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Update docs with GPU fitting info
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nickjcroucher committed Feb 27, 2024
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Expand Up @@ -111,4 +111,15 @@ Using a GPU
By default, PopPUNK will use not use GPUs. To use them, you will need to add
the flag ``--gpu-sketch`` (when constructing or querying a database using reads),
``--gpu-dist`` (when constructing or querying a database from assemblies or reads),
or ``--gpu-graph`` (when querying or visualising a database, or fitting a model).
``--gpu-model`` (when fitting a DBSCAN model on the GPU), or ``--gpu-graph``
(when querying or visualising a database, or fitting a model).

Note that fitting a model with a GPU is fast, even with a large subsample of points,
but may be limited by the memory of the GPU device. Therefore it is recommended that
either the model is only fitted to a subsample of points, resulting in an incomplete
model fit that must then be refined before use (option ``--for-refine``), or that
the transfer of data between CPU and GPU is optimised using the ``--assign-subsample``
variable. Larger values of ``--assign-subsample`` will result in fewer batches being
transferred to the GPU memory, speeding up the process, but also increasing the risks
that your device will run out of memory, particularly if a large, complex model object
is already being stored on the device.

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