readme.pcg2
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| 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 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. | ||
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| + | 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. | ||
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| See PREGSF90 with genotypes (SNP) for options. | See PREGSF90 with genotypes (SNP) for options. | ||
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| Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse). | Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse). | ||
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| + | //For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) or Daniela Lourenco (danilino@uga.edu) at the University of Georgia.// | ||
| ====== Options ====== | ====== Options ====== | ||
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| OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
| </ | </ | ||
| - | Set a convergence criterion (default 1e-12). Usually, a stricter criterion (e.g., 1e-14 to 1e-16) is needed with a single-trait model than a multiple-start model. | + | Set a convergence criterion (default 1e-12). Usually, a stricter criterion (e.g., 1e-14 to 1e-16) is needed with a single-trait model than a multiple-trait model. |
| < | < | ||
| OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
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| OPTION blksize 3 | 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, | + | Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, |
| < | < | ||
| OPTION init_eq 10 | OPTION init_eq 10 | ||
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| OPTION cont 1 | OPTION cont 1 | ||
| </ | </ | ||
| - | To restart the program from the last solutions. | + | To restart the program from the last solutions |
| < | < | ||
| OPTION missing -999 | OPTION missing -999 | ||
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| OPTION restart 100 | OPTION restart 100 | ||
| </ | </ | ||
| - | Set the number of iteration | + | Set the number of iterations |
| < | < | ||
| OPTION prior_solutions | OPTION prior_solutions | ||
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| OPTION SNP_file snp | OPTION SNP_file snp | ||
| </ | </ | ||
| - | Specify the SNP file name to use genotype data. | + | Specify the SNP file name to use genotype data. \\ |
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| - | //For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.// | + | ==== Storing solutions with original ID ==== |
| + | blup90iod2 allows storing solutions with original ID. To do it, simply add the following option: | ||
| + | OPTION origID | ||
| + | The output is //trait effect level original_id solution//, and is stored in '' | ||
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readme.pcg2.1579739172.txt.gz · Last modified: 2024/03/25 18:22 (external edit)