Quickstart Guide

This workflow uses PyCOMPSs as Workflow Managment System and GROMACS with PMX for MD and Free Energy evaluations.

1. Get the repository

Clone this repository where you want to use it:

git clone https://github.com/GANANA-EU-INDIA/WP3-P3-workflow.git
cd WP3-P3-workflow

Optionally, create a branch to keep the original workflow intact and allow future updates via git pull:

git switch -c new-branch-name

2. Install PyCOMPSs on HPC

Info

Full details in PyCOMPSs installation section.

Dependencies

Java (11+), Boost, Python (3.11+), gcc, autotools. Load via your cluster's module system.

Manual installation

wget https://compss.bsc.es/repo/sc/stable/COMPSs_<version>.tar.gz
tar -xvzf COMPSs_<version>.tar.gz
cd COMPSs
./install -T <targetDir> [<supercomputer.cfg>]

Create a TCL module file to expose $COMPSS_HOME, PATH, CLASSPATH, PYTHONPATH. See PyCOMPSs.md for a template.

Verify

enqueue_compss -h

3. Set up and run the workflow

Info

Full details: workflow setup and usage.

Python environment

python -m venv ../envs/<venv_name> --system-site-packages
source ../envs/<venv_name>/bin/activate
pip install -r requirements.txt

--system-site-packages exposes PyCOMPSs to the venv.

Gromacs

The user is responsible to install Gromacs in the machine. Please refer to the official installation guide or an example for the Leonardo cluster.

File structure

File	Purpose	When to edit
`Makefile`	Entry point, default arguments	Change workflow execution defaults
`workflow/md.py`	Task definitions, pipeline logic	Adapt workflow steps
`wrapper/env_config_<cluster>.sh`	Cluster modules, `enqueue_compss` flags	New cluster or queue settings
`wrapper/submit_workflow.sh`	Submission wrapper to `enqueue_compss`	Rarely

Submit

make                                # list targets
make md                             # default run
make CLUSTERNAME=dardel NODES=4     # override defaults

Outputs and .COMPSs/ runtime logs appear in the workflow directory.

Clean up

make clean

4. Contribute back

Info

See more info in the contribution documentation

Made an improvement? Open a Pull Request:

git add -A
git commit -m "Describe your changes"
git push origin feat-branch-name

Then open a PR to the main repository and wait for review.

For bugs or feature requests, open an issue using the provided templates.