readme.pcg2
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
readme.pcg2 [2016/10/21 22:17] – [Options] shogo | readme.pcg2 [2024/03/25 18:22] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 5: | Line 5: | ||
\\ | \\ | ||
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. | ||
+ | \\ | ||
+ | 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. | 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). | Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse). | ||
+ | |||
+ | //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 ====== | ||
Line 14: | Line 18: | ||
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 | OPTION blksize 3 | ||
</ | </ | ||
- | Set block size for preconditioner (default 1). | + | Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, use the number of traits. |
< | < | ||
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) to accelerate convergence (usually, 10% to 50% faster). |
< | < | ||
OPTION solv_method FSPAK | OPTION solv_method FSPAK | ||
Line 34: | Line 38: | ||
OPTION tol 1d-12 | OPTION tol 1d-12 | ||
</ | </ | ||
- | Tolerance to get a positive definite matrix (default=1d-12). | + | Tolerance to get a positive definite |
< | < | ||
OPTION residual | OPTION residual | ||
Line 42: | Line 46: | ||
OPTION avgeps 50 | OPTION avgeps 50 | ||
</ | </ | ||
- | Using the last 50 average eps for convergence. | + | Using the last 50 average eps for convergence, |
< | < | ||
OPTION cont 1 | OPTION cont 1 | ||
</ | </ | ||
- | To restart the program from the previous | + | To restart the program from the last solutions |
< | < | ||
OPTION missing -999 | OPTION missing -999 | ||
Line 54: | Line 58: | ||
OPTION restart 100 | OPTION restart 100 | ||
</ | </ | ||
- | Set the number of iteration | + | Set the number of iterations |
< | < | ||
OPTION prior_solutions | OPTION prior_solutions | ||
Line 66: | Line 70: | ||
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. \\ |
\\ | \\ | ||
- | //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 '' | ||
+ | |||
readme.pcg2.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1