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title: Large-scale genetic evaluation author: Yutaka Masuda date: September 2019 subject: "Introduction to BLUPF90 suite programs" tags: [introduction,tutorial] ...

Iteration on data with preconditioned conjugate gradient (PCG)

Algorithm

Preconditioned conjugate gradient (PCG) is an iterative method to solve the linear equations. This method is easily harmonized with the "iteration on data" technique. The intermediate status is kept in 4 vectors, and the one iteration will be done by updating the vectors. BLUP90IOD2 is a program implementing this algorithm. Here we will introduce a basic idea needed to understand what the program performs. See Stranden and Lidauer (2000) and Tsuruta et al. (2001) for the detailed algorithm.

The mixed model equations can be written as $$ \mathbf{Cx} = \mathbf{b} $$ where $\mathbf{C}$ is the left-hand side matrix, $\mathbf{x}$ is the solution vector, and $\mathbf{b}$ is the right-hand side vector. If we have a matrix $\mathbf{M}$ which is an approximation of $\mathbf{C}$, above equations are equivalent to $$ \mathbf{M}^{-1}\mathbf{Cx} = \mathbf{M}^{-1}\mathbf{b}. $$ This matrix $\mathbf{M}$ is called preconditioner. If $\mathbf{M = C}$, the equations are immediately solved. BLUPF90 uses $\mathbf{M} = \mathrm{diag}(\mathbf{C})$ so its inverse is easily calculated.

The residual is expressed as $$ \mathbf{r} = \mathbf{b} - \mathbf{Cx} $$ and the algorithm tries to reduce with statistics containing the residual. The convergence criterion with the current solution $\mathbf{\hat{x}}$ is $$ \varepsilon = \frac{||\mathbf{b} - \mathbf{C\hat{x}}||^2}{||\mathbf{b}||^2} $$ where $||\cdot||$ means the norm. The default of $\varepsilon$ in BLUPF90IOD2 is $10^{-12}$.

Note that some other software, e.g., MiX99, uses $\sqrt{\varepsilon}$. The users should be careful about the definition of convergence criterion when they have switched the software to BLUPF90IOD2.

Programs

BLUP90IOD2 is the current program to perform the iteration on data with PCG. CBLUP90IOD can handle a threshold model or threshold-linear models with 1 threshold trait. BLUP90MBE is specialized in multibreed models with external information (see Legarra et al., 2007). In this example, we use the BLUP90IOD2 program.

A parallel version of BLUPF90IOD2 is now available. BLUP90IOD2OMP1 is a program supporting parallel processing in reading data and pedigree files using OpenMP. This program is useful especially for very large data set with a complicated model (like the multiple-trait model). There is no advantage to use this program for small or moderate data set. The usage of this program is the same as BLUP90IOD2.

Files and analysis

Here we will use the same sample files as used in REML estimation.

We will apply a 4-trait animal model to this data set with the following parameter file.

DATAFILE
simdata.txt
NUMBER_OF_TRAITS
4
NUMBER_OF_EFFECTS
4
OBSERVATION(S)
9 10 11 12
WEIGHT(S)

EFFECTS:
6 6 6 6   155 cross
7 7 7 7     2 cross
8 8 8 8    11 cross
1 1 1 1  4641 cross
RANDOM_RESIDUAL VALUES
 63.568  35.276  26.535  13.533
 35.276  84.627  37.831  23.306
 26.535  37.831  75.156  28.079
 13.533  23.306  28.079  46.839
RANDOM_GROUP
4
RANDOM_TYPE
add_animal
FILE
simped.txt
(CO)VARIANCES
 37.150  19.471  23.885  24.246
 19.471  16.128  19.571  22.239
 23.885  19.571  31.315  33.782
 24.246  22.239  33.782  51.706

Run BLUP90IOD2 with the parameter file. It takes 185 rounds to meet the convergence.

round =   183  eps =  0.1707E-11  time =    0.01
round =   184  eps =  0.1139E-11  time =    0.01
round =   185  eps =  0.9976E-12  time =    0.01
  7.1286485E-03 seconds per round
 * END iteration: 11-14-2016  17h 52m 05s 737
 solutions stored in file: "solutions"

Options

OPTION conv_crit tol

This option defines the convergence criterion ($\varepsilon$) to stop the iterations. A real value tol should be a small value. The default is 1.0E-12. The criterion should be carefully decided because the default value could be too loose but the strict criterion requires too many rounds to converge. The best practice is to compare solutions from different convergence criterions and determine enough convergence criterion.

OPTION blksize n

This option creates a block diagonal matrix for pre-conditioner ($\mathbf{M}$). The integer value n defines the block size. By default, the pre-conditioner is the diagonal matrix (i.e. n is 1). The block size should be the same as the number of traits. This option will reduce the number of iterations if the specified value is valid.