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[WIP] added missing 'partition' argument to slurm launcher #25

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merged 1 commit into from
Oct 11, 2023
Merged

[WIP] added missing 'partition' argument to slurm launcher #25

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6 changes: 4 additions & 2 deletions R/crew_controller_slurm.R
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,8 @@ crew_controller_slurm <- function(
slurm_log_error = "/dev/null",
slurm_memory_gigabytes_per_cpu = NULL,
slurm_cpus_per_task = NULL,
slurm_time_minutes = 1440
slurm_time_minutes = 1440,
slurm_partition = NULL
) {
if (!is.null(seconds_exit)) {
crew::crew_deprecate(
Expand Down Expand Up @@ -96,7 +97,8 @@ crew_controller_slurm <- function(
slurm_log_error = slurm_log_error,
slurm_memory_gigabytes_per_cpu = slurm_memory_gigabytes_per_cpu,
slurm_cpus_per_task = slurm_cpus_per_task,
slurm_time_minutes = slurm_time_minutes
slurm_time_minutes = slurm_time_minutes,
slurm_partition = slurm_partition
)
controller <- crew::crew_controller(client = client, launcher = launcher)
controller$validate()
Expand Down
22 changes: 18 additions & 4 deletions R/crew_launcher_slurm.R
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,8 @@
#' SLURM cluster. `slurm_time_minutes = 60` translates to a line of
#' `#SBATCH --time=60` in the SLURM job script. `slurm_time_minutes = NULL`
#' omits this line.
#' @param slurm_partition Character of length 1, name of the slurm partition to
#' create workers on.
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Would be great to have a mention of how this translates into the --partition flag, as in the above @param descriptions. Also how a NULL value omits the flag.

crew_launcher_slurm <- function(
name = NULL,
seconds_interval = NULL,
Expand All @@ -72,7 +74,8 @@ crew_launcher_slurm <- function(
slurm_log_error = "/dev/null",
slurm_memory_gigabytes_per_cpu = NULL,
slurm_cpus_per_task = NULL,
slurm_time_minutes = 1440
slurm_time_minutes = 1440,
slurm_partition = NULL
) {
crew_deprecate(
name = "seconds_interval",
Expand Down Expand Up @@ -106,7 +109,8 @@ crew_launcher_slurm <- function(
slurm_log_error = slurm_log_error,
slurm_memory_gigabytes_per_cpu = slurm_memory_gigabytes_per_cpu,
slurm_cpus_per_task = slurm_cpus_per_task,
slurm_time_minutes = slurm_time_minutes
slurm_time_minutes = slurm_time_minutes,
slurm_partition = slurm_partition
)
launcher$validate()
launcher
Expand All @@ -133,6 +137,8 @@ crew_class_launcher_slurm <- R6::R6Class(
slurm_cpus_per_task = NULL,
#' @field slurm_time_minutes See [crew_launcher_slurm()].
slurm_time_minutes = NULL,
#' @field slurm_partition See See [crew_launcher_slurm()].
slurm_partition = NULL,
#' @description SLURM launcher constructor.
#' @return an SLURM launcher object.
#' @param name See [crew_launcher_slurm()].
Expand All @@ -157,6 +163,7 @@ crew_class_launcher_slurm <- R6::R6Class(
#' @param slurm_memory_gigabytes_per_cpu See [crew_launcher_slurm()].
#' @param slurm_cpus_per_task See [crew_launcher_slurm()].
#' @param slurm_time_minutes See [crew_launcher_slurm()].
#' @param slurm_partition See [crew_launcher_slurm()].
initialize = function(
name = NULL,
seconds_launch = NULL,
Expand All @@ -179,7 +186,8 @@ crew_class_launcher_slurm <- R6::R6Class(
slurm_log_error = NULL,
slurm_memory_gigabytes_per_cpu = NULL,
slurm_cpus_per_task = NULL,
slurm_time_minutes = NULL
slurm_time_minutes = NULL,
slurm_partition = NULL
) {
super$initialize(
name = name,
Expand All @@ -205,12 +213,13 @@ crew_class_launcher_slurm <- R6::R6Class(
self$slurm_memory_gigabytes_per_cpu <- slurm_memory_gigabytes_per_cpu
self$slurm_cpus_per_task <- slurm_cpus_per_task
self$slurm_time_minutes <- slurm_time_minutes
self$slurm_partition <- slurm_partition
},
#' @description Validate the launcher.
#' @return `NULL` (invisibly). Throws an error if a field is invalid.
validate = function() {
super$validate()
fields <- c("slurm_log_output", "slurm_log_error")
fields <- c("slurm_log_output", "slurm_log_error", "slurm_partition")
for (field in fields) {
if (!is.null(self[[field]])) {
crew::crew_assert(
Expand Down Expand Up @@ -299,6 +308,11 @@ crew_class_launcher_slurm <- R6::R6Class(
character(0L),
paste0("#SBATCH --time=", self$slurm_time_minutes)
),
if_any(
is.null(self$slurm_partition),
character(0L),
paste0("#SBATCH --partition=", self$slurm_partition)
),
self$script_lines
)
},
Expand Down
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