Install PolyzyMD with pixi

Use this page when you want a working PolyzyMD install quickly.

By the end of this guide, you will have a pixi-managed environment where polyzymd --help and polyzymd info run successfully.

Note

PolyzyMD’s simulation stack depends on packages distributed through conda-forge. pixi handles that solver stack for you, so you do not need conda or mamba installed separately.

Before You Start

• Linux x86-64

• Git

• a shell where you can install pixi

If you are setting up PolyzyMD on a GPU cluster, read this page first and then use the short HPC section below.

1. Install pixi

If pixi is not already available on your system:

curl -fsSL https://pixi.sh/install.sh | sh
source ~/.bashrc

Check that it is available:

pixi --version

2. Install on a Local Machine

The default local setup uses the build environment. This is the right choice for project scaffolding, validation, system building, documentation work, and most local development tasks.

git clone https://github.com/joelaforet/polyzymd.git
cd polyzymd

pixi install -e build
pixi shell -e build

polyzymd --help
polyzymd info

If those last two commands work, your install is ready.

3. If You Are Installing on HPC

Use one of the CUDA environments instead of build.

git clone https://github.com/joelaforet/polyzymd.git
cd polyzymd

# Pick the environment that matches your cluster
pixi install -e cuda-12-6
# or
pixi install -e cuda-12-4

pixi shell -e cuda-12-6
polyzymd info

Built-in presets include configurations for CU Boulder Alpine/Blanca and PSC Bridges2. For submission details and cluster-specific notes, see Run PolyzyMD on SLURM Clusters.

Choose the Right CUDA Environment

On a GPU node, check the driver version:

nvidia-smi | head -1

Use this mapping:

CUDA driver version	Environment	Example clusters
12.6	cuda-12-6	PSC Bridges2
12.4	cuda-12-4	CU Boulder Blanca

4. Verify the Commands You Can Use

In the build environment, these commands should work directly:

Command	Works in build?	Notes
polyzymd init	Yes	Project scaffolding
polyzymd build	Yes	System building
polyzymd validate	Yes	Config validation
polyzymd clean-pdb	Yes	PDB cleanup
polyzymd info	Yes	Version/dependency summary
polyzymd submit	No	Requires a CUDA environment
polyzymd run-segment	No	Requires a CUDA environment

Common Installation Checks

If something looks wrong, try these first:

pixi: command not found

curl -fsSL https://pixi.sh/install.sh | sh
source ~/.bashrc
which pixi

polyzymd: command not found

pixi shell -e build
which polyzymd

OpenMM cannot see CUDA

Make sure you activated the CUDA environment that matches your cluster:

pixi shell -e cuda-12-6
python -c "import openmm; print(openmm.Platform.getPlatformByName('CUDA').getName())"

For broader installation and workflow issues, see Troubleshooting.

Contributor Setup

If you are modifying PolyzyMD itself, use the contributor environment guide:

• Set Up a Contributor Environment

Next Step

Continue to Run Your First PolyzyMD Simulation to create a project scaffold and run your first simulation.