https://github.com/glotzerlab/hoomd-validation
Longer Running Validation Tests for HOOMD-blue
https://github.com/glotzerlab/hoomd-validation
Last synced: 11 months ago
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Longer Running Validation Tests for HOOMD-blue
- Host: GitHub
- URL: https://github.com/glotzerlab/hoomd-validation
- Owner: glotzerlab
- License: bsd-3-clause
- Created: 2022-04-26T20:16:03.000Z (about 4 years ago)
- Default Branch: trunk
- Last Pushed: 2024-11-08T13:41:22.000Z (over 1 year ago)
- Last Synced: 2024-11-08T14:35:50.674Z (over 1 year ago)
- Language: Python
- Size: 843 KB
- Stars: 3
- Watchers: 9
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
# 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:
```bash
git clone https://github.com/glotzerlab/hoomd-validation.git
```
Then change to the repository's directory:
```bash
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`.
```bash
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`.
[row]: https://row.readthedocs.io
## Execute tests
Run
```bash
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:
```bash
python3 dashboard.py run
```
[signac]: https://signac.readthedocs.io
[signac-dashboard]: https://signac-dashboard.readthedocs.io
## Requirements
* h5py
* hoomd >= 4.6.0
* matplotlib
* numpy
* rtoml
* scipy
* signac >= 2.2.0
* signac-dashboard [optional]