lynxkite-graph-analytics/README.md

LynxKite Graph Analytics

This is a LynxKite plugin that provides a graph analytics environment. Includes a batch executor operating on graph bundles and a collection of GPU-accelerated graph data science operations.

To use this, install both LynxKite and this plugin. Then "LynxKite Graph Analytics" will show up as one of the workspace types in LynxKite.

pip install lynxkite lynxkite-graph-analytics

Run LynxKite with NX_CUGRAPH_AUTOCONFIG=True to enable GPU-accelerated graph data science operations.

BioNemo

If you want to use BioNemo operations, then you will have to use the provided Docker image, or install BioNemo manually in your environment. Take into account that BioNemo needs a GPU to work, you can find the specific requirements here.

The import of BioNemo operations is gate keeped behing the LYNXKITE_BIONEMO_INSTALLED variable. BioNemo operations will only be imported if this environment variable is set to true.

To build the image:

# in lynxkite-graph-analytics folder
$ docker build -f Dockerfile.bionemo -t lynxkite-bionemo ..
$ docker run --name bionemo -d -p8000:8000 --gpus=all lynxkite-bionemo

Take into account that this Dockerfile does not include the lynxkite-lynxscribe package. If you want to include it you will need to set up git credentials inside the container.

If you want to do some development, then it is recommend to use the devcontainers vscode extension. The following is a basic configuration to get started:

// .devcontainer/devcontainer.json
{
    "name": "Existing Dockerfile",
    "runArgs": [
        "--gpus=all",
        "--shm-size=4g"
    ],
    "build": {
        "context": "..",
        "dockerfile": "../lynxkite-graph-analytics/Dockerfile.bionemo"
    }
}