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Command used: wombat ggroups.par
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wombat ggroups.par
Script started on 2025-05-26 17:25:31+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "ggroups.par"
**RUNOP -v --s1step**
**COMMENT Example18/C: Illustrate fitting of explict genetic groups**
**ANAL	UNI**
  Analysis type = 1  "UNI"
  No. of traits =  1
**DATA	../muwex2.d**
  Data file : "../muwex2.d"
**TR1  traitno			      2**
  Data - column :	 1  "traitno"	      2
**TR1  animal			    555**
  Data - column :	 2  "animal"	   555
**TR1  sire**
  Data - column :	 3  "sire"	  -1
**TR1  dam**
  Data - column :	 4  "dam"	 -1
**TR1  generation		      4**
  Data - column :	 5  "generation"	 4
**TR1  sex			      2**
  Data - column :	 6  "sex"	  2
**TR1  littersize		      7**
  Data - column :	 7  "littersize"	 7
**TR1  litterno 		     55**
  Data - column :	 8  "litterno"	      55
**TR1  weight			      0**
  Data - column :	 9  "weight"	     0
**END**
**MODEL**
**FIX  generation**
**FIX  sex**
**FIX  littersize**
**SUBJ	animal**
**RAN  animal		     GIN**
**RAN  gggrps		     IDE**
**RAN  litterno 	     IDE**
**TR   weight		     "1"->1  -123456789**
  Trait no.  1	"weight"  Missing value  -123456789
**END**
**VAR  residual 	     1	1**
**1.700000000000000**
**VAR  animal		     1	1**
**4.900000000000000**
**VAR  gggrps		     1	1**
**1.000000000000000**
**VAR  litterno 	     1	1**
**1.500000000000000**
**SPECIAL**
**GENGROUPS gggrps 5 1000 animal**
 HACK_NUMBER GGRPS
 SPECIAL: Fit "explicit" genetic groups
 No. of groups given	       :	   5
 Scale factor for proportions  :   1000.00000000000
 Random effect in model        : "gggrps"
 Corresponding "animal" effect : "animal"
**END**

 End of parameter file reached :  35 lines read
 "Animal" effect corresponding to genetic groups
 set to "animal" GIN
 Read genetic group proportions from .codes file!
  skipping check for sorting of data
 No. of "subjects" in data			   =	      284
 Maximum no. of records/individual =		   =		1	   399
 File						   = "animal.gin"
 No. of records 				   =	     1014
 Denseness of matrix				   =  1.75950	 %
 No. of diagonal elements found 		   =	      339
 No. of zero elements found			   =		0
 No. of elements close to zero			   =		0    0.00%
 Log determinant given				   =  0.00000
 ***** Found more levels of RE in GIN^{-1} than in data
       No. of levels found in data		   =	      284
       Max. row/column no. in GIN^{-1}		   =	      339



 ***** Looking for file with codes "animal.codes"
 Have read					   =	      339 codes from file "animal.codes"
 Max. number of levels for "animal" set to	   =	      339
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	       30
 No. of genotyped animals in total		   =	      309
 Total no. of "animals" 			   =	      339

    Zero out: 1st level  1  sex 	     1	 EqNo.	      4
    Zero out: 1st level  1  littersize	     2	 EqNo.	      6
 No. of "subjects" in data			   =	      284
 No. of combinations of records 		   =		1
 No. of effect codes/ind. (maxnr)		   =		6
 nq,neqns,nnginv	   1	     398	1014	       0	   0  xx   33955.2000000000	       33955  2147483646
 Will try to allocate large array: "LL91" next
   ... size required		 :	     60. elements
   ... individual dimensions	 :	    12		 5
S1STEP: build MME - before genetic groups			2064
 ***Time: begin add91			      0 	  0 Used since last	    0.0 	0.0
S1STEP: build MME - AFTER genetic groups			2124
 ***Time: end add91			      0 	  0 Used since last	    0.0 	0.0
 build MME - data part complete 		   =	     2124
 S1STEP: build MME - random effects part	   =	     2189
  end of peds	     2189
 S1STEP: build MME - 1st pass complete
 Total no. of equations in MME			   =	      398
 No. of non-zero off-diagonal elements (triangle)  =	     2189
 S1STEP: sort linked list - 2nd pass complete
 ZHZ successfully allocated		     2189.
 ZHZDDD successfully allocated		    95481.
 GHG successfully allocated	      5 	  5
 Will try to allocate large array: "QQ91" next
   ... size required		 :	     60. elements
   ... individual dimensions	 :	    12		 5
 ***Time: begin add91			      0 	  0 Used since last	    0.0 	0.0
 ***Time: end add91			      0 	  0 Used since last	    0.0 	0.0
  end of peds	     2189
 S1STEP: build MME - 3rd pass complete
 No. of zero elements in ZHZ			   =	     1961
 No. of "genotyped" animals			   =	      309
 No. of "dense" equations - genotyped animals	   =	      309
 ... divided into how many sub-blocks		   =		1
 ... non-zero elements (triangle)		   =  919.000	   1.91878
 No. of "dense" equations - genetic groups	   =		5
 ... non-zero elements (triangle)		   =  15.0000	   100.000
 Total no. of non-zero coefficients LHS (inc.diag) =  3205.00
 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    0.138000E-01
 S1STEP: start PCG iterations at -  cpu 	      0 system		 0 wmb		 0
   PCG	  50	 2.67990	0.861758E-06	0.586858E-09	 5675.45      sys-time		     0.0
   PCG	  50	 2.67990	0.861758E-06	0.586858E-09	 5675.45      sys-time		     0.0
 Final SS(solutions)				   =  5675.45
 Final SS(deviations)				   = 0.586858E-09
 Final SS(dev)/SS(sol)				   = 0.103403E-12
 S1STEP: end PCG iterations at - cpu		  0 system	     0
						 0 system	    0 min
 wtime						   = 0.170000E-01 0.283333E-03 0.472222E-05
 since precond					   = 0.260000E-02 0.433333E-04
	 no. of iterates carried out		   =	       50 imprssor
 No. of OMP threads used			   =		8
 Time for setting up preconditioner		   =  0.00000	   0.00000
Example18/C: Illustrate fitting of explict genetic groups
   1  animal		       339  zero soln.s       0
   2  gggrps			 5  zero soln.s       0
   3  litterno			42  zero soln.s       0
 Total time used (secs): CPU =		 0  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


0.060u 0.004s 0:00.02 300.0%	0+0k 0+288io 0pf+0w

Script done on 2025-05-26 17:25:31+1000
