Update transformer.py #210
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I get a numpy cuda / cpu conversion error due to the `batches` being moved to `device` before the `collate()` function.
```
Traceback (most recent call last):
File "/local-scratch-nvme/nigam/ehrshot/lib/python3.10/pdb.py", line 1723, in main
pdb._runscript(mainpyfile)
File "/local-scratch-nvme/nigam/ehrshot/lib/python3.10/pdb.py", line 1583, in _runscript
self.run(statement)
File "/local-scratch-nvme/nigam/ehrshot/lib/python3.10/bdb.py", line 598, in run
exec(cmd, globals, locals)
File "<string>", line 1, in <module>
File "/share/pi/nigam/mwornow/ehrshot-benchmark/ehrshot/4_generate_clmbr_features.py", line 123, in <module>
results: Dict[str, Any] = compute_features(dataset, model_name, labels, ontology=None, num_proc=num_threads, tokens_per_batch=tokens_per_batch, device=device)
File "/share/pi/nigam/mwornow/ehrshot-benchmark/ehrshot/4_generate_clmbr_features.py", line 69, in compute_features
batch = processor.collate([batch])["batch"]
File "/local-scratch-nvme/nigam/ehrshot/lib/python3.10/site-packages/femr/models/processor.py", line 401, in collate
return {"batch": _add_dimension(self.creator.cleanup_batch(batches[0]))}
File "/local-scratch-nvme/nigam/ehrshot/lib/python3.10/site-packages/femr/models/processor.py", line 322, in cleanup_batch
batch["transformer"]["patient_lengths"] = np.array(batch["transformer"]["patient_lengths"])
File "/local-scratch-nvme/nigam/ehrshot/lib/python3.10/site-packages/torch/_tensor.py", line 1062, in __array__
return self.numpy()
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.
```
This fixes that by waiting until after `collate()` to move to device.
for more information, see https://pre-commit.ci
EthanSteinberg
approved these changes
Apr 25, 2024
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I get a numpy cuda / cpu conversion error due to the
batchesbeing moved todevicebefore thecollate()function.This fixes that by waiting until after
collate()to move to device.