SLURM Job Templates Repository for Tribhuvan University Super Computing Center

This repository provides standardized, reproducible, and well-documented SLURM job templates for a variety of scientific software packages. It is designed for HPC users who need reliable job scripts, helper tools, and examples for running simulations, analyses, and computational workflows.

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1. Overview

This repository centralizes SLURM job scripts and support files used for scientific computing workloads. Each software package has its own directory containing:

• SLURM job templates
• Wrapper scripts
• Example input files
• Documentation specific to that software

The goal is to ensure reproducibility, portability across HPC systems, and simplify onboarding for new users.

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2. Repository Structure

README.md
LICENSE
CONTRIBUTING.md
CI/
  checks.sh
  lint.yml

templates/
  common_header.sh
  slurm_header.sbatch

softwares/
  fplo/
    README.md
    run_qe.sh
    jobs/
      fplo_short.sbatch
      fplo_long.sbatch
    inputs/
      example.in
    outputs/

  gromacs/
    README.md
    jobs/
      gmx_md.sbatch
    container/

examples/
  benchmark_matrix.csv
  submit_all.sh

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3. Naming Conventions

• Job scripts: software_task_resources.sbatch
  • Example: qe_relax_4h_1node.sbatch
• Wrapper scripts: run_software.sh
• All templates include version tags in comments.

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4. Usage Instructions

4.1 Submitting a Job

cd softwares/fplo/jobs
sbatch fplo_short.sbatch

4.2 Monitoring Jobs

squeue -u $USER
sacct -j <JOBID>

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5. Standard SLURM Template Specification

Each .sbatch file should include the following structure:

Header

#!/bin/bash
#SBATCH --job-name=<JOB_NAME>
#SBATCH --account=<ACCOUNT>
#SBATCH --partition=<PARTITION>
#SBATCH --nodes=<NODES>
#SBATCH --ntasks-per-node=<NTASKS_PER_NODE>
#SBATCH --cpus-per-task=<CPUS_PER_TASK>
#SBATCH --time=<TIME>
#SBATCH --mem=<MEMORY>
##SBATCH --gres=gpu:<GPUS> Since we have single gpu on the system on each node. It doesnot require now. 
#SBATCH --output=logs/%x-%j.out
#SBATCH --error=logs/%x-%j.err

Variables Section

ACCOUNT="project_x"
PARTITION="compute"
MODULE="fplo/22"
INPUT_FILE="inputs/example.in"
OUTPUT_DIR="$SLURM_SUBMIT_DIR/outputs"

Execution Section

module purge
module load $MODULE

mkdir -p $OUTPUT_DIR
srun pw.x -in $INPUT_FILE > $OUTPUT_DIR/pw.out

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6. Per-Software Documentation

Each software directory includes:

• Typical HPC resource requirements
• Recommended MPI/OMP settings
• Pre/post-processing workflow
• Known issues and best practices

Example (Quantum ESPRESSO):

• CPU-only: Match tasks per node with physical CPU cores.
• Hybrid: Use MPI ranks × OpenMP threads.
• Suggested command: srun pw.x -in input.in

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7. Modules and Containers Support

Templates support:

• Environment Modules / Lmod
• Apptainer/Singularity

Container Example

singularity exec qe.sif pw.x -in $INPUT_FILE > output.out

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8. Input/Output Organization

• inputs/: Minimal example input files
• outputs/: Output generated after job completion
• For large datasets, store externally and reference them

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9. Testing & CI

Included tests:

• Syntax validation for .sbatch files
• ShellCheck linting for wrapper scripts
• Placeholder checks (no unresolved )

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10. Contribution Guidelines

To contribute:

• Add software under softwares/<name>/
• Provide minimal + advanced templates
• Include documentation and version tags
• Follow formatting conventions

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11. License and Citation

• Default license: MIT
• Cite software authors properly in each submodule

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12. Troubleshooting

PENDING job:

• Account/partition mismatch
• Requested nodes unavailable

MPI errors:

• Use correct srun or mpirun based on cluster policy

Slow I/O:

• Use $SCRATCH rather than home directories
• We have scratch directory, under maintenance, So you cannot use until further notice.

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13. Contact

Maintain the list of maintainers here:

• Primary Maintainer: Aatiz Ghimire
• Email: hpc@tu.edu.np

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This repository aims to become a standard reference for reproducible HPC job submissions across scientific disciplines.