readme.pcg2
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readme.pcg2 [2012/05/28 13:47] – created shogo | readme.pcg2 [2016/10/21 22:17] – [Options] shogo | ||
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- | The documentation for blupf90 is available separately as a PDF document. | + | ====== BLUP90IOD2 ====== |
- | The following lines can be added at the end of parameter file for blupf90: | + | |
- | Available | + | ===== Summary ===== |
+ | The original program was written by Shogo Tsuruta in 1999. | ||
+ | \\ | ||
+ | BLUP90IOD2 is a BLUP program for solving a large number of mixed model equations, using preconditioned conjugate gradient (PCG). Another version for heterogeneous residual variances is also available. | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
+ | \\ | ||
+ | Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse). | ||
+ | ====== Options ====== | ||
+ | < | ||
OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
- | + | </ | |
- | Set convergence criteria (deault 1e-12). | + | Set convergence criteria (deault 1e-12). |
+ | < | ||
OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
- | + | </ | |
- | Set maximum number of rounds (default 1000). | + | Set maximum number of rounds (default 1000). |
+ | < | ||
+ | OPTION blksize 3 | ||
+ | </ | ||
+ | Set block size for preconditioner (default 1). | ||
+ | < | ||
+ | OPTION init_eq 10 | ||
+ | </ | ||
+ | Set the number of effects to be solved directly (default=0). | ||
+ | < | ||
OPTION solv_method FSPAK | OPTION solv_method FSPAK | ||
- | + | </ | |
- | | + | Solving method |
- | + | < | |
- | OPTION r_factor 1.6 | + | OPTION |
- | + | </ | |
- | Set relaxation factor | + | Tolerance to get a positive definite matrix |
- | + | < | |
- | OPTION | + | |
- | + | ||
- | Store solutions and s.e. | + | |
- | + | ||
- | OPTION missing | + | |
- | + | ||
- | | + | |
OPTION residual | OPTION residual | ||
- | + | </ | |
- | y-hat and residual | + | y-hat and residuals |
- | + | < | |
- | OPTION | + | OPTION |
- | + | </ | |
- | Set block size for preconditioner (default 1). | + | Using the last 50 average eps for convergence. |
- | [shogo@dodo6 thr1pcg]$ cd .. | + | <file> |
- | [shogo@dodo6 f90-05]$ cat pcg2/ | + | |
- | BLUP90IOD2 - Optimized version of BLUP90IOD with options for block diagonal preconditioner and direct | + | |
- | solving | + | |
- | + | ||
- | Modified by Shogo Tsuruta, University of Georgia | + | |
- | + | ||
- | The following lines can be added at the end of parameter | + | |
- | + | ||
- | OPTION conv_crit | + | |
- | set convergence criterion to given level (default 1e-12) | + | |
- | + | ||
- | OPTION maxrounds | + | |
- | set maximum number of rounds to given number (default=5000) | + | |
- | + | ||
- | OPTION solv_method | + | |
- | | + | |
- | + | ||
- | OPTION blksize 3 | + | |
- | set block size for preconditioner (default=1) | + | |
- | + | ||
- | OPTION init_eq 10 | + | |
- | set the number of effects to be solved directly (default=0) | + | |
OPTION cont 1 | OPTION cont 1 | ||
- | | + | </ |
- | + | To restart the program from the previous solutions. | |
- | OPTION missing -1 | + | < |
- | set the missing value (default 0). | + | OPTION missing -999 |
+ | </ | ||
+ | Set the missing value (default 0) in integer. | ||
+ | < | ||
OPTION restart 100 | OPTION restart 100 | ||
- | | + | </ |
- | + | Set the number of iteration to recompute residuals (default=100). | |
- | OPTION | + | < |
- | implement one-step genomic selection updating animal effects with genomic relationship matrix | + | OPTION |
- | + | </ | |
- | For information on availability of BLUP90IOD, please contact Ignacy | + | Using the previous solution file to start the iteration. An additional software is required to use this option. |
- | Misztal (ignacy@uga.edu) at the University of Georgia. | + | < |
+ | OPTION random_upg 1 2 | ||
+ | </ | ||
+ | Set the UPG random. " | ||
+ | < | ||
+ | OPTION SNP_file snp | ||
+ | </ | ||
+ | Specify the SNP file name to use genotype data. | ||
+ | \\ | ||
+ | //For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.// | ||
readme.pcg2.txt · Last modified: 2024/05/16 14:16 by dani