From d18240bd293dc5be0d0c418553e963bc5ec69a8f Mon Sep 17 00:00:00 2001 From: wlandau-lilly Date: Mon, 8 Jan 2024 10:55:57 -0500 Subject: [PATCH] Document SGE monitor --- R/crew_monitor_sge.R | 4 +++- README.Rmd | 22 ++++++++++++++++++++++ README.md | 25 +++++++++++++++++++++++++ man/crew_class_monitor_sge.Rd | 4 +++- 4 files changed, 53 insertions(+), 2 deletions(-) diff --git a/R/crew_monitor_sge.R b/R/crew_monitor_sge.R index a6a5e14..1ced44c 100644 --- a/R/crew_monitor_sge.R +++ b/R/crew_monitor_sge.R @@ -120,7 +120,9 @@ crew_class_monitor_sge <- R6::R6Class( #' @param jobs Character vector of job names or job IDs to terminate. #' Ignored if `all` is set to `TRUE`. #' @param all Logical of length 1, whether to terminate all the jobs - #' under your user name. If `TRUE`, the `jobs` argument is ignored. + #' under your user name. This terminates ALL your SGE jobs, + #' regardless of whether `crew.cluster` launched them, + #' so use with caution! terminate = function(jobs = NULL, all = FALSE) { # Cannot be tested with automated tests. # Tested in tests/sge/monitor.R. diff --git a/README.Rmd b/README.Rmd index 09d4e0e..79b4b9c 100644 --- a/README.Rmd +++ b/README.Rmd @@ -73,6 +73,28 @@ Remember to terminate the controller when you are done. controller$terminate() ``` +# Monitoring + +To manage resource usage, you may choose to list and manually terminate cluster jobs using `crew_monitor_sge()` and other supported monitors. Example for SGE: + +```{r} +monitor <- crew_monitor_sge() +job_list <- monitor$jobs() +job_list +#> # A tibble: 2 × 9 +#> job_number prio name owner state start_time queue_name jclass_name slots +#> +#> 1 131853812 0.05000 crew-m… USER… r 2024-01-0… all.norma… NA 1 +#> 2 131853813 0.05000 crew-m… USER… r 2024-01-0… all.norma… NA 1 +monitor$terminate(jobs = job_list$job_number) +#> USER has registered the job 131853812 for deletion +#> USER has registered the job 131853813 for deletion +monitor$jobs() +#> data frame with 0 columns and 0 rows +``` + +`monitor$terminate(all = TRUE)` terminates all your SGE jobs, regardless of whether `crew.cluster` created them. + # Tips * `crew.cluster` submits jobs over the local network using system calls to the resource manager (e.g SGE or SLURM). Please invoke `crew.cluster` on a node of the cluster, either a login node (head node) or a compute node. diff --git a/README.md b/README.md index 4d18f7c..7a11cb5 100644 --- a/README.md +++ b/README.md @@ -76,6 +76,31 @@ Remember to terminate the controller when you are done. controller$terminate() ``` +# Monitoring + +To manage resource usage, you may choose to list and manually terminate +cluster jobs using `crew_monitor_sge()` and other supported monitors. +Example for SGE: + +``` r +monitor <- crew_monitor_sge() +job_list <- monitor$jobs() +job_list +#> # A tibble: 2 × 9 +#> job_number prio name owner state start_time queue_name jclass_name slots +#> +#> 1 131853812 0.05000 crew-m… USER… r 2024-01-0… all.norma… NA 1 +#> 2 131853813 0.05000 crew-m… USER… r 2024-01-0… all.norma… NA 1 +monitor$terminate(jobs = job_list$job_number) +#> USER has registered the job 131853812 for deletion +#> USER has registered the job 131853813 for deletion +monitor$jobs() +#> data frame with 0 columns and 0 rows +``` + +`monitor$terminate(all = TRUE)` terminates all your SGE jobs, regardless +of whether `crew.cluster` created them. + # Tips - `crew.cluster` submits jobs over the local network using system calls diff --git a/man/crew_class_monitor_sge.Rd b/man/crew_class_monitor_sge.Rd index 9394536..77efc05 100644 --- a/man/crew_class_monitor_sge.Rd +++ b/man/crew_class_monitor_sge.Rd @@ -112,7 +112,9 @@ Terminate one or more SGE jobs. Ignored if \code{all} is set to \code{TRUE}.} \item{\code{all}}{Logical of length 1, whether to terminate all the jobs -under your user name. If \code{TRUE}, the \code{jobs} argument is ignored.} +under your user name. This terminates ALL your SGE jobs, +regardless of whether \code{crew.cluster} launched them, +so use with caution!} } \if{html}{\out{}} }