Our Gibbs sampling programs can continue the sampling only if you have prepared something for the accidental stop before running the program. Otherwise, please run it again.
There are two options:
The idea is to save the current samples of “solutions” and variance components.
By default, the samples of variance components will be saved in
gibbs_samples but the samples of “solutions” are saved only in the last round of sampling.
To continue the sampling, the program needs both
save_halfway_samples THRGIBBS1F90 saves
last_solutions in every *n* rounds.
If the option is not available, you can perform small sampling repeatedly.
For example, you can get 1000 samples in one run to get “last_solutions” and continue the next run using the previous results.
A shell script can automate this process. It is not elegant but it will work.
In both methods, the continued sampling may give you slightly different results from the non-breaking run. This is because of numerical error. The saved samples of variance components have limited precision and it creates errors in subsequent sampling. In general, this error is trivial and you can ignore it.
See THRGIBBS1F90 for details.
Modify the following shell script according to your analysis and run it with bash (terminal in Linux and macOS). Before running the script, make sure this script works in your environment. Please read the comment lines in the script to continue the sampling.
#!/bin/bash # # A suggested script to save last_solutions in every N rounds. # Please change the variables according to your analysis. # # To continue the sampling, 1) rename last_run.* to the # original file i.e. # last_run.gibbs_samples -> gubbs_samples # last_run.last_solutions -> last_solutions # last_run.fort.99 -> fort.99 # last_run.binary_final_solutions -> binary_final_solutions # # and 2) put the number of previous samples to the variable # "previous_samples" below. # # This is 0 for the first time. # Put appropriate value if you continue the sampling. previous_samples=0 # Put your favorite value here. total_samples=100000 # Save the intermediate samples every this rounds. save_rounds=10000 # set your parameter file parameter_file=renf90.par # thinning: samples saved in every n rounds thinning=1 # program name program=thrgibbs1f90 # run the program for previous in `seq $previous_samples $save_rounds $total_samples`; do # the current + last current_start=`expr $previous + 1` current_end=`expr $previous + $save_rounds` if [ $current_start -gt $total_samples ]; then break fi # create a parameter file with "OPTION cont" parameter_file_cont=$parameter_file.cont if [ $previous -eq 0 ]; then cp $parameter_file $parameter_file_cont else cp $parameter_file $parameter_file_cont echo OPTION cont $previous >> $parameter_file_cont fi # input echo $parameter_file_cont > input.txt echo $save_rounds 0 >> input.txt echo $thinning >> input.txt echo "#" Running from $current_start to $current_end >> input.txt # run the program $program < input.txt if [ $? -ne 0 ]; then break fi # backup the files echo 'The files last_run.* have the previous' $current_end 'samples.' > last_run.txt cp gibbs_samples last_run.gibbs_samples cp last_solutions last_run.last_solutions cp fort.99 last_run.fort.99 cp binary_final_solutions last_run.binary_final_solutions done