Merge pull request #23 from A2-ai/cleanup

Cleanup

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: slurmtools
 Title: slurm tooling 
-Version: 0.0.0.9003
+Version: 0.0.0.9004
 Authors@R: c(person("Devin", "Pastoor", , "[email protected]", role = c("aut", "cre")),
     person("Jenna", "Elwing", email = "[email protected]", role = "aut"),
     person("Matthew", "Smith", email = "[email protected]", role = "aut"))
@@ -25,7 +25,8 @@ Imports:
     here,
     cli,
     stringi,
-    hms
+    hms,
+    lifecycle
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -13,7 +13,7 @@ export(cancel_slurm_job)
 export(generate_nmm_config)
 export(get_slurm_jobs)
 export(get_slurm_partitions)
-export(submit_nonmem_model)
+export(submit_slurm_job)
 importFrom(brio,read_file)
 importFrom(brio,write_file)
 importFrom(dplyr,"%>%")

R/cancel-job.R

@@ -1,7 +1,7 @@
 #' Cancels a running job
 #'
 #' @param job_id job id to cancel
-#' @param user optional if not the current user.
+#' @param confirm requires confirmation to cancel job
 #' @importFrom rlang .data
 #' @importFrom rlang .env
 #'
@@ -10,38 +10,43 @@
 #' @examples \dontrun{
 #' cancel_job(243)
 #' }
-cancel_slurm_job <- function(job_id, user = NULL) {
+cancel_slurm_job <- function(job_id, confirm = TRUE) {
 
   current_user = if (is.null(Sys.getenv("USER"))) Sys.info()['user'] else Sys.getenv("USER")
 
-  if (!is.null(user) && user != current_user) {
-    cat("The supplied user does not match the current user.\n")
-    cat(paste0("\tsupplied user: ", user, "\n\tcurrent_user: ", current_user, "\n"))
-    cat("You might be cancelling someone elses job.")
-    continue <- readline("Are you sure you want to cancel this job? (Y/n)\n")
-    if (continue == "Y") {
-      current_user <- user
-    } else if (tolower(continue) == "n") {
-      stop(paste0("Not cancelling job: ", job_id))
-    } else {
-      stop("Please enter Y or n")
-    }
-  }
-
   jobs <- get_slurm_jobs(user = current_user)
 
   if (!job_id %in% jobs$job_id) {
-    stop("Please ensure the job id is correct.")
+    if (job_id %in% get_slurm_jobs()$job_id) {
+      message("This job is associated with a different user")
+    }
+    message(paste0("Below are the available jobs for you to cancel:"))
+    print(get_slurm_jobs(user = current_user))
+    stop(paste0("Please ensure the job id is associated your user_name: ", current_user))
   }
 
   job_id_filtered <- jobs %>% dplyr::filter(.data$job_id == .env$job_id)
   if (!job_id_filtered$job_state %in% c("RUNNING", "CONFIGURING")) {
     stop(paste0("Job: ", job_id, " is not running"))
   }
 
-  result <- processx::run("scancel", args = c(as.character(job_id)))
-  if (result$status != 0) {
-    print(paste0("Stdout: ", result$stdout))
-    print(paste0("Stderr: ", result$stderr))
+  if (confirm) {
+    continue <- readline(
+      paste0("You are about to cancel job: ", job_id, ". Are you sure you want to cancel? [Y/n]\n")
+    )
+  } else {
+    continue <- "Y"
+  }
+
+  if (continue == "Y") {
+    result <- processx::run("scancel", args = c(as.character(job_id)))
+    if (result$status != 0) {
+      print(paste0("Stdout: ", result$stdout))
+      print(paste0("Stderr: ", result$stderr))
+    }
+  } else if (tolower(continue) == 'n') {
+    stop("Job NOT cancelled.")
+  } else {
+    stop("You must enter Y or n")
   }
 }

R/slurmtools.R

@@ -5,7 +5,7 @@
 #'
 #' @section submitting jobs:
 #' \itemize{
-#'  \item \code{\link{submit_nonmem_model}}: Submits a job to slurm
+#'  \item \code{\link{submit_slurm_job}}: Submits a job to slurm
 #'  \item \code{\link{generate_nmm_config}}: Generates a NONMEMmonitor config
 #'  file
 #' }

R/submit-model.R

@@ -11,7 +11,11 @@
 #' @param bbi_config_path path to bbi.yaml file for bbi configuration
 #' @param slurm_template_opts choose slurm template
 #'
-#' @export
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#'
+#' @keywords internal
 submit_nonmem_model <-
   function(.mod,
            partition = get_slurm_partitions(),
@@ -23,7 +27,7 @@ submit_nonmem_model <-
            submission_root = getOption('slurmtools.submission_root'),
            bbi_config_path = getOption('slurmtools.bbi_config_path'),
            slurm_template_opts = list()) {
-
+    lifecycle::deprecate_soft("0.1.0", "submit_nonmem_model()", "submit_slurm_job()")
     if (is.null(partition)) {
       rlang::abort("no partition selected")
     }
@@ -127,3 +131,134 @@ submit_nonmem_model <-
       processx::run(cmd$cmd, cmd$args, ...)
     })
   }
+
+#' submit a nonmem model to slurm in parallel
+#'
+#' @param .mod a path to a model or a bbi nonmem model object
+#' @param partition name of the partition to submit the model
+#' @param ncpu number of cpus to run the model against
+#' @param overwrite whether to overwrite existing model results
+#' @param dry_run return the command that would have been invoked, without invoking
+#' @param ... arguments to pass to processx::run
+#' @param slurm_job_template_path path to slurm job template
+#' @param submission_root directory to track job submission scripts and output
+#' @param bbi_config_path path to bbi.yaml file for bbi configuration
+#' @param slurm_template_opts choose slurm template
+#'
+#' @export
+submit_slurm_job <-
+  function(.mod,
+           partition = get_slurm_partitions(),
+           ncpu = 1,
+           overwrite = FALSE,
+           dry_run = FALSE,
+           ...,
+           slurm_job_template_path = getOption('slurmtools.slurm_job_template_path'),
+           submission_root = getOption('slurmtools.submission_root'),
+           bbi_config_path = getOption('slurmtools.bbi_config_path'),
+           slurm_template_opts = list()) {
+
+    if (is.null(partition)) {
+      rlang::abort("no partition selected")
+    }
+    partition <- match.arg(partition)
+
+    check_slurm_partitions(ncpu, partition)
+
+    if (!inherits(.mod, "bbi_nonmem_model") &&
+        !fs::file_exists(.mod)) {
+      stop(
+        "please provide a bbi_nonmem_model created via read_model/new_model, or a path to the model file"
+      )
+    }
+    if (!inherits(.mod, "bbi_nonmem_model")) {
+      # its a file path that exists so lets convert that into the structure bbi
+      # provides for now
+      .mod <- list(absolute_model_path = fs::path_abs(.mod))
+    }
+    parallel <- if (ncpu > 1) {
+      TRUE
+    } else {
+      FALSE
+    }
+
+    if (!fs::file_exists(slurm_job_template_path)) {
+      rlang::abort(sprintf("slurm job template path not valid: `%s`", slurm_job_template_path))
+    }
+    if (overwrite && fs::dir_exists(.mod$absolute_model_path)) {
+      fs::dir_delete(.mod$absolute_model_path)
+    }
+
+    config_toml_path <- paste0(.mod$absolute_model_path, ".toml")
+    #if (!fs::file_exists(config_toml_path)) {
+    #  rlang::warn(sprintf("config.toml file not found, if submitting the job with nmm this is required. Please run generate_nmm_config()"))
+    #}
+
+    if (is.null(slurm_template_opts$nmm_exe_path)) {
+      nmm_exe_path <- Sys.which("nmm")
+    } else {
+      nmm_exe_path <- slurm_template_opts$nmm_exe_path
+    }
+
+    if (is.null(slurm_template_opts$bbi_exe_path)) {
+      bbi_exe_path <- Sys.which("bbi")
+    } else {
+      bbi_exe_path <- slurm_template_opts$bbi_exe_path
+    }
+
+    if (is.null(slurm_template_opts$project_path)) {
+      project_path <- here::here()
+    } else {
+      project_path <- slurm_template_opts$project_path
+    }
+    if (is.null(slurm_template_opts$project_name)) {
+      project_name <- here::here() %>% basename()
+    } else {
+      project_name <- slurm_template_opts$project_name
+    }
+
+    default_template_list = list(
+      partition = partition,
+      parallel = parallel,
+      ncpu = ncpu,
+      job_name = sprintf("%s-nonmem-run", basename(.mod$absolute_model_path)),
+      project_path = project_path,
+      project_name = project_name,
+      bbi_exe_path = bbi_exe_path,
+      bbi_config_path = bbi_config_path,
+      model_path = .mod$absolute_model_path,
+      config_toml_path = config_toml_path,
+      nmm_exe_path = nmm_exe_path
+    )
+
+    template_list = c(
+      default_template_list,
+      slurm_template_opts)
+
+    template_script <-
+      withr::with_dir(dirname(.mod$absolute_model_path), {
+        tmpl <- brio::read_file(slurm_job_template_path)
+        whisker::whisker.render(
+          tmpl,
+          template_list
+        )
+      })
+
+    script_file_path <-
+      file.path(submission_root, sprintf("%s.sh", basename(.mod$absolute_model_path)))
+    if (!dry_run) {
+      if (!fs::dir_exists(submission_root)) {
+        fs::dir_create(submission_root)
+      }
+      brio::write_file(template_script, script_file_path)
+      fs::file_chmod(script_file_path, "0755")
+    }
+    cmd <- list(cmd = Sys.which("sbatch"), args = script_file_path, template_script = template_script, partition = partition)
+    if (dry_run) {
+      return(cmd)
+    }
+    withr::with_dir(submission_root, {
+      processx::run(cmd$cmd, cmd$args, ...)
+    })
+  }
+

_pkgdown.yml

@@ -37,7 +37,7 @@ navbar:
 reference:
 - title: Data Processing Functions
   contents:
-  - submit_nonmem_model
+  - submit_slurm_job
   - generate_nmm_config
   - get_slurm_jobs
   - cancel_slurm_job