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Prepare SLURM file for failed / Unfitted Models

Source: R/Mod_SLURM_Refit.R
Mod_SLURM_Refit.Rd

This function prepares SLURM files for models that have not been successfully fitted yet. It generates command files for refitting and creates corresponding SLURM batch files to execute these commands on a HPC environment.

Usage

Mod_SLURM_Refit(
  ModelDir = NULL,
  NumArrayJobs = 210,
  JobName = NULL,
  MemPerCpu = NULL,
  Time = NULL,
  Partition = "small-g",
  EnvFile = ".env",
  CatJobInfo = TRUE,
  ntasks = 1,
  CpusPerTask = 1,
  GpusPerNode = 1,
  FromHPC = TRUE,
  PrepSLURM = TRUE,
  Path_Hmsc = NULL,
  Refit_Prefix = "Commands2Refit",
  SLURM_Prefix = "Bash_Refit"
)

Arguments

ModelDir

String. Path to the model files directory. Must not end with a slash.

NumArrayJobs

Integer specifying the maximum number of array jobs per SLURM script. Default: 210. See LUMI documentation for more details.

JobName

String. The name of the submitted job(s).

MemPerCpu

String. Memory per CPU allocation for the SLURM job. Example: 32G for 32 gigabytes. Defaults to NULL. If not provided, the function will throw an error.

Time

String. Duration for which the job should run. Example: 01:00:00 for one hour. If not provided, the function will throw an error.

Partition

String. The name of the partition. Default: small-g for running the array jobs on the GPU.

EnvFile

String. Path to read the environment variables. Default value: .env.

CatJobInfo

Logical. Add bash lines to print information on the submitted job. Default: TRUE.

ntasks

Integer. The value for the #SBATCH --ntasks= SLURM argument. Default: 1.

CpusPerTask

Integer. The value for the #SBATCH --cpus-per-task= SLURM argument. Default: 1.

GpusPerNode

Integer. The value for the #SBATCH --gpus-per-node= SLURM argument. Default: 1.

FromHPC

Logical. Indicates if the operation is being performed from an HPC environment. This adjusts file paths accordingly. Default: TRUE.

PrepSLURM

Logical indicating whether to prepare SLURM command files. If TRUE (default), the SLURM commands will be saved to disk using the Mod_SLURM function.

Path_Hmsc

String. Path for the Hmsc-HPC.

Refit_Prefix

String. Prefix for the files that contain the commands to refit the models.

SLURM_Prefix

String. Prefix for the exported SLURM file.

Value

The function does not return any value but creates command and SLURM batch files for refitting models.

Author

Ahmed El-Gabbas