Package 'slurmtools'

Cancels a running job

Description

Cancels a running job

Usage

cancel_slurm_job(job_id, auto_confirm = FALSE)

Arguments

job_id	job id to cancel
auto_confirm	does not prompt user before cancelling job

Examples

## Not run: 
cancel_job(243)

## End(Not run)

---

Gets the jobs run on slurm as a tibble

Description

Gets the jobs run on slurm as a tibble

Usage

get_slurm_jobs(user = NULL)

Arguments

user	optional user name to filter jobs only submitted by user

Value

a tibble containing the jobs submitted to slurm

Examples

## Not run: 
get_slurm_jobs()

## End(Not run)

---

Gets the available slurm partitions the user can use.

Description

Gets the available slurm partitions the user can use.

Usage

get_slurm_partitions(cache = TRUE)

Arguments

cache

optional argument to forgo caching

Value

vector of available partitions

Examples

## Not run: 
get_slurm_partitions

## End(Not run)

---

slurmtools: An R package for easily submitting NONMEM jobs to slurm.

Description

This package aims to ease the submission and monitoring of NONMEM jobs running on slurm.

submitting jobs

• submit_slurm_job: Submits a job to slurm

monitoring jobs

• get_slurm_jobs: Gives a table of submitted jobs to slurm that shows status and other information given with squeue

cancelling jobs

• cancel_slurm_job: Cancels the specified job

slurm partitions

• get_slurm_partitions: Gives a vector of available partitions a user can submit jobs to.

Author(s)

Maintainer: Devin Pastoor [email protected]

Authors:

• Jenna Elwing [email protected]

• Matthew Smith [email protected]

• Jacob Dumbleton [email protected]

---

submit a nonmem model to slurm in parallel

Description

submit a nonmem model to slurm in parallel

Usage

submit_slurm_job(
  .mod,
  partition = get_slurm_partitions(),
  ncpu = 1,
  overwrite = FALSE,
  dry_run = FALSE,
  ...,
  slurm_job_template_path = getOption("slurmtools.slurm_job_template_path"),
  submission_root = getOption("slurmtools.submission_root"),
  bbi_config_path = getOption("slurmtools.bbi_config_path"),
  slurm_template_opts = list()
)

Arguments

.mod	a path to a model or a bbi nonmem model object
partition	name of the partition to submit the model
ncpu	number of cpus to run the model against
overwrite	whether to overwrite existing model results
dry_run	return the command that would have been invoked, without invoking
...	arguments to pass to processx::run
slurm_job_template_path	path to slurm job template
submission_root	directory to track job submission scripts and output
bbi_config_path	path to bbi.yaml file for bbi configuration
slurm_template_opts	choose slurm template

---

Updates the logging level for functions. Default is set to WARN

Description

Updates the logging level for functions. Default is set to WARN

Usage

toggle_logger(quiet = FALSE)

Arguments

quiet

suppresses messaging about log level.

Examples

## Not run: 
Sys.setenv("RPFY_VERBOSE" = "DEBUG")
toggle_logger()

## End(Not run)

---