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The documentation for blupf90 is available separately as a PDF document. The following lines can be added at the end of parameter file for blupf90:
Available options:
OPTION conv_crit 1e-12
Set convergence criteria (deault 1e-12).
OPTION maxrounds 10000
Set maximum number of rounds (default 1000).
OPTION solv_method FSPAK
Selection solutions by FSPAK, SOR or PCG (default PCG).
OPTION r_factor 1.6
Set relaxation factor for SOR (default 1.4).
OPTION sol se
Store solutions and s.e.
OPTION missing -999
Missing observation (default 0).
OPTION residual
y-hat and residual will be shown in yhat_residual.
OPTION blksize 3
Set block size for preconditioner (default 1).
[shogo@dodo6 thr1pcg]$ cd .. [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
OPTION missing -1
set the missing value (default 0).
OPTION restart 100
set the number of iteration to recompute residuals (default=100)
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.