Found no NVIDIA driver for CPU (run_bern2_cpu.sh)

[anopperl]

CPU : bern2

• Hello all and @mjeensung , I am trying to run run_bern2_cpu.sh. I have checked logs "nohup_multi_ner.out" file and it is saying that "Found no NVIDIA driver". I thing, for CPU user there no need to have NVIDIA driver. right ?
• sorry for my English

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]

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]

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]

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)