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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/slurm_call.R
\name{slurm_call}
\alias{slurm_call}
\title{Execution of a single function call on the Slurm cluster}
\usage{
slurm_call(
f,
params = list(),
jobname = NA,
global_objects = NULL,
add_objects = NULL,
pkgs = rev(.packages()),
libPaths = NULL,
rscript_path = NULL,
r_template = NULL,
sh_template = NULL,
slurm_options = list(),
submit = TRUE
)
}
\arguments{
\item{f}{Any R function.}
\item{params}{A named list of parameters to pass to \code{f}.}
\item{jobname}{The name of the Slurm job; if \code{NA}, it is assigned a
random name of the form "slr####".}
\item{global_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
\code{f}.}
\item{add_objects}{Older deprecated name of \code{global_objects}, retained for
backwards compatibility.}
\item{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 \code{slurm_call} is called.}
\item{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 \code{.libPaths()} on a cluster node.
Non-existent library trees are silently ignored.}
\item{rscript_path}{The location of the Rscript command. If not specified,
defaults to the location of Rscript within the R installation being run.}
\item{r_template}{The path to the template file for the R script run on each node.
If NULL, uses the default template "rslurm/templates/slurm_run_single_R.txt".}
\item{sh_template}{The path to the template file for the sbatch submission script.
If NULL, uses the default template "rslurm/templates/submit_single_sh.txt".}
\item{slurm_options}{A named list of options recognized by \code{sbatch}; see
Details below for more information.}
\item{submit}{Whether or not to submit the job to the cluster with
\code{sbatch}; see Details below for more information.}
}
\value{
A \code{slurm_job} object containing the \code{jobname} and the number
of \code{nodes} effectively used.
}
\description{
Use \code{slurm_call} to perform a single function evaluation a the Slurm
cluster.
}
\details{
This function creates a temporary folder ("_rslurm_[jobname]") in the current
directory, holding .RData and .RDS data files, the R script to run and the
Bash submission script generated for the Slurm job.
The names of any other R objects (besides \code{params}) that \code{f} needs
to access should be listed in the \code{global_objects} argument.
Use \code{slurm_options} to set any option recognized by \code{sbatch}, e.g.
\code{slurm_options = list(time = "1:00:00", share = TRUE)}. See
\url{http://slurm.schedmd.com/sbatch.html} for details on possible options.
Note that full names must be used (e.g. "time" rather than "t") and that
flags (such as "share") must be specified as TRUE. The "job-name", "ntasks"
and "output" options are already determined by \code{slurm_call} and should
not be manually set.
When processing the computation job, the Slurm cluster will output two files
in the temporary folder: one with the return value of the function
("results_0.RDS") and one containing any console or error output produced by
R ("slurm_[node_id].out").
If \code{submit = TRUE}, the job is sent to the cluster and a confirmation
message (or error) is output to the console. If \code{submit = FALSE}, a
message indicates the location of the saved data and script files; the job
can be submitted manually by running the shell command \code{sbatch
submit.sh} from that directory.
After sending the job to the Slurm cluster, \code{slurm_call} returns a
\code{slurm_job} object which can be used to cancel the job, get the job
status or output, and delete the temporary files associated with it. See the
description of the related functions for more details.
}
\seealso{
\code{\link{slurm_apply}} to parallelize a function over a parameter
set.
\code{\link{cancel_slurm}}, \code{\link{cleanup_files}},
\code{\link{get_slurm_out}} and \code{\link{get_job_status}} which use
the output of this function.
}
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