- Language: en
METHOD_OPTIONS¶
Type: dict_record
method options for comp_script
Example:-
METHOD_OPTIONS:
py_module: comp
rand_seed: 12345
float_format: default
py_module¶
Type: one_of(comp)
Python module required to process this script file
Example:-
py_module: comp
rand_seed¶
Option to set seed to make run result reproducible -e.g. when debugging.
Example:-
rand_seed: 12345
PARALLEL¶
Type: one_of_record
one of many possible servers
Example:-
PARALLEL:
SINGLE: {}
MPI_WORKERS¶
Type: dict_record
MPI local server spec.
Example:-
MPI_WORKERS:
n_workers: auto
cpu_load: 1.0
n_workers¶
Number of workers to use on this machine, defaults to number of processors, but could be more or fewer.
Example:-
n_workers: auto
DESCRIPTION¶
Type: dict_record
Description fields for script.
Example:-
DESCRIPTION:
name: my_pkpd_model
title: My PKPD model
author: My Name
abstract: |
Abstract describing the model
keywords: ['pkpd']
FILE_PATHS¶
Type: dict_record
File paths for comp script
Example:-
FILE_PATHS:
output_folder: auto
temp_folder: auto
log_folder: auto
output_file_ext: ['svg']
delete_old_files_flag: False
gen_script_path: my_pkpd_model_gen.pyml
gen_output_folder: my_pkpd_model_gen.pyml_output
fit_script_path: my_pkpd_model_fit.pyml
fit_output_folder: my_pkpd_model_fit.pyml_output
solutions:
fit_obs: input_observations_soln.pyml
gen_pred: my_pkpd_model_gen.pyml_output\generated_data\solution.pyml
gen_sim_pred: my_pkpd_model_gen.pyml_output\my_pkpd_model_sim.pyml_output\gen_pred\solution.pyml
final_fit_ipred: my_pkpd_model_fit.pyml_output\solN\solution.pyml
final_fit_sim_ipred: my_pkpd_model_fit.pyml_output\my_pkpd_model_sim.pyml_output\final_fit_ipred\solution.pyml
output_folder¶
Type: output_folder / auto
Output folder - results of computation stored here
Example:-
output_folder: auto
temp_folder¶
Type: output_folder / auto
Temp folder - temporary files stored here
Example:-
temp_folder: auto
log_folder¶
Type: output_folder / auto
Log folder - log files stored here
Example:-
log_folder: auto
output_file_ext¶
Type: list_of(pdf,png,svg)
Output file extension - determines graphical output file format.
Example:-
output_file_ext: ['svg']
delete_old_files_flag¶
Type: bool
Option to delete any existing files before running.
Example:-
delete_old_files_flag: False
gen_script_path¶
Type: input_file / auto
Path to gen_script.
Example:-
gen_script_path: my_pkpd_model_gen.pyml
gen_output_folder¶
Type: output_folder / auto
Gen script output folder.
Example:-
gen_output_folder: my_pkpd_model_gen.pyml_output
fit_script_path¶
Type: input_file / auto
Path to fit_script.
Example:-
fit_script_path: my_pkpd_model_fit.pyml
fit_output_folder¶
Type: output_folder / auto
Fit script output folder.
Example:-
fit_output_folder: my_pkpd_model_fit.pyml_output
solutions¶
Type: dict
Solutions to compare
Example:-
solutions:
fit_obs: input_observations_soln.pyml
gen_pred: my_pkpd_model_gen.pyml_output\generated_data\solution.pyml
gen_sim_pred: my_pkpd_model_gen.pyml_output\my_pkpd_model_sim.pyml_output\gen_pred\solution.pyml
final_fit_ipred: my_pkpd_model_fit.pyml_output\solN\solution.pyml
final_fit_sim_ipred: my_pkpd_model_fit.pyml_output\my_pkpd_model_sim.pyml_output\final_fit_ipred\solution.pyml
COMP_OPTIONS¶
Type: dict_record
Options for comp script
Example:-
COMP_OPTIONS:
compute_gen_objective_value: True
compute_fit_objective_value: True
OUTPUT_SCRIPTS¶
Type: dict_record
scripts to output for further processing
Example:-
OUTPUT_SCRIPTS:
GRPH: {output_mode: none, grph_list: ['OBS_vs_TIME']}
GRPH¶
Type: dict_record
options to pass to grph script.
Example:-
GRPH:
output_mode: none
grph_list: ['OBS_vs_TIME']