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Model does not build #13

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GemmaTuron opened this issue Feb 20, 2025 · 0 comments
Open

Model does not build #13

GemmaTuron opened this issue Feb 20, 2025 · 0 comments

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@GemmaTuron
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The current version of this model in DockerHub produces all None outputs.

I am trying to build it locally but even from a simple fetch_from_dir I run into this issue due to trying to package it with BentoML. I certainly think this model should be packaged with FAST API and I do not know why it choses bentoML. Does not help that the history in the model has been erased.
Here the error. I'll push the changes as I have improved and updated the code anyways to calculate the descriptors:

(zairadescribe) gturon@pujarnol:~/github/ersilia-os$ ersilia -v fetch eos5axz --from_dir eos5axz
15:27:26 | DEBUG    | Repo path specified: eos5axz
15:27:26 | DEBUG    | Absolute path: /home/gturon/github/ersilia-os/eos5axz
⬇️  Fetching model eos5axz: morgan-counts
15:27:26 | DEBUG    | Initialized with URL: None
15:27:26 | DEBUG    | Getting model source
15:27:26 | DEBUG    | Model getting fetched from Local Repository
15:27:26 | INFO     | Model doesn't exist on your system, fetching it now.
15:27:26 | DEBUG    | Starting fetching procedure
15:27:26 | DEBUG    | Fetching in your system, not from DockerHub
15:27:26 | DEBUG    | Deciding fetcher (BentoML or FastAPI)
15:27:26 | DEBUG    | Fetching using BentoML
15:27:26 | DEBUG    | Checking if the model is installable with BentoML
15:27:26 | DEBUG    | Starting fetching procedure
15:27:26 | DEBUG    | GitHub CLI is installed
15:27:26 | DEBUG    | Git LFS is installed
Git LFS initialized.
15:27:26 | DEBUG    | Git LFS has been activated
15:27:27 | DEBUG    | Connected to the internet
15:27:27 | DEBUG    | Conda is installed
15:27:27 | DEBUG    | EOS Home path exists
15:27:27 | INFO     | Starting delete of model eos5axz
15:27:27 | DEBUG    | Attempting Bento delete
15:27:28 | DEBUG    | No BentoML Catalog available
15:27:28 | INFO     | Deleting conda environment eos5axz
15:27:28 | DEBUG    | Attempting temporary folder delete
15:27:28 | DEBUG    | Attempting lake delete (local)
15:27:28 | DEBUG    | Deleting /home/gturon/eos/isaura/lake/eos5axz_local.h5
15:27:28 | DEBUG    | Attempting lake delete (public)
15:27:28 | DEBUG    | Deleting /home/gturon/eos/isaura/lake/eos5axz_public.h5
15:27:28 | INFO     | Removing docker images and stopping containers related to eos5axz
Total reclaimed space: 0B
15:27:28 | DEBUG    | Running docker images > /tmp/ersilia-kizixpki/docker-images.txt
15:27:28 | DEBUG    | Model entry eos5axz was not available in the fetched models registry
15:27:28 | SUCCESS  | Model eos5axz deleted successfully
15:27:28 | DEBUG    | Getting repository
15:27:28 | DEBUG    | Preparing inner template if necessary
15:27:28 | DEBUG    | The pack.py file already exists
15:27:28 | DEBUG    | The Dockerfile file already exists
15:27:28 | DEBUG    | The src folder already exists
15:27:28 | DEBUG    | Changing python version if necessary
15:27:28 | DEBUG    | {'version': '0.11.0', 'slim': False, 'python': 'py312'}
15:27:28 | DEBUG    | User is not root
15:27:28 | DEBUG    | Copying example file if available
15:27:28 | DEBUG    | Example file exists
15:27:28 | DEBUG    | Done getting model
15:27:28 | DEBUG    | Check if model can be run with vanilla (system) code (i.e. dockerfile has no installs)
15:27:28 | DEBUG    | Check bentoml and python version
15:27:28 | INFO     | BentoML version {'version': '0.11.0', 'slim': False, 'python': 'py312'}
15:27:28 | DEBUG    | Custom Ersilia BentoML is used, no need for modifying protobuf version
15:27:28 | DEBUG    | Model needs some installs
15:27:28 | DEBUG    | Checking if only python/conda install will be sufficient
15:27:28 | DEBUG    | Mode: conda
15:27:28 | DEBUG    | Trying to remove path: /home/gturon/bentoml/repository/eos5axz
15:27:28 | DEBUG    | ...successfully
15:27:28 | DEBUG    | ...but path did not exist!
15:27:28 | DEBUG    | Initializing conda packer
15:27:28 | DEBUG    | Packing model with Conda
15:27:28 | DEBUG    | Writing install commands
15:27:28 | DEBUG    | Run commands: ['pip install rdkit==2024.9.5', 'pip install numpy==2.2.3']
15:27:28 | DEBUG    | Writing install commands in /home/gturon/eos/dest/eos5axz/model_install_commands.sh
15:27:28 | DEBUG    | Setting up
15:27:28 | DEBUG    | Installs file /home/gturon/eos/dest/eos5axz/model_install_commands.sh
15:27:28 | DEBUG    | Conda environment eos5axz
15:27:29 | DEBUG    | Environment eos5axz does not exist
15:27:30 | INFO     | Cloning base conda environment and adding model dependencies
Source:      /home/gturon/miniconda3/envs/eosbase-bentoml-0.11.0-py312
Destination: /home/gturon/miniconda3/envs/eos5axz
Packages: 23
Files: 5948

Downloading and Extracting Packages:


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate eos5axz
#
# To deactivate an active environment, use
#
#     $ conda deactivate

15:27:37 | DEBUG    | Run commandlines on eos5axz
15:27:37 | DEBUG    | python -m pip --disable-pip-version-check install rdkit==2024.9.5
python -m pip --disable-pip-version-check install numpy==2.2.3
python -m pip --disable-pip-version-check install git+https://github.com/ersilia-os/bentoml-ersilia.git

15:27:37 | DEBUG    | Activating base environment
15:27:37 | DEBUG    | Current working directory: /home/gturon/eos/dest/eos5axz
15:27:37 | DEBUG    | Running bash /tmp/ersilia-0aqlmr05/script.sh 2>&1 | tee -a /tmp/ersilia-q0zng1uy/command_outputs.log
Collecting rdkit==2024.9.5
  Using cached rdkit-2024.9.5-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (4.0 kB)
Requirement already satisfied: numpy in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from rdkit==2024.9.5) (2.2.2)
Collecting Pillow (from rdkit==2024.9.5)
  Using cached pillow-11.1.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
Using cached rdkit-2024.9.5-cp312-cp312-manylinux_2_28_x86_64.whl (34.3 MB)
Using cached pillow-11.1.0-cp312-cp312-manylinux_2_28_x86_64.whl (4.5 MB)
Installing collected packages: Pillow, rdkit
Successfully installed Pillow-11.1.0 rdkit-2024.9.5
Collecting numpy==2.2.3
  Using cached numpy-2.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Using cached numpy-2.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.1 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 2.2.2
    Uninstalling numpy-2.2.2:
      Successfully uninstalled numpy-2.2.2
Successfully installed numpy-2.2.3
Collecting git+https://github.com/ersilia-os/bentoml-ersilia.git
  Cloning https://github.com/ersilia-os/bentoml-ersilia.git to /tmp/pip-req-build-72i0e3d_
  Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/bentoml-ersilia.git /tmp/pip-req-build-72i0e3d_
  Resolved https://github.com/ersilia-os/bentoml-ersilia.git to commit d9d9f342294da3f1a69c9e81adb17f77bc010aac
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: docker in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (7.1.0)
Requirement already satisfied: alembic in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (1.14.1)
Requirement already satisfied: packaging in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (24.2)
Requirement already satisfied: boto3 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (1.36.19)
Requirement already satisfied: psutil in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (6.1.1)
Requirement already satisfied: cerberus in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (1.3.7)
Requirement already satisfied: sqlalchemy in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (2.0.38)
Requirement already satisfied: sqlalchemy-utils in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (0.41.2)
Requirement already satisfied: tabulate in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (0.9.0)
Requirement already satisfied: humanfriendly in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (10.0)
Requirement already satisfied: flask in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (3.1.0)
Requirement already satisfied: chardet in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (5.2.0)
Requirement already satisfied: numpy in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (2.2.3)
Requirement already satisfied: multidict in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (6.1.0)
Requirement already satisfied: requests in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (2.32.3)
Requirement already satisfied: python-json-logger in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (3.2.1)
Requirement already satisfied: ruamel.yaml in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (0.18.10)
Requirement already satisfied: werkzeug in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (3.1.3)
Requirement already satisfied: protobuf<3.19,>=3.8.0 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (3.18.3)
Requirement already satisfied: prometheus_client in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (0.21.1)
Requirement already satisfied: Mako in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from alembic->bentoml==0.11.0) (1.3.9)
Requirement already satisfied: typing-extensions>=4 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from alembic->bentoml==0.11.0) (4.12.2)
Requirement already satisfied: greenlet!=0.4.17 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from sqlalchemy->bentoml==0.11.0) (3.1.1)
Requirement already satisfied: botocore<1.37.0,>=1.36.19 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from boto3->bentoml==0.11.0) (1.36.19)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from boto3->bentoml==0.11.0) (1.0.1)
Requirement already satisfied: s3transfer<0.12.0,>=0.11.0 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from boto3->bentoml==0.11.0) (0.11.2)
Requirement already satisfied: urllib3>=1.26.0 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from docker->bentoml==0.11.0) (2.3.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from requests->bentoml==0.11.0) (3.4.1)
Requirement already satisfied: idna<4,>=2.5 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from requests->bentoml==0.11.0) (3.10)
Requirement already satisfied: certifi>=2017.4.17 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from requests->bentoml==0.11.0) (2025.1.31)
Requirement already satisfied: Jinja2>=3.1.2 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from flask->bentoml==0.11.0) (3.1.5)
Requirement already satisfied: itsdangerous>=2.2 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from flask->bentoml==0.11.0) (2.2.0)
Requirement already satisfied: click>=8.1.3 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from flask->bentoml==0.11.0) (8.1.8)
Requirement already satisfied: blinker>=1.9 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from flask->bentoml==0.11.0) (1.9.0)
Requirement already satisfied: MarkupSafe>=2.1.1 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from werkzeug->bentoml==0.11.0) (3.0.2)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from ruamel.yaml->bentoml==0.11.0) (0.2.12)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from botocore<1.37.0,>=1.36.19->boto3->bentoml==0.11.0) (2.9.0.post0)
Requirement already satisfied: six>=1.5 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.37.0,>=1.36.19->boto3->bentoml==0.11.0) (1.17.0)
15:27:50 | DEBUG    | Collecting rdkit==2024.9.5
  Using cached rdkit-2024.9.5-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (4.0 kB)
Requirement already satisfied: numpy in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from rdkit==2024.9.5) (2.2.2)
Collecting Pillow (from rdkit==2024.9.5)
  Using cached pillow-11.1.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
Using cached rdkit-2024.9.5-cp312-cp312-manylinux_2_28_x86_64.whl (34.3 MB)
Using cached pillow-11.1.0-cp312-cp312-manylinux_2_28_x86_64.whl (4.5 MB)
Installing collected packages: Pillow, rdkit
Successfully installed Pillow-11.1.0 rdkit-2024.9.5
Collecting numpy==2.2.3
  Using cached numpy-2.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Using cached numpy-2.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.1 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 2.2.2
    Uninstalling numpy-2.2.2:
      Successfully uninstalled numpy-2.2.2
Successfully installed numpy-2.2.3
Collecting git+https://github.com/ersilia-os/bentoml-ersilia.git
  Cloning https://github.com/ersilia-os/bentoml-ersilia.git to /tmp/pip-req-build-72i0e3d_
  Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/bentoml-ersilia.git /tmp/pip-req-build-72i0e3d_
  Resolved https://github.com/ersilia-os/bentoml-ersilia.git to commit d9d9f342294da3f1a69c9e81adb17f77bc010aac
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: docker in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (7.1.0)
Requirement already satisfied: alembic in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (1.14.1)
Requirement already satisfied: packaging in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (24.2)
Requirement already satisfied: boto3 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (1.36.19)
Requirement already satisfied: psutil in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (6.1.1)
Requirement already satisfied: cerberus in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (1.3.7)
Requirement already satisfied: sqlalchemy in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (2.0.38)
Requirement already satisfied: sqlalchemy-utils in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (0.41.2)
Requirement already satisfied: tabulate in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (0.9.0)
Requirement already satisfied: humanfriendly in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (10.0)
Requirement already satisfied: flask in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (3.1.0)
Requirement already satisfied: chardet in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (5.2.0)
Requirement already satisfied: numpy in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (2.2.3)
Requirement already satisfied: multidict in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (6.1.0)
Requirement already satisfied: requests in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (2.32.3)
Requirement already satisfied: python-json-logger in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (3.2.1)
Requirement already satisfied: ruamel.yaml in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (0.18.10)
Requirement already satisfied: werkzeug in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (3.1.3)
Requirement already satisfied: protobuf<3.19,>=3.8.0 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (3.18.3)
Requirement already satisfied: prometheus_client in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from bentoml==0.11.0) (0.21.1)
Requirement already satisfied: Mako in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from alembic->bentoml==0.11.0) (1.3.9)
Requirement already satisfied: typing-extensions>=4 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from alembic->bentoml==0.11.0) (4.12.2)
Requirement already satisfied: greenlet!=0.4.17 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from sqlalchemy->bentoml==0.11.0) (3.1.1)
Requirement already satisfied: botocore<1.37.0,>=1.36.19 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from boto3->bentoml==0.11.0) (1.36.19)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from boto3->bentoml==0.11.0) (1.0.1)
Requirement already satisfied: s3transfer<0.12.0,>=0.11.0 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from boto3->bentoml==0.11.0) (0.11.2)
Requirement already satisfied: urllib3>=1.26.0 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from docker->bentoml==0.11.0) (2.3.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from requests->bentoml==0.11.0) (3.4.1)
Requirement already satisfied: idna<4,>=2.5 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from requests->bentoml==0.11.0) (3.10)
Requirement already satisfied: certifi>=2017.4.17 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from requests->bentoml==0.11.0) (2025.1.31)
Requirement already satisfied: Jinja2>=3.1.2 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from flask->bentoml==0.11.0) (3.1.5)
Requirement already satisfied: itsdangerous>=2.2 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from flask->bentoml==0.11.0) (2.2.0)
Requirement already satisfied: click>=8.1.3 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from flask->bentoml==0.11.0) (8.1.8)
Requirement already satisfied: blinker>=1.9 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from flask->bentoml==0.11.0) (1.9.0)
Requirement already satisfied: MarkupSafe>=2.1.1 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from werkzeug->bentoml==0.11.0) (3.0.2)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from ruamel.yaml->bentoml==0.11.0) (0.2.12)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from botocore<1.37.0,>=1.36.19->boto3->bentoml==0.11.0) (2.9.0.post0)
Requirement already satisfied: six>=1.5 in /home/gturon/miniconda3/envs/eos5axz/lib/python3.12/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.37.0,>=1.36.19->boto3->bentoml==0.11.0) (1.17.0)

15:27:50 | DEBUG    | Activation done
15:27:50 | DEBUG    | Creating environment YAML file
15:27:52 | DEBUG    | Storing Conda environment in the local environment database
15:27:52 | DEBUG    | Done with the Conda setup
15:27:52 | DEBUG    | Using environment eos5axz
15:27:52 | DEBUG    | Running command: python pack.py
15:27:52 | DEBUG    | Run commandlines on eos5axz
15:27:52 | DEBUG    | 
        python pack.py
        
15:27:52 | DEBUG    | Activating base environment
15:27:52 | DEBUG    | Current working directory: /home/gturon/eos/dest/eos5axz
15:27:52 | DEBUG    | Running bash /tmp/ersilia-j2fbn0fd/script.sh 2>&1 | tee -a /tmp/ersilia-1xiy526c/command_outputs.log
[2025-02-20 15:27:53,448] WARNING - Python 3.12.9 found in current environment is not officially supported by BentoML. The docker base image used is'bentoml/model-server:0.11.0' which will use conda to install Python 3.12.9 in the build process. Supported Python versions are: f3.6, 3.7, 3.8
[2025-02-20 15:27:54,478] INFO - BentoService bundle 'eos5axz:20250220152753_8BE1EB' saved to: /home/gturon/bentoml/repository/eos5axz/20250220152753_8BE1EB
15:27:54 | DEBUG    | [2025-02-20 15:27:53,448] WARNING - Python 3.12.9 found in current environment is not officially supported by BentoML. The docker base image used is'bentoml/model-server:0.11.0' which will use conda to install Python 3.12.9 in the build process. Supported Python versions are: f3.6, 3.7, 3.8
[2025-02-20 15:27:54,478] INFO - BentoService bundle 'eos5axz:20250220152753_8BE1EB' saved to: /home/gturon/bentoml/repository/eos5axz/20250220152753_8BE1EB

15:27:54 | DEBUG    | Activation done
15:27:54 | DEBUG    | Previous command successfully run inside eos5axz conda environment
15:27:54 | DEBUG    | Now trying to establish symlinks
15:27:54 | DEBUG    | BentoML location is /home/gturon/bentoml/repository/eos5axz/20250220152753_8BE1EB
15:27:54 | DEBUG    | Ersilia Bento location is /home/gturon/eos/repository/eos5axz/20250220152753_8BE1EB
15:27:54 | DEBUG    | Building symlinks between /home/gturon/eos/repository/eos5axz/20250220152753_8BE1EB and /home/gturon/bentoml/repository/eos5axz/20250220152753_8BE1EB
15:27:54 | DEBUG    | Creating model symlink bundle artifacts > dest
15:27:54 | DEBUG    | Creating model_install_commands.sh symlink dest <> bundle
15:27:54 | INFO     | Could not create symbolic link from /home/gturon/eos/dest/eos5axz/data.h5 to /home/gturon/eos/isaura/lake/eos5axz_public.h5
15:27:54 | DEBUG    | Run file found in framework: /home/gturon/eos/repository/eos5axz/20250220152753_8BE1EB/eos5axz/artifacts/framework/run.sh
15:27:54 | DEBUG    | Run commandlines on eos5axz
15:27:54 | DEBUG    | which python > /tmp/ersilia-kfkco100/tmp.txt
15:27:55 | DEBUG    | Activating base environment
15:27:55 | DEBUG    | Current working directory: /home/gturon/github/ersilia-os
15:27:55 | DEBUG    | Running bash /tmp/ersilia-5yc4a6kc/script.sh 2>&1 | tee -a /tmp/ersilia-khifn357/command_outputs.log
15:27:55 | DEBUG    | 
15:27:55 | DEBUG    | Activation done
15:27:55 | DEBUG    | Python executable: /home/gturon/miniconda3/envs/eos5axz/bin/python
15:27:55 | DEBUG    | Conda is needed
15:27:55 | DEBUG    | Checking if model needs to be integrated to a tool
15:27:55 | DEBUG    | Getting model card of eos5axz
15:27:55 | DEBUG    | Trying to get metadata from: /home/gturon/eos/dest/eos5axz
15:27:55 | DEBUG    | Card saved at /home/gturon/eos/dest/eos5axz/card.json
15:27:55 | DEBUG    | Saving slug morgan-counts
15:27:55 | DEBUG    | Checking that autoservice works
15:27:55 | DEBUG    | Setting BentoML AutoService for eos5axz
15:27:55 | DEBUG    | No service class provided, deciding automatically
15:27:55 | DEBUG    | No service class file exists in /home/gturon/eos/repository/eos5axz/20250220152753_8BE1EB/service_class.txt
15:27:55 | DEBUG    | Pack method is: bentoml
15:27:55 | DEBUG    | Pack method is: bentoml
15:27:55 | DEBUG    | Setting virtual environment at /home/gturon/eos/dest/eos5axz
15:27:55 | DEBUG    | Pack method is: bentoml
15:27:56 | DEBUG    | Pack method is: bentoml
15:27:56 | DEBUG    | Service class: conda
15:27:56 | DEBUG    | Getting APIs from list file
15:27:56 | DEBUG    | Getting APIs from BentoML
15:27:56 | DEBUG    | Getting APIs from Bento
15:27:56 | DEBUG    | Getting info from BentoML and storing in /tmp/ersilia-_2d5a44m/information.json
🚨🚨🚨 Something went wrong with Ersilia 🚨🚨🚨

Error message:

Expecting value: line 1 column 1 (char 0)
If this error message is not helpful, open an issue at:
 - https://github.com/ersilia-os/ersilia
Or feel free to reach out to us at:
 - hello[at]ersilia.io

If you haven't, try to run your command in verbose mode (-v in the CLI)
 - You will find the console log file in: /home/gturon/eos/current.log
Task exception was never retrieved
future: <Task finished name='Task-1' coro=<ModelFetcher.fetch() done, defined at /home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch.py:345> exception=SystemExit(1)>
Traceback (most recent call last):
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/utils/exceptions_utils/throw_ersilia_exception.py", line 25, in inner_function
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch.py", line 203, in _fetch_from_bentoml
    mf.fetch(model_id=self.model_id)
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch_bentoml.py", line 213, in fetch
    self._fetch(model_id)
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch_bentoml.py", line 171, in _fetch
    self._fetch_not_from_dockerhub(model_id=model_id)
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch_bentoml.py", line 154, in _fetch_not_from_dockerhub
    self._check()
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch_bentoml.py", line 127, in _check
    mc.check()
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/actions/check.py", line 27, in check
    AutoService(self.model_id)
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/serve/autoservice.py", line 216, in __init__
    self._set_apis()
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/serve/autoservice.py", line 257, in _set_apis
    for api_name in self.service._get_apis_from_where_available():
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/serve/services.py", line 124, in _get_apis_from_where_available
    apis_list = self._get_apis_from_bento()
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/serve/services.py", line 98, in _get_apis_from_bento
    info = self._get_info_from_bento()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/serve/services.py", line 92, in _get_info_from_bento
    info = json.load(f)
           ^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/json/__init__.py", line 293, in load
    return loads(fp.read(),
           ^^^^^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/cli/commands/__init__.py", line 31, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/cli/commands/fetch.py", line 142, in fetch
    fetch_result = _fetch(mf, model_id)
                   ^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/cli/commands/fetch.py", line 37, in _fetch
    res = asyncio.run(mf.fetch(model_id))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/site-packages/nest_asyncio.py", line 30, in run
    return loop.run_until_complete(task)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/site-packages/nest_asyncio.py", line 92, in run_until_complete
    self._run_once()
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/site-packages/nest_asyncio.py", line 133, in _run_once
    handle._run()
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/asyncio/events.py", line 84, in _run
    self._context.run(self._callback, *self._args)
  File "/home/gturon/miniconda3/envs/zairadescribe/lib/python3.11/asyncio/tasks.py", line 277, in __step
    result = coro.send(None)
             ^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch.py", line 366, in fetch
    fr = await self._fetch(model_id)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch.py", line 334, in _fetch
    self._fetch_not_from_dockerhub(model_id=model_id)
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/utils/exceptions_utils/throw_ersilia_exception.py", line 25, in inner_function
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/hub/fetch/fetch.py", line 228, in _fetch_not_from_dockerhub
    self._fetch_from_bentoml()
  File "/home/gturon/github/ersilia-os/ersilia/ersilia/utils/exceptions_utils/throw_ersilia_exception.py", line 41, in inner_function
    sys.exit(DEFAULT_ERSILIA_ERROR_EXIT_CODE)
SystemExit: 1
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@GemmaTuron