Run TMB Model on SLURM Cluster — run_tmb_on

Creates and optionally submits a SLURM job to run a TMB model on a computing cluster.

run_tmb_on_slurm(
  data,
  params,
  random = NULL,
  map_words = NULL,
  dll = "model",
  n_cores = NULL,
  job_name = "TMBjob",
  partition = "fuchs",
  time = "8:00:00",
  ntasks = 1,
  nodes = 1,
  conda_env = "kinh",
  rscript = "run_tmb.r",
  work_dir = ".",
  submit = FALSE,
  submit_cmd = "sbatch",
  data_path = "tmb_data.RData",
  param_path = "tmb_params.RData",
  map_path = "tmb_param_map.RData"
)

Arguments

data: Data list for TMB model
params: Parameter list for TMB model
random: Character vector of random effect parameter names
map_words: Named list of parameter mapping specifications
dll: Character name of compiled TMB model (without extension)
n_cores: Number of cores for OpenMP parallelization
job_name: Character name for SLURM job
partition: Character name of SLURM partition
time: Character time limit for job ("HH:MM:SS")
ntasks: Number of tasks for SLURM
nodes: Number of nodes for SLURM
conda_env: Character name of conda environment
rscript: Character name for generated R script
work_dir: Character path to working directory
submit: Logical whether to submit job immediately
submit_cmd: Character command to submit SLURM job
data_path: Character path to save data
param_path: Character path to save parameters
map_path: Character path to save parameter map

Value

Invisibly returns a list with:

submitted: Logical indicating if job was submitted
output: System output from job submission if applicable
rscript: Path to generated R script
slurm: Path to generated SLURM script
data: Path to saved data
param: Path to saved parameters
map: Path to saved parameter map if applicable

Details

This function generates necessary R and SLURM scripts to run a TMB model on a SLURM-based computing cluster. It saves model data and parameters to files, creates an R script to fit the model, and a SLURM submission script. The job can be submitted immediately or the scripts can be saved for later submission.