Add Continuous Integration script to reproduce error assert q.is_cuda and k.is_cuda and v.is_cuda

[richelbilderbeek]

Dear DNABERT 2 maintainer,

With this Pull Request I'd like to prove that the documentation is incomplete, by reproducing the error

assert q.is_cuda and k.is_cuda and v.is_cuda

This error is reported too in #11, #20, #34, #96 and #112.

I made the error reproducible with the script in .github/workflow/check_build.yaml, where I copy-paste the install process only. I simply followed the install procedure in the README, using the recommended Python 3.8, yet without the conda setup:

- uses: actions/setup-python@v2
  with:
    python-version: 3.8

- name: install required packages
  run: python3 -m pip install -r requirements.txt

- name: run example code shown in README
  run: python3 .github/workflows/example_huggingface_v4_28.py

The script it runs is copied from the README too:

import torch
from transformers import AutoTokenizer, AutoModel

tokenizer = AutoTokenizer.from_pretrained("zhihan1996/DNABERT-2-117M", trust_remote_code=True)
model = AutoModel.from_pretrained("zhihan1996/DNABERT-2-117M", trust_remote_code=True)

dna = "ACGTAGCATCGGATCTATCTATCGACACTTGGTTATCGATCTACGAGCATCTCGTTAGC"
inputs = tokenizer(dna, return_tensors = 'pt')["input_ids"]
hidden_states = model(inputs)[0] # [1, sequence_length, 768]

# embedding with mean pooling
embedding_mean = torch.mean(hidden_states[0], dim=0)
print(embedding_mean.shape) # expect to be 768

# embedding with max pooling
embedding_max = torch.max(hidden_states[0], dim=0)[0]
print(embedding_max.shape) # expect to be 768

The error log is shown in the next message below.

I think that a user should be able to install a Python module and run example code with success by reading the documentation, hence I think the documentation is incomplete or the error message given is not helpful enough (#112).

I hope you appreciate the effort I put in to make DNABERT 2 even better for everyone. Maybe using CI scripts is new to you, I'd be happy to discuss their pros and cons and I'd be happy to maintain such scripts for my users :-)

Cheers, Richel Bilderbeek

[richelbilderbeek]

Ah, you cannot see the errors. They are here (you need to have been logged in to GitHub) and pasted below for convenience:

2024-09-09T06:46:10.2938687Z Current runner version: '2.319.1'
2024-09-09T06:46:10.2962786Z ##[group]Operating System
2024-09-09T06:46:10.2963370Z Ubuntu
2024-09-09T06:46:10.2963723Z 22.04.4
2024-09-09T06:46:10.2964154Z LTS
2024-09-09T06:46:10.2964445Z ##[endgroup]
2024-09-09T06:46:10.2964852Z ##[group]Runner Image
2024-09-09T06:46:10.2965344Z Image: ubuntu-22.04
2024-09-09T06:46:10.2965696Z Version: 20240901.1.0
2024-09-09T06:46:10.2966684Z Included Software: https://github.com/actions/runner-images/blob/ubuntu22/20240901.1/images/ubuntu/Ubuntu2204-Readme.md
2024-09-09T06:46:10.2968198Z Image Release: https://github.com/actions/runner-images/releases/tag/ubuntu22%2F20240901.1
2024-09-09T06:46:10.2969034Z ##[endgroup]
2024-09-09T06:46:10.2969442Z ##[group]Runner Image Provisioner
2024-09-09T06:46:10.2969985Z 2.0.384.1
2024-09-09T06:46:10.2970286Z ##[endgroup]
2024-09-09T06:46:10.2986839Z ##[group]GITHUB_TOKEN Permissions
2024-09-09T06:46:10.2988502Z Actions: write
2024-09-09T06:46:10.2989503Z Attestations: write
2024-09-09T06:46:10.2989965Z Checks: write
2024-09-09T06:46:10.2990430Z Contents: write
2024-09-09T06:46:10.2990815Z Deployments: write
2024-09-09T06:46:10.2991198Z Discussions: write
2024-09-09T06:46:10.2991672Z Issues: write
2024-09-09T06:46:10.2992029Z Metadata: read
2024-09-09T06:46:10.2992362Z Packages: write
2024-09-09T06:46:10.2992828Z Pages: write
2024-09-09T06:46:10.2993205Z PullRequests: write
2024-09-09T06:46:10.2993596Z RepositoryProjects: write
2024-09-09T06:46:10.2994130Z SecurityEvents: write
2024-09-09T06:46:10.2994549Z Statuses: write
2024-09-09T06:46:10.2994905Z ##[endgroup]
2024-09-09T06:46:10.2997970Z Secret source: Actions
2024-09-09T06:46:10.2998549Z Prepare workflow directory
2024-09-09T06:46:10.3617057Z Prepare all required actions
2024-09-09T06:46:10.3774031Z Getting action download info
2024-09-09T06:46:10.5835179Z Download action repository 'actions/checkout@v2' (SHA:ee0669bd1cc54295c223e0bb666b733df41de1c5)
2024-09-09T06:46:10.6967864Z Download action repository 'actions/setup-python@v2' (SHA:e9aba2c848f5ebd159c070c61ea2c4e2b122355e)
2024-09-09T06:46:10.9506973Z Complete job name: check_build
2024-09-09T06:46:11.0433490Z ##[group]Run actions/checkout@v2
2024-09-09T06:46:11.0434144Z with:
2024-09-09T06:46:11.0434534Z   repository: UPPMAX/DNABERT_2
2024-09-09T06:46:11.0435238Z   token: ***
2024-09-09T06:46:11.0435695Z   ssh-strict: true
2024-09-09T06:46:11.0436117Z   persist-credentials: true
2024-09-09T06:46:11.0436588Z   clean: true
2024-09-09T06:46:11.0436986Z   fetch-depth: 1
2024-09-09T06:46:11.0437363Z   lfs: false
2024-09-09T06:46:11.0437741Z   submodules: false
2024-09-09T06:46:11.0438179Z   set-safe-directory: true
2024-09-09T06:46:11.0438619Z ##[endgroup]
2024-09-09T06:46:11.2418144Z Syncing repository: UPPMAX/DNABERT_2
2024-09-09T06:46:11.2421190Z ##[group]Getting Git version info
2024-09-09T06:46:11.2422619Z Working directory is '/home/runner/work/DNABERT_2/DNABERT_2'
2024-09-09T06:46:11.2424325Z [command]/usr/bin/git version
2024-09-09T06:46:11.2425025Z git version 2.46.0
2024-09-09T06:46:11.2426866Z ##[endgroup]
2024-09-09T06:46:11.2443840Z Temporarily overriding HOME='/home/runner/work/_temp/7cc918d7-80a2-43f5-8989-ca3f806b7ae2' before making global git config changes
2024-09-09T06:46:11.2446343Z Adding repository directory to the temporary git global config as a safe directory
2024-09-09T06:46:11.2448649Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/DNABERT_2/DNABERT_2
2024-09-09T06:46:11.2479589Z Deleting the contents of '/home/runner/work/DNABERT_2/DNABERT_2'
2024-09-09T06:46:11.2484425Z ##[group]Initializing the repository
2024-09-09T06:46:11.2487214Z [command]/usr/bin/git init /home/runner/work/DNABERT_2/DNABERT_2
2024-09-09T06:46:11.2601124Z hint: Using 'master' as the name for the initial branch. This default branch name
2024-09-09T06:46:11.2602926Z hint: is subject to change. To configure the initial branch name to use in all
2024-09-09T06:46:11.2604609Z hint: of your new repositories, which will suppress this warning, call:
2024-09-09T06:46:11.2605728Z hint:
2024-09-09T06:46:11.2607018Z hint: 	git config --global init.defaultBranch <name>
2024-09-09T06:46:11.2607856Z hint:
2024-09-09T06:46:11.2608490Z hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and
2024-09-09T06:46:11.2609644Z hint: 'development'. The just-created branch can be renamed via this command:
2024-09-09T06:46:11.2610393Z hint:
2024-09-09T06:46:11.2610763Z hint: 	git branch -m <name>
2024-09-09T06:46:11.2611587Z Initialized empty Git repository in /home/runner/work/DNABERT_2/DNABERT_2/.git/
2024-09-09T06:46:11.2615514Z [command]/usr/bin/git remote add origin https://github.com/UPPMAX/DNABERT_2
2024-09-09T06:46:11.2651417Z ##[endgroup]
2024-09-09T06:46:11.2652213Z ##[group]Disabling automatic garbage collection
2024-09-09T06:46:11.2654679Z [command]/usr/bin/git config --local gc.auto 0
2024-09-09T06:46:11.2682477Z ##[endgroup]
2024-09-09T06:46:11.2683342Z ##[group]Setting up auth
2024-09-09T06:46:11.2688532Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2024-09-09T06:46:11.2716981Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :"
2024-09-09T06:46:11.3032797Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2024-09-09T06:46:11.3061212Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :"
2024-09-09T06:46:11.3298213Z [command]/usr/bin/git config --local http.https://github.com/.extraheader AUTHORIZATION: basic ***
2024-09-09T06:46:11.3340161Z ##[endgroup]
2024-09-09T06:46:11.3341094Z ##[group]Fetching the repository
2024-09-09T06:46:11.3352685Z [command]/usr/bin/git -c protocol.version=2 fetch --no-tags --prune --progress --no-recurse-submodules --depth=1 origin +105bb1c14e24d28516b4898ef25acb0d400671a5:refs/remotes/origin/main
2024-09-09T06:46:11.7336901Z remote: Enumerating objects: 25, done.        
2024-09-09T06:46:11.7338081Z remote: Counting objects:   4% (1/25)        
2024-09-09T06:46:11.7338837Z remote: Counting objects:   8% (2/25)        
2024-09-09T06:46:11.7339595Z remote: Counting objects:  12% (3/25)        
2024-09-09T06:46:11.7340444Z remote: Counting objects:  16% (4/25)        
2024-09-09T06:46:11.7341208Z remote: Counting objects:  20% (5/25)        
2024-09-09T06:46:11.7341834Z remote: Counting objects:  24% (6/25)        
2024-09-09T06:46:11.7342478Z remote: Counting objects:  28% (7/25)        
2024-09-09T06:46:11.7343073Z remote: Counting objects:  32% (8/25)        
2024-09-09T06:46:11.7343629Z remote: Counting objects:  36% (9/25)        
2024-09-09T06:46:11.7344287Z remote: Counting objects:  40% (10/25)        
2024-09-09T06:46:11.7344964Z remote: Counting objects:  44% (11/25)        
2024-09-09T06:46:11.7346036Z remote: Counting objects:  48% (12/25)        
2024-09-09T06:46:11.7346898Z remote: Counting objects:  52% (13/25)        
2024-09-09T06:46:11.7347522Z remote: Counting objects:  56% (14/25)        
2024-09-09T06:46:11.7348084Z remote: Counting objects:  60% (15/25)        
2024-09-09T06:46:11.7349055Z remote: Counting objects:  64% (16/25)        
2024-09-09T06:46:11.7349677Z remote: Counting objects:  68% (17/25)        
2024-09-09T06:46:11.7350369Z remote: Counting objects:  72% (18/25)        
2024-09-09T06:46:11.7350959Z remote: Counting objects:  76% (19/25)        
2024-09-09T06:46:11.7351550Z remote: Counting objects:  80% (20/25)        
2024-09-09T06:46:11.7352248Z remote: Counting objects:  84% (21/25)        
2024-09-09T06:46:11.7352848Z remote: Counting objects:  88% (22/25)        
2024-09-09T06:46:11.7353421Z remote: Counting objects:  92% (23/25)        
2024-09-09T06:46:11.7354029Z remote: Counting objects:  96% (24/25)        
2024-09-09T06:46:11.7354613Z remote: Counting objects: 100% (25/25)        
2024-09-09T06:46:11.7355276Z remote: Counting objects: 100% (25/25), done.        
2024-09-09T06:46:11.7356222Z remote: Compressing objects:   5% (1/18)        
2024-09-09T06:46:11.7356932Z remote: Compressing objects:  11% (2/18)        
2024-09-09T06:46:11.7357549Z remote: Compressing objects:  16% (3/18)        
2024-09-09T06:46:11.7358176Z remote: Compressing objects:  22% (4/18)        
2024-09-09T06:46:11.7358881Z remote: Compressing objects:  27% (5/18)        
2024-09-09T06:46:11.7359520Z remote: Compressing objects:  33% (6/18)        
2024-09-09T06:46:11.7360112Z remote: Compressing objects:  38% (7/18)        
2024-09-09T06:46:11.7382932Z remote: Compressing objects:  44% (8/18)        
2024-09-09T06:46:11.7388261Z remote: Compressing objects:  50% (9/18)        
2024-09-09T06:46:11.7393335Z remote: Compressing objects:  55% (10/18)        
2024-09-09T06:46:11.7397214Z remote: Compressing objects:  61% (11/18)        
2024-09-09T06:46:11.7398172Z remote: Compressing objects:  66% (12/18)        
2024-09-09T06:46:11.7398854Z remote: Compressing objects:  72% (13/18)        
2024-09-09T06:46:11.7399486Z remote: Compressing objects:  77% (14/18)        
2024-09-09T06:46:11.7400247Z remote: Compressing objects:  83% (15/18)        
2024-09-09T06:46:11.7400874Z remote: Compressing objects:  88% (16/18)        
2024-09-09T06:46:11.7634026Z remote: Compressing objects:  94% (17/18)        
2024-09-09T06:46:11.7634867Z remote: Compressing objects: 100% (18/18)        
2024-09-09T06:46:11.7635925Z remote: Compressing objects: 100% (18/18), done.        
2024-09-09T06:46:11.9654375Z remote: Total 25 (delta 5), reused 18 (delta 5), pack-reused 0 (from 0)        
2024-09-09T06:46:11.9811307Z From https://github.com/UPPMAX/DNABERT_2
2024-09-09T06:46:11.9813223Z  * [new ref]         105bb1c14e24d28516b4898ef25acb0d400671a5 -> origin/main
2024-09-09T06:46:11.9839185Z ##[endgroup]
2024-09-09T06:46:11.9840074Z ##[group]Determining the checkout info
2024-09-09T06:46:11.9841206Z ##[endgroup]
2024-09-09T06:46:11.9841840Z ##[group]Checking out the ref
2024-09-09T06:46:11.9845430Z [command]/usr/bin/git checkout --progress --force -B main refs/remotes/origin/main
2024-09-09T06:46:11.9927056Z Switched to a new branch 'main'
2024-09-09T06:46:11.9930290Z branch 'main' set up to track 'origin/main'.
2024-09-09T06:46:11.9935374Z ##[endgroup]
2024-09-09T06:46:11.9969983Z [command]/usr/bin/git log -1 --format='%H'
2024-09-09T06:46:11.9997311Z '105bb1c14e24d28516b4898ef25acb0d400671a5'
2024-09-09T06:46:12.0320500Z ##[group]Run actions/setup-python@v2
2024-09-09T06:46:12.0321023Z with:
2024-09-09T06:46:12.0321344Z   python-version: 3.8
2024-09-09T06:46:12.0321978Z   token: ***
2024-09-09T06:46:12.0322316Z ##[endgroup]
2024-09-09T06:46:12.1438659Z Successfully setup CPython (3.8.18)
2024-09-09T06:46:12.1572949Z ##[group]Run python3 -m pip install -r requirements.txt
2024-09-09T06:46:12.1573730Z �[36;1mpython3 -m pip install -r requirements.txt�[0m
2024-09-09T06:46:12.1604063Z shell: /usr/bin/bash -e {0}
2024-09-09T06:46:12.1604635Z env:
2024-09-09T06:46:12.1605076Z   pythonLocation: /opt/hostedtoolcache/Python/3.8.18/x64
2024-09-09T06:46:12.1605719Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.8.18/x64/lib
2024-09-09T06:46:12.1606309Z ##[endgroup]
2024-09-09T06:46:14.9741529Z Collecting einops (from -r requirements.txt (line 1))
2024-09-09T06:46:15.0189087Z   Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB)
2024-09-09T06:46:15.1044411Z Collecting transformers==4.29.2 (from -r requirements.txt (line 2))
2024-09-09T06:46:15.1202289Z   Downloading transformers-4.29.2-py3-none-any.whl.metadata (112 kB)
2024-09-09T06:46:15.4164429Z Collecting peft (from -r requirements.txt (line 3))
2024-09-09T06:46:15.4319485Z   Downloading peft-0.12.0-py3-none-any.whl.metadata (13 kB)
2024-09-09T06:46:15.4976424Z Collecting omegaconf (from -r requirements.txt (line 4))
2024-09-09T06:46:15.5138249Z   Downloading omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB)
2024-09-09T06:46:15.5802719Z Collecting torch (from -r requirements.txt (line 5))
2024-09-09T06:46:15.5958546Z   Downloading torch-2.4.1-cp38-cp38-manylinux1_x86_64.whl.metadata (26 kB)
2024-09-09T06:46:15.6257299Z Collecting evaluate (from -r requirements.txt (line 6))
2024-09-09T06:46:15.6411781Z   Downloading evaluate-0.4.2-py3-none-any.whl.metadata (9.3 kB)
2024-09-09T06:46:15.6991133Z Collecting accelerate (from -r requirements.txt (line 7))
2024-09-09T06:46:15.7140826Z   Downloading accelerate-0.34.2-py3-none-any.whl.metadata (19 kB)
2024-09-09T06:46:15.7696730Z Collecting filelock (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:15.7843174Z   Downloading filelock-3.16.0-py3-none-any.whl.metadata (3.0 kB)
2024-09-09T06:46:15.8521465Z Collecting huggingface-hub<1.0,>=0.14.1 (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:15.8671007Z   Downloading huggingface_hub-0.24.6-py3-none-any.whl.metadata (13 kB)
2024-09-09T06:46:16.1223348Z Collecting numpy>=1.17 (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:16.1380430Z   Downloading numpy-1.24.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)
2024-09-09T06:46:16.2401486Z Collecting packaging>=20.0 (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:16.2552108Z   Downloading packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
2024-09-09T06:46:16.3156493Z Collecting pyyaml>=5.1 (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:16.3320088Z   Downloading PyYAML-6.0.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
2024-09-09T06:46:16.7977207Z Collecting regex!=2019.12.17 (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:16.8134008Z   Downloading regex-2024.7.24-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (40 kB)
2024-09-09T06:46:16.8667485Z Collecting requests (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:16.8817692Z   Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
2024-09-09T06:46:17.0998032Z Collecting tokenizers!=0.11.3,<0.14,>=0.11.1 (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:17.1157805Z   Downloading tokenizers-0.13.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB)
2024-09-09T06:46:17.2328115Z Collecting tqdm>=4.27 (from transformers==4.29.2->-r requirements.txt (line 2))
2024-09-09T06:46:17.2476088Z   Downloading tqdm-4.66.5-py3-none-any.whl.metadata (57 kB)
2024-09-09T06:46:17.3701616Z Collecting psutil (from peft->-r requirements.txt (line 3))
2024-09-09T06:46:17.3856195Z   Downloading psutil-6.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
2024-09-09T06:46:17.5529495Z Collecting safetensors (from peft->-r requirements.txt (line 3))
2024-09-09T06:46:17.5684707Z   Downloading safetensors-0.4.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.8 kB)
2024-09-09T06:46:17.6129222Z Collecting antlr4-python3-runtime==4.9.* (from omegaconf->-r requirements.txt (line 4))
2024-09-09T06:46:17.6276881Z   Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)
2024-09-09T06:46:17.6633691Z   Installing build dependencies: started
2024-09-09T06:46:19.2865068Z   Installing build dependencies: finished with status 'done'
2024-09-09T06:46:19.2875702Z   Getting requirements to build wheel: started
2024-09-09T06:46:19.5363569Z   Getting requirements to build wheel: finished with status 'done'
2024-09-09T06:46:19.5374425Z   Preparing metadata (pyproject.toml): started
2024-09-09T06:46:19.7415493Z   Preparing metadata (pyproject.toml): finished with status 'done'
2024-09-09T06:46:19.7790538Z Collecting typing-extensions>=4.8.0 (from torch->-r requirements.txt (line 5))
2024-09-09T06:46:19.7936956Z   Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
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2024-09-09T06:46:51.2495981Z Building wheels for collected packages: antlr4-python3-runtime
2024-09-09T06:46:51.2516430Z   Building wheel for antlr4-python3-runtime (pyproject.toml): started
2024-09-09T06:46:51.4982178Z   Building wheel for antlr4-python3-runtime (pyproject.toml): finished with status 'done'
2024-09-09T06:46:51.4991466Z   Created wheel for antlr4-python3-runtime: filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144553 sha256=6d2e44ed622233b1354891d31fc7e181a86941bda27bcec3f7e22d41f9dd82ed
2024-09-09T06:46:51.4993548Z   Stored in directory: /home/runner/.cache/pip/wheels/b1/a3/c2/6df046c09459b73cc9bb6c4401b0be6c47048baf9a1617c485
2024-09-09T06:46:51.5018049Z Successfully built antlr4-python3-runtime
2024-09-09T06:46:52.1546564Z Installing collected packages: tokenizers, pytz, mpmath, antlr4-python3-runtime, xxhash, urllib3, tzdata, typing-extensions, tqdm, sympy, six, safetensors, regex, pyyaml, psutil, packaging, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, multidict, MarkupSafe, idna, fsspec, frozenlist, filelock, einops, dill, charset-normalizer, certifi, attrs, async-timeout, aiohappyeyeballs, yarl, triton, requests, python-dateutil, pyarrow, omegaconf, nvidia-cusparse-cu12, nvidia-cudnn-cu12, multiprocess, jinja2, aiosignal, pandas, nvidia-cusolver-cu12, huggingface-hub, aiohttp, transformers, torch, datasets, accelerate, peft, evaluate
2024-09-09T06:47:46.1354132Z Successfully installed MarkupSafe-2.1.5 accelerate-0.34.2 aiohappyeyeballs-2.4.0 aiohttp-3.10.5 aiosignal-1.3.1 antlr4-python3-runtime-4.9.3 async-timeout-4.0.3 attrs-24.2.0 certifi-2024.8.30 charset-normalizer-3.3.2 datasets-2.21.0 dill-0.3.8 einops-0.8.0 evaluate-0.4.2 filelock-3.16.0 frozenlist-1.4.1 fsspec-2024.6.1 huggingface-hub-0.24.6 idna-3.8 jinja2-3.1.4 mpmath-1.3.0 multidict-6.0.5 multiprocess-0.70.16 networkx-3.1 numpy-1.24.4 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-9.1.0.70 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.20.5 nvidia-nvjitlink-cu12-12.6.68 nvidia-nvtx-cu12-12.1.105 omegaconf-2.3.0 packaging-24.1 pandas-2.0.3 peft-0.12.0 psutil-6.0.0 pyarrow-17.0.0 python-dateutil-2.9.0.post0 pytz-2024.1 pyyaml-6.0.2 regex-2024.7.24 requests-2.32.3 safetensors-0.4.5 six-1.16.0 sympy-1.13.2 tokenizers-0.13.3 torch-2.4.1 tqdm-4.66.5 transformers-4.29.2 triton-3.0.0 typing-extensions-4.12.2 tzdata-2024.1 urllib3-2.2.2 xxhash-3.5.0 yarl-1.11.0
2024-09-09T06:47:47.4051347Z ##[group]Run python3 .github/workflows/example_huggingface_v4_28.py
2024-09-09T06:47:47.4052143Z �[36;1mpython3 .github/workflows/example_huggingface_v4_28.py�[0m
2024-09-09T06:47:47.4078444Z shell: /usr/bin/bash -e {0}
2024-09-09T06:47:47.4078799Z env:
2024-09-09T06:47:47.4079223Z   pythonLocation: /opt/hostedtoolcache/Python/3.8.18/x64
2024-09-09T06:47:47.4079943Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.8.18/x64/lib
2024-09-09T06:47:47.4080408Z ##[endgroup]
2024-09-09T06:47:51.5606159Z /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/huggingface_hub/file_download.py:1150: FutureWarning: `resume_download` is deprecated and will be removed in version 1.0.0. Downloads always resume when possible. If you want to force a new download, use `force_download=True`.
2024-09-09T06:47:51.5609564Z   warnings.warn(
2024-09-09T06:47:51.5612286Z A new version of the following files was downloaded from https://huggingface.co/zhihan1996/DNABERT-2-117M:
2024-09-09T06:47:51.5614612Z - configuration_bert.py
2024-09-09T06:47:51.5616252Z . Make sure to double-check they do not contain any added malicious code. To avoid downloading new versions of the code file, you can pin a revision.
2024-09-09T06:47:52.1983088Z A new version of the following files was downloaded from https://huggingface.co/zhihan1996/DNABERT-2-117M:
2024-09-09T06:47:52.1984150Z - flash_attn_triton.py
2024-09-09T06:47:52.1985689Z . Make sure to double-check they do not contain any added malicious code. To avoid downloading new versions of the code file, you can pin a revision.
2024-09-09T06:47:52.4467079Z A new version of the following files was downloaded from https://huggingface.co/zhihan1996/DNABERT-2-117M:
2024-09-09T06:47:52.4469055Z - bert_padding.py
2024-09-09T06:47:52.4471368Z . Make sure to double-check they do not contain any added malicious code. To avoid downloading new versions of the code file, you can pin a revision.
2024-09-09T06:47:52.4473726Z A new version of the following files was downloaded from https://huggingface.co/zhihan1996/DNABERT-2-117M:
2024-09-09T06:47:52.4474979Z - bert_layers.py
2024-09-09T06:47:52.4475541Z - flash_attn_triton.py
2024-09-09T06:47:52.4476174Z - bert_padding.py
2024-09-09T06:47:52.4477749Z . Make sure to double-check they do not contain any added malicious code. To avoid downloading new versions of the code file, you can pin a revision.
2024-09-09T06:48:00.3505333Z /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/huggingface_hub/file_download.py:1150: FutureWarning: `resume_download` is deprecated and will be removed in version 1.0.0. Downloads always resume when possible. If you want to force a new download, use `force_download=True`.
2024-09-09T06:48:00.3507940Z   warnings.warn(
2024-09-09T06:48:00.3516506Z /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/transformers/modeling_utils.py:446: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.
2024-09-09T06:48:00.3524230Z   return torch.load(checkpoint_file, map_location="cpu")
2024-09-09T06:48:00.3527912Z Some weights of the model checkpoint at zhihan1996/DNABERT-2-117M were not used when initializing BertModel: ['cls.predictions.transform.LayerNorm.bias', 'cls.predictions.transform.dense.bias', 'cls.predictions.transform.LayerNorm.weight', 'cls.predictions.transform.dense.weight', 'cls.predictions.decoder.weight', 'cls.predictions.decoder.bias']
2024-09-09T06:48:00.3532486Z - This IS expected if you are initializing BertModel from the checkpoint of a model trained on another task or with another architecture (e.g. initializing a BertForSequenceClassification model from a BertForPreTraining model).
2024-09-09T06:48:00.3535875Z - This IS NOT expected if you are initializing BertModel from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).
2024-09-09T06:48:00.3539030Z Some weights of BertModel were not initialized from the model checkpoint at zhihan1996/DNABERT-2-117M and are newly initialized: ['bert.pooler.dense.weight', 'bert.pooler.dense.bias']
2024-09-09T06:48:00.3541582Z You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.
2024-09-09T06:48:00.6324226Z Traceback (most recent call last):
2024-09-09T06:48:00.6336888Z   File ".github/workflows/example_huggingface_v4_28.py", line 9, in <module>
2024-09-09T06:48:00.6338032Z     hidden_states = model(inputs)[0] # [1, sequence_length, 768]
2024-09-09T06:48:00.6339997Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
2024-09-09T06:48:00.6341525Z     return self._call_impl(*args, **kwargs)
2024-09-09T06:48:00.6342966Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
2024-09-09T06:48:00.6344286Z     return forward_call(*args, **kwargs)
2024-09-09T06:48:00.6346224Z   File "/home/runner/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/d064dece8a8b41d9fb8729fbe3435278786931f1/bert_layers.py", line 609, in forward
2024-09-09T06:48:00.6347913Z     encoder_outputs = self.encoder(
2024-09-09T06:48:00.6349826Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
2024-09-09T06:48:00.6351212Z     return self._call_impl(*args, **kwargs)
2024-09-09T06:48:00.6352741Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
2024-09-09T06:48:00.6354126Z     return forward_call(*args, **kwargs)
2024-09-09T06:48:00.6356001Z   File "/home/runner/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/d064dece8a8b41d9fb8729fbe3435278786931f1/bert_layers.py", line 447, in forward
2024-09-09T06:48:00.6357614Z     hidden_states = layer_module(hidden_states,
2024-09-09T06:48:00.6359282Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
2024-09-09T06:48:00.6361114Z     return self._call_impl(*args, **kwargs)
2024-09-09T06:48:00.6362655Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
2024-09-09T06:48:00.6364022Z     return forward_call(*args, **kwargs)
2024-09-09T06:48:00.6365922Z   File "/home/runner/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/d064dece8a8b41d9fb8729fbe3435278786931f1/bert_layers.py", line 328, in forward
2024-09-09T06:48:00.6367720Z     attention_output = self.attention(hidden_states, cu_seqlens, seqlen,
2024-09-09T06:48:00.6369584Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
2024-09-09T06:48:00.6370949Z     return self._call_impl(*args, **kwargs)
2024-09-09T06:48:00.6372389Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
2024-09-09T06:48:00.6374062Z     return forward_call(*args, **kwargs)
2024-09-09T06:48:00.6376466Z   File "/home/runner/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/d064dece8a8b41d9fb8729fbe3435278786931f1/bert_layers.py", line 241, in forward
2024-09-09T06:48:00.6378605Z     self_output = self.self(input_tensor, cu_seqlens, max_s, indices,
2024-09-09T06:48:00.6380583Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1553, in _wrapped_call_impl
2024-09-09T06:48:00.6382050Z     return self._call_impl(*args, **kwargs)
2024-09-09T06:48:00.6383810Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1562, in _call_impl
2024-09-09T06:48:00.6385251Z     return forward_call(*args, **kwargs)
2024-09-09T06:48:00.6387243Z   File "/home/runner/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/d064dece8a8b41d9fb8729fbe3435278786931f1/bert_layers.py", line 182, in forward
2024-09-09T06:48:00.6389336Z     attention = flash_attn_qkvpacked_func(qkv, bias)
2024-09-09T06:48:00.6391031Z   File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/torch/autograd/function.py", line 574, in apply
2024-09-09T06:48:00.6392458Z     return super().apply(*args, **kwargs)  # type: ignore[misc]
2024-09-09T06:48:00.6393811Z   File "/home/runner/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/d064dece8a8b41d9fb8729fbe3435278786931f1/flash_attn_triton.py", line 1021, in forward
2024-09-09T06:48:00.6394934Z     o, lse, ctx.softmax_scale = _flash_attn_forward(
2024-09-09T06:48:00.6396302Z   File "/home/runner/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/d064dece8a8b41d9fb8729fbe3435278786931f1/flash_attn_triton.py", line 781, in _flash_attn_forward
2024-09-09T06:48:00.6397479Z     assert q.is_cuda and k.is_cuda and v.is_cuda
2024-09-09T06:48:00.6397922Z AssertionError
2024-09-09T06:48:01.0374956Z ##[error]Process completed with exit code 1.
2024-09-09T06:48:01.0463010Z Post job cleanup.
2024-09-09T06:48:01.1352861Z [command]/usr/bin/git version
2024-09-09T06:48:01.1389483Z git version 2.46.0
2024-09-09T06:48:01.1434352Z Temporarily overriding HOME='/home/runner/work/_temp/96bbb5ec-9f75-4741-afea-a408eb4fbb5e' before making global git config changes
2024-09-09T06:48:01.1436388Z Adding repository directory to the temporary git global config as a safe directory
2024-09-09T06:48:01.1438605Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/DNABERT_2/DNABERT_2
2024-09-09T06:48:01.1472032Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2024-09-09T06:48:01.1502683Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :"
2024-09-09T06:48:01.1743468Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2024-09-09T06:48:01.1765235Z http.https://github.com/.extraheader
2024-09-09T06:48:01.1775314Z [command]/usr/bin/git config --local --unset-all http.https://github.com/.extraheader
2024-09-09T06:48:01.1806715Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :"
2024-09-09T06:48:01.2307258Z Cleaning up orphan processes