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makenewzGenericSpecial.c
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makenewzGenericSpecial.c
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/* RAxML-VI-HPC (version 2.2) a program for sequential and parallel estimation of phylogenetic trees
* Copyright August 2006 by Alexandros Stamatakis
*
* Partially derived from
* fastDNAml, a program for estimation of phylogenetic trees from sequences by Gary J. Olsen
*
* and
*
* Programs of the PHYLIP package by Joe Felsenstein.
*
* This program is free software; you may redistribute it and/or modify its
* under the terms of the GNU General Public License as published by the Free
* Software Foundation; either version 2 of the License, or (at your option)
* any later version.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
* for more details.
*
*
* For any other enquiries send an Email to Alexandros Stamatakis
* Alexandros.Stamatakis@epfl.ch
*
* When publishing work that is based on the results from RAxML-VI-HPC please cite:
*
* Alexandros Stamatakis:"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
* thousands of taxa and mixed models".
* Bioinformatics 2006; doi: 10.1093/bioinformatics/btl446
*/
#ifndef WIN32
#include <unistd.h>
#endif
#include <math.h>
#include <time.h>
#include <stdlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include "axml.h"
#ifdef __SIM_SSE3
#include <xmmintrin.h>
#include <pmmintrin.h>
/*#include <tmmintrin.h>*/
#endif
#ifdef _USE_PTHREADS
extern volatile double *reductionBuffer;
extern volatile double *reductionBufferTwo;
extern volatile int NumberOfThreads;
#endif
#ifdef _FINE_GRAIN_MPI
extern double *globalResult;
#endif
extern const unsigned int mask32[32];
/*******************/
static inline boolean isGap(unsigned int *x, int pos)
{
return (x[pos / 32] & mask32[pos % 32]);
}
static void coreGTRGAMMAPROT_perSite(siteAAModels *siteProtModel, int* perSiteAA, double *gammaRates, double *sumtable, int upper, int *wrptr,
volatile double *ext_dlnLdlz, volatile double *ext_d2lnLdlz2, double lz)
{
double
*sum,
diagptable0[80 * (NUM_PROT_MODELS - 2)] __attribute__ ((aligned (BYTE_ALIGNMENT))),
diagptable1[80 * (NUM_PROT_MODELS - 2)] __attribute__ ((aligned (BYTE_ALIGNMENT))),
diagptable2[80 * (NUM_PROT_MODELS - 2)] __attribute__ ((aligned (BYTE_ALIGNMENT))),
*d0,
*d1,
*d2;
int i, j, l, p;
double dlnLdlz = 0;
double d2lnLdlz2 = 0;
double ki, kisqr;
double inv_Li, dlnLidlz, d2lnLidlz2;
for(p = 0; p < (NUM_PROT_MODELS - 2); p++)
{
double
*d0 = &diagptable0[80 * p],
*d1 = &diagptable1[80 * p],
*d2 = &diagptable2[80 * p],
*EIGN = siteProtModel[p].EIGN;
for(i = 0; i < 4; i++)
{
ki = gammaRates[i];
kisqr = ki * ki;
d0[i * 20] = 1.0;
d1[i * 20] = 0.0;
d2[i * 20] = 0.0;
for(l = 1; l < 20; l++)
{
d0[i * 20 + l] = EXP(EIGN[l-1] * ki * lz);
d1[i * 20 + l] = EIGN[l-1] * ki;
d2[i * 20 + l] = EIGN[l-1] * EIGN[l-1] * kisqr;
}
}
}
for (i = 0; i < upper; i++)
{
__m128d a0 = _mm_setzero_pd();
__m128d a1 = _mm_setzero_pd();
__m128d a2 = _mm_setzero_pd();
d0 = &diagptable0[80 * perSiteAA[i]];
d1 = &diagptable1[80 * perSiteAA[i]];
d2 = &diagptable2[80 * perSiteAA[i]];
sum = &sumtable[i * 80];
for(j = 0; j < 4; j++)
{
double
*_d0 = &d0[j * 20],
*_d1 = &d1[j * 20],
*_d2 = &d2[j * 20];
for(l = 0; l < 20; l+=2)
{
__m128d tmpv = _mm_mul_pd(_mm_load_pd(&_d0[l]), _mm_load_pd(&sum[j * 20 +l]));
a0 = _mm_add_pd(a0, tmpv);
a1 = _mm_add_pd(a1, _mm_mul_pd(tmpv, _mm_load_pd(&_d1[l])));
a2 = _mm_add_pd(a2, _mm_mul_pd(tmpv, _mm_load_pd(&_d2[l])));
}
}
a0 = _mm_hadd_pd(a0, a0);
a1 = _mm_hadd_pd(a1, a1);
a2 = _mm_hadd_pd(a2, a2);
_mm_storel_pd(&inv_Li, a0);
_mm_storel_pd(&dlnLidlz, a1);
_mm_storel_pd(&d2lnLidlz2, a2);
inv_Li = 1.0 / inv_Li;
dlnLidlz *= inv_Li;
d2lnLidlz2 *= inv_Li;
dlnLdlz += wrptr[i] * dlnLidlz;
d2lnLdlz2 += wrptr[i] * (d2lnLidlz2 - dlnLidlz * dlnLidlz);
}
*ext_dlnLdlz = dlnLdlz;
*ext_d2lnLdlz2 = d2lnLdlz2;
}
static void sumGAMMAPROT_perSite(int *perSiteAA,
siteAAModels *siteProtModel,
int tipCase, double *sumtable, double *x1, double *x2,
unsigned char *tipX1, unsigned char *tipX2, int n)
{
int i, l, k;
double *left, *right, *sum;
switch(tipCase)
{
case TIP_TIP:
for(i = 0; i < n; i++)
{
double
*tipVector = siteProtModel[perSiteAA[i]].tipVector;
left = &(tipVector[20 * tipX1[i]]);
right = &(tipVector[20 * tipX2[i]]);
for(l = 0; l < 4; l++)
{
sum = &sumtable[i * 80 + l * 20];
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
}
}
break;
case TIP_INNER:
for(i = 0; i < n; i++)
{
double
*tipVector = siteProtModel[perSiteAA[i]].tipVector;
left = &(tipVector[20 * tipX1[i]]);
for(l = 0; l < 4; l++)
{
right = &(x2[80 * i + l * 20]);
sum = &sumtable[i * 80 + l * 20];
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
}
}
break;
case INNER_INNER:
for(i = 0; i < n; i++)
{
for(l = 0; l < 4; l++)
{
left = &(x1[80 * i + l * 20]);
right = &(x2[80 * i + l * 20]);
sum = &(sumtable[i * 80 + l * 20]);
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
}
}
break;
default:
assert(0);
}
}
static void sumCAT_SAVE(int tipCase, double *sum, double *x1_start, double *x2_start, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n, double *x1_gapColumn, double *x2_gapColumn, unsigned int *x1_gap, unsigned int *x2_gap)
{
int i;
double
*x1,
*x2,
*x1_ptr = x1_start,
*x2_ptr = x2_start;
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &(tipVector[4 * tipX2[i]]);
_mm_store_pd( &sum[i*4 + 0], _mm_mul_pd( _mm_load_pd( &x1[0] ), _mm_load_pd( &x2[0] )));
_mm_store_pd( &sum[i*4 + 2], _mm_mul_pd( _mm_load_pd( &x1[2] ), _mm_load_pd( &x2[2] )));
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
if(isGap(x2_gap, i))
x2 = x2_gapColumn;
else
{
x2 = x2_ptr;
x2_ptr += 4;
}
_mm_store_pd( &sum[i*4 + 0], _mm_mul_pd( _mm_load_pd( &x1[0] ), _mm_load_pd( &x2[0] )));
_mm_store_pd( &sum[i*4 + 2], _mm_mul_pd( _mm_load_pd( &x1[2] ), _mm_load_pd( &x2[2] )));
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
if(isGap(x1_gap, i))
x1 = x1_gapColumn;
else
{
x1 = x1_ptr;
x1_ptr += 4;
}
if(isGap(x2_gap, i))
x2 = x2_gapColumn;
else
{
x2 = x2_ptr;
x2_ptr += 4;
}
_mm_store_pd( &sum[i*4 + 0], _mm_mul_pd( _mm_load_pd( &x1[0] ), _mm_load_pd( &x2[0] )));
_mm_store_pd( &sum[i*4 + 2], _mm_mul_pd( _mm_load_pd( &x1[2] ), _mm_load_pd( &x2[2] )));
}
break;
default:
assert(0);
}
}
static void sumGAMMA_GAPPED_SAVE(int tipCase, double *sumtable, double *x1_start, double *x2_start, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n,
double *x1_gapColumn, double *x2_gapColumn, unsigned int *x1_gap, unsigned int *x2_gap)
{
double
*x1,
*x2,
*sum,
*x1_ptr = x1_start,
*x2_ptr = x2_start;
int i, j, k;
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &(tipVector[4 * tipX2[i]]);
sum = &sumtable[i * 16];
#ifndef __SIM_SSE3
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k++)
sum[j * 4 + k] = x1[k] * x2[k];
#else
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k+=2)
_mm_store_pd( &sum[j*4 + k], _mm_mul_pd( _mm_load_pd( &x1[k] ), _mm_load_pd( &x2[k] )));
#endif
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
if(x2_gap[i / 32] & mask32[i % 32])
x2 = x2_gapColumn;
else
{
x2 = x2_ptr;
x2_ptr += 16;
}
sum = &sumtable[16 * i];
#ifndef __SIM_SSE3
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k++)
sum[j * 4 + k] = x1[k] * x2[j * 4 + k];
#else
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k+=2)
_mm_store_pd( &sum[j*4 + k], _mm_mul_pd( _mm_load_pd( &x1[k] ), _mm_load_pd( &x2[j * 4 + k] )));
#endif
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
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;
}
sum = &sumtable[16 * i];
#ifndef __SIM_SSE3
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k++)
sum[j * 4 + k] = x1[j * 4 + k] * x2[j * 4 + k];
#else
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k+=2)
_mm_store_pd( &sum[j*4 + k], _mm_mul_pd( _mm_load_pd( &x1[j * 4 + k] ), _mm_load_pd( &x2[j * 4 + k] )));
#endif
}
break;
default:
assert(0);
}
}
static void sumGAMMA(int tipCase, double *sumtable, double *x1_start, double *x2_start, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n)
{
double *x1, *x2, *sum;
int i, j, k;
/* C-OPT once again switch over possible configurations at inner node */
switch(tipCase)
{
case TIP_TIP:
/* C-OPT main for loop overt alignment length */
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &(tipVector[4 * tipX2[i]]);
sum = &sumtable[i * 16];
#ifndef __SIM_SSE3
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k++)
sum[j * 4 + k] = x1[k] * x2[k];
#else
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k+=2)
_mm_store_pd( &sum[j*4 + k], _mm_mul_pd( _mm_load_pd( &x1[k] ), _mm_load_pd( &x2[k] )));
#endif
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &x2_start[16 * i];
sum = &sumtable[16 * i];
#ifndef __SIM_SSE3
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k++)
sum[j * 4 + k] = x1[k] * x2[j * 4 + k];
#else
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k+=2)
_mm_store_pd( &sum[j*4 + k], _mm_mul_pd( _mm_load_pd( &x1[k] ), _mm_load_pd( &x2[j * 4 + k] )));
#endif
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
x1 = &x1_start[16 * i];
x2 = &x2_start[16 * i];
sum = &sumtable[16 * i];
#ifndef __SIM_SSE3
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k++)
sum[j * 4 + k] = x1[j * 4 + k] * x2[j * 4 + k];
#else
for(j = 0; j < 4; j++)
for(k = 0; k < 4; k+=2)
_mm_store_pd( &sum[j*4 + k], _mm_mul_pd( _mm_load_pd( &x1[j * 4 + k] ), _mm_load_pd( &x2[j * 4 + k] )));
#endif
}
break;
default:
assert(0);
}
}
static void sumCAT(int tipCase, double *sum, double *x1_start, double *x2_start, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n)
{
int i;
double
*x1,
*x2;
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &(tipVector[4 * tipX2[i]]);
_mm_store_pd( &sum[i*4 + 0], _mm_mul_pd( _mm_load_pd( &x1[0] ), _mm_load_pd( &x2[0] )));
_mm_store_pd( &sum[i*4 + 2], _mm_mul_pd( _mm_load_pd( &x1[2] ), _mm_load_pd( &x2[2] )));
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &x2_start[4 * i];
_mm_store_pd( &sum[i*4 + 0], _mm_mul_pd( _mm_load_pd( &x1[0] ), _mm_load_pd( &x2[0] )));
_mm_store_pd( &sum[i*4 + 2], _mm_mul_pd( _mm_load_pd( &x1[2] ), _mm_load_pd( &x2[2] )));
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
x1 = &x1_start[4 * i];
x2 = &x2_start[4 * i];
_mm_store_pd( &sum[i*4 + 0], _mm_mul_pd( _mm_load_pd( &x1[0] ), _mm_load_pd( &x2[0] )));
_mm_store_pd( &sum[i*4 + 2], _mm_mul_pd( _mm_load_pd( &x1[2] ), _mm_load_pd( &x2[2] )));
}
break;
default:
assert(0);
}
}
static void coreGTRGAMMA(const int upper, double *sumtable,
volatile double *ext_dlnLdlz, volatile double *ext_d2lnLdlz2, double *EIGN, double *gammaRates, double lz, int *wrptr)
{
double
dlnLdlz = 0.0,
d2lnLdlz2 = 0.0,
ki,
kisqr,
inv_Li,
dlnLidlz,
d2lnLidlz2,
*sum,
diagptable0[16] __attribute__ ((aligned (BYTE_ALIGNMENT))),
diagptable1[16] __attribute__ ((aligned (BYTE_ALIGNMENT))),
diagptable2[16] __attribute__ ((aligned (BYTE_ALIGNMENT)));
int
i,
j,
l;
for(i = 0; i < 4; i++)
{
ki = gammaRates[i];
kisqr = ki * ki;
diagptable0[i * 4] = 1.0;
diagptable1[i * 4] = 0.0;
diagptable2[i * 4] = 0.0;
for(l = 1; l < 4; l++)
{
diagptable0[i * 4 + l] = EXP(EIGN[l-1] * ki * lz);
diagptable1[i * 4 + l] = EIGN[l-1] * ki;
diagptable2[i * 4 + l] = EIGN[l-1] * EIGN[l-1] * kisqr;
}
}
for (i = 0; i < upper; i++)
{
__m128d a0 = _mm_setzero_pd();
__m128d a1 = _mm_setzero_pd();
__m128d a2 = _mm_setzero_pd();
sum = &sumtable[i * 16];
for(j = 0; j < 4; j++)
{
double
*d0 = &diagptable0[j * 4],
*d1 = &diagptable1[j * 4],
*d2 = &diagptable2[j * 4];
for(l = 0; l < 4; l+=2)
{
__m128d tmpv = _mm_mul_pd(_mm_load_pd(&d0[l]), _mm_load_pd(&sum[j * 4 + l]));
a0 = _mm_add_pd(a0, tmpv);
a1 = _mm_add_pd(a1, _mm_mul_pd(tmpv, _mm_load_pd(&d1[l])));
a2 = _mm_add_pd(a2, _mm_mul_pd(tmpv, _mm_load_pd(&d2[l])));
}
}
a0 = _mm_hadd_pd(a0, a0);
a1 = _mm_hadd_pd(a1, a1);
a2 = _mm_hadd_pd(a2, a2);
_mm_storel_pd(&inv_Li, a0);
_mm_storel_pd(&dlnLidlz, a1);
_mm_storel_pd(&d2lnLidlz2, a2);
inv_Li = 1.0 / inv_Li;
dlnLidlz *= inv_Li;
d2lnLidlz2 *= inv_Li;
dlnLdlz += wrptr[i] * dlnLidlz;
d2lnLdlz2 += wrptr[i] * (d2lnLidlz2 - dlnLidlz * dlnLidlz);
}
*ext_dlnLdlz = dlnLdlz;
*ext_d2lnLdlz2 = d2lnLdlz2;
}
static void coreGTRCAT(int upper, int numberOfCategories, double *sum,
volatile double *d1, volatile double *d2, double *wrptr, double *wr2ptr,
double *rptr, double *EIGN, int *cptr, double lz)
{
int i;
double
*d, *d_start,
inv_Li, dlnLidlz, d2lnLidlz2,
dlnLdlz = 0.0,
d2lnLdlz2 = 0.0;
double e1[4] __attribute__ ((aligned (BYTE_ALIGNMENT)));
double e2[4] __attribute__ ((aligned (BYTE_ALIGNMENT)));
double dd1, dd2, dd3;
__m128d
e1v[2],
e2v[2];
e1[0] = 0.0;
e2[0] = 0.0;
e1[1] = EIGN[0];
e2[1] = EIGN[0] * EIGN[0];
e1[2] = EIGN[1];
e2[2] = EIGN[1] * EIGN[1];
e1[3] = EIGN[2];
e2[3] = EIGN[2] * EIGN[2];
e1v[0]= _mm_load_pd(&e1[0]);
e1v[1]= _mm_load_pd(&e1[2]);
e2v[0]= _mm_load_pd(&e2[0]);
e2v[1]= _mm_load_pd(&e2[2]);
d = d_start = (double *)malloc_aligned(numberOfCategories * 4 * sizeof(double));
dd1 = EIGN[0] * lz;
dd2 = EIGN[1] * lz;
dd3 = EIGN[2] * lz;
for(i = 0; i < numberOfCategories; i++)
{
d[i * 4 + 0] = 1.0;
d[i * 4 + 1] = EXP(dd1 * rptr[i]);
d[i * 4 + 2] = EXP(dd2 * rptr[i]);
d[i * 4 + 3] = EXP(dd3 * rptr[i]);
}
for (i = 0; i < upper; i++)
{
double *s = &sum[4 * i];
d = &d_start[4 * cptr[i]];
__m128d tmp_0v =_mm_mul_pd(_mm_load_pd(&d[0]),_mm_load_pd(&s[0]));
__m128d tmp_1v =_mm_mul_pd(_mm_load_pd(&d[2]),_mm_load_pd(&s[2]));
__m128d inv_Liv = _mm_add_pd(tmp_0v, tmp_1v);
__m128d dlnLidlzv = _mm_add_pd(_mm_mul_pd(tmp_0v, e1v[0]), _mm_mul_pd(tmp_1v, e1v[1]));
__m128d d2lnLidlz2v = _mm_add_pd(_mm_mul_pd(tmp_0v, e2v[0]), _mm_mul_pd(tmp_1v, e2v[1]));
inv_Liv = _mm_hadd_pd(inv_Liv, inv_Liv);
dlnLidlzv = _mm_hadd_pd(dlnLidlzv, dlnLidlzv);
d2lnLidlz2v = _mm_hadd_pd(d2lnLidlz2v, d2lnLidlz2v);
_mm_storel_pd(&inv_Li, inv_Liv);
_mm_storel_pd(&dlnLidlz, dlnLidlzv);
_mm_storel_pd(&d2lnLidlz2, d2lnLidlz2v);
inv_Li = 1.0/inv_Li;
dlnLidlz *= inv_Li;
d2lnLidlz2 *= inv_Li;
dlnLdlz += wrptr[i] * dlnLidlz;
d2lnLdlz2 += wr2ptr[i] * (d2lnLidlz2 - dlnLidlz * dlnLidlz);
}
*d1 = dlnLdlz;
*d2 = d2lnLdlz2;
free(d_start);
}
static void sumGAMMAPROT_GAPPED_SAVE(int tipCase, double *sumtable, double *x1, double *x2, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n,
double *x1_gapColumn, double *x2_gapColumn, unsigned int *x1_gap, unsigned int *x2_gap)
{
int i, l, k;
double
*left,
*right,
*sum,
*x1_ptr = x1,
*x2_ptr = x2,
*x1v,
*x2v;
switch(tipCase)
{
case TIP_TIP:
for(i = 0; i < n; i++)
{
left = &(tipVector[20 * tipX1[i]]);
right = &(tipVector[20 * tipX2[i]]);
for(l = 0; l < 4; l++)
{
sum = &sumtable[i * 80 + l * 20];
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
}
}
break;
case TIP_INNER:
for(i = 0; i < n; i++)
{
left = &(tipVector[20 * tipX1[i]]);
if(x2_gap[i / 32] & mask32[i % 32])
x2v = x2_gapColumn;
else
{
x2v = x2_ptr;
x2_ptr += 80;
}
for(l = 0; l < 4; l++)
{
right = &(x2v[l * 20]);
sum = &sumtable[i * 80 + l * 20];
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
}
}
break;
case INNER_INNER:
for(i = 0; i < n; i++)
{
if(x1_gap[i / 32] & mask32[i % 32])
x1v = x1_gapColumn;
else
{
x1v = x1_ptr;
x1_ptr += 80;
}
if(x2_gap[i / 32] & mask32[i % 32])
x2v = x2_gapColumn;
else
{
x2v = x2_ptr;
x2_ptr += 80;
}
for(l = 0; l < 4; l++)
{
left = &(x1v[l * 20]);
right = &(x2v[l * 20]);
sum = &(sumtable[i * 80 + l * 20]);
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
}
}
break;
default:
assert(0);
}
}
static void sumGAMMAPROT(int tipCase, double *sumtable, double *x1, double *x2, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n)
{
int i, l, k;
double *left, *right, *sum;
switch(tipCase)
{
case TIP_TIP:
for(i = 0; i < n; i++)
{
left = &(tipVector[20 * tipX1[i]]);
right = &(tipVector[20 * tipX2[i]]);
for(l = 0; l < 4; l++)
{
sum = &sumtable[i * 80 + l * 20];
#ifdef __SIM_SSE3
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
#else
for(k = 0; k < 20; k++)
sum[k] = left[k] * right[k];
#endif
}
}
break;
case TIP_INNER:
for(i = 0; i < n; i++)
{
left = &(tipVector[20 * tipX1[i]]);
for(l = 0; l < 4; l++)
{
right = &(x2[80 * i + l * 20]);
sum = &sumtable[i * 80 + l * 20];
#ifdef __SIM_SSE3
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
#else
for(k = 0; k < 20; k++)
sum[k] = left[k] * right[k];
#endif
}
}
break;
case INNER_INNER:
for(i = 0; i < n; i++)
{
for(l = 0; l < 4; l++)
{
left = &(x1[80 * i + l * 20]);
right = &(x2[80 * i + l * 20]);
sum = &(sumtable[i * 80 + l * 20]);
#ifdef __SIM_SSE3
for(k = 0; k < 20; k+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[k]), _mm_load_pd(&right[k]));
_mm_store_pd(&sum[k], sumv);
}
#else
for(k = 0; k < 20; k++)
sum[k] = left[k] * right[k];
#endif
}
}
break;
default:
assert(0);
}
}
static void sumGTRCATPROT(int tipCase, double *sumtable, double *x1, double *x2, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n)
{
int i, l;
double *sum, *left, *right;
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
left = &(tipVector[20 * tipX1[i]]);
right = &(tipVector[20 * tipX2[i]]);
sum = &sumtable[20 * i];
#ifdef __SIM_SSE3
for(l = 0; l < 20; l+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[l]), _mm_load_pd(&right[l]));
_mm_store_pd(&sum[l], sumv);
}
#else
for(l = 0; l < 20; l++)
sum[l] = left[l] * right[l];
#endif
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
left = &(tipVector[20 * tipX1[i]]);
right = &x2[20 * i];
sum = &sumtable[20 * i];
#ifdef __SIM_SSE3
for(l = 0; l < 20; l+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[l]), _mm_load_pd(&right[l]));
_mm_store_pd(&sum[l], sumv);
}
#else
for(l = 0; l < 20; l++)
sum[l] = left[l] * right[l];
#endif
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
left = &x1[20 * i];
right = &x2[20 * i];
sum = &sumtable[20 * i];
#ifdef __SIM_SSE3
for(l = 0; l < 20; l+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[l]), _mm_load_pd(&right[l]));
_mm_store_pd(&sum[l], sumv);
}
#else
for(l = 0; l < 20; l++)
sum[l] = left[l] * right[l];
#endif
}
break;
default:
assert(0);
}
}
static void sumGTRCATPROT_SAVE(int tipCase, double *sumtable, double *x1, double *x2, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n,
double *x1_gapColumn, double *x2_gapColumn, unsigned int *x1_gap, unsigned int *x2_gap)
{
int
i,
l;
double
*sum,
*left,
*right,
*left_ptr = x1,
*right_ptr = x2;
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
left = &(tipVector[20 * tipX1[i]]);
right = &(tipVector[20 * tipX2[i]]);
sum = &sumtable[20 * i];
for(l = 0; l < 20; l+=2)
{
__m128d sumv = _mm_mul_pd(_mm_load_pd(&left[l]), _mm_load_pd(&right[l]));
_mm_store_pd(&sum[l], sumv);
}
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
left = &(tipVector[20 * tipX1[i]]);
if(isGap(x2_gap, i))
right = x2_gapColumn;
else
{
right = right_ptr;
right_ptr += 20;
}
sum = &sumtable[20 * i];