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google-deepmind / alphafold3

AlphaFold 3 inference pipeline.
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Question regarding multiple tasks #51

Closed sky1ove closed 2 hours ago

sky1ove commented 2 hours ago

I'm curious what are the commands you use if you have multiple json files in your af_input folder? Do you use a shell loop in a container with --rm, or do you use docker exec in a persistent container, or batch processing, or GNU Parallel? What do you recommend?

jsspencer commented 2 hours ago

--input_dir allows you to specify a directory of input JSON files. AF3 is then run on all JSON files in the specified directory.

If you have multiple GPUs, then you can use a shell script to run AF3 in parallel.