slurmtools

slurmtools is a collection of utility functions suitable for interacting with slurm and submitting nonmem jobs. There are three main functions of slurmtools

1. submit_slurm_jobs - submits a job to slurm via sbatch. The job is defined by a template file that is filled in during the call of this function
2. get_slurm_jobs - gives a tibble of currently runing jobs via squeue.
3. cancel_slurm_jobs - cancels a running slurm job via scancel.

Installation

You can install the development version of slurmtools from GitHub with:

# install.packages("pak")
pak::pkg_install("a2-ai/slurmtools")

Examples

This block sets up options used by slurmtools:

nonmem = file.path(here::here(), "vignettes", "model", "nonmem")

options('slurmtools.submission_root' = file.path(nonmem, "submission-log"))
options('slurmtools.bbi_config_path' = file.path(nonmem, "bbi.yaml"))
options('slurmtools.slurm_job_template_path' = file.path(nonmem, 'slurm-job-bbi.tmpl'))

library(slurmtools)
#> 
#> 
#> ── Set slurmtools options ──────────────────────────────────────────────────────
#> ✔ slurmtools.slurm_jon_template_path: /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/slurm-job-bbi.tmpl
#> ✔ slurmtools.submission_root: /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log
#> ✔ slurmtools.bbi_config_path: /cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/bbi.yaml

This block reads in a nonmem model with bbr and submits the job to slurm:

mod_number <- "1001"
mod <- bbr::read_model(file.path(nonmem, mod_number))

submit_slurm_job(mod, overwrite = TRUE)
#> $status
#> [1] 0
#> 
#> $stdout
#> [1] "Submitted batch job 612\n"
#> 
#> $stderr
#> [1] ""
#> 
#> $timeout
#> [1] FALSE

This block shows recently submitted and completed jobs:

knitr::kable(get_slurm_jobs(user = 'matthews'))

job_id	partition	job_name	user_name	job_state	time	cpus	standard_input	standard_output	submit_time	start_time	end_time	current_working_directory
609	cpu2mem4gb	1001-nonmem-run	matthews	COMPLETED	00:00:14	1	/dev/null	/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-609.out	2024-11-26 13:51:15	2024-11-26 13:51:15	2024-11-26 13:51:29	/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log
610	cpu2mem4gb	1001-nonmem-run	matthews	COMPLETED	00:00:14	1	/dev/null	/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-610.out	2024-11-26 13:52:17	2024-11-26 13:52:17	2024-11-26 13:52:31	/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log
611	cpu2mem4gb	1001-nonmem-run	matthews	COMPLETED	00:00:15	1	/dev/null	/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-611.out	2024-11-26 13:52:40	2024-11-26 13:52:40	2024-11-26 13:52:55	/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log
612	cpu2mem4gb	1001-nonmem-run	matthews	PENDING	00:00:00	1	/dev/null	/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log/slurm-612.out	2024-11-26 13:54:48	1970-01-01 00:00:00	1970-01-01 00:00:00	/cluster-data/user-homes/matthews/Packages/slurmtools/vignettes/model/nonmem/submission-log