Deleting temporary files created by cmdstanr

General
1

I am running cmdstanr within an mclapply loop, e.g.

                                                   
mod <- cmdstan_model(stan_file='myModel.stan') 
results <-do.call(rbind,mclapply(1:1000,mc.cores=4,function(i) {  
  ...
  fit <- mod$sample(data=input_data,
                    chains=4,
                  parallel_chains=4)
  ...
})

Stan runs fine but it creates several large files within the rtmpfile /tmp/RtmpXXX and they do not get removed, but actually accumulate as the mclapply loop progresses and take up more and more space.

What can I do? Is there a way to figure out the temporary files that rcmdstan is creating so that I can delete them after each run? Any other suggestions?

2

The sample() function allows you to manually specify the name and location of the temp file where draws are written to. See Run Stan's MCMC algorithms — model-method-sample • cmdstanr

3 Likes
4

This works, one can get the output files from the fit and then delete them…

files_to_remove ← fit$output_files()
file.remove(files_to_remove)

1 Like