Runs R commands on a cluster

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.

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.

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.

Examples

# \donttest{
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")
    )
}
# }