readme.pcg2
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readme.pcg2 [2012/05/30 14:05] – shogo | readme.pcg2 [2024/05/15 19:48] – [Summary] dani | ||
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- | ====== BLUP90IOD2====== | + | ====== BLUP90IOD2 ====== |
- | \\ | + | |
+ | ===== Summary ===== | ||
The original program was written by Shogo Tsuruta in 1999. | 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. | ||
+ | \\ | ||
+ | It implements single-step genomic evaluations updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse). | ||
- | ===== Summary===== | + | //For information on availability |
- | BLUP90IOD2 is a BLUP program for solving a large number | + | |
====== Options ====== | ====== Options ====== | ||
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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 | + | OPTION solv_method |
</ | </ | ||
Solving method for initial equations (default=DIRECT). | Solving method for initial equations (default=DIRECT). | ||
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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 | ||
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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 -1 | + | OPTION missing -999 |
</ | </ | ||
- | Set the missing value (default 0). | + | Set the missing value (default 0) in integer. |
< | < | ||
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 random_upg 1 2 | OPTION random_upg 1 2 | ||
</ | </ | ||
- | Set the UPG random. " | + | Set the UPG random. " |
< | < | ||
- | OPTION SNP_file | + | OPTION SNP_file |
</ | </ | ||
- | implement one-step genomic selection updating animal effects | + | Specify the SNP file name to use genotype data. \\ |
+ | \\ | ||
+ | ==== Storing solutions | ||
+ | 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 '' | ||
- | //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