R/clean.R

In jokergoo/bsub: Submitter and Monitor of the 'LSF Cluster'

#' Clear temporary dir
#' 
#' @param ask Whether to promote.
#'
#' @details
#' The temporary files might be used by the running/pending jobs. Deleting them would affect some jobs.
#' You should better delete them after all jobs are done.
#'
#' @export
#' @examples
#' \dontrun{
#' list_temp_files()
#' }
#' 
list_temp_files = function() {

    if(!under_same_file_system()) {
        stop("Temporary files can only be detected on the same file system as submission nodes.")
    }

    attached_vars = job_attached_vars_by_id()
    temp_dir = attached_vars$temp_dir
    temp_dir = temp_dir[!is.na(temp_dir)]

    files = unlist(lapply(temp_dir, function(x) {
        list.files(x, full.names = TRUE)
    }))

    unname(files)
}

#' @rdname list_temp_files
#' @export
remove_temp_files = function(ask = TRUE) {

    if(!under_same_file_system()) {
        stop("Temporary files can only be detected on the same file system as submission nodes.")
    }

    files = list_temp_files()

    if(length(files) == 0) {
        if(ask) qqcat("All temporary directories are empty.\n")
        return(invisible(NULL))
    }
    if(!ask) {
        if(length(files)) {
            file.remove(files)
            return(invisible(NULL))
        }
    }

    file_types = gsub("^.*\\.([^.]+)$", "\\1", files)
    tb = table(file_types)
    job_tb = bjobs(status = "all", print = FALSE)
    if(any(job_tb$JOB_STAT %in% c("RUN", "PEND"))) {
        cat("There are still running/pending jobs. Deleting temporary files might affect some of the jobs.\n")
    }
    cat(qq("There @{ifelse(length(files) > 1, 'are', 'is')} "), qq("@{tb} .@{names(tb)} file@{ifelse(tb > 1, 's', '')}, "), "delete all? [y|n|s] ", sep = "")
    while(1) {
        answer = readline()
        if(answer == "y" || answer == "Y") {
            file.remove(files)
            break
        } else if(answer == "n" || answer == "N") {
            break
        } else if(answer == "s" || answer == "S") {
            for(nm in names(tb)) {
                qqcat("Remove all @{tb[nm]} .@{nm} file@{ifelse(tb[nm] > 1, 's', '')}? [y|n] ")
                while(1) {
                    answer2 = readline()
                    if(answer2 == "y" || answer2 == "Y") {
                        file.remove(files[file_types == nm])
                        break
                    } else if(answer2 == "n" || answer2 == "N") {
                        break
                    } else {
                        qqcat("Remove all @{tb[nm]} .@{nm} file@{ifelse(tb[nm] > 1, 's', '')}? [y|n] ")
                    }
                }
                
            }
            break
        } else {
            cat(qq("There @{ifelse(length(files) > 1, 'are', 'is')} "), qq("@{tb} .@{names(tb)} file@{ifelse(tb > 1, 's', '')}, "), "delete all? [y|n|s] ", sep = "")
        }
    }
    return(invisible(NULL))
}

#' Check whether there are dump files
#' 
#' @param print Whether to print messages.
#'
#' @details
#' For the failed jobs, LSF cluster might generate a core dump file and R might generate a `.RDataTmp` file.
#'
#' Note if you manually set working directory in your R code/script, the R dump file can be not caught.
#'
#' @returns A vector of file names.
#' @export
#' @examples
#' \dontrun{
#' list_dump_files()
#' }
list_dump_files = function(print = TRUE) {

    if(!under_same_file_system()) {
        stop("Dump files can only be detected on the same file system as submission nodes.")
    }

    job_tb = bjobs(status = "all", print = FALSE)
    wd = job_tb$EXEC_CWD
    wd = wd[wd != "-"]
    wd = unique(wd)

    dump_files = NULL
    for(w in wd) {
        if(print) {
            qqcat("checking @{w}\n")
        }
        dump_files = c(dump_files, list.files(path = w, pattern = "^core.\\d$", all.files = TRUE, full.names = TRUE))
        dump_files = c(dump_files, list.files(path = w, pattern = "^\\.RDataTmp", all.files = TRUE, full.names = TRUE))
    }

    return(dump_files)
}