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How to run the CPU search and the GPU fold on different machines with Alphafold3

Use the run flags to do genetic and template search on a CPU box and inference on a GPU box.

Short answer: Install AlphaFold 3 as described in docs/installation.md; then run python run_alphafold.py --help to list all the available flags; run the data pipeline alone with --run_data_pipeline set to true and --run_inference set to false on a machine without a GPU. All steps.

Credentials. Keep the model parameters and their terms of use in mind when copying files between machines.

Who it is forA lab sharing one GPU across many predictions.

The problemThe data pipeline is slow and does not need the GPU, so it wastes GPU hours.

The outcomeA split workflow where the expensive search runs where it is cheap.

What you need first

  • The model parameters, which you may only use if received directly from Google, under the weights terms of use
  • Docker and an NVIDIA GPU for the inference step
  • The genetic and template databases for the data pipeline, mounted into the container
  • A fold_input.json describing your sequences, model seeds, dialect and version

Steps

  1. Install AlphaFold 3 as described in docs/installation.md
  2. Run python run_alphafold.py --help to list all the available flags
  3. Run the data pipeline alone with --run_data_pipeline set to true and --run_inference set to false on a machine without a GPU
  4. Run inference alone on the GPU machine with --run_data_pipeline false and --run_inference true, reading docs/performance.md for tuning

Prompt for your agent

With google-deepmind/alphafold3, show me how to run the data pipeline on my CPU server and inference on my GPU server using --run_data_pipeline and --run_inference, and what to copy between them.

Caveat. The data pipeline needs the genetic and template databases, which are large.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for google-deepmind/alphafold3 and "Run the CPU search and the GPU fold on different machines"

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