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dmis-lab / BERN2

BERN2: an advanced neural biomedical namedentity recognition and normalization tool
http://bern2.korea.ac.kr
BSD 2-Clause "Simplified" License
175 stars 42 forks source link

Found no NVIDIA driver for CPU (run_bern2_cpu.sh) #61

Closed anopperl closed 7 months ago

anopperl commented 8 months ago

CPU : bern2

Logs: "nohup_multi_ner.out"

Traceback (most recent call last): File "/bern2local/multi_ner/ner_server.py", line 89, in mt_ner = MTNER(args) File "/bern2local/multi_ner/main.py", line 521, in init self.model = self.model.cuda() File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/nn/modules/module.py", line 911, in cuda return self._apply(lambda t: t.cuda(device)) File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/nn/modules/module.py", line 802, in _apply module._apply(fn) File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/nn/modules/module.py", line 802, in _apply module._apply(fn) File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/nn/modules/module.py", line 802, in _apply module._apply(fn) File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/nn/modules/module.py", line 825, in _apply param_applied = fn(param) File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/nn/modules/module.py", line 911, in return self._apply(lambda t: t.cuda(device)) File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/cuda/init.py", line 302, in _lazy_init torch._C._cuda_init() RuntimeError: Found no NVIDIA driver on your system. Please check that you have an NVIDIA GPU and installed a driver from http://www.nvidia.com/Download/inde x.aspx

mjeensung commented 8 months ago

Hi @anopperl

Thank you for reporting the issue! We have resolved it, so could you please update the code and run BERN2 again? (see https://github.com/dmis-lab/BERN2/commit/3bb255c7ff3e02e9c1c2cdd44caed13c2afe1518)

anopperl commented 8 months ago

Hi @mjeensung thanks. there is no error in "nohup_multi_ner.out" but now errors are in nohup_bern2.out

` [27/Mar/2024 06:51:44.937765] id: 93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab [27/Mar/2024 06:51:45.448458] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] tmVar 2.0 0.5086250305175781 sec [27/Mar/2024 06:51:45.804228] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] GNormPlus 0.8629016876220703 sec [27/Mar/2024 06:51:48.531194] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] Multi-task NER 3.589254856109619 sec, #entities: 64 [27/Mar/2024 06:51:51.088236] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] ALL NER 6.149087190628052 sec ent_type = diseaseent_type = drug [27/Mar/2024 06:51:51.089104] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] [drug] 0.000 sec, CUI-less: 7.7% (1/13)

ent_type = geneent_type = speciesent_type = cell_line

[27/Mar/2024 06:51:51.089867] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] [species] 0.000 sec, CUI-less: 0.0% (0/2)

[27/Mar/2024 06:51:51.090215]ent_type = DNA ent_type = cell_typeWARN! DNA is not supported yet [27/Mar/2024 06:51:51.090808][93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] [cell_line] 0.001 sec, CUI-less: 100.0% (4/4)

[27/Mar/2024 06:51:51.090951] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] [DNA] 0.000 sec, CUI-less: 100.0% (6/6) [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] [cell_type] 0.000 sec, CUI-less: 100.0% (5/5) [27/Mar/2024 06:51:51.291597] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] [disease] 0.203 sec, CUI-less: 31.2% (5/16) [27/Mar/2024 06:51:51.333462] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] [gene] 0.244 sec, CUI-less: 22.2% (4/18) [27/Mar/2024 06:51:51.333631] [93ef66feb48de91c1a58a22f1d8afae0bbd27996720e1bb02f5ca1ab] Rule-based normalization 0.245 sec (1 article(s), 7 entity type(s))

cui-less in disease=5

Traceback (most recent call last): File "/bern2local/bern2/bern2.py", line 107, in annotate_text output = self.tag_entities(text, base_name) File "/bern2local/bern2/bern2.py", line 403, in tag_entities tagged_docs = self.normalizer.neural_normalize( File "/bern2local/bern2/normalizer.py", line 195, in neural_normalize norm_entities = self.neural_disease_normalizer.normalize( File "/bern2local/normalizers/neural_normalizer.py", line 85, in normalize for batch in name_dataloader: File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/utils/data/dataloader.py", line 631, in next data = self._next_data() File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/utils/data/dataloader.py", line 675, in _next_data data = self._dataset_fetcher.fetch(index) # may raise StopIteration File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/utils/data/_utils/fetch.py", line 51, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/utils/data/_utils/fetch.py", line 51, in data = [self.dataset[idx] for idx in possibly_batched_index] File "/bern2local/normalizers/neural_normalizer.py", line 25, in getitem return {key: torch.tensor(val[idx]).cuda() for key, val in self.encodings.items()} if not self.no_cuda else \ File "/bern2local/normalizers/neural_normalizer.py", line 25, in return {key: torch.tensor(val[idx]).cuda() for key, val in self.encodings.items()} if not self.no_cuda else \ File "/usr/local/envs/bern2/lib/python3.9/site-packages/torch/cuda/init.py", line 302, in _lazy_init torch._C._cuda_init() RuntimeError: Found no NVIDIA driver on your system. Please check that you have an NVIDIA GPU and installed a driver from http://www.nvidia.com/Download/index.aspx `

mjeensung commented 8 months ago

My bad, we've found another missing part that controls the usage of CUDA. We have resolved it, so could you please update the code and run BERN2 again?

(see https://github.com/dmis-lab/BERN2/commit/b508e01fd6b1afff8d017110b5e653d800e2c802)