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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).

For information on availability of BLUP90IOD, please contact Ignacy Misztal ( or Daniela Lourenco ( at the University of Georgia.


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.

OPTION maxrounds 10000

Set maximum number of rounds (default 5000).

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, use 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

Solving method for initial equations (default=DIRECT).

OPTION tol 1d-12

Tolerance to get a positive definite covariance component matrix (default=1d-12).

OPTION residual

y-hat and residuals will be included in “yhat_residual”.

OPTION avgeps 50

Using the last 50 average eps for convergence, depending on the fluctuation of convergence. When using this option, the convergence criterion can be loosen (e.g., 1e-12 → 1e-10, 1e-14 → 1e-12), also depending on how convergence fluctuates.

OPTION cont 1

To restart the program from the last solutions (required file: solutions_rsd).

OPTION missing -999

Set the missing value (default 0) in integer.

OPTION restart 100

Set the number of iterations to reset the residuals (default=100).

OPTION prior_solutions

Using the previous solution file to start the iteration. An additional software is required to use this option.

OPTION random_upg 1 2

Set the UPG random. “1” the weight for random UPG = 1. If the second number exits, the weight will be inverted (e.g., 1/2=0.5).

OPTION SNP_file snp

Specify the SNP file name to use genotype data.

Storing solutions with original ID

blup90iod2 allows storing solutions with original ID. To do it, simply add the following option:


The output is trait effect level original_id solution, and is stored in solutions.original.

readme.pcg2.txt · Last modified: 2023/01/07 03:08 by shogo