paml speed test: x3400

large:

 

This is large in speed 2.

It runs an MCMC algorithm

Reading options from mcmctree.ctl..

Reading master tree.

(((a, b), ((c, d), e)), (f, (g, (h, i))));

 

Reading sequence data..  1 loci

*** Locus 1 ***

 

ns = 9   ls = 215833

Reading sequences, sequential format..

Reading seq # 1: a     

Reading seq # 2: b     

Reading seq # 3: c     

Reading seq # 4: d     

Reading seq # 5: e     

Reading seq # 6: f     

Reading seq # 7: g     

Reading seq # 8: h     

Reading seq # 9: i     

 

215833 site patterns read, 200000000 sites

Counting frequencies..

215833 patterns, clean

442025984 bytes for conP, 0 bytes for conP0

0 burnin, sampled every 1, 20 samples

Approximating posterior (Settings: cleandata=1.  print=0  saveconP=1.)

 

getting initial values to start MCMC.

 

priors: 

G(6.0000, 2.0000) for kappa

G(1.0000, 1.0000) for alpha

G(2.0000, 2.0000) for rgene

Initial parameters (np = 11):

 0.945 0.606 0.448 0.563 0.372 0.872 0.640 0.452 0.739 2.152 0.588

 

lnL0 = -2197386427.52

 

Starting MCMC...

finetune steps (time rate mixing para RatePara?):  0.001  0.001  0.800  0.010

    paras: times, rates, sigma2, correl, kappa, alpha

  5% 0.50 0.00 1.00 0.50  0.832 0.534 0.394 0.495 0.327 -2197178046.0  0:05

 10% 0.50 0.00 1.00 0.50  0.798 0.512 0.378 0.475 0.314 -2196902682.8  0:10

 15% 0.50 0.33 0.67 0.50  0.787 0.505 0.372 0.468 0.309 -2196706637.4  0:14

 20% 0.53 0.25 0.75 0.62  0.783 0.503 0.370 0.466 0.308 -2196363815.4  0:19

 25% 0.55 0.20 0.60 0.50  0.781 0.501 0.369 0.464 0.307 -2196270005.3  0:23

 30% 0.54 0.33 0.50 0.50  0.779 0.500 0.368 0.463 0.306 -2195987932.5  0:28

 35% 0.52 0.43 0.43 0.50  0.778 0.500 0.368 0.463 0.306 -2195823430.1  0:33

 40% 0.52 0.38 0.38 0.50  0.778 0.499 0.368 0.462 0.306 -2195414814.2  0:37

 45% 0.51 0.33 0.33 0.44  0.777 0.499 0.367 0.462 0.305 -2195262951.6  0:41

 50% 0.53 0.40 0.30 0.45  0.777 0.499 0.367 0.462 0.305 -2194870827.1  0:46

 55% 0.49 0.36 0.36 0.45  0.766 0.492 0.362 0.455 0.301 -2194829851.6  0:51

 60% 0.50 0.42 0.42 0.42  0.767 0.493 0.362 0.456 0.301 -2194659620.3  0:55

 65% 0.49 0.46 0.38 0.42  0.769 0.493 0.363 0.456 0.302 -2194147677.2  1:00

 70% 0.48 0.50 0.36 0.43  0.770 0.494 0.363 0.457 0.302 -2193958431.0  1:05

 75% 0.48 0.53 0.33 0.43  0.771 0.495 0.364 0.457 0.302 -2193662346.9  1:09

 80% 0.48 0.50 0.38 0.44  0.766 0.492 0.361 0.454 0.300 -2193210952.2  1:14

 85% 0.49 0.53 0.35 0.44  0.762 0.489 0.359 0.452 0.299 -2192798742.2  1:19

 90% 0.49 0.50 0.33 0.47  0.758 0.487 0.357 0.450 0.297 -2192286505.2  1:24

 95% 0.48 0.53 0.32 0.45  0.754 0.485 0.356 0.448 0.296 -2192133162.8  1:28

100% 0.49 0.55 0.35 0.45  0.753 0.484 0.355 0.447 0.295 -2191882540.7  1:33

 

Time used:  1:33

 

This is small in speed 2.

It calculates 20 transition-probability matrices of size 400x400.

 

(A) repeated squaring

  1/ 20  P00(4.19) = 0.386203729 0:02

  2/ 20  P00(2.53) = 0.537066951 0:05

  3/ 20  P00(0.84) = 0.799213805 0:07

  4/ 20  P00(0.68) = 0.832898484 0:10

  5/ 20  P00(3.70) = 0.399355478 0:12

  6/ 20  P00(0.46) = 0.889539120 0:15

  7/ 20  P00(4.31) = 0.335684843 0:17

  8/ 20  P00(4.82) = 0.325967311 0:20

  9/ 20  P00(0.93) = 0.793737266 0:22

 10/ 20  P00(0.38) = 0.918190395 0:25

 11/ 20  P00(0.91) = 0.801778102 0:27

 12/ 20  P00(3.30) = 0.429690709 0:29

 13/ 20  P00(0.01) = 0.996570165 0:32

 14/ 20  P00(0.33) = 0.924427670 0:34

 15/ 20  P00(2.25) = 0.593340081 0:37

 16/ 20  P00(0.45) = 0.904184404 0:39

 17/ 20  P00(4.96) = 0.297681422 0:42

 18/ 20  P00(0.89) = 0.794941530 0:44

 19/ 20  P00(0.49) = 0.885739119 0:47

 20/ 20  P00(2.26) = 0.583081265 0:49

 

(B) eigensolution

  1/ 20  P00(4.19) = 0.386203676 0:50

  2/ 20  P00(2.53) = 0.537066931 0:50

  3/ 20  P00(0.84) = 0.799213804 0:51

  4/ 20  P00(0.68) = 0.832898483 0:52

  5/ 20  P00(3.70) = 0.399355428 0:53

  6/ 20  P00(0.46) = 0.889539119 0:53

  7/ 20  P00(4.31) = 0.335684773 0:54

  8/ 20  P00(4.82) = 0.325967237 0:55

  9/ 20  P00(0.93) = 0.793737264 0:55

 10/ 20  P00(0.38) = 0.918190395 0:56

 11/ 20  P00(0.91) = 0.801778101 0:57

 12/ 20  P00(3.30) = 0.429690667 0:57

 13/ 20  P00(0.01) = 0.996570165 0:58

 14/ 20  P00(0.33) = 0.924427670 0:59

 15/ 20  P00(2.25) = 0.593340068 0:59

 16/ 20  P00(0.45) = 0.904184403 1:00

 17/ 20  P00(4.96) = 0.297681337 1:01

 18/ 20  P00(0.89) = 0.794941529 1:02

 19/ 20  P00(0.49) = 0.885739119 1:02

 20/ 20  P00(2.26) = 0.583081251 1:03