======================================================
Command used: wombat hinv_gin.par
======================================================

wombat hinv_gin.par
Script started on 2025-05-26 17:31:13+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "hinv_gin.par"
**RUNOP  --hinv -v**
**COM Example12/A: Step 1 - generate H^{-1}**
**PED ../pedigree.dat**
  Pedigree file : "../pedigree.dat"
**MRK ../MarkerCounts.dat**
  Marker counts file : "../MarkerCounts.dat"
**SPECIAL**
**HINVERSE SNP 1000**
  HINV: nsnp, msnp	   1000        1000
 HACK_NUMBER NSNPS
**HINVERSE lambda 1.0**
  HINV: lambda	  1.00000000000000
**HINVERSE epsilon 0.05d0**
  HINV: epsilon   5.000000000000000E-002
**HINVERSE OUT GIN animal**
  HINV: how_houtput GIN
 animal.gin
**END**

 End of parameter file reached :  10 lines read
 Colleau's method specified for calculation of A22 - but not needed
 "In core" storage for NRM Inverse switched on
 ***Time: begin idvec			      0 	  0 Used since last	    0.0 	0.0
 ***Time: end idvec			      0 	  0 Used since last	    0.0 	0.0
 Pedigree file					   = ../pedigree.dat
 Total no. of animal IDs found			   =	      600
 no. of NRM matrices		1	    1
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	      313
 No. of genotyped animals in total		   =	      287
 Total no. of "animals" 			   =	      600

 Begin: read M2 from ../MarkerCounts.dat       sys-time 	    0.0 	    0.0
 tvec4	      1000
 chevck marks	     1000	 1000
 No. of rows in ../MarkerCounts.dat read	   =	      287
 No. of marker allele counts per row read	   =	     1000
 End: read M2 from .dat 		       sys-time 	    0.1 	    0.1
 Successfully allocated arrays for in-core NRM

 Inbreeding coefficients for random effect	   =		1 computed
 ... TIER's algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =	       24
 Average inbreeding coefficient 		   = 0.500000	  (in %)
 ... amongst inbred animals			   =  12.5000	  (in %)

 NRM Inverse no. :	     1	 "X"
 No. of elements =	  1780	 log determinant =  -277.258872223979
 A22: No. genotyped animals + ancestors 	   =	      368
 End: calculating A22 (Colleau) 	       sys-time 	    0.2 	    0.2
 End: centering M2			       sys-time 	    0.2 	    0.2
 End: calculating GRM			       sys-time 	    0.2 	    0.2
 end calc g22 F
 F
 End: inverting g22			       sys-time 	    0.2 	    0.2
 End: inverting a22			       sys-time 	    0.2 	    0.2
 Start writing out "animal.gin"
 H^{-1} : No. of non-zero elements in A^11, A^21   =	   42505.000
	 0.00000		  alpha 	  0.00000
 Total time used (secs): CPU =		 1  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


0.942u 0.130s 0:00.30 356.6%	0+0k 0+4184io 0pf+0w

Script done on 2025-05-26 17:31:13+1000
======================================================
Command used: wombat s1step.par
======================================================

wombat s1step.par
Script started on 2025-05-26 17:31:13+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

	   1 xone
	   2 xtwo
  skipping check for sorting of data
	  50	      50 0   1.00000
 File						   = "animal.gin"
 No. of records 				   =	    42505
 Denseness of matrix				   =  23.5746	 %
 No. of diagonal elements found 		   =	      600
 No. of zero elements found			   =		0
 No. of elements close to zero			   =		0    0.00%
 Log determinant given				   =  0.00000
 Have read					   =	      600 codes from file "animal.codes"
 Max. number of levels for "animal" set to	   =	      600
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	      313
 No. of genotyped animals in total		   =	      287
 Total no. of "animals" 			   =	      600

 No. of "subjects" in data			   =	      600
 No. of combinations of records 		   =		1
 No. of effect codes/ind. (maxnr)		   =		4
 Random effect no.	     0
  1   1.19670
  2   1.16150	    12.5249
 Eigenvalues   12.6428	     1.07884
 in %	       92.1377	     7.86232
 Random effect no.	     1
  1   1.19670
  2  0.666500	    3.13120
 Eigenvalues   3.33860	    0.989303
 in %	       77.1413	     22.8587
 build MME - data part complete 		   =	     3020
 S1STEP: build MME - random effects part	   =	     6476
 S1STEP: build MME - 1st pass complete
 Total no. of equations in MME			   =	     1814
 No. of non-zero off-diagonal elements (triangle)  =	     6476
 S1STEP: sort linked list - 2nd pass complete
 S1STEP: build MME - 3rd pass complete
 No. of zero elements in ZHZ			   =	     6476
 No. of "genotyped" animals			   =	      287
 No. of "dense" equations - genotyped animals	   =	      574
 ... divided into how many sub-blocks		   =		1
 ... non-zero elements (triangle)		   =  165025.	   100.000
 Total no. of non-zero coefficients LHS (inc.diag) =  172741.
 Pre-conditioning scheme selected		   = "imprssor "
 Dense Cholesky factorisation option		   = "dpotrf"
 Dense LHS multiplication option		   = "dsymv "
 Sparse LHS multiplication option		   = "dsymv "
 Maximum no. of iterates			   =	    50000
 Interval (iterates) to reset residuals 	   =	       75
 Convergence criterion: SS deviations		   = 0.100000E-08
 Convergence criterion: SS dev.s/SS sol.s	   = 0.100000E-06
 S1STEP: start preconditioner at -  cpu 	      0 system		 0 wmb		 0    0.144600
 S1STEP: start PCG iterations at -  cpu 	      0 system		 0 wmb		 0
   PCG	  41	 2.98723	0.685910E-06	0.760190E-09	 14418.7      sys-time		     0.2
 Final SS(solutions)				   =  14418.7
 Final SS(deviations)				   = 0.760190E-09
 Final SS(dev)/SS(sol)				   = 0.527225E-13
 S1STEP: end PCG iterations at - cpu		  0 system	     0
						 0 system	    0 min
 wtime						   = 0.151000	  0.251667E-02 0.419444E-04
 since precond					   = 0.670000E-02 0.111667E-03
	 no. of iterates carried out		   =	       41 imprssor
 No. of OMP threads used			   =		8
 Time for setting up preconditioner		   =  0.00000	   0.00000
Example21/A: Step 2 - SS-GBLUP analysis
   1  animal		      1200  zero soln.s       0
 Total time used (secs): CPU =		 0  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


0.248u 0.012s 0:00.16 156.2%	0+0k 0+584io 0pf+0w

Script done on 2025-05-26 17:31:14+1000
