submit simulation examples

This page is generated from docs/submit-simulation/examples.md. Edit the repository source; automated publishing replaces direct wiki edits.

Submission examples

Run these commands on ifarm from a csh/tcsh login shell. Preview is the default and is the recommended first step for every sample.

Preview one completed sample

source run.csh \
  --workflow submit \
  --lund-dir /shared/runs/Uniform__1e__5986MeV/lundfiles

Preview first inspects both mchipo/ and reconhipo/ paths. It preserves files in an existing directory and says that --execute would delete and recreate it. It creates and verifies either directory when missing. It does not call sbatch.

Submit only the first five LUND files

source run.csh \
  --workflow submit \
  --lund-dir /shared/runs/Uniform__1e__5986MeV/lundfiles \
  --num-jobs 5 \
  --execute

--execute warns before deleting an existing mchipo/ or reconhipo/ directory and all its contents, then recreates both directories empty while preserving lundfiles/.

Override the shared per-task event limit

source run.csh \
  --workflow submit \
  --lund-dir /shared/runs/Uniform__enFD__4029MeV/lundfiles \
  --num-jobs 3 \
  --events-per-job 5000

Without the override, the largest selected manifest file count becomes the shared GEMC/reconstruction limit.

Preview several samples in one invocation

source run.csh \
  --workflow submit \
  --lund-dir /shared/runs/Uniform__1e__2070MeV/lundfiles \
  --lund-dir /shared/runs/Uniform__epFD__2070MeV/lundfiles \
  --lund-dir /shared/runs/Uniform__enFD__2070MeV/lundfiles \
  --num-jobs 2

Each distinct sample becomes a separate Slurm array.

Use a submission profile with explicit overrides

source run.csh \
  --workflow submit \
  --config config/submission.conf \
  --lund-dir /shared/runs/physical/lundfiles \
  --gemc-version 5.14 \
  --torus -1.0 \
  --job-name C12_GENIE_validation

Select detector and reconstruction resources explicitly

source run.csh \
  --workflow submit \
  --lund-dir /shared/runs/physical/lundfiles \
  --gemc-target-variation rgm_fall2021_Ar \
  --gcard config/detector/Generation_files_6GeV/5.14/rgm_fall2021_Ar_6GeV.gcard \
  --yaml config/detector/Generation_files_6GeV/5.14/rgm_fall2021-ai_6Gev.yaml

Use paths that exist in the refreshed ifarm checkout. The GCARD controls detector simulation; the YAML controls reconstruction.

Test a custom clas12Tags checkout

source run.csh \
  --workflow submit \
  --lund-dir /shared/runs/physical/lundfiles \
  --clas12tags-dir /shared/development/clas12Tags

This changes GEMC_DATA_DIR for detector-development testing while retaining the selected GEMC executable checks.

Optional direct farm-log cleanup

source run.csh \
  --workflow submit \
  --lund-dir /shared/runs/physical/lundfiles \
  --clear-farm-out true \
  --farm-out /shared/farm_out \
  --execute

Use cleanup only with an exact reviewed directory. It deletes files directly inside that directory once per invocation; it does not broaden simulation-output replacement. The --farm-out DIRECTORY option is required whenever --clear-farm-out true is selected. Omit both options to preserve existing Slurm logs.

Verify reconstructed output

The workflow does not monitor array tasks after sbatch accepts them. Once the jobs finish, review the Slurm states and logs and test at least one file under the run's reconhipo/ directory:

hipo-utils -dump /shared/runs/physical/reconhipo/<hipo-file-name>.hipo

Confirm that hipo-utils opens the file and displays CLAS12 data banks. Also check the remaining task states and output inventory; one valid HIPO file does not guarantee that the complete array succeeded.

The repository also contains a matched uniform submission command list for 1e, enFD, and epFD at the three established beam energies.