm256_load_pd(&extEV[20 * k + 12]);
#ifdef _FMA
vv[3] = FMAMACC(vv[3],x1px2v,extEvv);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[12],vv[3]);
extEvv = _mm256_load_pd(&extEV[20 * k + 16]);
#ifdef _FMA
vv[4] = FMAMACC(vv[4],x1px2v,extEvv);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
}
for(i = 0; i < n; i++)
{
if(!(x3_gap[i / 32] & mask32[i % 32]))
{
uX1 = &umpX1[80 * tipX1[i]];
uX2 = &umpX2[80 * tipX2[i]];
for(j = 0; j < 4; j++)
{
__m256d vv[5];
v = &x3_ptr[j * 20];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(k = 0; k < 20; k++)
{
x1px2 = uX1[j * 20 + k] * uX2[j * 20 + k];
__m256d x1px2v = _mm256_set1_pd(x1px2);
__m256d extEvv = _mm256_load_pd(&extEV[20 * k]);
#ifdef _FMA
vv[0] = FMAMACC(vv[0],x1px2v,extEvv);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[0],vv[0]);
extEvv = _mm256_load_pd(&extEV[20 * k + 4]);
#ifdef _FMA
vv[1] = FMAMACC(vv[1],x1px2v,extEvv);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[4],vv[1]);
extEvv = _mm256_load_pd(&extEV[20 * k + 8]);
#ifdef _FMA
vv[2] = FMAMACC(vv[2],x1px2v,extEvv);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[8],vv[2]);
extEvv = _mm256_load_pd(&extEV[20 * k + 12]);
#ifdef _FMA
vv[3] = FMAMACC(vv[3],x1px2v,extEvv);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[12],vv[3]);
extEvv = _mm256_load_pd(&extEV[20 * k + 16]);
#ifdef _FMA
vv[4] = FMAMACC(vv[4],x1px2v,extEvv);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(x1px2v,extEvv));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
x3_ptr += 80;
}
}
}
break;
case TIP_INNER:
{
double
umpX1[1840] __attribute__ ((aligned (BYTE_ALIGNMENT))),
ump_x2[20] __attribute__ ((aligned (BYTE_ALIGNMENT)));
for(i = 0; i < 23; i++)
{
v = &(tipVector[20 * i]);
for(k = 0; k < 80; k++)
{
__m256d umpX1v = _mm256_setzero_pd();
for(l = 0; l < 20; l+=4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d leftv = _mm256_load_pd(&left[k * 20 + l]);
#ifdef _FMA
umpX1v = FMAMACC(umpX1v, vv, leftv);
#else
umpX1v = _mm256_add_pd(umpX1v, _mm256_mul_pd(vv, leftv));
#endif
}
umpX1v = hadd3(umpX1v);
_mm256_maskstore_pd(&umpX1[80 * i + k], bitmask, umpX1v);
}
}
{
uX1 = &umpX1[1760];
for(k = 0; k < 4; k++)
{
v = &(x2_gapColumn[k * 20]);
for(l = 0; l < 20; l++)
{
__m256d ump_x2v = _mm256_setzero_pd();
__m256d vv = _mm256_load_pd(&v[0]);
__m256d rightv = _mm256_load_pd(&right[k*400+l*20+0]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[4]);
rightv = _mm256_load_pd(&right[k*400+l*20+4]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[8]);
rightv = _mm256_load_pd(&right[k*400+l*20+8]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[12]);
rightv = _mm256_load_pd(&right[k*400+l*20+12]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[16]);
rightv = _mm256_load_pd(&right[k*400+l*20+16]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
ump_x2v = hadd3(ump_x2v);
_mm256_maskstore_pd(&ump_x2[l], bitmask, ump_x2v);
}
v = &x3_gapColumn[20 * k];
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
x1px2 = uX1[k * 20 + l] * ump_x2[l];
__m256d x1px2v = _mm256_set1_pd(x1px2);
#ifdef _FMA
__m256d ev = _mm256_load_pd(&extEV[l * 20 + 0]);
vv[0] = FMAMACC(vv[0],x1px2v, ev);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 0])));
#endif
_mm256_store_pd(&v[0],vv[0]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 4]);
vv[1] = FMAMACC(vv[1],x1px2v, ev);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 4])));
#endif
_mm256_store_pd(&v[4],vv[1]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 8]);
vv[2] = FMAMACC(vv[2],x1px2v, ev);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 8])));
#endif
_mm256_store_pd(&v[8],vv[2]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 12]);
vv[3] = FMAMACC(vv[3],x1px2v, ev);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 12])));
#endif
_mm256_store_pd(&v[12],vv[3]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 16]);
vv[4] = FMAMACC(vv[4],x1px2v, ev);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 16])));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
v = x3_gapColumn;
__m256d minlikelihood_avx = _mm256_set1_pd(minlikelihood);
scale = 1;
for(l = 0; scale && (l < 80); l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d vv_abs = _mm256_and_pd(vv,absMask_AVX.m);
vv_abs = _mm256_cmp_pd(vv_abs,minlikelihood_avx,_CMP_LT_OS);
if(_mm256_movemask_pd(vv_abs) != 15)
scale = 0;
}
if(scale)
{
__m256d twotothe256v = _mm256_set_pd(twotothe256,twotothe256,twotothe256,twotothe256);
gapScaling = 1;
for(l = 0; l < 80; l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
_mm256_store_pd(&v[l],_mm256_mul_pd(vv,twotothe256v));
}
}
}
for (i = 0; i < n; i++)
{
if((x3_gap[i / 32] & mask32[i % 32]))
{
if(gapScaling)
{
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
else
{
uX1 = &umpX1[80 * tipX1[i]];
if(x2_gap[i / 32] & mask32[i % 32])
x2 = x2_gapColumn;
else
{
x2 = x2_ptr;
x2_ptr += 80;
}
for(k = 0; k < 4; k++)
{
v = &(x2[k * 20]);
for(l = 0; l < 20; l++)
{
__m256d ump_x2v = _mm256_setzero_pd();
__m256d vv = _mm256_load_pd(&v[0]);
__m256d rightv = _mm256_load_pd(&right[k*400+l*20+0]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[4]);
rightv = _mm256_load_pd(&right[k*400+l*20+4]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[8]);
rightv = _mm256_load_pd(&right[k*400+l*20+8]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[12]);
rightv = _mm256_load_pd(&right[k*400+l*20+12]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
vv = _mm256_load_pd(&v[16]);
rightv = _mm256_load_pd(&right[k*400+l*20+16]);
#ifdef _FMA
ump_x2v = FMAMACC(ump_x2v,vv,rightv);
#else
ump_x2v = _mm256_add_pd(ump_x2v, _mm256_mul_pd(vv, rightv));
#endif
ump_x2v = hadd3(ump_x2v);
_mm256_maskstore_pd(&ump_x2[l], bitmask, ump_x2v);
}
v = &x3_ptr[k * 20];
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
x1px2 = uX1[k * 20 + l] * ump_x2[l];
__m256d x1px2v = _mm256_set1_pd(x1px2);
#ifdef _FMA
__m256d ev = _mm256_load_pd(&extEV[l * 20 + 0]);
vv[0] = FMAMACC(vv[0],x1px2v, ev);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 0])));
#endif
_mm256_store_pd(&v[0],vv[0]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 4]);
vv[1] = FMAMACC(vv[1],x1px2v, ev);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 4])));
#endif
_mm256_store_pd(&v[4],vv[1]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 8]);
vv[2] = FMAMACC(vv[2],x1px2v, ev);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 8])));
#endif
_mm256_store_pd(&v[8],vv[2]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 12]);
vv[3] = FMAMACC(vv[3],x1px2v, ev);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 12])));
#endif
_mm256_store_pd(&v[12],vv[3]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[l * 20 + 16]);
vv[4] = FMAMACC(vv[4],x1px2v, ev);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(x1px2v, _mm256_load_pd(&extEV[l * 20 + 16])));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
v = x3_ptr;
__m256d minlikelihood_avx = _mm256_set1_pd(minlikelihood);
scale = 1;
for(l = 0; scale && (l < 80); l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d vv_abs = _mm256_and_pd(vv,absMask_AVX.m);
vv_abs = _mm256_cmp_pd(vv_abs,minlikelihood_avx,_CMP_LT_OS);
if(_mm256_movemask_pd(vv_abs) != 15)
scale = 0;
}
if(scale)
{
__m256d twotothe256v = _mm256_set_pd(twotothe256,twotothe256,twotothe256,twotothe256);
for(l = 0; l < 80; l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
_mm256_store_pd(&v[l],_mm256_mul_pd(vv,twotothe256v));
}
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
x3_ptr += 80;
}
}
}
break;
case INNER_INNER:
for(k = 0; k < 4; k++)
{
vl = &(x1_gapColumn[20 * k]);
vr = &(x2_gapColumn[20 * k]);
v = &(x3_gapColumn[20 * k]);
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d al = _mm256_setzero_pd();
__m256d ar = _mm256_setzero_pd();
__m256d leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 0]);
__m256d rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 0]);
__m256d vlv = _mm256_load_pd(&vl[0]);
__m256d vrv = _mm256_load_pd(&vr[0]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 4]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 4]);
vlv = _mm256_load_pd(&vl[4]);
vrv = _mm256_load_pd(&vr[4]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 8]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 8]);
vlv = _mm256_load_pd(&vl[8]);
vrv = _mm256_load_pd(&vr[8]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 12]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 12]);
vlv = _mm256_load_pd(&vl[12]);
vrv = _mm256_load_pd(&vr[12]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 16]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 16]);
vlv = _mm256_load_pd(&vl[16]);
vrv = _mm256_load_pd(&vr[16]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
/**************************************************************************************************************/
al = hadd3(al);
ar = hadd3(ar);
al = _mm256_mul_pd(ar,al);
/************************************************************************************************************/
#ifdef _FMA
__m256d ev = _mm256_load_pd(&extEV[20 * l + 0]);
vv[0] = FMAMACC(vv[0], al, ev);
#else
vv[0] = _mm256_add_pd(vv[0],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 0])));
#endif
_mm256_store_pd(&v[0],vv[0]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[20 * l + 4]);
vv[1] = FMAMACC(vv[1], al, ev);
#else
vv[1] = _mm256_add_pd(vv[1],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 4])));
#endif
_mm256_store_pd(&v[4],vv[1]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[20 * l + 8]);
vv[2] = FMAMACC(vv[2], al, ev);
#else
vv[2] = _mm256_add_pd(vv[2],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 8])));
#endif
_mm256_store_pd(&v[8],vv[2]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[20 * l + 12]);
vv[3] = FMAMACC(vv[3], al, ev);
#else
vv[3] = _mm256_add_pd(vv[3],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 12])));
#endif
_mm256_store_pd(&v[12],vv[3]);
#ifdef _FMA
ev = _mm256_load_pd(&extEV[20 * l + 16]);
vv[4] = FMAMACC(vv[4], al, ev);
#else
vv[4] = _mm256_add_pd(vv[4],_mm256_mul_pd(al, _mm256_load_pd(&extEV[20 * l + 16])));
#endif
_mm256_store_pd(&v[16],vv[4]);
}
}
v = x3_gapColumn;
scale = 1;
__m256d minlikelihood_avx = _mm256_set1_pd(minlikelihood);
for(l = 0; scale && (l < 80); l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
__m256d vv_abs = _mm256_and_pd(vv,absMask_AVX.m);
vv_abs = _mm256_cmp_pd(vv_abs,minlikelihood_avx,_CMP_LT_OS);
if(_mm256_movemask_pd(vv_abs) != 15)
scale = 0;
}
if(scale)
{
__m256d twotothe256v = _mm256_set_pd(twotothe256,twotothe256,twotothe256,twotothe256);
gapScaling = 1;
for(l = 0; l < 80; l += 4)
{
__m256d vv = _mm256_load_pd(&v[l]);
_mm256_store_pd(&v[l],_mm256_mul_pd(vv,twotothe256v));
}
}
for(i = 0; i < n; i++)
{
if(x3_gap[i / 32] & mask32[i % 32])
{
if(gapScaling)
{
if(useFastScaling)
addScale += wgt[i];
else
ex3[i] += 1;
}
}
else
{
if(x1_gap[i / 32] & mask32[i % 32])
x1 = x1_gapColumn;
else
{
x1 = x1_ptr;
x1_ptr += 80;
}
if(x2_gap[i / 32] & mask32[i % 32])
x2 = x2_gapColumn;
else
{
x2 = x2_ptr;
x2_ptr += 80;
}
for(k = 0; k < 4; k++)
{
vl = &(x1[20 * k]);
vr = &(x2[20 * k]);
v = &(x3_ptr[20 * k]);
__m256d vv[5];
vv[0] = _mm256_setzero_pd();
vv[1] = _mm256_setzero_pd();
vv[2] = _mm256_setzero_pd();
vv[3] = _mm256_setzero_pd();
vv[4] = _mm256_setzero_pd();
for(l = 0; l < 20; l++)
{
__m256d al = _mm256_setzero_pd();
__m256d ar = _mm256_setzero_pd();
__m256d leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 0]);
__m256d rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 0]);
__m256d vlv = _mm256_load_pd(&vl[0]);
__m256d vrv = _mm256_load_pd(&vr[0]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 4]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 4]);
vlv = _mm256_load_pd(&vl[4]);
vrv = _mm256_load_pd(&vr[4]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 8]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 8]);
vlv = _mm256_load_pd(&vl[8]);
vrv = _mm256_load_pd(&vr[8]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 12]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 12]);
vlv = _mm256_load_pd(&vl[12]);
vrv = _mm256_load_pd(&vr[12]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));
ar = _mm256_add_pd(ar,_mm256_mul_pd(vrv,rightv));
#endif
leftv = _mm256_load_pd(&left[k * 400 + l * 20 + 16]);
rightv = _mm256_load_pd(&right[k * 400 + l * 20 + 16]);
vlv = _mm256_load_pd(&vl[16]);
vrv = _mm256_load_pd(&vr[16]);
#ifdef _FMA
al = FMAMACC(al, vlv, leftv);
ar = FMAMACC(ar, vrv, rightv);
#else
al = _mm256_add_pd(al,_mm256_mul_pd(vlv,leftv));