readme.pcg2
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readme.pcg2 [2012/05/28 13:47] – created shogo | readme.pcg2 [2012/05/29 16:02] – 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: | + | \\ |
+ | The original program was written by Shogo Tsuruta in 1999. | ||
- | Available options: | + | ===== Summary===== |
+ | BLUP90IOD2 is a BLUP program for solving a large number of mixed model equations, using preconditioned conjugate gradient (PCG). | ||
+ | ====== Options ====== | ||
+ | < | ||
OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
- | + | </ | |
- | | + | set convergence criteria (deault 1e-12). |
+ | < | ||
OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
- | + | </ | |
- | | + | set maximum number of rounds (default 1000). |
- | + | < | |
- | OPTION solv_method FSPAK | + | |
- | + | ||
- | Selection solutions by FSPAK, SOR or PCG (default PCG). | + | |
- | + | ||
- | OPTION r_factor 1.6 | + | |
- | + | ||
- | Set relaxation factor for SOR (default 1.4). | + | |
- | + | ||
- | OPTION sol se | + | |
- | + | ||
- | Store solutions and s.e. | + | |
- | + | ||
- | OPTION missing -999 | + | |
- | + | ||
- | Missing observation (default 0). | + | |
- | + | ||
- | OPTION residual | + | |
- | + | ||
- | y-hat and residual will be shown in yhat_residual. | + | |
OPTION blksize 3 | OPTION blksize 3 | ||
- | + | </file> | |
- | Set block size for preconditioner (default 1). | + | set block size for preconditioner (default 1). |
- | [shogo@dodo6 thr1pcg]$ cd .. | + | < |
- | [shogo@dodo6 f90-05]$ cat pcg2/Readme.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 | OPTION init_eq 10 | ||
- | set the number of effects to be solved directly (default=0) | + | </ |
+ | 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 | + | </ |
+ | to restart the program from the previous solutions | ||
+ | < | ||
OPTION missing -1 | OPTION missing -1 | ||
- | set the missing value (default 0). | + | </ |
+ | set the missing value (default 0). | ||
+ | < | ||
OPTION restart 100 | OPTION restart 100 | ||
- | set the number of iteration to recompute residuals (default=100) | + | </ |
+ | set the number of iteration to recompute residuals (default=100) | ||
+ | < | ||
OPTION SNP_file snps | OPTION SNP_file snps | ||
- | implement one-step genomic selection updating animal effects with genomic relationship matrix (H-Inverse) | + | </ |
+ | implement one-step genomic selection updating animal effects with genomic relationship matrix (H-Inverse) | ||
- | For information on availability of BLUP90IOD, please contact Ignacy | + | //For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.// |
- | Misztal (ignacy@uga.edu) at the University of Georgia. | + | |
readme.pcg2.txt · Last modified: 2024/05/16 14:16 by dani