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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
*
* 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
extern const unsigned int mask32[32];
/*******************/
static void sumCAT_BINARY(int tipCase, double *sum, double *x1_start, double *x2_start, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n)
{
int i;
#ifndef __SIM_SSE3
int j;
#endif
double *x1, *x2;
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[2 * tipX1[i]]);
x2 = &(tipVector[2 * tipX2[i]]);
#ifndef __SIM_SSE3
for(j = 0; j < 2; j++)
sum[i * 2 + j] = x1[j] * x2[j];
#else
_mm_store_pd(&sum[i * 2], _mm_mul_pd( _mm_load_pd(x1), _mm_load_pd(x2)));
#endif
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[2 * tipX1[i]]);
x2 = &x2_start[2 * i];
#ifndef __SIM_SSE3
for(j = 0; j < 2; j++)
sum[i * 2 + j] = x1[j] * x2[j];
#else
_mm_store_pd(&sum[i * 2], _mm_mul_pd( _mm_load_pd(x1), _mm_load_pd(x2)));
#endif
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
x1 = &x1_start[2 * i];
x2 = &x2_start[2 * i];
#ifndef __SIM_SSE3
for(j = 0; j < 2; j++)
sum[i * 2 + j] = x1[j] * x2[j];
#else
_mm_store_pd(&sum[i * 2], _mm_mul_pd( _mm_load_pd(x1), _mm_load_pd(x2)));
#endif
}
break;
default:
assert(0);
}
}
#ifndef __SIM_SSE3
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, j;
double *x1, *x2;
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &(tipVector[4 * tipX2[i]]);
for(j = 0; j < 4; j++)
sum[i * 4 + j] = x1[j] * x2[j];
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
x1 = &(tipVector[4 * tipX1[i]]);
x2 = &x2_start[4 * i];
for(j = 0; j < 4; j++)
sum[i * 4 + j] = x1[j] * x2[j];
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
x1 = &x1_start[4 * i];
x2 = &x2_start[4 * i];
for(j = 0; j < 4; j++)
sum[i * 4 + j] = x1[j] * x2[j];
}
break;
default:
assert(0);
}
}
#else
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 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);
}
}
#endif
static void coreGTRCAT_BINARY(int upper, int numberOfCategories, double *sum,
volatile double *d1, volatile double *d2,
double *rptr, double *EIGN, int *cptr, double lz, int *wgt)
{
int i;
double
*d, *d_start,
tmp_0, inv_Li, dlnLidlz, d2lnLidlz2,
dlnLdlz = 0.0,
d2lnLdlz2 = 0.0;
double e[2];
double dd1;
e[0] = EIGN[0];
e[1] = EIGN[0] * EIGN[0];
d = d_start = (double *)rax_malloc(numberOfCategories * sizeof(double));
dd1 = e[0] * lz;
for(i = 0; i < numberOfCategories; i++)
d[i] = EXP(dd1 * rptr[i]);
for (i = 0; i < upper; i++)
{
double
r = rptr[cptr[i]],
wr1 = r * wgt[i],
wr2 = r * r * wgt[i];
d = &d_start[cptr[i]];
inv_Li = sum[2 * i];
inv_Li += (tmp_0 = d[0] * sum[2 * i + 1]);
inv_Li = 1.0/FABS(inv_Li);
dlnLidlz = tmp_0 * e[0];
d2lnLidlz2 = tmp_0 * e[1];
dlnLidlz *= inv_Li;
d2lnLidlz2 *= inv_Li;
dlnLdlz += wr1 * dlnLidlz;
d2lnLdlz2 += wr2 * (d2lnLidlz2 - dlnLidlz * dlnLidlz);
}
*d1 = dlnLdlz;
*d2 = d2lnLdlz2;
rax_free(d_start);
}
#ifdef __SIM_SSE3
static void coreGTRCAT(int upper, int numberOfCategories, double *sum,
volatile double *d1, volatile double *d2,
double *rptr, double *EIGN, int *cptr, double lz, int *wgt)
{
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 *)rax_malloc(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],
r = rptr[cptr[i]],
wr1 = r * wgt[i],
wr2 = r * r * wgt[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/FABS(inv_Li);
dlnLidlz *= inv_Li;
d2lnLidlz2 *= inv_Li;
dlnLdlz += wr1 * dlnLidlz;
d2lnLdlz2 += wr2 * (d2lnLidlz2 - dlnLidlz * dlnLidlz);
}
*d1 = dlnLdlz;
*d2 = d2lnLdlz2;
rax_free(d_start);
}
#else
static void coreGTRCAT(int upper, int numberOfCategories, double *sum,
volatile double *d1, volatile double *d2,
double *rptr, double *EIGN, int *cptr, double lz, int *wgt)
{
int i;
double
*d, *d_start,
tmp_0, tmp_1, tmp_2, inv_Li, dlnLidlz, d2lnLidlz2,
dlnLdlz = 0.0,
d2lnLdlz2 = 0.0;
double e[6];
double dd1, dd2, dd3;
e[0] = EIGN[0];
e[1] = EIGN[0] * EIGN[0];
e[2] = EIGN[1];
e[3] = EIGN[1] * EIGN[1];
e[4] = EIGN[2];
e[5] = EIGN[2] * EIGN[2];
d = d_start = (double *)rax_malloc(numberOfCategories * 4 * sizeof(double));
dd1 = e[0] * lz;
dd2 = e[2] * lz;
dd3 = e[4] * lz;
for(i = 0; i < numberOfCategories; i++)
{
d[i * 4] = EXP(dd1 * rptr[i]);
d[i * 4 + 1] = EXP(dd2 * rptr[i]);
d[i * 4 + 2] = EXP(dd3 * rptr[i]);
}
for (i = 0; i < upper; i++)
{
double
r = rptr[cptr[i]],
wr1 = r * wgt[i],
wr2 = r * r * wgt[i];
d = &d_start[4 * cptr[i]];
inv_Li = sum[4 * i];
inv_Li += (tmp_0 = d[0] * sum[4 * i + 1]);
inv_Li += (tmp_1 = d[1] * sum[4 * i + 2]);
inv_Li += (tmp_2 = d[2] * sum[4 * i + 3]);
inv_Li = 1.0/FABS(inv_Li);
dlnLidlz = tmp_0 * e[0];
d2lnLidlz2 = tmp_0 * e[1];
dlnLidlz += tmp_1 * e[2];
d2lnLidlz2 += tmp_1 * e[3];
dlnLidlz += tmp_2 * e[4];
d2lnLidlz2 += tmp_2 * e[5];
dlnLidlz *= inv_Li;
d2lnLidlz2 *= inv_Li;
dlnLdlz += wr1 * dlnLidlz;
d2lnLdlz2 += wr2 * (d2lnLidlz2 - dlnLidlz * dlnLidlz);
}
*d1 = dlnLdlz;
*d2 = d2lnLdlz2;
rax_free(d_start);
}
#endif
#ifdef __SIM_SSE3
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];
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 INNER_INNER:
for (i = 0; i < n; i++)
{
if(isGap(x1_gap, i))
left = x1_gapColumn;
else
{
left = left_ptr;
left_ptr += 20;
}
if(isGap(x2_gap, i))
right = x2_gapColumn;
else
{
right = right_ptr;
right_ptr += 20;
}
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;
default:
assert(0);
}
}
#endif
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 sumGTRCATSECONDARY(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[16 * tipX1[i]]);
right = &(tipVector[16 * tipX2[i]]);
sum = &sumtable[16 * i];
for(l = 0; l < 16; l++)
sum[l] = left[l] * right[l];
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
left = &(tipVector[16 * tipX1[i]]);
right = &x2[16 * i];
sum = &sumtable[16 * i];
for(l = 0; l < 16; l++)
sum[l] = left[l] * right[l];
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
left = &x1[16 * i];
right = &x2[16 * i];
sum = &sumtable[16 * i];
for(l = 0; l < 16; l++)
sum[l] = left[l] * right[l];
}
break;
default:
assert(0);
}
}
static void sumCatFlex(int tipCase, double *sumtable, double *x1, double *x2, double *tipVector,
unsigned char *tipX1, unsigned char *tipX2, int n, const int numStates)
{
int i, l;
double *sum, *left, *right;
switch(tipCase)
{
case TIP_TIP:
for (i = 0; i < n; i++)
{
left = &(tipVector[numStates * tipX1[i]]);
right = &(tipVector[numStates * tipX2[i]]);
sum = &sumtable[numStates * i];
for(l = 0; l < numStates; l++)
sum[l] = left[l] * right[l];
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
left = &(tipVector[numStates * tipX1[i]]);
right = &x2[numStates * i];
sum = &sumtable[numStates * i];
for(l = 0; l < numStates; l++)
sum[l] = left[l] * right[l];
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
left = &x1[numStates * i];
right = &x2[numStates * i];
sum = &sumtable[numStates * i];
for(l = 0; l < numStates; l++)
sum[l] = left[l] * right[l];
}
break;
default:
assert(0);
}
}
static void sumGTRCATSECONDARY_6(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[6 * tipX1[i]]);
right = &(tipVector[6 * tipX2[i]]);
sum = &sumtable[6 * i];
for(l = 0; l < 6; l++)
sum[l] = left[l] * right[l];
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
left = &(tipVector[6 * tipX1[i]]);
right = &x2[6 * i];
sum = &sumtable[6 * i];
for(l = 0; l < 6; l++)
sum[l] = left[l] * right[l];
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
left = &x1[6 * i];
right = &x2[6 * i];
sum = &sumtable[6 * i];
for(l = 0; l < 6; l++)
sum[l] = left[l] * right[l];
}
break;
default:
assert(0);
}
}
static void sumGTRCATSECONDARY_7(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[7 * tipX1[i]]);
right = &(tipVector[7 * tipX2[i]]);
sum = &sumtable[7 * i];
for(l = 0; l < 7; l++)
sum[l] = left[l] * right[l];
}
break;
case TIP_INNER:
for (i = 0; i < n; i++)
{
left = &(tipVector[7 * tipX1[i]]);
right = &x2[7 * i];
sum = &sumtable[7 * i];
for(l = 0; l < 7; l++)
sum[l] = left[l] * right[l];
}
break;
case INNER_INNER:
for (i = 0; i < n; i++)
{
left = &x1[7 * i];
right = &x2[7 * i];
sum = &sumtable[7 * i];
for(l = 0; l < 7; l++)
sum[l] = left[l] * right[l];
}
break;
default:
assert(0);
}
}
#ifdef __SIM_SSE3
static void coreGTRCATPROT(double *EIGN, double lz, int numberOfCategories, double *rptr, int *cptr, int upper,
volatile double *ext_dlnLdlz, volatile double *ext_d2lnLdlz2, double *sumtable, int *wgt)
{
int i, l;
double *d1, *d_start, *sum;
double
e[20] __attribute__ ((aligned (BYTE_ALIGNMENT))),
s[20] __attribute__ ((aligned (BYTE_ALIGNMENT))),
dd[20] __attribute__ ((aligned (BYTE_ALIGNMENT)));
double inv_Li, dlnLidlz, d2lnLidlz2;
double dlnLdlz = 0.0;
double d2lnLdlz2 = 0.0;
d1 = d_start = (double *)rax_malloc(numberOfCategories * 20 * sizeof(double));
e[0] = 0.0;
s[0] = 0.0;
for(l = 1; l < 20; l++)
{
e[l] = EIGN[l-1] * EIGN[l-1];
s[l] = EIGN[l-1];
dd[l] = s[l] * lz;
}
for(i = 0; i < numberOfCategories; i++)
{
d1[20 * i] = 1.0;
for(l = 1; l < 20; l++)
d1[20 * i + l] = EXP(dd[l] * rptr[i]);
}
for (i = 0; i < upper; i++)
{
double
r = rptr[cptr[i]],
wr1 = r * wgt[i],
wr2 = r * r * wgt[i];
__m128d a0 = _mm_setzero_pd();
__m128d a1 = _mm_setzero_pd();
__m128d a2 = _mm_setzero_pd();
d1 = &d_start[20 * cptr[i]];
sum = &sumtable[20 * i];
for(l = 0; l < 20; l+=2)
{
__m128d tmpv = _mm_mul_pd(_mm_load_pd(&d1[l]), _mm_load_pd(&sum[l]));
a0 = _mm_add_pd(a0, tmpv);
__m128d sv = _mm_load_pd(&s[l]);
a1 = _mm_add_pd(a1, _mm_mul_pd(tmpv, sv));
__m128d ev = _mm_load_pd(&e[l]);
a2 = _mm_add_pd(a2, _mm_mul_pd(tmpv, ev));
}
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/FABS(inv_Li);
dlnLidlz *= inv_Li;
d2lnLidlz2 *= inv_Li;
dlnLdlz += wr1 * dlnLidlz;
d2lnLdlz2 += wr2 * (d2lnLidlz2 - dlnLidlz * dlnLidlz);
}
*ext_dlnLdlz = dlnLdlz;
*ext_d2lnLdlz2 = d2lnLdlz2;
rax_free(d_start);
}
#else
static void coreGTRCATPROT(double *EIGN, double lz, int numberOfCategories, double *rptr, int *cptr, int upper,
volatile double *ext_dlnLdlz, volatile double *ext_d2lnLdlz2, double *sumtable, int *wgt)
{
int i, l;
double *d1, *d_start, *sum;
double e[20], s[20], dd[20];
double tmp;
double inv_Li, dlnLidlz, d2lnLidlz2;
double dlnLdlz = 0.0;
double d2lnLdlz2 = 0.0;
d1 = d_start = (double *)rax_malloc(numberOfCategories * 20 * sizeof(double));
for(l = 1; l < 20; l++)
{
e[l] = EIGN[l-1] * EIGN[l-1];
s[l] = EIGN[l-1];
dd[l] = s[l] * lz;
}
for(i = 0; i < numberOfCategories; i++)
{
for(l = 1; l < 20; l++)
d1[20 * i + l] = EXP(dd[l] * rptr[i]);
}
for (i = 0; i < upper; i++)
{
double
r = rptr[cptr[i]],
wr1 = r * wgt[i],
wr2 = r * r * wgt[i];
d1 = &d_start[20 * cptr[i]];
sum = &sumtable[20 * i];
inv_Li = sum[0];
dlnLidlz = 0.0;
d2lnLidlz2 = 0.0;
for(l = 1; l < 20; l++)
{
inv_Li += (tmp = d1[l] * sum[l]);
dlnLidlz += tmp * s[l];
d2lnLidlz2 += tmp * e[l];