qsub_lapply: Apply a Function over a List or Vector on a gridengine...

In rcannood/qsub: Running Commands Remotely on 'Gridengine' Clusters

Description

Apply a Function over a List or Vector on a gridengine system!

Usage

qsub_lapply(
  X,
  FUN,
  object_envir = environment(FUN),
  qsub_config = NULL,
  qsub_environment = NULL,
  qsub_packages = NULL,
  ...
)

Arguments

X	A vector (atomic or list) or an expression object. Other objects (including classed objects) will be coerced by base::as.list.
FUN	The function to be applied to each element of X.
object_envir	The environment in which to go looking for the qsub_environment variables, if these are characters.
qsub_config	The configuration to use for this execution.
qsub_environment	NULL, a character vector or an environment. Specifies what data and functions will be uploaded to the server.
qsub_packages	The packages to be loaded on the cluster.
...	optional arguments to FUN.

See Also

create_qsub_config, set_default_qsub_config

Examples

## Not run: 
# Initial configuration and execution
qsub_config <- create_qsub_config(
  remote = "myserver",
  local_tmp_path = "/home/myuser/workspace/.r2gridengine",
  remote_tmp_path = "/scratch/myuser/.r2gridengine"
)
qsub_lapply(
  X = seq_len(3),
  FUN = function(i) { Sys.sleep(1); i+1 },
  qsub_config = qsub_config
)

# Setting a default configuration and short hand notation for execution
set_default_qsub_config(qsub_config, permanent = T)
qsub_lapply(seq_len(3), function(i) { Sys.sleep(1); i+1 })

# Overriding a default qsub_config
qsub_lapply(seq_len(3), function(i) i + 1,
  qsub_config = override_qsub_config(name = "MyJob"))

# Don't wait for results, get a handle instead and retrieve later.
handle <- qsub_lapply(seq_len(3), function(i) i + 1,
  qsub_config = override_qsub_config(wait = F))

# Wait until results have been generated on the remote

# Retrieve results
qsub_retrieve(handle)

## End(Not run)

rcannood/qsub documentation built on Sept. 26, 2021, 8:55 a.m.