Basecalling settings

❗ This section is under construction

optimising Guppy Base Calling on Jetson Xavier NX

General formula:

runners * chunks_per_runner * chunk_size < 100'000 * [max GPU memory in GB] * 2

Xavier NX

So the current settings I am running on the Xavier NX are:

• --gpu_runners_per_device = 4 (1 default MinIT config)
• --chunks_per_runner = 256 (48 default MinIT config)
• --chunk_size = 1000 (1000 default MinIT config)

4 * 256 * 1000 ~= 100'000 * 8 * 2 which is 1'024'000 < 1'600'000

this is leaving some overhead for the likes of the OS and MinKnow.

Running with the default settings (as above) took ~5.3 mins on a test data set. Running with the selected settings reduced this down to ~2.7 mins.

Increasing the chunks_per_runner led to the largest gains in speed.

Xavier AGX

The current 'optimal' settings I am running on the Xavier AGX are:

• --num_callers (num basecallers) = 2
• --gpu_runners_per_device = 3 (1 default MinIT config)
• --chunks_per_runner = 1024 (48 default MinIT config)
• --chunk_size = 1000 (1000 default MinIT config)

3 * 1024 * 1000 ~= 100'000 * 16 * 2 which is 3'072'000 < 3'200'000

This is giving me a base calling rate of ~9.43x10⁶ samples/s.