slurm_apply: SLURM Apply

In Saint-Louis-University/sluhpc: Submit R Code to the Saint Louis University High Performance Cluster

Description

SLURM Apply

Usage

slurm_apply(f, params, jobname, nodes = 2, cpus_per_node = 2,
  add_objects = NULL, pkgs = rev(attached_packages()),
  libPaths = NULL, slurm_options = list(), submit = FALSE)

Arguments

f	a function that accepts one or many single values as parameters and may return any type of R object
params	a data frame of parameter values to apply f to. Each column corresponds to a parameter of f (Note: names must match) and each row corresponds to a separate function call
jobname	the name of the slurm job
nodes	the (maximum) number of cluster nodes to spread the calculation over. slurm_apply automatically divides params in chunks of approximately equal size to send to each node. Less nodes are allocated if the parameter set is too small to use all CPUs on the requested nodes
cpus_per_node	the number of CPUs per node on the cluster; determines how many processes are run in parallel per node
add_objects	a character vector containing the name of R objects to be saved in a .RData file and loaded on each cluster node prior to calling f.
pkgs	a character vector containing the names of packages that must be loaded on each cluster node. By default, it includes all packages loaded by the user when slurm_apply is called with the exception of the sluhpc package.
libPaths	a character vector describing the location of additional R library trees to search through, or NULL. The default value of NULL corresponds to libraries returned by .libPaths() on a cluster node. Non-existent library trees are silently ignored.
slurm_options	a named list of options recognized by sbatch; see Details below for more information.
submit	whether or not to submit the job to the cluster with sbatch. See slurm_apply details for more information

Value

a slurm_job object containing the job name and the number of nodes effectively used

Note

this function overrides slurm_apply to add a command in the submission script to load R on APEX and call RScript with a relative path

Examples

## Not run: 
do_search <- function(x, y) x + y
slurm_job <- slurm_apply(do_search,
                         data.frame(x = seq( 0, 42,  21),
                                    y = seq(42,  0, -21)),
                         "find_meaning")

## End(Not run)

Saint-Louis-University/sluhpc documentation built on Oct. 30, 2019, 11:47 p.m.