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bzhanglab / DeepRescore

DeepRescore: rescore PSMs leveraging deep learning-derived peptide features
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GPU usage #5

Open kudpolser opened 3 years ago

kudpolser commented 3 years ago

Dear developers,

DeepRescore does not use the GPU on our server. How do I get him to see our graphic cards? I assume I need to pass the parameters to Docker --runtime=nvidia --NVIDIA_VISIBLE_DEVICES=all, but due to the fact that I am using nextflow, I don't understand how to do this.

Thanks in advance.

Polina

wenbostar commented 3 years ago

Have you installed https://github.com/NVIDIA/nvidia-docker?

Bo

nukaemon commented 3 years ago

Hello @kudpolser

I encountered with the same problem when running on AWS server. Add '--gpus all' to nextflow.config like as

docker {

        enabled    = true
        remove     = true
        runOptions = '-u $(id -u):$(id -g) --gpus all'
        temp       = "/tmp/"
}

then you should pass train_autoRT process.