Submit models to be run in batch

Submits a group of models to be run in batch by calling out to bbi in as few external calls as possible (see "Details").

submit_models(
  .mods,
  .bbi_args = NULL,
  .mode = getOption("bbr.bbi_exe_mode"),
  ...,
  .config_path = NULL,
  .wait = TRUE,
  .dry_run = FALSE
)

# S3 method for list
submit_models(
  .mods,
  .bbi_args = NULL,
  .mode = getOption("bbr.bbi_exe_mode"),
  ...,
  .config_path = NULL,
  .wait = TRUE,
  .dry_run = FALSE
)

Arguments

.mods

The model objects to submit.

.bbi_args

A named list specifying arguments to pass to bbi formatted like list("nm_version" = "nm74gf_nmfe", "json" = T, "threads" = 4). Run print_bbi_args() to see valid arguments. Note that bbr does not support changing the output directory (including through the model or global YAML files).

.mode

Either "sge", the default, to submit model(s) to the grid or "local" for local execution. This can be passed directly to this argument or set globally with options("bbr.bbi_exe_mode").

...

args passed through to bbi_exec()

.config_path

Path to a bbi configuration file. If NULL, the default, will attempt to use a bbi.yaml in the same directory as the model.

.wait

If TRUE, the default, wait for the bbi process to return before this function call returns. If FALSE function will return while bbi process runs in the background.

.dry_run

Returns an object detailing the command that would be run, insted of running it. This is primarily for testing but also a debugging tool.

Details

The number of bbi calls to make is determined by the number of distinct sets of bbi arguments passed to the submission calls, either explicitly through .bbi_args, as specified in the bbi_args field of the model YAML, or specified globally in bbi.yaml.

Methods (by class)

• list: Takes a list of bbi_nonmem_model objects.

See also

submit_model()