Merge pull request #18 from A2-ai/cancel_job

added ability to cancel a running job

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: slurmtools
 Title: slurm tooling 
-Version: 0.0.0.9001
+Version: 0.0.0.9002
 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"))

NAMESPACE

@@ -9,6 +9,7 @@ S3method(format_toml,integer)
 S3method(format_toml,list)
 S3method(format_toml,logical)
 S3method(format_toml,name)
+export(cancel_job)
 export(generate_nmm_config)
 export(get_slurm_jobs)
 export(get_slurm_partitions)
@@ -36,6 +37,8 @@ importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map2_chr)
 importFrom(purrr,map_if)
+importFrom(rlang,.data)
+importFrom(rlang,.env)
 importFrom(rlang,abort)
 importFrom(rlang,as_function)
 importFrom(rlang,dots_list)

R/cancel-job.R

@@ -0,0 +1,48 @@
+#' Cancels a running job
+#'
+#' @param job_id job id to cancel
+#' @param user optional if not the current user.
+#' @importFrom rlang .data
+#' @importFrom rlang .env
+#'
+#' @export
+#'
+#' @examples \dontrun{
+#' cancel_job(243)
+#' }
+cancel_job <- function(job_id, user = NULL) {
+
+  current_user = Sys.getenv("USER") %||% Sys.info()['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$job_id) {
+    stop("Please ensure the job id is correct.")
+  }
+
+  job_id_filtered <- jobs %>% dplyr::filter(.data$job_id == .env$job_id)
+  print(job_id_filtered)
+  if (job_id_filtered$job_state != "RUNNING") {
+    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))
+  }
+}

R/slurmtools.R

@@ -16,6 +16,11 @@
 #'  that shows status and other information given with `squeue`
 #' }
 #'
+#' @section cancelling jobs:
+#' \itemize{
+#'  \item \code{\link{cancel_job}}: Cancels the specified job
+#' }
+#'
 #' @section slurm partitions:
 #' \itemize{
 #'  \item \code{\link{get_slurm_partitions}}: Gives a vector of available

_pkgdown.yml

@@ -40,6 +40,7 @@ reference:
   - submit_nonmem_model
   - generate_nmm_config
   - get_slurm_jobs
+  - cancel_job
   - get_slurm_partitions
   - slurmtools
 

vignettes/Running-nonmem.Rmd

@@ -6,18 +6,6 @@ vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
-
-```{r, include = FALSE}
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
-```
-
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -259,13 +247,19 @@ curl -d "Finished model run: 1001-nonmem-run $JOBID" ntfy.sh/ntfy_demo
 
 To reiterate, this template file is run as a bash shell script so anything you can do in bash you can put into the template and pass the needed arguments and customize the behavior to your liking.
 
-```{r, include = FALSE}
-#removing generated files from running this vignette
-# nonmem <- file.path("model", "nonmem")
-# 
+```{r cleanup, include = FALSE}
+# cancelling any running nonmem jobs
+jobs <- get_slurm_jobs(user = "matthews") %>%
+  dplyr::filter(job_state == "RUNNING") %>% 
+  dplyr::pull(job_id)
+
+for (job in jobs) {
+  cancel_job(job)
+}
+
 unlink(file.path(nonmem, "1001"), recursive = TRUE)
 unlink(file.path(nonmem, "1001.yaml"))
 unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
+unlink(file.path(nonmem, "submission-log"), recursive = TRUE)
 unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
 ```

vignettes/custom-alerts.Rmd

@@ -10,17 +10,6 @@ editor_options:
     wrap: 72
 ---
 
-```{r, include = FALSE}
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
-```
-
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -40,12 +29,13 @@ options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
 ## Submitting a NONMEM job with nmm
 
 Instead of using bbi we can use `nmm` ([NONMEM
-Monitor](https://github.com/A2-ai/nonmem-monitor/releases)) which currently has
-some additional functionality of sending notifications about zero
-gradients, missing -1E9 lines in ext file, and some very basic control
-stream errors. Nonmem-monitor also allows for setting up an alerter to
-be better fed these messages - more on that later. To use `nmm` you can
-install the latest release from the github repository linked above.
+Monitor](https://github.com/A2-ai/nonmem-monitor/releases)) which
+currently has some additional functionality of sending notifications
+about zero gradients, missing -1E9 lines in ext file, and some very
+basic control stream errors. Nonmem-monitor also allows for setting up
+an alerter to be better fed these messages - more on that later. To use
+`nmm` you can install the latest release from the github repository
+linked above.
 
 We can update the template file accordingly:
 
@@ -70,7 +60,8 @@ it's not on our path.
 The `config.toml` file controls what `nmm` will monitor and where to
 look for files and how to alert you. We'll use `generate_nmm_config()`
 to create this file. First we can look at the documentation to see what
-type of information we should pass to this function. `?generate_nmm_config()`
+type of information we should pass to this function.
+`?generate_nmm_config()`
 
 ```{r}
 mod_number <- "1001"
@@ -239,19 +230,16 @@ This gives us the notifications in a much more digestible format
 
 ![nmm ntfy.sh alerts](data/images/nmm_ntfy_alerts.png)
 
-```{r, include = FALSE}
-# #cancelling any running nonmem jobs
-# state <- slurmtools::get_slurm_jobs(user = "matthews")
-# 
-# if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
-#   for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
-#     processx::run("scancel", args = paste0(job_id))
-#   }
-# }
-# 
-# #removing generated files from running this vignette
-# nonmem <- file.path("model", "nonmem")
-# 
+```{r cleanup, include = FALSE}
+# cancelling any running nonmem jobs
+jobs <- get_slurm_jobs(user = "matthews") %>%
+  dplyr::filter(job_state == "RUNNING") %>% 
+  dplyr::pull(job_id)
+
+for (job in jobs) {
+  cancel_job(job)
+}
+
 unlink(file.path(nonmem, "1001"), recursive = TRUE)
 unlink(file.path(nonmem, "1001.yaml"))
 unlink(file.path(nonmem, "1001.toml"))

vignettes/slack-alerts.Rmd

@@ -9,18 +9,6 @@ editor_options:
   markdown: 
     wrap: 72
 ---
-
-```{r, include = FALSE}
-#removing generated files from running this vignette
-nonmem <- file.path("model", "nonmem")
-
-unlink(file.path(nonmem, "1001"), recursive = TRUE)
-unlink(file.path(nonmem, "1001.yaml"))
-unlink(file.path(nonmem, "1001.toml"))
-unlink(file.path(nonmem, "submission-log"), recursive = TRUE) 
-unlink(file.path(nonmem, "in_progress"), recursive = TRUE)
-```
-
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -151,19 +139,16 @@ slurmtools::get_slurm_jobs(user = 'matthews')
 
 ![nmm slack alerts](data/images/nmm_slack_notifications.png)
 
-```{r, include = FALSE}
-# #cancelling any running nonmem jobs
-# state <- slurmtools::get_slurm_jobs(user = "matthews")
-# 
-# if (any(state$job_state %in% c("RUNNING", "CONFIGURING"))) {
-#   for (job_id in state %>% dplyr::filter(job_state == "RUNNING") %>% dplyr::pull("job_id")) {
-#     processx::run("scancel", args = paste0(job_id))
-#   }
-# }
-# 
-# #removing generated files from running this vignette
-# nonmem <- file.path("model", "nonmem")
-# 
+```{r cleanup, include = FALSE}
+# cancelling any running nonmem jobs
+jobs <- get_slurm_jobs(user = "matthews") %>%
+  dplyr::filter(job_state == "RUNNING") %>% 
+  dplyr::pull(job_id)
+
+for (job in jobs) {
+  cancel_job(job)
+}
+
 unlink(file.path(nonmem, "1001"), recursive = TRUE)
 unlink(file.path(nonmem, "1001.yaml"))
 unlink(file.path(nonmem, "1001.toml"))