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
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
|
Description: filter SSE3 intrinsics
src/sse.c is compiled when SSE is active at least. However this file includes
some intrinsics which are specific to SSE3, so adjust the source code to make
sure the -msse3 option has been specified indeed. Unfortunately, this also
means that the code is unusable as is on x86 without proper sse3-support.
Author: Étienne Mollier <emollier@debian.org>
Forwarded: no
Last-Update: 2021-11-17
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/src/sse.h
+++ b/src/sse.h
@@ -25,7 +25,7 @@ the GNU public licence. See http://www.
#include "sse2neon.h"
#endif
-#if (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || defined(__ARM_NEON))
+#if defined(__SSE3__)
void SSE_Update_Partial_Lk(t_tree *tree,t_edge *b_fcus,t_node *n);
void SSE_Update_Eigen_Lr(t_edge *b, t_tree *tree);
--- a/src/lk.c
+++ b/src/lk.c
@@ -791,7 +791,7 @@ phydbl Lk_Core(int state, int ambiguity_
{
#if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
tree->site_lk_cat[catg] = AVX_Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,tPij_rr,pi,ns,ambiguity_check,state);
-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
+#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
tree->site_lk_cat[catg] = SSE_Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,tPij_rr,pi,ns,ambiguity_check,state);
#else
tree->site_lk_cat[catg] = Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,pi,ns,ambiguity_check,state);
@@ -882,7 +882,7 @@ phydbl Lk_Core_Eigen_Lr(phydbl *expl, ph
{
#if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
tree->site_lk_cat[catg] = AVX_Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
+#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
tree->site_lk_cat[catg] = SSE_Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
#else
tree->site_lk_cat[catg] = Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
@@ -975,7 +975,7 @@ void Lk_dLk_Core_Eigen_Lr(phydbl *expl,
AVX_Lk_dLk_Core_One_Class_Eigen_Lr(dot_prod,
expl ? expl : NULL,
ns,&core_lk,&core_dlk);
-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
+#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
SSE_Lk_dLk_Core_One_Class_Eigen_Lr(dot_prod,
expl ? expl : NULL,
ns,&core_lk,&core_dlk);
@@ -1057,7 +1057,7 @@ void Update_Eigen_Lr(t_edge *b, t_tree *
#if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
AVX_Update_Eigen_Lr(b,tree);
return;
-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
+#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
SSE_Update_Eigen_Lr(b,tree);
return;
#endif
@@ -1305,7 +1305,7 @@ void Update_Partial_Lk(t_tree *tree, t_e
{
#if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
AVX_Update_Partial_Lk(tree,b,d);
-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
+#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
SSE_Update_Partial_Lk(tree,b,d);
#else
Default_Update_Partial_Lk(tree,b,d);
--- a/src/utilities.h
+++ b/src/utilities.h
@@ -40,7 +40,7 @@ the GNU public licence. See http://www.o
#include <xmmintrin.h>
#elif defined(__ARM_NEON)
#include "sse2neon.h"
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif defined __SSE3__
#include <emmintrin.h>
#include <pmmintrin.h>
#endif
@@ -151,8 +151,8 @@ static inline int isinf_ld(long double x
#if (defined __AVX__ || defined __AVX2__)
#define BYTE_ALIGN 32
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || \
- defined(__ARM_NEON))
+#elif defined(__SSE3__) || \
+ defined(__ARM_NEON)
#define BYTE_ALIGN 16
#else
#define BYTE_ALIGN 1
@@ -873,10 +873,12 @@ typedef struct __Tree
#if (defined(__AVX__) || defined(__AVX2__))
__m256d *_tPij1, *_tPij2, *_pmat1plk1, *_pmat2plk2, *_plk0, *_l_ev, *_r_ev,
*_prod_left, *_prod_rght;
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || \
- defined(__ARM_NEON))
+#elif defined(__SSE3__) || \
+ defined(__ARM_NEON)
__m128d *_tPij1, *_tPij2, *_pmat1plk1, *_pmat2plk2, *_plk0, *_l_ev, *_r_ev,
*_prod_left, *_prod_rght;
+#else
+ long *_tPij1,*_tPij2,*_pmat1plk1,*_pmat2plk2,*_plk0,*_l_ev,*_r_ev,*_prod_left,*_prod_rght;
#endif
phydbl *p_lk_left_pi, *l_ev;
@@ -2975,7 +2977,7 @@ int Number_Of_Free_Params(t_tree *mix
#if (defined(__AVX__) || defined(__AVX2__))
#include "avx.h"
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || \
+#elif (defined(__SSE3__) || \
defined(__ARM_NEON))
#include "sse.h"
#endif
--- a/src/free.c
+++ b/src/free.c
@@ -410,7 +410,7 @@ void Free_Tree_Lk(t_tree *tree)
Free(tree->p_lk_left_pi);
Free(tree->l_ev);
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
Free(tree->_tPij1);
Free(tree->_tPij2);
Free(tree->_pmat1plk1);
--- a/src/make.c
+++ b/src/make.c
@@ -28,8 +28,8 @@ void Make_Tree_For_Lk(t_tree *tree)
const unsigned int ns = tree->mod->ns;
const unsigned int nsns = ns * ns;
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
const unsigned int sz = (int)BYTE_ALIGN / 8;
const unsigned int ncatg = tree->mod->ras->n_catg;
#endif
@@ -134,7 +134,7 @@ void Make_Tree_For_Lk(t_tree *tree)
sizeof(phydbl),
BYTE_ALIGN);
#endif
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif (defined(__SSE3__))
#ifndef WIN32
if (posix_memalign(
(void **)&tree->dot_prod, BYTE_ALIGN,
@@ -221,8 +221,8 @@ void Make_Tree_For_Lk(t_tree *tree)
sizeof(phydbl),
BYTE_ALIGN);
#endif
-#elif (!(defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__)))
+#elif (!(defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__)))
tree->dot_prod = (phydbl *)mCalloc(
tree->data->n_pattern * tree->mod->ns *
MAX(tree->mod->ras->n_catg, tree->mod->n_mixt_classes),
@@ -579,8 +579,8 @@ void Make_Edge_Lk_Left(t_edge *b, t_tree
{
b->p_lk_left = NULL;
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign((void **)&b->p_lk_tip_l, BYTE_ALIGN,
(size_t)tree->data->n_pattern * tree->mod->ns *
@@ -686,8 +686,8 @@ void Make_Edge_Lk_Rght(t_edge *b, t_tree
}
else if (b->rght->tax)
{
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign((void **)&b->p_lk_tip_r, BYTE_ALIGN,
(size_t)tree->data->n_pattern * tree->mod->ns *
@@ -761,8 +761,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
MAX(tree->mod->ras->n_catg, tree->mod->n_mixt_classes),
sizeof(int));
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign(
(void **)&tree->p_lk_extra_0, BYTE_ALIGN,
@@ -785,8 +785,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
sizeof(phydbl));
#endif
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign((void **)&tree->p_lk_tip_extra_0, BYTE_ALIGN,
(size_t)tree->data->n_pattern * tree->mod->ns *
@@ -813,8 +813,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
MAX(tree->mod->ras->n_catg, tree->mod->n_mixt_classes),
sizeof(int));
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign(
(void **)&tree->p_lk_extra_1, BYTE_ALIGN,
@@ -837,8 +837,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
sizeof(phydbl));
#endif
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign((void **)&tree->p_lk_tip_extra_1, BYTE_ALIGN,
(size_t)tree->data->n_pattern * tree->mod->ns *
@@ -1265,8 +1265,8 @@ void Make_Model_Complete(t_mod *mod)
mod->Pij_rr = (vect_dbl *)mCalloc(1, sizeof(vect_dbl));
Init_Vect_Dbl(0, mod->Pij_rr);
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign((void **)&mod->Pij_rr->v, BYTE_ALIGN,
(size_t)mod->ras->n_catg * mod->ns * mod->ns *
@@ -1377,8 +1377,8 @@ t_efrq *Make_Efrq(int ns)
e_frq->pi = (vect_dbl *)mCalloc(1, sizeof(vect_dbl));
e_frq->pi->len = ns;
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign((void **)&e_frq->pi->v, BYTE_ALIGN,
(size_t)ns * sizeof(phydbl)))
@@ -1504,8 +1504,8 @@ eigen *Make_Eigen_Struct(int ns)
eig->r_e_vect_im = (phydbl *)mCalloc(ns * ns, sizeof(phydbl));
eig->q = (phydbl *)mCalloc(ns * ns, sizeof(phydbl));
-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
- defined(__SSE2__) || defined(__SSE3__))
+#if (defined(__AVX__) || defined(__AVX2__) || \
+ defined(__SSE3__))
#ifndef WIN32
if (posix_memalign((void **)&eig->r_e_vect, BYTE_ALIGN,
ns * ns * sizeof(phydbl)))
--- a/src/sse.c
+++ b/src/sse.c
@@ -19,7 +19,7 @@ the GNU public licence. See http://www.o
//////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////
-#if (((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || defined(__ARM_NEON)) && !((defined __AVX__ || defined __AVX2__))) && !defined(DISABLE_NATIVE))
+#if (((defined(__SSE3__) || defined(__ARM_NEON)) && !((defined __AVX__ || defined __AVX2__))) && !defined(DISABLE_NATIVE))
void SSE_Update_Eigen_Lr(t_edge *b, t_tree *tree)
{
|
