-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathlikelihood.h
488 lines (429 loc) · 13.1 KB
/
likelihood.h
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
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
#ifndef __LIKELIHOOD_H__
#define __LIKELIHOOD_H__
//#define TIMING_ANALIZ
#if defined (TIMING_ANALIZ)
static clock_t CPUCondLikeDown;
static clock_t CPUScalers;
static clock_t CPUScalersRemove;
static clock_t CPUCondLikeRoot;
static clock_t CPULilklihood;
#define TIME(X1,CPUtime)\
{CPUTimeStart = clock();\
X1;\
CPUtime += (clock()-CPUTimeStart);}
#else
#define TIME(X1,CPUtime)\
X1;
#endif
#define A 0
#define C 1
#define G 2
#define T 3
#define AA 0
#define AC 1
#define AG 2
#define AT 3
#define CA 4
#define CC 5
#define CG 6
#define CT 7
#define GA 8
#define GC 9
#define GG 10
#define GT 11
#define TA 12
#define TC 13
#define TG 14
#define TT 15
CLFlt *preLikeL; /* precalculated cond likes for left descendant */
CLFlt *preLikeR; /* precalculated cond likes for right descendant*/
CLFlt *preLikeA; /* precalculated cond likes for ancestor */
typedef struct{
CLFlt *pL;
CLFlt *pR;
CLFlt *clL;
CLFlt *clR;
CLFlt *clP;
int nStates;
int *lState;
int *rState;
int shortCut;
int preLikeJump;
int k;
int c;
int numChars;
int numGammaCats;
}cld_gen_prmt_t;
typedef struct{
CLFlt *pL;
CLFlt *pR;
CLFlt *pA;
CLFlt *clL;
CLFlt *clR;
CLFlt *clP;
CLFlt *clA;
int nStates;
int *lState;
int *rState;
int *aState;
int shortCut;
int preLikeJump;
int k;
int c;
int numChars;
int numGammaCats;
}clr_gen_prmt_t;
typedef struct{
CLFlt **clP;
int nStates;
int c;
int numChars;
int numGammaCats;
CLFlt *scP;
CLFlt *lnScaler;
CLFlt *clPtr;
CLFlt scaler;
}cls_gen_prmt_t;
typedef struct{
CLFlt **clP;
CLFlt *clPtr;
CLFlt *lnScaler;
CLFlt *nSitesOfPat;
CLFlt *clInvar;
MrBFlt lnL;
MrBFlt freq;
MrBFlt *bs;
MrBFlt pInvar;
int hasPInvar;
int numChars;
int numGammaCats;
int nStates;
int c;
}likeh_gen_prmt_t;
typedef struct{
CLFlt *pL;
CLFlt *pR;
CLFlt *clL;
CLFlt *clR;
CLFlt *clP;
int *lState;
int *rState;
int shortCut;
int k;
int c;
int h;
int numChars;
int numGammaCats;
}cld_nuc4_prmt_t;
typedef struct{
CLFlt *pL;
CLFlt *pR;
CLFlt *pA;
CLFlt *clL;
CLFlt *clR;
CLFlt *clP;
CLFlt *clA;
int *lState;
int *rState;
int *aState;
int shortCut;
int k;
int c;
int h;
int numChars;
int numGammaCats;
}clr_nuc4_prmt_t;
typedef struct{
CLFlt **clP;
int c;
int numChars;
int numGammaCats;
CLFlt *scP;
CLFlt *lnScaler;
CLFlt *clPtr;
CLFlt scaler;
}cls_nuc4_prmt_t;
typedef struct{
CLFlt **clP;
int c;
int numChars;
int numGammaCats;
CLFlt *clPtr;
CLFlt *scP;
CLFlt *lnScaler;
CLFlt *nSitesOfPat;
CLFlt *clInvar;
MrBFlt lnL;
MrBFlt freq;
MrBFlt *bs;
MrBFlt pInvar;
int hasPInvar;
}likeh_nuc4_prmt_t;
#ifdef AVX_ENABLED
typedef struct{
CLFlt *pL;
CLFlt *pR;
__m256 *clL;
__m256 *clR;
__m256 *clP;
int numAVXChars;
int numGammaCats;
int c;
}cld_nuc4_AVX_prmt_t;
typedef struct{
CLFlt *pL;
CLFlt *pR;
CLFlt *pA;
__m256 *clL;
__m256 *clR;
__m256 *clA;
__m256 *clP;
int numAVXChars;
int numGammaCats;
int c;
}clr_nuc4_AVX_prmt_t;
typedef struct{
CLFlt *scP;
CLFlt *lnScaler;
__m256 *clPtr, **clP, *scP_AVX, *lnScaler_AVX;
int numAVXChars;
int numGammaCats;
int c;
int c1;
}cls_nuc4_AVX_prmt_t;
typedef struct{
CLFlt *pL;
CLFlt *pR;
__m256 *clL;
__m256 *clR;
__m256 *clP;
int nStates;
int *lState;
int *rState;
int shortCut;
int preLikeJump;
int c;
int numAVXChars;
int numGammaCats;
}cld_gen_AVX_prmt_t;
typedef struct{
CLFlt *pL;
CLFlt *pR;
CLFlt *pA;
__m256 *clL;
__m256 *clR;
__m256 *clP;
__m256 *clA;
int nStates;
int *lState;
int *rState;
int *aState;
int shortCut;
int preLikeJump;
int c;
int numAVXChars;
int numGammaCats;
}clr_gen_AVX_prmt_t;
typedef struct{
CLFlt *scP;
CLFlt *lnScaler;
__m256 *clPtr, **clP, *scP_AVX, *lnScaler_AVX;
int numAVXChars;
int numGammaCats;
int c;
int c1;
int nStates;
}cls_gen_AVX_prmt_t;
#endif
int CondLikeDown_Bin (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeDown_Bin_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeDown_Bin_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeDown_Gen (TreeNode *p, int division, int chain);
#if defined (FINE_GRAINED)
void ThreadCLDown_Gen (int id);
void ThreadCLRoot_Gen (int id);
void ThreadCLScaler_Gen (int id);
void ThreadLikeH_Gen (int id);
void *ThreadCLMix_Gen(void *prmt);
void ThreadCLDown_NUC4 (int id);
void ThreadCLRoot_NUC4 (int id);
void ThreadCLScaler_NUC4 (int id);
void ThreadLikeH_NUC4 (int id);
void *ThreadCLMix_NUC4 (void *prmt);
#endif
#if defined (SSE_ENABLED)
int CondLikeDown_Gen_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeDown_Gen_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeDown_Gen_GibbsGamma (TreeNode *p, int division, int chain);
int CondLikeDown_NUC4 (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeDown_NUC4_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeDown_NUC4_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeDown_NUC4_GibbsGamma (TreeNode *p, int division, int chain);
int CondLikeDown_NY98 (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeDown_NY98_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeDown_NY98_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeDown_Std (TreeNode *p, int division, int chain);
int CondLikeRoot_Bin (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeRoot_Bin_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeRoot_Bin_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeRoot_Gen (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeRoot_Gen_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeRoot_Gen_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeRoot_Gen_GibbsGamma (TreeNode *p, int division, int chain);
int CondLikeRoot_NUC4 (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeRoot_NUC4_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeRoot_NUC4_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeRoot_NUC4_GibbsGamma (TreeNode *p, int division, int chain);
int CondLikeRoot_NY98 (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeRoot_NY98_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeRoot_NY98_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeRoot_Std (TreeNode *p, int division, int chain);
int CondLikeScaler_Gen (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeScaler_Gen_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeScaler_Gen_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeScaler_Gen_GibbsGamma (TreeNode *p, int division, int chain);
int CondLikeScaler_NUC4 (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeScaler_NUC4_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeScaler_NUC4_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeScaler_NUC4_GibbsGamma (TreeNode *p, int division, int chain);
int CondLikeScaler_NY98 (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int CondLikeScaler_NY98_SSE (TreeNode *p, int division, int chain);
#endif
#if defined (AVX_ENABLED)
int CondLikeScaler_NY98_AVX (TreeNode *p, int division, int chain);
#endif
int CondLikeScaler_Std (TreeNode *p, int division, int chain);
int CondLikeUp_Bin (TreeNode *p, int division, int chain);
int CondLikeUp_Gen (TreeNode *p, int division, int chain);
int CondLikeUp_NUC4 (TreeNode *p, int division, int chain);
int CondLikeUp_Std (TreeNode *p, int division, int chain);
void LaunchLogLikeForDivision (int chain, int d, MrBFlt* lnL);
int Likelihood_Adgamma (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
int Likelihood_Gen (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#if defined (SSE_ENABLED)
int Likelihood_Gen_SSE (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#endif
#if defined (AVX_ENABLED)
int Likelihood_Gen_AVX (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#endif
int Likelihood_Gen_GibbsGamma (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
int Likelihood_NUC4 (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#if defined (SSE_ENABLED)
int Likelihood_NUC4_SSE (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#endif
#if defined (AVX_ENABLED)
int Likelihood_NUC4_AVX (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#endif
int Likelihood_NUC4_GibbsGamma (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
int Likelihood_NY98 (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#if defined (SSE_ENABLED)
int Likelihood_NY98_SSE (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#endif
#if defined (AVX_ENABLED)
int Likelihood_NY98_AVX (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#endif
int Likelihood_Pars (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
int Likelihood_ParsStd (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
int Likelihood_Res (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#if defined (SSE_ENABLED)
int Likelihood_Res_SSE (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#endif
#if defined (AVX_ENABLED)
int Likelihood_Res_AVX (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
#endif
int Likelihood_Std (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats);
int TiProbs_Fels (TreeNode *p, int division, int chain);
int TiProbs_Gen (TreeNode *p, int division, int chain);
#ifdef AVX_ENABLED
int TiProbs_Gen_AVX (TreeNode *p, int division, int chain);
#endif
int TiProbs_GenCov (TreeNode *p, int division, int chain);
int TiProbs_Hky (TreeNode *p, int division, int chain);
int TiProbs_JukesCantor (TreeNode *p, int division, int chain);
int TiProbs_Std (TreeNode *p, int division, int chain);
int TiProbs_Res (TreeNode *p, int division, int chain);
#ifdef FINE_GRAINED
#define NUM_THREADS 4
#define CLDOWN 1
#define CLROOT 2
#define CLSCALER 3
#define LIKEH 4
#define GEN 1
#define NUC4 2
int charNum[NUM_THREADS];
pthread_t clmix_gen_thd[NUM_THREADS];
int clmix_gen_id[NUM_THREADS];
cld_gen_prmt_t cld_gen_prmt[NUM_THREADS];
clr_gen_prmt_t clr_gen_prmt[NUM_THREADS];
cls_gen_prmt_t cls_gen_prmt[NUM_THREADS];
likeh_gen_prmt_t likeh_gen_prmt[NUM_THREADS];
pthread_t clmix_nuc4_thd[NUM_THREADS];
int clmix_nuc4_id[NUM_THREADS];
cld_nuc4_prmt_t cld_nuc4_prmt[NUM_THREADS];
clr_nuc4_prmt_t clr_nuc4_prmt[NUM_THREADS];
cls_nuc4_prmt_t cls_nuc4_prmt[NUM_THREADS];
likeh_nuc4_prmt_t likeh_nuc4_prmt[NUM_THREADS];
pthread_barrier_t start_barrier;
pthread_barrier_t stop_barrier;
pthread_barrier_t half_barrier;
#if defined (AVX_ENABLED)
cld_nuc4_AVX_prmt_t cld_nuc4_AVX_prmt[NUM_THREADS];
clr_nuc4_AVX_prmt_t clr_nuc4_AVX_prmt[NUM_THREADS];
cls_nuc4_AVX_prmt_t cls_nuc4_AVX_prmt[NUM_THREADS];
int charNumScaler[NUM_THREADS];
int ThreadCLDown_NUC4_AVX (int id);
int ThreadCLRoot_NUC4_AVX (int id);
int ThreadCLScaler_NUC4_AVX (int id);
pthread_t clmix_nuc4_AVX_thd[NUM_THREADS];
void *ThreadCLMix_NUC4_AVX(void *prmt);
cld_gen_AVX_prmt_t cld_gen_AVX_prmt[NUM_THREADS];
clr_gen_AVX_prmt_t clr_gen_AVX_prmt[NUM_THREADS];
cls_gen_AVX_prmt_t cls_gen_AVX_prmt[NUM_THREADS];
int ThreadCLDown_Gen_AVX(int id);
int ThreadCLRoot_Gen_AVX(int id);
int ThreadCLScaler_Gen_AVX(int id);
pthread_t clmix_gen_AVX_thd[NUM_THREADS];
void *ThreadCLMix_Gen_AVX(void *prmt);
#endif
#endif
#endif /* __LIKELIHOOD_H__ */