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--- readme.pcg2 [2012/05/28 13:47] – created shogo
+++ readme.pcg2 [2012/05/30 14:08] – shogo
@@ 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:
+\\
+The original program was written by Shogo Tsuruta in 1999.
-Available options:
+===== Summary=====
+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.
+====== Options ======
+<file>
 OPTION conv_crit 1e-12
+</file>
-    Set convergence criteria (deault 1e-12).
+Set convergence criteria (deault 1e-12).
+<file>
 OPTION maxrounds 10000
+</file>
-    Set maximum number of rounds (default 1000).
+Set maximum number of rounds (default 1000).
+<file>
+OPTION blksize 3
+</file>
+Set block size for preconditioner (default 1).
+<file>
+OPTION init_eq 10
+</file>
+Set the number of effects to be solved directly (default=0).
+<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 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.
-[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 previous solutions.
+<file>
 OPTION missing -1
-   set the missing value (default 0).
+</file>
+Set the missing value (default 0).
+<file>
 OPTION restart 100
-   set the number of iteration to recompute residuals (default=100)
+</file>
+Set the number of iteration to recompute 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 snps
-   implement one-step genomic selection updating animal effects with genomic relationship matrix (H-Inverse)
+</file>
+implement one-step genomic selection updating animal effects with genomic relationship matrix (H-Inverse).
-For information on availability of BLUP90IOD, please contact Ignacy
+//For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.//
-Misztal (ignacy@uga.edu) at the University of Georgia.