HOOMD-blue Validation

This repository contains validation tests for HOOMD-blue. The workflows are organized in a signac workspace and use row.

Preparation

Clone this repository:

git clone https://github.com/glotzerlab/hoomd-validation.git

Then change to the repository's directory:

cd hoomd-validation

Configuration

1. Install the requirements (see below) into a Python environment of your choice.
2. Copy hoomd_validation/config-sample.toml to hoomd_validation/config.toml and set the parameters as desired. Each option is documented by a comment in the sample configuration file.
3. Initialize the signac project directories and create workflow.toml.

   python3 hoomd_validation/project.py init

4. Configure row as necessary for your workstation or HPC resources.

   Note: project.py init will overwrite workflow.toml.

Execute tests

Run

row submit

To submit the first stage of the workflow. Wait for all the jobs to complete, then run row submit again to start the second stage. Most subprojects in the validation workflow have 4 stages ending with compare_modes.

Note: You can execute a single subproject with `row submit --action 'subproject_name.*'

After you execute compare_mode, inspect the svg files saved in the repository root. You can also run the provided signac-dashboard application to explore the results in a web browser:

python3 dashboard.py run

Requirements

• h5py
• hoomd >= 4.6.0
• matplotlib
• numpy
• rtoml
• scipy
• signac >= 2.2.0
• signac-dashboard [optional]