Docker Installation

Use Docker for GPU inference on a Linux host with an NVIDIA GPU. All examples below are one-shot docker run commands executed from the host. For non-Docker installation, see inference_instructions.md.

1. Verify Docker GPU support

Install Docker and the NVIDIA Container Toolkit, then verify that containers can see the GPU:

docker run --rm --gpus all nvidia/cuda:12.6.3-base-ubuntu24.04 nvidia-smi

2. Get the image

Pull the prebuilt image:

docker pull aurekaresearch/opendde:v1

Or build from the repository root:

docker build -t aurekaresearch/opendde:v1 .

3. Prepare runtime data

OpenDDE reads checkpoints and runtime data from OPENDDE_ROOT_DIR. If you have local checkpoints, place opendde.pt and/or opendde_abag.pt under checkpoint/ in that directory:

export OPENDDE_ROOT_DIR="$PWD/opendde_data"

mkdir -p "$OPENDDE_ROOT_DIR/checkpoint"
cp /absolute/path/to/opendde.pt "$OPENDDE_ROOT_DIR/checkpoint/opendde.pt"

Released checkpoints:

Checkpoint	Use case	Download
`opendde.pt`	General-purpose OpenDDE checkpoint.	opendde.pt
`opendde_abag.pt`	ABAG-optimized checkpoint for antibody-antigen complexes.	opendde_abag.pt

For the default Docker command below, place the general-purpose checkpoint at $OPENDDE_ROOT_DIR/checkpoint/opendde.pt. When using the ABAG-optimized checkpoint, add this to the opendde pred command:

--load_checkpoint_path /opendde_data/checkpoint/opendde_abag.pt

Download one checkpoint directly into the default host path:

# General-purpose checkpoint:
curl -L \
  -o "$OPENDDE_ROOT_DIR/checkpoint/opendde.pt" \
  https://huggingface.co/aurekaresearch/OpenDDE/resolve/main/opendde.pt

# ABAG-optimized checkpoint:
curl -L \
  -o "$OPENDDE_ROOT_DIR/checkpoint/opendde_abag.pt" \
  https://huggingface.co/aurekaresearch/OpenDDE/resolve/main/opendde_abag.pt

Download or verify the remaining runtime files with Docker:

docker run --rm \
  -v "$OPENDDE_ROOT_DIR":/opendde_data \
  aurekaresearch/opendde:v1 \
  bash scripts/download_opendde_data.sh \
    --root /opendde_data

For protein-only smoke tests that disable MSA/template/RNA-MSA preprocessing, you can skip search databases:

docker run --rm \
  -v "$OPENDDE_ROOT_DIR":/opendde_data \
  aurekaresearch/opendde:v1 \
  bash scripts/download_opendde_data.sh \
    --root /opendde_data \
    --skip-search-database

4. Run inference

The command below assumes tiny.json exists in the current host directory. See ../README.md for the minimal input example.

mkdir -p output

docker run --rm --gpus all --shm-size=4g \
  -e OPENDDE_ROOT_DIR=/opendde_data \
  -v "$OPENDDE_ROOT_DIR":/opendde_data:ro \
  -v "$PWD":/workspace \
  -v "$PWD/output":/output \
  aurekaresearch/opendde:v1 \
  opendde pred \
    -i /workspace/tiny.json \
    -o /output \
    -n opendde_v1 \
    --use_msa false \
    --use_template false \
    --use_rna_msa false \
    --sample 1 \
    --step 200 \
    --cycle 10

For production inference options, MSA/template preprocessing, and checkpoint configuration, see inference_instructions.md.