Merge pull request #6 from A2-ai/get_job_fix

Get job fix

.Rhistory

@@ -0,0 +1,271 @@
+here::here()
+devtools::check()
+devtools::check()
+here::here()
+devtools::check()
+here::here()
+library(here)
+install.packages("here")
+install.packages("devtools")
+devtools::check()
+install.packages("dplyr")
+install.packages("extendr")
+install.packages("rextendr")
+devtools::check()
+install.packages("bbr")
+devtools::check()
+as.POSIXct("2024-08-23 12:34:56")
+build_site()
+library(pkgdown)
+build_site()
+getwd()
+setwd("../scicalc")
+getwd()
+build_site()
+library(scicalc)
+getwd()
+library(pkgdown)
+sink("_pkgdown.yml")
+template_navbar()
+template_reference()
+sink()
+build_site()
+build_site()
+library(slurmtools)
+#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)
+knitr::opts_chunk$set(
+collapse = TRUE,
+comment = ""
+)
+library(slurmtools)
+options(repos = c(
+"slurmtools" = "https://a2-ai.github.io/gh-pkg-mirror/slurmtools",
+getOption("repos")))
+install.packages("slurmtools")
+library(slurmtools)
+library(bbr)
+library(here)
+nonmem = file.path(here::here(), "vignettes", "model", "nonmem")
+options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
+mod_number <- "1001"
+if (file.exists(file.path(nonmem, paste0(mod_number, ".yaml")))) {
+mod <- bbr::read_model(file.path(nonmem, mod_number))
+} else {
+mod <- bbr::new_model(file.path(nonmem, mod_number))
+}
+submission <- slurmtools::submit_nonmem_model(
+mod,
+slurm_job_template_path = file.path(nonmem, "slurm-job-bbi.tmpl"),
+slurm_template_opts = list(
+bbi_exe_path = Sys.which("bbi"),
+bbi_config_path = file.path(nonmem, "bbi.yaml"))
+)
+submission
+submitted_job_id <- submission$stdout
+submitted_job_id <- strsplit(submitted_job_id, "\n")[[1]]
+submitted_job_id <- tail(strsplit(submitted_job_id, " ")[[1]], 1)
+slurmtools::get_slurm_jobs() %>%
+dplyr::filter(job_id == submitted_job_id)
+?tail
+?get_slurm_jobs
+get_slurm_jobs
+cmd <- list(cmd = "squeue", args = "--json")
+res <- processx::run(cmd$cmd, args = cmd$args)
+if (res$status != 0) {
+# todo: better handle returning why
+rlang::abort("unable to get slurm jobs, test what the output would be by running `squeue --json`")
+}
+res_df <- parse_jobs_json(jsonlite::fromJSON(res$stdout, simplifyVector = FALSE))
+?parse_jobs_json
+??parse_jobs_json
+parse_jobs_json <- function(.json) {
+if (!length(.json$jobs)) {
+return(NULL)
+}
+purrr::list_rbind(purrr::map(.json$jobs, parse_job_to_row))
+}
+res_df <- parse_jobs_json(jsonlite::fromJSON(res$stdout, simplifyVector = FALSE))
+parse_job_to_row <- function(job) {
+tibble::tibble(
+job_id = job$job_id,
+job_state = job$job_state,
+cpus = job$cpus$number,
+partition = job$partition,
+standard_input = job$standard_input,
+standard_output = job$standard_output,
+submit_time = job$submit_time,
+start_time = job$start_time,
+user_name = job$user_name,
+current_working_directory = job$current_working_directory
+)
+}
+res_df <- parse_jobs_json(jsonlite::fromJSON(res$stdout, simplifyVector = FALSE))
+res_df$submit_time
+class(res_df$submit_time)
+?as.POSIXct
+?jsonlite:::fromJSON
+as.POSIXct(res_df$submit_time$number, origin = "1970-01-01")
+res_df$start_time
+build_site()
+#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)
+knitr::opts_chunk$set(
+collapse = TRUE,
+comment = ""
+)
+library(slurmtools)
+library(bbr)
+library(here)
+nonmem = file.path(here::here(), "vignettes", "model", "nonmem")
+options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
+mod_number <- "1001"
+if (file.exists(file.path(nonmem, paste0(mod_number, ".yaml")))) {
+mod <- bbr::read_model(file.path(nonmem, mod_number))
+} else {
+mod <- bbr::new_model(file.path(nonmem, mod_number))
+}
+submission <- slurmtools::submit_nonmem_model(
+mod,
+slurm_job_template_path = file.path(nonmem, "slurm-job-bbi.tmpl"),
+slurm_template_opts = list(
+bbi_exe_path = Sys.which("bbi"),
+bbi_config_path = file.path(nonmem, "bbi.yaml"))
+)
+submission
+submitted_job_id <- submission$stdout
+submitted_job_id <- strsplit(submitted_job_id, "\n")[[1]]
+submitted_job_id <- tail(strsplit(submitted_job_id, " ")[[1]], 1)
+slurmtools::get_slurm_jobs() %>%
+dplyr::filter(job_id == submitted_job_id)
+open slurmtools::get_slurm_jobs()
+open(slurmtools::get_slurm_jobs())
+open(slurmtools::get_slurm_jobs
+)
+squeue --version
+library(pkgdown)
+build_site()
+.Last.error
+library(slurmtools)
+#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)
+knitr::opts_chunk$set(
+collapse = TRUE,
+comment = ""
+)
+library(slurmtools)
+library(bbr)
+library(here)
+nonmem = file.path(here::here(), "vignettes", "model", "nonmem")
+options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
+mod_number <- "1001"
+if (file.exists(file.path(nonmem, paste0(mod_number, ".yaml")))) {
+mod <- bbr::read_model(file.path(nonmem, mod_number))
+} else {
+mod <- bbr::new_model(file.path(nonmem, mod_number))
+}
+submission <- slurmtools::submit_nonmem_model(
+mod,
+slurm_job_template_path = file.path(nonmem, "slurm-job-bbi.tmpl"),
+slurm_template_opts = list(
+bbi_exe_path = Sys.which("bbi"),
+bbi_config_path = file.path(nonmem, "bbi.yaml"))
+)
+submission
+submitted_job_id <- submission$stdout
+submitted_job_id <- strsplit(submitted_job_id, "\n")[[1]]
+submitted_job_id <- tail(strsplit(submitted_job_id, " ")[[1]], 1)
+slurmtools::get_slurm_jobs() %>%
+dplyr::filter(job_id == submitted_job_id)
+.libPaths()
+install.packages("~/packages/slurmtools", repos = NULL, type = "source")
+library(slurmtools)
+#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)
+knitr::opts_chunk$set(
+collapse = TRUE,
+comment = ""
+)
+library(slurmtools)
+library(bbr)
+library(here)
+nonmem = file.path(here::here(), "vignettes", "model", "nonmem")
+options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
+mod_number <- "1001"
+if (file.exists(file.path(nonmem, paste0(mod_number, ".yaml")))) {
+mod <- bbr::read_model(file.path(nonmem, mod_number))
+} else {
+mod <- bbr::new_model(file.path(nonmem, mod_number))
+}
+View(as.data.frame(available.packages()))
+mod_number <- "1001"
+if (file.exists(file.path(nonmem, paste0(mod_number, ".yaml")))) {
+mod <- bbr::read_model(file.path(nonmem, mod_number))
+} else {
+mod <- bbr::new_model(file.path(nonmem, mod_number))
+}
+submission <- slurmtools::submit_nonmem_model(
+mod,
+slurm_job_template_path = file.path(nonmem, "slurm-job-bbi.tmpl"),
+slurm_template_opts = list(
+bbi_exe_path = Sys.which("bbi"),
+bbi_config_path = file.path(nonmem, "bbi.yaml"))
+)
+submission
+submitted_job_id <- submission$stdout
+submitted_job_id <- strsplit(submitted_job_id, "\n")[[1]]
+submitted_job_id <- tail(strsplit(submitted_job_id, " ")[[1]], 1)
+slurmtools::get_slurm_jobs() %>%
+dplyr::filter(job_id == submitted_job_id)
+parse_job_to_row <- function(job) {
+tibble::tibble(
+job_id = job$job_id,
+job_state = job$job_state,
+cpus = job$cpus$number,
+partition = job$partition,
+standard_input = job$standard_input,
+standard_output = job$standard_output,
+submit_time = job$submit_time,
+start_time = job$start_time,
+user_name = job$user_name,
+current_working_directory = job$current_working_directory
+)
+}
+parse_jobs_json <- function(.json) {
+if (!length(.json$jobs)) {
+return(NULL)
+}
+purrr::list_rbind(purrr::map(.json$jobs, parse_job_to_row))
+}
+cmd <- list(cmd = "squeue", args = "--json")
+res <- processx::run(cmd$cmd, args = cmd$args)
+if (res$status != 0) {
+# todo: better handle returning why
+rlang::abort("unable to get slurm jobs, test what the output would be by running `squeue --json`")
+}
+res_df <- parse_jobs_json(jsonlite::fromJSON(res$stdout, simplifyVector = FALSE))
+View(res_df)
+View(res_df)
+get_slurm_jobs
+installed.packages()
+View(as.data.frame(installed.packages()))

DESCRIPTION

@@ -8,7 +8,7 @@ Description: What the package does (one paragraph).
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Imports: 
     brio,
     dplyr,
@@ -29,7 +29,6 @@ Suggests:
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
-    bbr,
-    pdftools,
+    bbr
 Config/testthat/edition: 3
 VignetteBuilder: knitr

R/attach.R

@@ -1,4 +1,3 @@
-
 #' Generates a tidyverse-esque onAttach message
 #'
 #' @return a message to display on attach

R/get-jobs.R

@@ -2,15 +2,33 @@ utils::globalVariables(c("user_name"))
 
 # Function to parse each job into a tibble row
 parse_job_to_row <- function(job) {
+  # check options for squeue version
+  # alter parsing based on result
+
+  if (getOption("squeue.version") > package_version("23.02.4")){
+    submit_time = job$submit_time$number
+    start_time = job$start_time$number
+    ### This is "hacky", it looks like for configuring model the list is 3 {"Running", "Configuring", "Power_up_node"}
+    if (length(job$job_state) > 1){
+      job_state = job$job_state[[2]]
+    } else {
+      job_state = job$job_state[[1]]
+    }
+  } else {
+    submit_time = job$submit_time
+    start_time = job$start_time
+    job_state = job$job_state
+  }
+
   tibble::tibble(
     job_id = job$job_id,
-    job_state = job$job_state,
+    job_state = job_state,
     cpus = job$cpus$number,
     partition = job$partition,
     standard_input = job$standard_input,
     standard_output = job$standard_output,
-    submit_time = job$submit_time,
-    start_time = job$start_time,
+    submit_time = submit_time,
+    start_time = start_time,
     user_name = job$user_name,
     current_working_directory = job$current_working_directory
   )

R/zzz.R

@@ -2,3 +2,16 @@
   msg <- slurmtools_options_message()
   packageStartupMessage(msg)
 }
+
+.onLoad <- function(libname, pkgname) {
+  processx_output <- processx::run("squeue", args = "--version")
+  if (processx_output$status != 0) {
+    warning("squeue not installed correctly")
+  } else {
+    # stdout format is "slurm major.minor.patch/n"
+    version <- strsplit(processx_output$stdout," ")[[1]][[2]] %>%
+      trimws() %>%
+      package_version()
+    options("squeue.version" = version)
+  }
+}