Runs R commands on a cluster that supports SGE.
gcluster.run(
...,
opt.flags = "",
max.jobs = 400,
debug = FALSE,
R = "R",
control_dir = NULL
)R commands
optional flags for qsub command
maximal number of simultaneously submitted jobs
if 'TRUE', additional reports are printed
command that launches R
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.
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. |
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.
# \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")
)
}
# }