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readme.gibbsf90new [2019/05/07 01:36] – [Command line options] yutakareadme.gibbsf90new [2019/09/24 17:47] – andres
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 </file> </file>
 The program saves every "5000" samples to restart or recover the job right after the last saved samples. It is useful when the program accidentally stopped. The program saves every "5000" samples to restart or recover the job right after the last saved samples. It is useful when the program accidentally stopped.
-<file> 
 <file> <file>
 OPTION cont 10000 OPTION cont 10000
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 "10000" is the number of samples run previously. The user can restart the program from the last run. This option requires "binary_final_solutions", "gibbs_samples", and "fort.99" files. "10000" is the number of samples run previously. The user can restart the program from the last run. This option requires "binary_final_solutions", "gibbs_samples", and "fort.99" files.
 When using "OPTION cont", all output files will be replaced by new ones. Before running with this option, all files should be backed up. When using "OPTION cont", all output files will be replaced by new ones. Before running with this option, all files should be backed up.
 +<file>
 OPTION prior 5 2 -1 5  OPTION prior 5 2 -1 5 
 </file> </file>
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 Specify the SNP file name to use genotype data. Specify the SNP file name to use genotype data.
 <file> <file>
-OPTION external_script name n+OPTION external_halfway_script name n
 </file> </file>
 program gibbstest will stop every //n// iterations, write samples of variances, unknowns and thresholds, wait for external program gibbstest will stop every //n// iterations, write samples of variances, unknowns and thresholds, wait for external
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 This option can help the 'cold start' (to continue the sampling when the program accidentally stops before completing the run). An integer value //n// is needed. In every //n// rounds, the program saves intermediate samples to 2 files (''last_solutions'' and ''binary_final_solutions''). The program can restart the sampling form the last round where the intermediate files were saved. The program also writes a log file ''save_halfway_samples.txt'' with useful information for the next run. This option can help the 'cold start' (to continue the sampling when the program accidentally stops before completing the run). An integer value //n// is needed. In every //n// rounds, the program saves intermediate samples to 2 files (''last_solutions'' and ''binary_final_solutions''). The program can restart the sampling form the last round where the intermediate files were saved. The program also writes a log file ''save_halfway_samples.txt'' with useful information for the next run.
  
-To restart, add ''OPTION cont 1'' to your parameter file and run ''thrgibbs1f90'' again. Input 3 numbers (samples, burn-in, and interval) according to save_halfway_samples.txt. Thrgibbs1f90 can take care of all restarting process by itself, so no other tools are needed.+To restart, add ''OPTION cont 1'' to your parameter file and run ''gibbsf90test'' again. Input 3 numbers (samples, burn-in, and interval) according to save_halfway_samples.txt. Gibbsf90test can take care of all restarting process by itself, so no other tools are needed.
  
 === Tips === === Tips ===
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 === Example === === Example ===
-Put the following option in your parameter file.+Put the following option in your parameter file for the first time when you run the program.
  
     OPTION save_halfway_samples 100     OPTION save_halfway_samples 100
  
-Run ''thrgibbs1f90''. You will see the following message on screen.+Run ''gibbsf90test''. You will see the following message on screen.
  
     '**** saving halfway samples in every         100  rounds (default=0)     '**** saving halfway samples in every         100  rounds (default=0)
  
-In this case, we assume the number of total samples is 3000, the burn-in is 0, and the interval is 10.+In this example, we assume the number of total samples is 3000, the burn-in is 0, and the interval is 10.
  
      number of samples and length of burn-in      number of samples and length of burn-in
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       interval                =         10       interval                =         10
          
-    Suggestion for the input in next run:+    Suggestion for input in the next run:
       total number of samples =       2200       total number of samples =       2200
       number of burn-in       =          0       number of burn-in       =          0
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        OPTION cont 1        OPTION cont 1
  
-Put the option ''OPTION cont 1'' to your parameter file. It can invoke the 'cold start' module in ''thrgibbs1f90''.+Put the option ''OPTION cont 1'' to your parameter file manually (by hand). It can invoke the 'cold start' module in ''gibbsf90test''.
  
     OPTION cont 1     OPTION cont 1
  
-Run ''thrgibbs1f90'' again. You will see the following message on screen. +Run ''gibbsf90test'' again. You will see the following message on screen. 
  
     '*** continuous sampling selected *** previous # samples =           1     '*** continuous sampling selected *** previous # samples =           1
  
-**NOTE: Although the message may say the previous number of sample is 1, you can ignore it. The program recognizes it is the cold start mode and works correctly.**+**NOTE: Although the message may say the previous number of sample is 1, you can safely ignore it. The program runs with the cold start mode and it works correctly.**
  
 Input the three numbers that are shown in ''save_halfway_samples.txt''. Input the three numbers that are shown in ''save_halfway_samples.txt''.
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        813.3       1303.       1778.            813.3       1303.       1778.    
  
-Just wait the analysis. You can interrupt the program again. The final results will be basically the same to ones from a non-stop analysis.+You can interrupt the program again. The results will be basically the same to ones from the non-stop analysis.
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