Base-calling server parameters¶

The default settings for Dorado GPU should be sufficient for most use cases.

The one trick we sometimes use, on a really high performance flow cell is to split the GPUs between readfish and dorado.

This of course assumes that you have a multiple GPU machine, such as PromethION tower. In the new P24 towers, there are 4x NVIDIA A100 GPUs.

  1. Stop dorado sudo systemctl stop doradod

  2. View the available CUDA devices. nvidia-smi

  3. Restart two dorado instances, splitting the devices between each.

Dorado:

/opt/ont/dorado/bin/dorado_basecall_server --log_path /var/log/dorado --config dna_r10.4.1_e8.2_400bps_fast.cfg --ipc_threads 3 --port /tmp/.guppy/5555 --dorado_download_path /opt/ont/dorado-models --device cuda:0

/opt/ont/dorado/bin/dorado_basecall_server --log_path /var/log/dorado --config dna_r10.4.1_e8.2_400bps_fast.cfg --ipc_threads 3 --port /tmp/.guppy/5556 --dorado_download_path /opt/ont/dorado-models --device cuda:1

  1. Start readfish, base calling on port 5556