opts_slurmR {slurmR}

Get and set default options for sbatch and slurmR internals

Description

Most of the functions in the slurmR package use tmp_path and job-name options to write and submit jobs to Slurm. These options have global defaults that are set and retrieved using opts_slurmR. These options also include SBATCH options and things to do before calling RScript, e.g., loading modules on an HPC cluster.

Usage

opts_slurmR

Format

An object of class opts_slurmR of length 17.

Details

Whatever the path specified on tmp_path, all nodes should have access to it. Moreover, it is recommended to use a path located in a high-performing drive. See for example disk staging.

The tmp_path directory is only created at the time that one of the functions needs to I/O files. Job creation calls like Slurm_EvalQ and Slurm_lapply do such.

The "preamble" options can be specified if, for example, the current cluster needs to load R, a compiler, or other programs via a module command.

Current supported options are:

Debugging mode

• ⁠debug_on : function ()⁠ Activates the debugging mode. When active, jobs will be submitted using sh and not sbatch. Also, only a single chunk of the data will be processed.

• ⁠debug_off : function ()⁠ Deactivates the debugging mode.

• ⁠get_debug : function ()⁠ Returns TRUE of debug mode is on

Verbose mode

• ⁠verbose_on : function ()⁠ Deactivates the verbose mode. When ON, sbatch prints the Rscript and batch files on screen so that the user knows what will be submitted to Slurm.

• ⁠verbose_off : function ()⁠ Deactivates the verbose mode.

• ⁠get_verbose : function ()⁠ Returns TRUE if verbose mode is on.

Slurm options

• ⁠set_tmp_path : function (path, recursive = TRUE)⁠ Sets the tempfile path for I/O

• ⁠get_tmp_path : function ()⁠ Retrieves tempfile path for I/O

• ⁠set_job_name : function (path, check = TRUE, overwrite = TRUE)⁠ Changes the job-name. When changing the name of the job the function will check whether the folder chdir/job-name is empty or not. If empty/not created it will create it, otherwise it will delete its contents (if 'overwrite = TRUE“, else it will return with an Error)..

• ⁠get_job_name : function (check = TRUE)⁠ Returns the current value of 'job-name'.

• ⁠set_preamble : function (...)⁠ Sets "preamble" to the RScript call. For example, it could be used for loading modules, setting env variables, etc., needed during the R session. Options are passed as characters.

• ⁠get_preamble : function ()⁠ Returns the preamble, e.g., module loads, environment variable definitions, etc., that will be included in sbatch submissions.

Other options

• ⁠get_cmd : function ()⁠ If debug mode is active, then it returns 'sh', otherwise 'sbatch'

For general set/retrieve options

• ⁠set_opts : function (...)⁠ A generic function to set options.

• ⁠get_opts_job : function (...)⁠ A generic function to retrieve options for the job (Slurm).

• ⁠get_opts_r : function (...)⁠ A generic function to retrieve options in R.

Nuke

• While reloading the package should reset all the options, if needed, the user can also use the function opts_slurmR$reset().

Examples

# Common setup
## Not run: 
opts_slurmR$set_tmp_path("/staging/pdt/vegayon")
opts_slurmR$set_job_name("simulations-1")
opts_slurm$set_opts(partition="thomas", account="lc_pdt")
opts_slurm$set_preamble("module load gcc")# if needed

## End(Not run)