I'm running BERN2 but server can't be reached

[Ufifus]

Running: bash run_bern2_cpu.sh [18/Oct/2022 17:29:56.854986] BERN2 LOADING.. ./output 0 ./resources/GNormPlusJava/input 0 ./resources/tmVarJava/input 0 start loading neural normalizer.. neural_disease_normalizer is loaded.. model=dmis-lab/biosyn-sapbert-bc5cdr-disease , dictionary=resources/normalization/normalizers/neural_norm_caches/dict_Disease_20210630.txt.pk Arguments: host: 0.0.0.0 port: 8888 mtner_home: ./multi_ner mtner_port: 18894 gnormplus_home: ./resources/GNormPlusJava gnormplus_port: 18895 tmvar2_home: ./resources/tmVarJava tmvar2_port: 18896 cache_host: localhost cache_port: 27017 gene_norm_port: 18888 disease_norm_port: 18892 use_neural_normalizer: True keep_files: False front_dev: False no_cuda: True [18/Oct/2022 17:31:25.741639] BERN2 LOADING.. ./output 0 ./resources/GNormPlusJava/input 0 ./resources/tmVarJava/input 0 start loading neural normalizer.. neural_disease_normalizer is loaded.. model=dmis-lab/biosyn-sapbert-bc5cdr-disease , dictionary=resources/normalization/normalizers/neural_norm_caches/dict_Disease_20210630.txt.pk

Error:

response = requests.get('http://localhost:8888/pubmed/30429607,29446767).json() ConnectionRefusedError: [Errno 111] Connection refused

During handling of the above exception, another exception occurred: urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=8888): Max retries exceeded with url: /pubmed/30429607,29446767 (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f00d7cad9c0>: Failed to establish a new connection: [Errno 111] Connection refused'))

Maybe i did something wrong, thank you for your time.

[mjeensung]

Hi @Ufifus Sorry for the late response.

Could you check if all processes for running BERN2 are alive?

ps auxww | grep ner_server.py
ps auxww | grep GNormPlusServer.main.jar
ps auxww | grep tmVar2Server.main.jar 
ps auxww | grep disease_normalizer_21.jar 
ps auxww | grep gnormplus-normalization_21.jar 
ps auxww | grep server.py

[mjeensung]

If you have any follow-up questions, please re-open this issue.

[Ufifus]

Sorry for the latest response too) Your answer helps me, on processes just dont working: artem 105084 0.0 0.0 17872 2316 pts/1 S+ 21:05 0:00 grep --color=auto ner_server.py artem 105086 0.0 0.0 17884 2256 pts/1 S+ 21:05 0:00 grep --color=auto GNormPlusServer.main.jar artem 105088 0.0 0.0 17880 2300 pts/1 S+ 21:05 0:00 grep --color=auto tmVar2Server.main.jar artem 105090 0.0 0.0 17880 2280 pts/1 S+ 21:05 0:00 grep --color=auto disease_normalizer_21.jar artem 105092 0.0 0.0 17884 2336 pts/1 S+ 21:05 0:00 grep --color=auto gnormplus-normalization_21.jar artem 105094 0.0 0.0 17872 2448 pts/1 S+ 21:05 0:00 grep --color=auto server.py

How much memory RAM i need for running BERN2 on CPU/GPU, more important GPU? Thanks you