readme.pcg2
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readme.pcg2 [2012/05/28 13:47] – created shogo | readme.pcg2 [2020/07/09 19:54] – [Summary] 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 options: | + | ===== 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. | ||
+ | \\ | ||
+ | BLUP90IOD2 has 2 additional versions: BLUP90IOD2OMP1 with OpenMP and BLUP90IOD2MPI with MPI. The OpenMP version is faster running with multiple cores. The MPI version has the same computing speed as the OpenMP version with less memory when we use SSD. | ||
+ | \\ | ||
+ | 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 | + | Set a convergence |
+ | < | ||
OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
- | + | </ | |
- | Set maximum number of rounds (default | + | Set maximum number of rounds (default |
+ | < | ||
+ | OPTION blksize 3 | ||
+ | </ | ||
+ | Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, the number can be the number of traits. | ||
+ | < | ||
+ | OPTION init_eq 10 | ||
+ | </ | ||
+ | Set the number of effects to be solved directly (default=0) to accelerate convergence (usually, 10% to 50% faster). | ||
+ | < | ||
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 covariance component matrix |
- | + | < | |
- | OPTION | + | |
- | + | ||
- | Store solutions and s.e. | + | |
- | + | ||
- | OPTION missing | + | |
- | + | ||
- | | + | |
OPTION residual | OPTION residual | ||
- | + | </ | |
- | y-hat and residual | + | y-hat and residuals |
- | + | < | |
- | OPTION | + | OPTION |
- | + | </file> | |
- | Set block size for preconditioner (default 1). | + | Using the last 50 average eps for convergence, depending on the fluctuation |
- | [shogo@dodo6 thr1pcg]$ cd .. | + | < |
- | [shogo@dodo6 f90-05]$ cat pcg2/Readme.pcg2 | + | |
- | BLUP90IOD2 - Optimized version of BLUP90IOD with options | + | |
- | solving | + | |
- | + | ||
- | Modified by Shogo Tsuruta, University | + | |
- | + | ||
- | The following lines can be added at the end of parameter file: | + | |
- | + | ||
- | OPTION conv_crit | + | |
- | set convergence criterion to given level (default | + | |
- | + | ||
- | 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 last 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