make.batch.file.yaml: Make yaml batch file

In bramkuijper/simulation.utils: Utilities for Working with Simulations in the Kuijper Lab

Make yaml batch file

Description

This function produces a batch file named batch_file_prefix.sh with the following contents:

/path/to/executable.exe -f parameter_file1.yaml
/path/to/executable.exe -f parameter_file2.yaml
/path/to/executable.exe -f parameter_file3.yaml

where parameter_file1.yaml then contains:

param_name1: 0.01
param_name2: 1
param_name3: 1
output_file: output_file_1.csv

If this is all done, you can then run the batch file in any UNIX terminal (e.g., Mac OS X terminal, MSYS2 on Windows) by giving the UNIX terminal the command

bash batch_file_prefix.sh

which causes all simulations to be run sequentially.

Usage

make.batch.file.yaml(
  parameter_list,
  executable_path,
  n_replicates = 1,
  n_cores = 1,
  batch_file_prefix = "batch_file",
  output_file_prefix = "output",
  yaml_file_prefix = "parameters",
  output_file_yaml_key = "base_name"
)

Arguments

parameter_list	a list or dataframe with all parameter combinations the order with which a parameter was added to the list will be maintained
executable_path	the path to the simulation executable (i.e., the exe file)
n_replicates	the number of replicates you'd like to run of each simulation
n_cores	the number of cores available. If n_cores>1, simulations can be run in parallel
batch_file_prefix	the prefix of the resulting batch file to which all the simulation commands will be written to
output_file_prefix	the prefix of the resulting output file to which each simulation will write its output.
yaml_file_prefix	the prefix of each individual .yaml file that iscontaining the parameters for a single simulation
output_file_yaml_key	the identifier key that a file name has in the yaml file. Default is base_name.

Value

This function returns NULL. However, a file with name batch_file_prefix will be written to disk. If the option yaml=TRUE, this will be accompanied by one or more .yaml files.

Examples

#initalize a parameter object
parameter_object <- list()
parameter_object$z <- c(0.0,0.01)
parameter_object$b <- 0.1

# call the batch file function
make.batch.file(parameter_list=parameter_object
                     ,executable_path="./my_simulation.exe")
# which produces a file named 'batch_file.sh' in the current directory
# containing:
# ./my_simulation.exe 0.0 0.1 output_file_1
# ./my_simulation.exe 0.001 0.1 output_file_2
# Note that the value of parameter z is
# printed first and then the value of parameter b, followed by the
# name of the output file for this simulation

bramkuijper/simulation.utils documentation built on Jan. 29, 2024, 11:23 a.m.