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--- readme.pcg2 [2012/05/28 13:47] – created shogo
+++ readme.pcg2 [2024/05/15 19:48] – [Summary] dani
@@ Line 1: / Line 1: @@
-The documentation for blupf90 is available separately as a PDF document.
+====== BLUP90IOD2 ======
-The following lines can be added at the end of parameter file for blupf90:
-Available options:
+===== Summary =====
+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 single-step genomic evaluations 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 ======
+<file>
 OPTION conv_crit 1e-12
+</file>
-    Set convergence criteria (deault 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-trait model.
+<file>
 OPTION maxrounds 10000
+</file>
-    Set maximum number of rounds (default 1000).
+Set maximum number of rounds (default 5000).
+<file>
+OPTION blksize 3
+</file>
+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.
+<file>
+OPTION init_eq 10
+</file>
+Set the number of effects to be solved directly (default=0) to accelerate convergence (usually, 10% to 50% faster).
+<file>
 OPTION solv_method FSPAK
+</file>
-    Selection solutions by FSPAK, SOR or PCG (default PCG).
+Solving method for initial equations (default=DIRECT).
+<file>
-OPTION r_factor 1.6
+OPTION tol 1d-12
+</file>
-    Set relaxation factor for SOR (default 1.4).
+Tolerance to get a positive definite covariance component matrix (default=1d-12).
+<file>
-OPTION sol se
-    Store solutions and s.e.
-OPTION missing -999
-    Missing observation (default 0).
 OPTION residual
+</file>
-    y-hat and residual will be shown in yhat_residual.
+y-hat and residuals will be included in "yhat_residual".
+<file>
-OPTION blksize 3
+OPTION avgeps 50
+</file>
-    Set block size for preconditioner (default 1).
+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.
-[shogo@dodo6 thr1pcg]$ cd ..
+<file>
-[shogo@dodo6 f90-05]$ cat pcg2/Readme.pcg2
-BLUP90IOD2 - Optimized version of BLUP90IOD with options for block diagonal preconditioner and direct
-solving
-Modified by Shogo Tsuruta, University of Georgia
-The following lines can be added at the end of parameter file:
-OPTION conv_crit  1e-10
-   set convergence criterion to given level (default 1e-12)
-OPTION maxrounds  10000
-   set maximum number of rounds to given number (default=5000)
-OPTION solv_method  FSPAK
-   selection initial solutions by FSPAK or DIRECT (default is DIRECT)
-OPTION blksize 3
-   set block size for preconditioner (default=1)
-OPTION init_eq 10
-   set the number of effects to be solved directly (default=0)
 OPTION cont 1
-   to restart the program from the previous solutions
+</file>
+To restart the program from the last solutions (required file: solutions_rsd).
-OPTION missing -1
+<file>
-   set the missing value (default 0).
+OPTION missing -999
+</file>
+Set the missing value (default 0) in integer.
+<file>
 OPTION restart 100
-   set the number of iteration to recompute residuals (default=100)
+</file>
+Set the number of iterations to reset the residuals (default=100).
+<file>
+OPTION prior_solutions
+</file>
+Using the previous solution file to start the iteration. An additional software is required to use this option.
+<file>
+OPTION random_upg 1 2
+</file>
+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).
+<file>
+OPTION SNP_file snp
+</file>
+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:
+  OPTION origID
+The output is //trait effect level original_id solution//, and is stored in ''solutions.original''.
-OPTION SNP_file snps
-   implement one-step genomic selection updating animal effects with genomic relationship matrix (H-Inverse)
-For information on availability of BLUP90IOD, please contact Ignacy
-Misztal (ignacy@uga.edu) at the University of Georgia.