View source: R/submit-models.R
submit_models | R Documentation |
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"),
...,
.overwrite = NULL,
.config_path = NULL,
.wait = TRUE,
.dry_run = FALSE
)
## S3 method for class 'list'
submit_models(
.mods,
.bbi_args = NULL,
.mode = getOption("bbr.bbi_exe_mode"),
...,
.overwrite = NULL,
.config_path = NULL,
.wait = TRUE,
.dry_run = FALSE
)
.mods |
The model objects to submit. |
.bbi_args |
A named list specifying arguments to pass to bbi
formatted like |
.mode |
Mode for model submission: "local", "sge", or "slurm". If
unspecified, the value is set to the value of the |
... |
args passed through to |
.overwrite |
Logical to specify whether or not to overwrite existing
model output from a previous run. If |
.config_path |
Path to a bbi configuration file. If |
.wait |
If |
.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. |
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
.
submit_models(list)
: Takes a list of bbi_base_model
objects.
NONMEM
model extensionsBefore executing the model, bbi
first copies the control stream file to a
subdirectory. Whether a relative path to the data file in the control stream
is adjusted for this change in directory depends on the control stream's file
extension:
For a model with a .mod
extension, bbi
automatically adjusts a
relative data path to make it relative to the execution directory,
following the behavior of PsN
.
For a model with a .ctl
extension, bbi
does not adjust the data
path. A relative data path in the control stream must be specified
one level deeper (i.e. with an additional ../
) to account for the
model being executed in a subdirectory.
submit_model()
Other NONMEM
model extensions:
get_data_path()
,
submit_model()
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