1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
/*
* phylotreeavx.cpp
*
* Created on: Dec 14, 2014
* Author: minh
*/
#include "vectorclass/vectormath_exp.h"
#include "vectorclass/vectorclass.h"
#include "phylokernel.h"
//#include "phylokernelsafe.h"
//#include "phylokernelmixture.h"
//#include "phylokernelmixrate.h"
//#include "phylokernelsitemodel.h"
#include "phylokernelnew.h"
#include "phylokernelnonrev.h"
#define KERNEL_FIX_STATES
#include "phylokernelnew.h"
#include "phylokernelnonrev.h"
#ifndef __AVX__
#error "You must compile this file with AVX enabled!"
#endif
void PhyloTree::setParsimonyKernelAVX() {
computeParsimonyBranchPointer = &PhyloTree::computeParsimonyBranchFastSIMD<Vec8ui>;
computePartialParsimonyPointer = &PhyloTree::computePartialParsimonyFastSIMD<Vec8ui>;
}
void PhyloTree::setDotProductAVX() {
#ifdef BOOT_VAL_FLOAT
dotProduct = &PhyloTree::dotProductSIMD<float, Vec8f>;
#else
dotProduct = &PhyloTree::dotProductSIMD<double, Vec4d>;
#endif
dotProductDouble = &PhyloTree::dotProductSIMD<double, Vec4d>;
}
void PhyloTree::setLikelihoodKernelAVX() {
vector_size = 4;
bool site_model = model_factory && model_factory->model->isSiteSpecificModel();
setParsimonyKernelAVX();
computeLikelihoodDervMixlenPointer = NULL;
if (site_model && safe_numeric) {
switch (aln->num_states) {
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD <Vec4d, SAFE_LH, 4, false, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD <Vec4d, SAFE_LH, 4, false, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD <Vec4d, SAFE_LH, 4, false, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, 4, false, true>;
break;
case 20:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD <Vec4d, SAFE_LH, 20, false, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD <Vec4d, SAFE_LH, 20, false, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD <Vec4d, SAFE_LH, 20, false, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, 20, false, true>;
break;
default:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchGenericSIMD <Vec4d, SAFE_LH, false, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervGenericSIMD <Vec4d, SAFE_LH, false, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodGenericSIMD <Vec4d, SAFE_LH, false, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferGenericSIMD<Vec4d, false, true>;
break;
}
return;
}
if (site_model) {
switch (aln->num_states) {
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD <Vec4d, NORM_LH, 4, false, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD <Vec4d, NORM_LH, 4, false, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD <Vec4d, NORM_LH, 4, false, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, 4, false, true>;
break;
case 20:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD <Vec4d, NORM_LH, 20, false, true>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD <Vec4d, NORM_LH, 20, false, true>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD <Vec4d, NORM_LH, 20, false, true>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, 20, false, true>;
break;
default:
ASSERT(0);
break;
}
return;
}
if ((model_factory && !model_factory->model->isReversible()) || params->kernel_nonrev) {
// if nonreversible model
switch (aln->num_states) {
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeNonrevLikelihoodBranchSIMD <Vec4d, 4>;
computeLikelihoodDervPointer = &PhyloTree::computeNonrevLikelihoodDervSIMD <Vec4d, 4>;
computePartialLikelihoodPointer = &PhyloTree::computeNonrevPartialLikelihoodSIMD<Vec4d, 4>;
break;
default:
computeLikelihoodBranchPointer = &PhyloTree::computeNonrevLikelihoodBranchGenericSIMD <Vec4d>;
computeLikelihoodDervPointer = &PhyloTree::computeNonrevLikelihoodDervGenericSIMD <Vec4d>;
computePartialLikelihoodPointer = &PhyloTree::computeNonrevPartialLikelihoodGenericSIMD<Vec4d>;
break;
}
computeLikelihoodFromBufferPointer = NULL;
return;
}
if (safe_numeric) {
switch(aln->num_states) {
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD <Vec4d, SAFE_LH, 4>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD <Vec4d, SAFE_LH, 4>;
computeLikelihoodDervMixlenPointer = &PhyloTree::computeLikelihoodDervMixlenSIMD<Vec4d, SAFE_LH, 4>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD <Vec4d, SAFE_LH, 4>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, 4>;
break;
case 20:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD <Vec4d, SAFE_LH, 20>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD <Vec4d, SAFE_LH, 20>;
computeLikelihoodDervMixlenPointer = &PhyloTree::computeLikelihoodDervMixlenSIMD<Vec4d, SAFE_LH, 20>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD <Vec4d, SAFE_LH, 20>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, 20>;
break;
default:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchGenericSIMD <Vec4d, SAFE_LH>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervGenericSIMD <Vec4d, SAFE_LH>;
computeLikelihoodDervMixlenPointer = &PhyloTree::computeLikelihoodDervMixlenGenericSIMD<Vec4d, SAFE_LH>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodGenericSIMD <Vec4d, SAFE_LH>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferGenericSIMD<Vec4d>;
break;
}
return;
}
switch(aln->num_states) {
case 4:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD <Vec4d, NORM_LH, 4>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD <Vec4d, NORM_LH, 4>;
computeLikelihoodDervMixlenPointer = &PhyloTree::computeLikelihoodDervMixlenSIMD<Vec4d, NORM_LH, 4>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD <Vec4d, NORM_LH, 4>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, 4>;
break;
case 20:
computeLikelihoodBranchPointer = &PhyloTree::computeLikelihoodBranchSIMD <Vec4d, NORM_LH, 20>;
computeLikelihoodDervPointer = &PhyloTree::computeLikelihoodDervSIMD <Vec4d, NORM_LH, 20>;
computeLikelihoodDervMixlenPointer = &PhyloTree::computeLikelihoodDervMixlenSIMD<Vec4d, NORM_LH, 20>;
computePartialLikelihoodPointer = &PhyloTree::computePartialLikelihoodSIMD <Vec4d, NORM_LH, 20>;
computeLikelihoodFromBufferPointer = &PhyloTree::computeLikelihoodFromBufferSIMD<Vec4d, 20>;
break;
default:
ASSERT(0);
break;
}
}
|
