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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", "batchtools",
"multiprocess", "future", "function"
)
attr(batchtools_lsf, "tweakable") <- c(
"finalize",
## Arguments to batchtools::makeClusterFunctionsLSF()
"scheduler.latency", "fs.latency"
)
#' @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", "batchtools",
"multiprocess", "future", "function"
)
attr(batchtools_openlava, "tweakable") <- c(
"finalize",
## Arguments to batchtools::makeClusterFunctionsOpenLava()
"scheduler.latency", "fs.latency"
)
#' @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", "batchtools",
"multiprocess", "future", "function"
)
attr(batchtools_sge, "tweakable") <- c(
"finalize",
## Arguments to batchtools::makeClusterFunctionsSGE()
"nodename", "scheduler.latency", "fs.latency"
)
#' @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", "batchtools",
"multiprocess", "future", "function"
)
attr(batchtools_slurm, "tweakable") <- c(
"finalize",
## Arguments to batchtools::makeClusterFunctionsSlurm()
"array.jobs", "nodename", "scheduler.latency", "fs.latency"
)
#' @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", "batchtools",
"multiprocess", "future", "function"
)
attr(batchtools_torque, "tweakable") <- c(
"finalize",
## Arguments to batchtools::makeClusterFunctionsTORQUE()
"scheduler.latency", "fs.latency"
)
#' @importFrom batchtools makeClusterFunctionsLSF
#' @importFrom batchtools makeClusterFunctionsOpenLava
#' @importFrom batchtools makeClusterFunctionsSGE
#' @importFrom batchtools makeClusterFunctionsSlurm
#' @importFrom batchtools makeClusterFunctionsTORQUE
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)
dotdotdot <- list(...)
make_cfs <- switch(type,
lsf = makeClusterFunctionsLSF,
openlava = makeClusterFunctionsOpenLava,
sge = makeClusterFunctionsSGE,
slurm = makeClusterFunctionsSlurm,
torque = makeClusterFunctionsTORQUE
)
constructor <- switch(type,
lsf = BatchtoolsLsfFuture,
openlava = BatchtoolsOpenLavaFuture,
sge = BatchtoolsSGEFuture,
slurm = BatchtoolsSlurmFuture,
torque = BatchtoolsTorqueFuture
)
make_cfs_formals <- formals(make_cfs)
## Get the default template?
if (is.null(template)) {
template <- make_cfs_formals$template
}
stop_if_not(is.character(template), length(template) == 1L,
!is.na(template), nzchar(template))
template <- find_template_file(template)
keep <- which(names(dotdotdot) %in% names(make_cfs_formals))
args <- c(list(template = template), dotdotdot[keep])
cluster.functions <- do.call(make_cfs, args = args)
attr(cluster.functions, "template") <- template
## Drop used '...' arguments
if (length(keep) > 0) dotdotdot <- dotdotdot[-keep]
args <- list(
expr = quote(expr), ## Avoid 'expr' being resolved by do.call()
substitute = FALSE, envir = envir,
globals = globals,
label = label,
cluster.functions = cluster.functions,
registry = registry,
resources = resources,
workers = workers
)
if (length(dotdotdot) > 0) args <- c(args, dotdotdot)
future <- do.call(constructor, args = args)
if (!future$lazy) future <- run(future)
invisible(future)
} ## batchtools_by_template()
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