create_qsub_config: Create a qsub configuration object.
In rcannood/qsub: Running Commands Remotely on 'Gridengine' Clusters

Description Usage Arguments Value See Also Examples

Create a qsub configuration object.

create_qsub_config(
  remote,
  local_tmp_path,
  remote_tmp_path,
  name = "r2qsub",
  num_cores = 1,
  memory = "4G",
  max_running_tasks = NULL,
  max_wall_time = "01:00:00",
  batch_tasks = 1,
  compress = c("gz", "bz2", "xz", "none"),
  modules = "R",
  execute_before = NULL,
  verbose = FALSE,
  wait = TRUE,
  remove_tmp_folder = TRUE,
  stop_on_error = TRUE
)

override_qsub_config(
  qsub_config = get_default_qsub_config(),
  remote = qsub_config$remote,
  local_tmp_path = qsub_config$local_tmp_path,
  remote_tmp_path = qsub_config$remote_tmp_path,
  name = qsub_config$name,
  num_cores = qsub_config$num_cores,
  memory = qsub_config$memory,
  max_running_tasks = qsub_config$max_running_tasks,
  max_wall_time = qsub_config$max_wall_time,
  batch_tasks = qsub_config$batch_tasks,
  compress = qsub_config$compress,
  modules = qsub_config$modules,
  execute_before = qsub_config$execute_before,
  verbose = qsub_config$verbose,
  wait = qsub_config$wait,
  remove_tmp_folder = qsub_config$remove_tmp_folder,
  stop_on_error = qsub_config$stop_on_error
)

`remote`	Remote machine specification for ssh, in format such as `user@server:port` that does not require interactive password entry.
`local_tmp_path`	A directory on the local machine in which to store temporary files. Should not contain a tilde ('~').
`remote_tmp_path`	A directory on the remote machine in which to store temporary files. Should not contain a tilde ('~').
`name`	The name of the execution. This will show up, for instance, in `qstat`.
`num_cores`	The number of cores to allocate per element in `X` in a `qsub_lapply` (default: `1`).
`memory`	The memory to allocate per core (default: `"4G"`). If this is set too high without it being required, you might not be able to make optimal use of the remote cluster.
`max_running_tasks`	limit concurrent array job task execution (default: `NULL`, infinite). If you have long jobs and there are many other users on the cluster, it is recommended you set this value to a reasonable number, such as 1/4th the total number of nodes * number of cores per node.
`max_wall_time`	The maximum time each task is allowed to run (default: `"01:00:00"`, 1 hour). If set to `NULL`, the job will be allowed to run indefinitely. Mind you, this might annoy other users of the cluster.
`batch_tasks`	How many values in `X` should be processed per task. Useful for when the 'length(X)' is very large (> 10000).
`compress`	Compression method to use: `"none"`, `"gz"` (default), `"bz2"`, or `"xz"`.
`modules`	Which modules to load (default: `"R"`). If set to `NULL`, it will be assumed Rscript will be available in the path through other means.
`execute_before`	Commands to execute in the bash shell before running R.
`verbose`	Whether or not to print out any ssh commands.
`wait`	If `TRUE`, will wait until the execution has finished by periodically checking the job status.
`remove_tmp_folder`	If `TRUE`, will remove everything that was created related to this execution at the end.
`stop_on_error`	If `TRUE`, will stop when an error occurs, else returns a NA for errored instances.
`qsub_config`	A qsub_config to be overridden

A qsub configuration object.

qsub_lapply, set_default_qsub_config

## Not run: 
qsub_config <- create_qsub_config(
  remote = "myuser@myserver.mylocation.com:22",
  local_tmp_path = "/home/myuser/workspace/.r2gridengine",
  remote_tmp_path = "/scratch/myuser/.r2gridengine"
)
qsub_lapply(1:10, function(x) x + 1, qsub_config = qsub_config)

set_default_qsub_config(qsub_config, permanent = TRUE)
qsub_lapply(1:10, function(x) x + 1)

qsub_lapply(
  X = 1:10,
  FUN = function(x) x + 1,
  qsub_config = override_qsub_config(verbose = TRUE)
)

## End(Not run)