gcluster.run: Runs R commands on a cluster

In misha: Toolkit for Analysis of Genomic Data

Runs R commands on a cluster

Description

Runs R commands on a cluster that supports SGE.

Usage

gcluster.run(
  ...,
  opt.flags = "",
  max.jobs = 400,
  debug = FALSE,
  R = "R",
  control_dir = NULL
)

Arguments

...	R commands
opt.flags	optional flags for qsub command
max.jobs	maximal number of simultaneously submitted jobs
debug	if 'TRUE', additional reports are printed
R	command that launches R
control_dir	directory where the control files are stored. Note that this directory should be accessible from all nodes. If 'NULL', a temporary directory would be created under the current misha database.

Details

This function runs R commands on a cluster by distributing them among cluster nodes. It must run on a machine that supports Sun Grid Engine (SGE). The order in which the commands are executed can not be guaranteed, therefore the commands must be inter-independent.

Optional flags to 'qsub' command can be passed through 'opt.flags' parameter. Users are strongly recommended to use only '-l' flag as other flags might interfere with those that are already used (-terse, -S, -o, -e, -V). For additional information please refer to the manual of 'qsub'.

The maximal number of simultaneously submitted jobs is controlled by 'max.jobs'.

Set 'debug' argument to 'TRUE to allow additional report prints.

'gcluster.run' launches R on the cluster nodes to execute the commands. 'R' argument specifies how R executable should be invoked.

Value

Return value ('retv') is a list, such that 'retv[[i]]' represents the result of the run of command number 'i'. Each result consists of 4 fields that can be accessed by 'retv[[i]]$FIELDNAME':

FIELDNAME	DESCRIPTION
exit.status	Exit status of the command. Possible values: 'success', 'failure' or 'interrupted'.
retv	Return value of the command.
stdout	Standard output of the command.
stderr	Standard error of the command.

Examples

gdb.init_examples()
# Run only on systems with Sun Grid Engine (SGE)
if (FALSE) {
    v <- 17
    gcluster.run(
        gsummary("dense_track + v"),
        {
            intervs <- gscreen("dense_track > 0.1", gintervals(1, 2))
            gsummary("sparse_track", intervs)
        },
        gsummary("rects_track")
    )
}

misha documentation built on Sept. 14, 2023, 5:08 p.m.