added installer.sh

[thisismygitrepo]

a slick installer.sh for convenience

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[thisismygitrepo]

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[Dontmindmes]

@thisismygitrepo have you managed to setup this model correctly? If so would you be willing to assist me please

[thisismygitrepo]

Hi Sumerian @Dontmindmes
Yes, just run my proposed installer script in a linux ubuntu. I made it a one liner.

https://raw.githubusercontent.com/microsoft/BioGPT/b3f88b7e7419ba333db24385392ffc70463facef/installer.sh

[Dontmindmes]

Hi Sumerian @Dontmindmes Yes, just run my proposed installer script in a linux ubuntu. I made it a one liner.

https://raw.githubusercontent.com/microsoft/BioGPT/b3f88b7e7419ba333db24385392ffc70463facef/installer.sh

@thisismygitrepo Thank you for the quick reply, I really appreciate it.
I have ran your script,seems like i needed a more powerful ec2 instance,

Also where would i put the python code to execute to test the model?

Thank you once again

Update: also when running the installer.sh for some reason the files it creates are now show anywhere

[thisismygitrepo]

• Yes, that takes a day or so to download as speed drops to hundreds of kilobytes occasionally.
• To get up and running quickly, only download of the models that you are interested in, e.g. jus this one that appears in first example of readme Pre-trained-BioGPT. Remove other download lines.
• Once the installer finalize, cd to repo location cd ~/code/BioGPT, then source . run.sh that will open a python console. In that console everything you see in README should work by copy pasting it. You can exit the console and install ipython for added convenience.

[Dontmindmes]

• Yes, that takes a day or so to download as speed drops to hundreds of kilobytes occasionally.
• To get up and running quickly, only download of the models that you are interested in, e.g. jus this one that appears in first example of readme Pre-trained-BioGPT. Remove other download lines.
• Once the installer finalize, cd to repo location cd ~/code/BioGPT, then source . run.sh that will open a python console. In that console everything you see in README should work by copy pasting it. You can exit the console and install ipython for added convenience.

Thank you for your response,
I just followed your exact instructions but i encounter this issue

2023-02-24 03:52:02 | INFO | fairseq.tasks.text_to_speech | Please install tensorboardX: pip install tensorboardX
2023-02-24 03:52:02 | INFO | fairseq.file_utils | loading archive file checkpoints/Pre-trained-BioGPT
2023-02-24 03:52:02 | INFO | fairseq.file_utils | loading archive file data/BioGPT
./run.sh: line 4: 3999 Killed python bio.py

the code im running is this

import torch
from fairseq.models.transformer_lm import TransformerLanguageModel
m = TransformerLanguageModel.from_pretrained(
"checkpoints/Pre-trained-BioGPT",
"checkpoint.pt",
"data/BioGPT",
tokenizer='moses',
bpe='fastbpe',
bpe_codes="data/BioGPT",
min_len=100,
max_len_b=1024)
m.cuda()
src_tokens = m.encode("COVID-19 is")
generate = m.generate([src_tokens], beam=5)[0]
output = m.decode(generate[0]["tokens"])
print(output)

I am using this model, https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/Pre-trained-BioGPT.tgz

[thisismygitrepo]

@Dontmindmes
Can you remove m.cuda() line from your code?
May be I should have said that when I claimed that all README code will work by copy paste.

[Dontmindmes]

@Dontmindmes Can you remove m.cuda() line from your code? May be I should have said that when I claimed that all README code will work by copy paste.

I attempted to comment out m.cuda() but it still gets killed for some reason

2023-02-24 04:33:05 | INFO | fairseq.tasks.text_to_speech | Please install tensorboardX: pip install tensorboardX
2023-02-24 04:33:06 | INFO | fairseq.file_utils | loading archive file checkpoints/Pre-trained-BioGPT
2023-02-24 04:33:06 | INFO | fairseq.file_utils | loading archive file data/BioGPT
./run.sh: line 4: 885 Killed python bio.py

[thisismygitrepo]

@Dontmindmes

Please post a longer tracceback of error. The best I can make from the short snippet you provided is that your system killed python, which can happen if python consumed too much memory?

This is what shows up on my console

2023-02-24 15:08:55 | INFO | fairseq.tasks.text_to_speech | Please install tensorboardX: pip install tensorboardX
2023-02-24 15:08:55 | INFO | fairseq.file_utils | loading archive file checkpoints/Pre-trained-BioGPT
2023-02-24 15:08:55 | INFO | fairseq.file_utils | loading archive file data
2023-02-24 15:09:00 | INFO | fairseq.tasks.language_modeling | dictionary: 42384 types

COVID-19 is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), which has spread to more than 200 countries and
territories, including the United States (US), Canada, Australia, New Zealand, the United Kingdom (UK), and the United States of America (USA), as of March 11, 2020, with more than 800,000 confirmed cases and
more than 800,000 deaths.

[Dontmindmes]

@Dontmindmes

Please post a longer tracceback of error. The best I can make from the short snippet you provided is that your system killed python, which can happen if python consumed too much memory?

This is what shows up on my console

2023-02-24 15:08:55 | INFO | fairseq.tasks.text_to_speech | Please install tensorboardX: pip install tensorboardX
2023-02-24 15:08:55 | INFO | fairseq.file_utils | loading archive file checkpoints/Pre-trained-BioGPT
2023-02-24 15:08:55 | INFO | fairseq.file_utils | loading archive file data
2023-02-24 15:09:00 | INFO | fairseq.tasks.language_modeling | dictionary: 42384 types

COVID-19 is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), which has spread to more than 200 countries and
territories, including the United States (US), Canada, Australia, New Zealand, the United Kingdom (UK), and the United States of America (USA), as of March 11, 2020, with more than 800,000 confirmed cases and
more than 800,000 deaths.

Hey thank you so much, i was able to get it to work but for some reason im given this response

', 'moses_no_dash_splits': False, 'moses_no_escape': False}, 'simul_type': None}
Loading codes from data ...
Read 0 codes from the codes file.
COVID -@ 19 is, COVIDs ø-1, COVIDs ø-2, COVIDs ø-3, COVIDs ø-4, COVIDs ø-5, COVIDs ø-6, COVIDs ø-7, COVIDs ø-8, COVIDs ø-9, COVIDs ø-10, COVIDs ø-11, and COVIDs ø-12.

it dumps a giant array of something then returns that

[Dontmindmes]

Update: thank you so much for all the help @thisismygitrepo i really appreciate it. Thank you for going out of your wait to assist me, i just got it to work!

[thisismygitrepo]

@Dontmindmes glad to have seen the installer working. Please share insights into what you went through for future readers or to make the installer better.