gcluster.run2: Runs R commands on a cluster that supports SGE

In tanaylab/misha.ext: A home to functions that extend the misha package

Runs R commands on a cluster that supports SGE

Description

Runs R commands on a cluster that supports SGE

Usage

gcluster.run2(
  ...,
  command_list = NULL,
  opt.flags = "",
  max.jobs = 400,
  debug = FALSE,
  R = paste0(R.home(component = "bin"), "/R"),
  packages = NULL,
  jobs_title = NULL,
  job_names = NULL,
  collapse_results = FALSE,
  queue = NULL,
  memory = NULL,
  mem_tot = NULL,
  threads = NULL,
  io_saturation = NULL,
  num_proc = NULL,
  queue_flag = "-q {queue}",
  memory_flag = "-l mem_free={memory}G",
  mem_tot_flag = "-l mem_total={mem_tot}G",
  threads_flag = "-pe threads {threads}",
  io_saturation_flag = "-l io_saturation={io_saturation}",
  num_proc_flag = "-l num_proc={num_proc}",
  script = system.file("bin", "sgjob.sh", package = "misha.ext"),
  verbose = FALSE
)

Arguments

...	R commands
command_list	list of strings with 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
packages	packages to load for each command
jobs_title	title of job names. names would have the title followed by a serial number
job_names	vector with the names of the jobs
collapse_results	collapse return values of the jobs to a data frame. if not possible - would return the usual list.
memory	memory requirments (would be called using memory_flag)
mem_tot	memory requirments for the machine (non-consumable)
threads	threads requirments (would be called using threads_flag)
io_saturation	io_saturation requirments (would be called using io_saturation_flag)
memory_flag	flag for memory requirment (formatted as in glue)
threads_flag	flag for threads requirment (formatted as in glue)
io_saturation_flag	flag for io_saturation requirment (formatted as in glue)
verbose	verbose output

Value

if collapse_results is TRUE: data frame with the results of all jobs (rbinded). if collapse_results is FALSE returns the same as: gcluster.run

See Also

gcluster.run

tanaylab/misha.ext documentation built on Oct. 1, 2024, 10:55 a.m.