Add a new 'wallclock_time' column to the output of 'job_report()'; ch…

…ange 'elapsed_time' to 'wallclock_time' for 'job_info()' for consistency
LieberInstitute · Oct 27, 2023 · 06f755c · 06f755c
1 parent 6f583f7
commit 06f755c
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Showing 6 changed files with 12 additions and 8 deletions.
diff --git a/R/job_info.R b/R/job_info.R
@@ -55,7 +55,7 @@ job_info <- function(user = Sys.getenv("USER"), partition = "shared") {
             PARTITION = as.factor(PARTITION),
             STATUS = as.factor(ST),
             JOB_ID = as.integer(JOBID),
-            ELAPSED_TIME = parse_slurm_time(TIME)
+            WALLCLOCK_TIME = parse_slurm_time(TIME)
         ) |>
         rename(REQUESTED_MEM_GB = MIN_MEMORY) |>
         select(-c(ST, JOBID, TIME))

diff --git a/R/job_report.R b/R/job_report.R
@@ -8,7 +8,7 @@
 #' @return A tibble with information about the requested job.
 #' @export
 #' @author Nicholas J. Eagles
-#' @import dplyr stringr utils
+#' @import dplyr stringr utils lubridate
 #'
 #' @family monitoring and informational functions
 #'
@@ -25,7 +25,7 @@ job_report <- function(job_id) {
     job_df <- read.csv(
         text = system(
             sprintf(
-                'sacct -j %s -P -o "JobID,JobIDRaw,User,JobName,Partition,AllocCPUS,ReqMem,State,MaxRSS,MaxVMSize,ExitCode" --units=G',
+                'sacct -j %s -P -o "JobID,JobIDRaw,User,JobName,Partition,AllocCPUS,ReqMem,State,MaxRSS,MaxVMSize,ExitCode,ElapsedRaw" --units=G',
                 job_id
             ),
             intern = TRUE
@@ -161,6 +161,9 @@ job_report <- function(job_id) {
             exit_code = as.integer(
                 str_extract(ExitCode, "^([0-9]+):", group = 1)
             ),
+            wallclock_time = ElapsedRaw |>
+                seconds() |>
+                as.difftime(),
             #   Some character columns should be factors
             Partition = as.factor(Partition),
             status = as.factor(State)
@@ -174,7 +177,7 @@ job_report <- function(job_id) {
             max_vmem_gb = MaxVMSize,
             max_rss_gb = MaxRSS,
         ) |>
-        select(-c(State, job_step, JobIDRaw, ExitCode))
+        select(-c(State, job_step, JobIDRaw, ExitCode, ElapsedRaw))
     colnames(job_df) <- tolower(colnames(job_df))
 
     #   Given a character vector containing an amount of memory (containing

diff --git a/data/job_info_df.rda b/data/job_info_df.rda
diff --git a/man/job_info_df.Rd b/man/job_info_df.Rd
diff --git a/tests/testthat/test-job_info.R b/tests/testthat/test-job_info.R
@@ -21,7 +21,7 @@ test_that(
         any_other_na <- job_df |>
             select(
                 job_id, user, name, partition, cpus, requested_mem_gb, status,
-                elapsed_time
+                wallclock_time
             ) |>
             is.na() |>
             any()
@@ -48,7 +48,7 @@ test_that(
             user = "character", array_task_id = "integer", name = "character",
             partition = "factor", cpus = "integer",
             requested_mem_gb = "numeric", status = "factor",
-            elapsed_time = "difftime"
+            wallclock_time = "difftime"
         )
         expected_types <- unname(expected_types[colnames(job_df)])
 

diff --git a/tests/testthat/test-job_report.R b/tests/testthat/test-job_report.R
@@ -19,7 +19,8 @@ test_that(
             cpus = "integer", requested_mem_gb = "numeric",
             max_rss_gb = "numeric", max_vmem_gb = "numeric",
             partition = "factor", array_task_id = "integer",
-            exit_code = "integer", status = "factor"
+            exit_code = "integer", status = "factor",
+            wallclock_time = "difftime"
         )
         expected_types <- unname(expected_types[colnames(job_df)])