1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
|
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/clusterFunctionsTORQUE.R
\name{makeClusterFunctionsTORQUE}
\alias{makeClusterFunctionsTORQUE}
\title{ClusterFunctions for OpenPBS/TORQUE Systems}
\usage{
makeClusterFunctionsTORQUE(
template = "torque",
scheduler.latency = 1,
fs.latency = 65
)
}
\arguments{
\item{template}{[\code{character(1)}]\cr
Either a path to a \pkg{brew} template file (with extension \dQuote{tmpl}), or a short descriptive name enabling the following heuristic for the file lookup:
\enumerate{
\item \dQuote{batchtools.[template].tmpl} in the path specified by the environment variable \dQuote{R_BATCHTOOLS_SEARCH_PATH}.
\item \dQuote{batchtools.[template].tmpl} in the current working directory.
\item \dQuote{[template].tmpl} in the user config directory (see \code{\link[rappdirs]{user_config_dir}}); on linux this is usually \dQuote{~/.config/batchtools/[template].tmpl}.
\item \dQuote{.batchtools.[template].tmpl} in the home directory.
\item \dQuote{[template].tmpl} in the package installation directory in the subfolder \dQuote{templates}.
}}
\item{scheduler.latency}{[\code{numeric(1)}]\cr
Time to sleep after important interactions with the scheduler to ensure a sane state.
Currently only triggered after calling \code{\link{submitJobs}}.}
\item{fs.latency}{[\code{numeric(1)}]\cr
Expected maximum latency of the file system, in seconds.
Set to a positive number for network file systems like NFS which enables more robust (but also more expensive) mechanisms to
access files and directories.
Usually safe to set to \code{0} to disable the heuristic, e.g. if you are working on a local file system.}
}
\value{
[\code{\link{ClusterFunctions}}].
}
\description{
Cluster functions for TORQUE/PBS (\url{https://adaptivecomputing.com/cherry-services/torque-resource-manager/}).
Job files are created based on the brew template \code{template.file}. This file is processed
with brew and then submitted to the queue using the \code{qsub} command. Jobs are killed using
the \code{qdel} command and the list of running jobs is retrieved using \code{qselect}. The user
must have the appropriate privileges to submit, delete and list jobs on the cluster (this is
usually the case).
The template file can access all resources passed to \code{\link{submitJobs}}
as well as all variables stored in the \code{\link{JobCollection}}.
It is the template file's job to choose a queue for the job and handle the desired resource
allocations.
}
\seealso{
Other ClusterFunctions:
\code{\link{makeClusterFunctionsDocker}()},
\code{\link{makeClusterFunctionsInteractive}()},
\code{\link{makeClusterFunctionsLSF}()},
\code{\link{makeClusterFunctionsMulticore}()},
\code{\link{makeClusterFunctionsOpenLava}()},
\code{\link{makeClusterFunctionsSGE}()},
\code{\link{makeClusterFunctionsSSH}()},
\code{\link{makeClusterFunctionsSlurm}()},
\code{\link{makeClusterFunctionsSocket}()},
\code{\link{makeClusterFunctions}()}
}
\concept{ClusterFunctions}
|
