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SLURM Run class to manage SLURM job execution

PMSlurmRun.Rd

This object represents a SLURM job that has been submitted. It provides methods to check job status, get results, and cancel the job.

Public fields

job_id

Character. The SLURM job ID

analysis_path

Character. Path to the analysis folder

result_path

Character. Path where results will be stored

log_path

Character. Path to the SLURM output log file

error_log_path

Character. Path to the SLURM error log file

Methods

Public methods

Method new()

Create a PMSlurmRun object

Usage

PMSlurmRun$new(job_id, analysis_path, result_path, log_path, error_log_path)

Arguments

job_id

Character. The SLURM job ID

analysis_path

Character. Path to the analysis folder

result_path

Character. Path where results will be stored

log_path

Character. Path to the SLURM output log file

error_log_path

Character. Path to the SLURM error log file

Method print()

Print method for PMSlurmRun

Usage

PMSlurmRun$print()

Method is_done()

Check if the SLURM job is done

Usage

PMSlurmRun$is_done()

Returns

Logical. TRUE if the job is done, FALSE otherwise.

Method is_successful()

Check if the SLURM job completed successfully

Usage

PMSlurmRun$is_successful()

Details

Returns FALSE if the job is still running or if it failed. Only returns TRUE if the job completed successfully.

Returns

Logical. TRUE if the job completed successfully, FALSE if it failed or is still running.

Method get_results()

Get the results from the SLURM job

Usage

PMSlurmRun$get_results(timeout = NULL)

Arguments

timeout

Numeric. Optional timeout in seconds. If provided, will wait for the job to complete (blocking) up to the timeout duration before failing. If NULL (default), returns immediately if job is not done.

Details

If timeout is provided, this method will block and wait for the job to complete. If the job fails or times out, an error is raised with details. The results are loaded from the intermediate folder.

Returns

The results object (loaded from the result file)

Method cancel()

Cancel the SLURM job

Usage

PMSlurmRun$cancel()

Returns

Invisibly returns TRUE if successful

Method clone()

The objects of this class are cloneable with this method.

Usage

PMSlurmRun$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
# Run a function in SLURM
analysis <- pm$get_analysis("my_analysis")
slurm_run <- analysis$run_in_slurm(function() {
  # Your analysis code here
  result <- compute_something()
  return(result)
})

# Check if job is done
slurm_run$is_done()

# Get results (errors if not done)
results <- slurm_run$get_results()

# Cancel the job
slurm_run$cancel()
} # }