submit_model | R Documentation |
Submits a model to be run by calling out to bbi
.
submit_model(
.mod,
.bbi_args = NULL,
.mode = getOption("bbr.bbi_exe_mode"),
...,
.overwrite = NULL,
.config_path = NULL,
.wait = TRUE,
.dry_run = FALSE
)
## S3 method for class 'bbi_base_model'
submit_model(
.mod,
.bbi_args = NULL,
.mode = getOption("bbr.bbi_exe_mode"),
...,
.overwrite = NULL,
.config_path = NULL,
.wait = TRUE,
.dry_run = FALSE
)
## S3 method for class 'bbi_nmsim_model'
submit_model(
.mod,
.bbi_args = NULL,
.mode = getOption("bbr.bbi_exe_mode"),
...,
.overwrite = NULL,
.config_path = NULL,
.wait = TRUE,
.dry_run = FALSE
)
## S3 method for class 'bbi_nmboot_model'
submit_model(
.mod,
.bbi_args = NULL,
.mode = "sge",
...,
.overwrite = FALSE,
.config_path = NULL,
.wait = FALSE,
.dry_run = FALSE,
.batch_size = 100
)
.mod |
The model object 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. |
.batch_size |
Number of models to submit to run concurrently as a
"batch." Passing |
While submit_model()
does return something, it is primarily
called for its side effects, specifically that it runs the model and writes
all model outputs to disk under get_output_dir(.mod)
.
NONMEM
For NONMEM models, a bbi_process
object is returned. The typical NONMEM
output files are all written into get_output_dir(.mod)
. A summary of the
contents of these files can be accessed with model_summary()
, and the path
to individual files can be easily constructed like
build_path_from_model(.mod, ".lst")
.
A bbi_config.json
file is also written, which stores information about the
configuration of the run. See config_log()
for more details about this
file.
submit_model(bbi_base_model)
: Takes a bbi_base_model
object.
submit_model(bbi_nmsim_model)
: Takes a bbi_base_model
object.
submit_model(bbi_nmboot_model)
: Takes a bbi_nmboot_model
object.
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_models()
Other NONMEM
model extensions:
get_data_path()
,
submit_models()
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