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	Convenience PDB cleanup, not biological-system selection
`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.