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#' Batchtools futures for LSF, OpenLava, SGE, Slurm, TORQUE etc.
#'
#' Batchtools futures for LSF, OpenLava, SGE, Slurm, TORQUE etc. are
#' asynchronous multiprocess futures that will be evaluated on a compute
#' cluster via a job scheduler.
#'
#' @inheritParams BatchtoolsFuture
#'
#' @param template (optional) A batchtools template file or a template string
#' (in \pkg{brew} format). If not specified, it is left to the
#' \pkg{batchtools} package to locate such file using its search rules.
#'
#' @param \ldots Additional arguments passed to [BatchtoolsFuture()].
#'
#' @return An object of class `BatchtoolsFuture`.
#'
#' @details
#' These type of batchtools futures rely on batchtools backends set
#' up using the following \pkg{batchtools} functions:
#'
#' * [batchtools::makeClusterFunctionsLSF()] for
#' [Load Sharing Facility (LSF)](https://en.wikipedia.org/wiki/Platform_LSF)
#' * [batchtools::makeClusterFunctionsOpenLava()] for
#' [OpenLava](https://en.wikipedia.org/wiki/OpenLava)
#' * [batchtools::makeClusterFunctionsSGE()] for
#' [Sun/Oracle Grid Engine (SGE)](https://en.wikipedia.org/wiki/Oracle_Grid_Engine)
#' * [batchtools::makeClusterFunctionsSlurm()] for
#' [Slurm](https://en.wikipedia.org/wiki/Slurm_Workload_Manager)
#' * [batchtools::makeClusterFunctionsTORQUE()] for
#' [TORQUE](https://en.wikipedia.org/wiki/TORQUE) / PBS
#'
#' @export
#' @rdname batchtools_template
#' @name batchtools_template
batchtools_lsf <- function(expr, envir = parent.frame(), substitute = TRUE,
globals = TRUE, label = NULL,
template = NULL, resources = list(),
workers = NULL,
registry = list(), ...) {
if (substitute) expr <- substitute(expr)
batchtools_by_template(expr, envir = envir, substitute = FALSE,
globals = globals, label = label, template = template,
type = "lsf", resources = resources,
workers = workers, registry = registry, ...)
}
class(batchtools_lsf) <- c("batchtools_lsf", "batchtools_template",
"batchtools", "multiprocess", "future",
"function")
#' @export
#' @rdname batchtools_template
batchtools_openlava <- function(expr, envir = parent.frame(), substitute = TRUE,
globals = TRUE, label = NULL,
template = NULL, resources = list(),
workers = NULL,
registry = list(), ...) {
if (substitute) expr <- substitute(expr)
batchtools_by_template(expr, envir = envir, substitute = FALSE,
globals = globals, label = label, template = template,
type = "openlava", resources = resources,
workers = workers, registry = registry, ...)
}
class(batchtools_openlava) <- c("batchtools_openlava", "batchtools_template",
"batchtools", "multiprocess", "future",
"function")
#' @export
#' @rdname batchtools_template
batchtools_sge <- function(expr, envir = parent.frame(), substitute = TRUE,
globals = TRUE, label = NULL,
template = NULL, resources = list(),
workers = NULL,
registry = list(), ...) {
if (substitute) expr <- substitute(expr)
batchtools_by_template(expr, envir = envir, substitute = FALSE,
globals = globals, label = label, template = template,
type = "sge", resources = resources,
workers = workers, registry = registry, ...)
}
class(batchtools_sge) <- c("batchtools_sge", "batchtools_template",
"batchtools", "multiprocess", "future",
"function")
#' @export
#' @rdname batchtools_template
batchtools_slurm <- function(expr, envir = parent.frame(), substitute = TRUE,
globals = TRUE, label = NULL,
template = NULL, resources = list(),
workers = NULL,
registry = list(), ...) {
if (substitute) expr <- substitute(expr)
batchtools_by_template(expr, envir = envir, substitute = FALSE,
globals = globals, label = label, template = template,
type = "slurm", resources = resources,
workers = workers, registry = registry, ...)
}
class(batchtools_slurm) <- c("batchtools_slurm", "batchtools_template",
"batchtools", "multiprocess", "future",
"function")
#' @export
#' @rdname batchtools_template
batchtools_torque <- function(expr, envir = parent.frame(), substitute = TRUE,
globals = TRUE, label = NULL,
template = NULL, resources = list(),
workers = NULL,
registry = list(), ...) {
if (substitute) expr <- substitute(expr)
batchtools_by_template(expr, envir = envir, substitute = FALSE,
globals = globals, label = label, template = template,
type = "torque", resources = resources,
workers = workers, registry = registry, ...)
}
class(batchtools_torque) <- c("batchtools_torque", "batchtools_template",
"batchtools", "multiprocess", "future",
"function")
#' @importFrom batchtools findTemplateFile
#' @importFrom batchtools makeClusterFunctionsLSF
#' @importFrom batchtools makeClusterFunctionsOpenLava
#' @importFrom batchtools makeClusterFunctionsSGE
#' @importFrom batchtools makeClusterFunctionsSlurm
#' @importFrom batchtools makeClusterFunctionsTORQUE
#' @importFrom utils file_test
batchtools_by_template <- function(expr, envir = parent.frame(),
substitute = TRUE, globals = TRUE,
template = NULL,
type = c("lsf", "openlava", "sge",
"slurm", "torque"),
resources = list(), label = NULL,
workers = NULL,
registry = list(), ...) {
if (substitute) expr <- substitute(expr)
type <- match.arg(type)
make_cfs <- switch(type,
lsf = makeClusterFunctionsLSF,
openlava = makeClusterFunctionsOpenLava,
sge = makeClusterFunctionsSGE,
slurm = makeClusterFunctionsSlurm,
torque = makeClusterFunctionsTORQUE
)
## Get the default template?
if (is.null(template)) {
template <- formals(make_cfs)$template
}
stop_if_not(is.character(template), length(template) == 1L,
!is.na(template), nzchar(template))
## Tweaked search for template file
pathname <- tryCatch({
findTemplateFile(template)
}, error = function(ex) {
## Try to find it in this package?
if (grepl("Argument 'template'", conditionMessage(ex))) {
pathname <- system.file("templates", sprintf("%s.tmpl", template),
package = "future.batchtools")
if (file_test("-f", pathname)) return(pathname)
}
stop(ex)
})
if (is.na(pathname)) {
stop(sprintf("Failed to locate a batchtools template file: *%s.tmpl",
template))
}
template <- pathname
cluster.functions <- make_cfs(template)
attr(cluster.functions, "template") <- template
future <- BatchtoolsFuture(expr = expr, envir = envir, substitute = FALSE,
globals = globals,
label = label,
cluster.functions = cluster.functions,
registry = registry,
resources = resources,
workers = workers,
...)
if (!future$lazy) future <- run(future)
future
} ## batchtools_by_template()
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