slurmR (version 0.5-4)

opts_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 () attr(slurmR::opts_slurmR$debug_on, "desc")

• debug_off : function () attr(slurmR::opts_slurmR$debug_off, "desc")

• get_debug : function () attr(slurmR::opts_slurmR$get_debug, "desc")

Verbose mode

• verbose_on : function () attr(slurmR::opts_slurmR$verbose_on, "desc")

• verbose_off : function () attr(slurmR::opts_slurmR$verbose_off, "desc")

• get_verbose : function () attr(slurmR::opts_slurmR$get_verbose, "desc")

Slurm options

• set_tmp_path : function (path, recursive = TRUE) attr(slurmR::opts_slurmR$set_tmp_path, "desc")

• get_tmp_path : function () attr(slurmR::opts_slurmR$get_tmp_path, "desc")

• set_job_name : function (path, check = TRUE, overwrite = TRUE) attr(slurmR::opts_slurmR$set_job_name, "desc").

• get_job_name : function (check = TRUE) attr(slurmR::opts_slurmR$get_job_name, "desc")

• set_preamble : function (...) attr(slurmR::opts_slurmR$set_preamble, "desc")

• get_preamble : function () attr(slurmR::opts_slurmR$get_preamble, "desc")

Other options

• get_cmd : function () attr(slurmR::opts_slurmR$get_cmd, "desc")

For general set/retrieve options

• set_opts : function (...) attr(slurmR::opts_slurmR$set_opts, "desc")

• get_opts_job : function (...) attr(slurmR::opts_slurmR$get_opts_job, "desc")

• get_opts_r : function (...) attr(slurmR::opts_slurmR$get_opts_r, "desc")

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
if (FALSE) {
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
}