AlexMikhalev

10:M 30 Apr 2021 21:27:20.002 * <rg> GEARS: QA cached called {'event': 'keymiss', 'key': 'cache_{06S}_{PMC261870.xml:{06S}:26}_Laser Correction', 'type': 'empty', 'value': None}


=== REDIS BUG REPORT START: Cut & paste starting from here ===
10:M 30 Apr 2021 21:27:20.002 # === ASSERTION FAILED ===
10:M 30 Apr 2021 21:27:20.002 # ==> module.c:4085 '(c->flags & CLIENT_BLOCKED) == 0' is not true

------ STACK TRACE ------

Backtrace:

AlexMikhalev

graph TD
    A[Christmas] -->|Get money| B(Go shopping)
    B --> C{Let me think}
    C -->|One| D[Laptop]
    C -->|Two| E[iPhone]
    C -->|Three| F[fa:fa-car Car]

AlexMikhalev

### This gears will pre-compute (encode) all sentences using BERT tokenizer for QA

tokenizer = None 

def loadTokeniser():
    global tokenizer
    from transformers import BertTokenizerFast
    tokenizer = BertTokenizerFast.from_pretrained("bert-large-uncased-whole-word-masking-finetuned-squad")
    return tokenizer

AlexMikhalev

tokenizer = None 
    
import numpy as np
import torch
import os 

config_switch=os.getenv('DOCKER', 'local')
if config_switch=='local':
    startup_nodes = [{"host": "127.0.0.1", "port": "30001"}, {"host": "127.0.0.1", "port":"30002"}, {"host":"127.0.0.1", "port":"30003"}]
else:

AlexMikhalev

tokenizer = None 
    
import numpy as np
import torch
import os 

config_switch=os.getenv('DOCKER', 'local')
if config_switch=='local':
    startup_nodes = [{"host": "127.0.0.1", "port": "30001"}, {"host": "127.0.0.1", "port":"30002"}, {"host":"127.0.0.1", "port":"30003"}]
else:

AlexMikhalev

#standard module
# peak memory usage (kilobytes on Linux, bytes on OS X)
import resource
resource.getrusage(resource.RUSAGE_SELF).ru_maxrss 
# pip install psutil
import os, psutil; print(psutil.Process(os.getpid()).memory_info().rss / 1024 ** 2)

AlexMikhalev

Problem

When I use docker to work with the shared workspace with host under Ubuntu, I find that files created by docker user is owned by root. This is not the same with macOS.

Maybe this is becuase docker is run by root user and the default user mapping mechanism is to map container-root to host-user or host-root. So can I map the container-root or container-any-user to host-current-user?

Fortunately the latest docker supports the re-map the container user to any host user via Linux namespace. Refer to this.

Linux namespace

AlexMikhalev

```
redis-cli -c -p 30001 -h 127.0.0.1
127.0.0.1:30001> keys *
 1) "processed_docs_stage1_para"
 2) "sentence:PMC293432.xml:{06S}"
 3) "sentence:PMC270701.xml:{06S}"
 4) "edges_matched_{06S}"
 5) "sentence:PMC222961.xml:{06S}"
 6) "processed_docs_stage3{06S}"
 7) "processed_docs_stage2_para{06S}"

AlexMikhalev

from transformers import AutoTokenizer, AutoModel
tokenizer = None 

def loadTokeniser():
    global tokenizer
    from transformers import AutoTokenizer
    tokenizer = AutoTokenizer.from_pretrained("t5-base",torchscript=True)
    # Try RobertaTokenizerFast and BART
    # tokenizer = AutoTokenizer.from_pretrained("emilyalsentzer/Bio_ClinicalBERT")
    return tokenizer

AlexMikhalev

from transformers import BertForQuestionAnswering
import torch

bert_name = "bert-large-uncased-whole-word-masking-finetuned-squad"

model = BertForQuestionAnswering.from_pretrained(bert_name, torchscript=True)
model.eval()

inputs = [torch.ones(1, 2, dtype=torch.int64),
          torch.ones(1, 2, dtype=torch.int64),