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ersilia-os / eos3ujl

GNU General Public License v3.0
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Cannot fetch model #3

Closed miquelduranfrigola closed 2 weeks ago

miquelduranfrigola commented 2 weeks ago

I am seeing the following error:

(base) root@codespaces-d29010:/workspaces/ersilia# ersilia -v fetch eos3ujl --from_github
20:06:03 | DEBUG    | Trying to get metadata from: /root/eos/dest/eos3ujl
⬇️  Fetching model eos3ujl: mtb-permeability
20:06:04 | DEBUG    | Initialized with URL: None
20:06:04 | DEBUG    | Getting model source
20:06:04 | DEBUG    | Model getting fetched from GitHub
20:06:04 | DEBUG    | Starting fetching procedure
20:06:04 | DEBUG    | Fetching in your system, not from DockerHub
20:06:04 | DEBUG    | Model doesn't exist in your local, fetching it now
20:06:04 | DEBUG    | Deciding fetcher (BentoML or FastAPI)
20:06:05 | DEBUG    | Fetching using Ersilia Pack (FastAPI)
20:06:06 | DEBUG    | Fetching from FastAPI...
20:06:09 | DEBUG    | GitHub CLI is installed
20:06:09 | DEBUG    | Git LFS is installed
Updated Git hooks.
Git LFS initialized.
20:06:09 | DEBUG    | Git LFS has been activated
20:06:09 | DEBUG    | Connected to the internet
20:06:09 | DEBUG    | Conda is installed
20:06:09 | DEBUG    | EOS Home path exists
20:06:09 | INFO     | Starting delete of model eos3ujl
20:06:09 | DEBUG    | Attempting Bento delete
  Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/bentoml-ersilia.git /tmp/pip-req-build-sdvpo1fu
20:06:19 | DEBUG    | No BentoML Catalog available
20:06:22 | INFO     | Deleting conda environment eos3ujl
20:06:24 | DEBUG    | Attempting temporary folder delete
20:06:24 | DEBUG    | Attempting lake delete (local)
20:06:24 | DEBUG    | Deleting /root/eos/isaura/lake/eos3ujl_local.h5
20:06:24 | DEBUG    | Attempting lake delete (public)
20:06:24 | DEBUG    | Deleting /root/eos/isaura/lake/eos3ujl_public.h5
20:06:24 | DEBUG    | Model entry eos3ujl was not available in the fetched models registry
20:06:24 | SUCCESS  | Model eos3ujl deleted successfully
20:06:24 | DEBUG    | Getting repository
Cloning into 'eos3ujl'...
remote: Enumerating objects: 49, done.
remote: Counting objects: 100% (42/42), done.
remote: Compressing objects: 100% (40/40), done.
ERROR: Pipe to stdout was broken 37.70 MiB | 18.85 MiB/s
Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
BrokenPipeError: [Errno 32] Broken pipe
remote: Total 49 (delta 6), reused 24 (delta 1), pack-reused 7 (from 1)
Receiving objects: 100% (49/49), 60.27 MiB | 20.16 MiB/s, done.
Resolving deltas: 100% (6/6), done.
rm: cannot remove '/tmp/ersilia-001oqn3c': Is a directory
Downloading large file mock.txt from S3 bucket.
[==================================================]✅

20:06:29 | INFO     | 🚀 Model starting...
20:06:29 | DEBUG    | User is root! Removing sudo commands
🚨🚨🚨 Something went wrong with Ersilia 🚨🚨🚨

Error message:

[Errno 2] No such file or directory: '/root/eos/dest/eos3ujl/Dockerfile'
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: /root/eos/current.log
miquelduranfrigola commented 2 weeks ago

Also, for some reason, the info API endpoint is not working. It only returns the API schema, not the full information. So, when using the FastAPI interface, it doesn't work.

DhanshreeA commented 2 weeks ago

For some reason while trying to fetch this model through github, git keeps crashing for me during the repo cloning stage:

Cloning into 'eos3ujl'...
remote: Enumerating objects: 49, done.
remote: Counting objects: 100% (42/42), done.
remote: Compressing objects: 100% (40/40), done.
error: RPC failed; curl 92 HTTP/2 stream 5 was not closed cleanly: CANCEL (err 8)
error: 84 bytes of body are still expected
fetch-pack: unexpected disconnect while reading sideband packet
fatal: early EOF
fatal: fetch-pack: invalid index-pack output
mv: cannot stat 'eos3ujl': No such file or directory
rm: cannot remove '/tmp/ersilia-tmzuxaq0': Is a directory
miquelduranfrigola commented 2 weeks ago

mmmm... can you clone it normally? it worked for me

DhanshreeA commented 2 weeks ago

Okay, so I can clone it normally, it is about 146MB which is not even that large. However, I switched my internet to one with higher speed, and now the model fetches successfully using the from_github flag. Nothing changed at all.

ersilia -v fetch eos3ujl --from_github
15:07:52 | DEBUG    | Trying to get metadata from: /home/dee/eos/dest/eos3ujl
⬇️  Fetching model eos3ujl: mtb-permeability
15:07:53 | DEBUG    | Initialized with URL: None
15:07:53 | DEBUG    | Getting model source
15:07:53 | DEBUG    | Model getting fetched from GitHub
15:07:53 | DEBUG    | Starting fetching procedure
15:07:53 | DEBUG    | Fetching in your system, not from DockerHub
15:07:53 | DEBUG    | Model doesn't exist in your local, fetching it now
15:07:53 | DEBUG    | Deciding fetcher (BentoML or FastAPI)
15:07:55 | DEBUG    | Fetching using Ersilia Pack (FastAPI)
15:07:56 | DEBUG    | Fetching from FastAPI...
15:07:56 | INFO     | GitHub CLI is not installed. Ersilia can work without it, but we highly recommend that you install this tool.
15:07:56 | DEBUG    | Git LFS is installed
Git LFS initialized.
15:07:56 | DEBUG    | Git LFS has been activated
15:07:56 | DEBUG    | Connected to the internet
15:07:56 | DEBUG    | Conda is installed
15:07:56 | DEBUG    | EOS Home path exists
15:07:56 | INFO     | Starting delete of model eos3ujl
15:07:56 | DEBUG    | Attempting Bento delete
15:07:57 | INFO     | Deleting conda environment eos3ujl
15:07:58 | DEBUG    | Attempting temporary folder delete
15:07:58 | DEBUG    | Attempting lake delete (local)
15:07:58 | DEBUG    | Deleting /home/dee/eos/isaura/lake/eos3ujl_local.h5
15:07:58 | DEBUG    | Attempting lake delete (public)
15:07:58 | DEBUG    | Deleting /home/dee/eos/isaura/lake/eos3ujl_public.h5
15:07:58 | INFO     | Removing docker images and stopping containers related to eos3ujl
Total reclaimed space: 0B
15:07:58 | DEBUG    | Running docker images > /tmp/ersilia-7d0dfag7/docker-images.txt
15:07:58 | DEBUG    | Model entry eos3ujl was not available in the fetched models registry
15:07:58 | SUCCESS  | Model eos3ujl deleted successfully
15:07:58 | DEBUG    | Getting repository
Cloning into 'eos3ujl'...
remote: Enumerating objects: 49, done.
remote: Counting objects: 100% (42/42), done.
remote: Compressing objects: 100% (40/40), done.
remote: Total 49 (delta 6), reused 24 (delta 1), pack-reused 7 (from 1)
Receiving objects: 100% (49/49), 60.27 MiB | 17.29 MiB/s, done.
Resolving deltas: 100% (6/6), done.
rm: cannot remove '/tmp/ersilia-b4squnpy': Is a directory
Downloading large file mock.txt from S3 bucket.
[==================================================]✅

15:08:04 | INFO     | 🚀 Model starting...
15:08:04 | DEBUG    | User is not root
15:08:04 | DEBUG    | Copying example file if available
15:08:04 | DEBUG    | Example file exists
15:08:04 | DEBUG    | Getting model parameters
15:08:04 | DEBUG    | Done getting model
15:08:04 | DEBUG    | Check if model can be run with vanilla (system) code. This is a default option when inside a docker container.
15:08:04 | DEBUG    | Initializing conda packer
15:08:04 | DEBUG    | Packing model with Conda
15:08:04 | DEBUG    | Setting up
15:08:04 | DEBUG    | Reading python version from install.yml
15:08:04 | DEBUG    | Conda environment eos3ujl
15:08:04 | DEBUG    | Environment eos3ujl does not exist
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 24.7.1
  latest version: 24.9.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=24.9.2

## Package Plan ##

  environment location: /home/dee/miniconda3/envs/eos3ujl

  added / updated specs:
    - python=3.10

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    python-3.10.15             |       he870216_1        26.8 MB
    tzdata-2024b               |       h04d1e81_0         115 KB
    ------------------------------------------------------------
                                           Total:        26.9 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main 
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu 
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6 
  ca-certificates    pkgs/main/linux-64::ca-certificates-2024.9.24-h06a4308_0 
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.40-h12ee557_0 
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1 
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0 
  openssl            pkgs/main/linux-64::openssl-3.0.15-h5eee18b_0 
  pip                pkgs/main/linux-64::pip-24.2-py310h06a4308_0 
  python             pkgs/main/linux-64::python-3.10.15-he870216_1 
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 
  setuptools         pkgs/main/linux-64::setuptools-75.1.0-py310h06a4308_0 
  sqlite             pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0 
  tk                 pkgs/main/linux-64::tk-8.6.14-h39e8969_0 
  tzdata             pkgs/main/noarch::tzdata-2024b-h04d1e81_0 
  wheel              pkgs/main/linux-64::wheel-0.44.0-py310h06a4308_0 
  xz                 pkgs/main/linux-64::xz-5.4.6-h5eee18b_1 
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1 

Downloading and Extracting Packages:

Preparing transaction: done                                                                                                       
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate eos3ujl
#
# To deactivate an active environment, use
#
#     $ conda deactivate

15:08:09 | DEBUG    | Creating base conda environment
15:08:09 | DEBUG    | Run commandlines on eos3ujl
15:08:09 | DEBUG    | python -m pip install git+https://github.com/ersilia-os/ersilia-pack.git
15:08:09 | DEBUG    | Activating base environment
15:08:09 | DEBUG    | Current working directory: /home/dee/ersilia-project
15:08:09 | DEBUG    | Running bash /tmp/ersilia-vozi1gx8/script.sh 2>&1 | tee -a /tmp/ersilia-m1n2z79v/command_outputs.log
Collecting git+https://github.com/ersilia-os/ersilia-pack.git
  Cloning https://github.com/ersilia-os/ersilia-pack.git to /tmp/pip-req-build-tr_vwdv7
  Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/ersilia-pack.git /tmp/pip-req-build-tr_vwdv7
  Resolved https://github.com/ersilia-os/ersilia-pack.git to commit 1f4795a35b9784907badf2f28711e8ab04d8a4ed
  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: fastapi in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from ersilia-pack==1.0.0) (0.115.0)
Requirement already satisfied: PyYAML in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from ersilia-pack==1.0.0) (6.0.2)
Requirement already satisfied: uvicorn[standard] in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from ersilia-pack==1.0.0) (0.31.0)
Requirement already satisfied: starlette<0.39.0,>=0.37.2 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from fastapi->ersilia-pack==1.0.0) (0.38.6)
Requirement already satisfied: pydantic!=1.8,!=1.8.1,!=2.0.0,!=2.0.1,!=2.1.0,<3.0.0,>=1.7.4 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from fastapi->ersilia-pack==1.0.0) (2.9.2)
Requirement already satisfied: typing-extensions>=4.8.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from fastapi->ersilia-pack==1.0.0) (4.12.2)
Requirement already satisfied: click>=7.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (8.1.7)
Requirement already satisfied: h11>=0.8 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (0.14.0)
Requirement already satisfied: httptools>=0.5.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (0.6.1)
Requirement already satisfied: python-dotenv>=0.13 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (1.0.1)
Requirement already satisfied: uvloop!=0.15.0,!=0.15.1,>=0.14.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (0.20.0)
Requirement already satisfied: watchfiles>=0.13 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (0.24.0)
Requirement already satisfied: websockets>=10.4 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (13.1)
Requirement already satisfied: annotated-types>=0.6.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from pydantic!=1.8,!=1.8.1,!=2.0.0,!=2.0.1,!=2.1.0,<3.0.0,>=1.7.4->fastapi->ersilia-pack==1.0.0) (0.7.0)
Requirement already satisfied: pydantic-core==2.23.4 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from pydantic!=1.8,!=1.8.1,!=2.0.0,!=2.0.1,!=2.1.0,<3.0.0,>=1.7.4->fastapi->ersilia-pack==1.0.0) (2.23.4)
Requirement already satisfied: anyio<5,>=3.4.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from starlette<0.39.0,>=0.37.2->fastapi->ersilia-pack==1.0.0) (4.6.0)
Requirement already satisfied: idna>=2.8 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from anyio<5,>=3.4.0->starlette<0.39.0,>=0.37.2->fastapi->ersilia-pack==1.0.0) (3.10)
Requirement already satisfied: sniffio>=1.1 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from anyio<5,>=3.4.0->starlette<0.39.0,>=0.37.2->fastapi->ersilia-pack==1.0.0) (1.3.1)
Requirement already satisfied: exceptiongroup>=1.0.2 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from anyio<5,>=3.4.0->starlette<0.39.0,>=0.37.2->fastapi->ersilia-pack==1.0.0) (1.2.2)
15:08:13 | DEBUG    | Collecting git+https://github.com/ersilia-os/ersilia-pack.git
  Cloning https://github.com/ersilia-os/ersilia-pack.git to /tmp/pip-req-build-tr_vwdv7
  Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/ersilia-pack.git /tmp/pip-req-build-tr_vwdv7
  Resolved https://github.com/ersilia-os/ersilia-pack.git to commit 1f4795a35b9784907badf2f28711e8ab04d8a4ed
  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: fastapi in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from ersilia-pack==1.0.0) (0.115.0)
Requirement already satisfied: PyYAML in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from ersilia-pack==1.0.0) (6.0.2)
Requirement already satisfied: uvicorn[standard] in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from ersilia-pack==1.0.0) (0.31.0)
Requirement already satisfied: starlette<0.39.0,>=0.37.2 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from fastapi->ersilia-pack==1.0.0) (0.38.6)
Requirement already satisfied: pydantic!=1.8,!=1.8.1,!=2.0.0,!=2.0.1,!=2.1.0,<3.0.0,>=1.7.4 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from fastapi->ersilia-pack==1.0.0) (2.9.2)
Requirement already satisfied: typing-extensions>=4.8.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from fastapi->ersilia-pack==1.0.0) (4.12.2)
Requirement already satisfied: click>=7.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (8.1.7)
Requirement already satisfied: h11>=0.8 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (0.14.0)
Requirement already satisfied: httptools>=0.5.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (0.6.1)
Requirement already satisfied: python-dotenv>=0.13 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (1.0.1)
Requirement already satisfied: uvloop!=0.15.0,!=0.15.1,>=0.14.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (0.20.0)
Requirement already satisfied: watchfiles>=0.13 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (0.24.0)
Requirement already satisfied: websockets>=10.4 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from uvicorn[standard]->ersilia-pack==1.0.0) (13.1)
Requirement already satisfied: annotated-types>=0.6.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from pydantic!=1.8,!=1.8.1,!=2.0.0,!=2.0.1,!=2.1.0,<3.0.0,>=1.7.4->fastapi->ersilia-pack==1.0.0) (0.7.0)
Requirement already satisfied: pydantic-core==2.23.4 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from pydantic!=1.8,!=1.8.1,!=2.0.0,!=2.0.1,!=2.1.0,<3.0.0,>=1.7.4->fastapi->ersilia-pack==1.0.0) (2.23.4)
Requirement already satisfied: anyio<5,>=3.4.0 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from starlette<0.39.0,>=0.37.2->fastapi->ersilia-pack==1.0.0) (4.6.0)
Requirement already satisfied: idna>=2.8 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from anyio<5,>=3.4.0->starlette<0.39.0,>=0.37.2->fastapi->ersilia-pack==1.0.0) (3.10)
Requirement already satisfied: sniffio>=1.1 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from anyio<5,>=3.4.0->starlette<0.39.0,>=0.37.2->fastapi->ersilia-pack==1.0.0) (1.3.1)
Requirement already satisfied: exceptiongroup>=1.0.2 in /home/dee/.pyenv/versions/3.10.14/envs/ersilia/lib/python3.10/site-packages (from anyio<5,>=3.4.0->starlette<0.39.0,>=0.37.2->fastapi->ersilia-pack==1.0.0) (1.2.2)

15:08:13 | DEBUG    | Activation done
15:08:13 | DEBUG    | Storing Conda environment in the local environment database
15:08:13 | DEBUG    | Done with the Conda setup
15:08:13 | DEBUG    | Using environment eos3ujl
15:08:13 | DEBUG    | Running command: ersilia_model_pack --repo_path /home/dee/eos/dest/eos3ujl --bundles_repo_path /home/dee/eos/repository --conda_env_name eos3ujl
15:08:13 | DEBUG    | Run commandlines on eos3ujl
15:08:13 | DEBUG    | ersilia_model_pack --repo_path /home/dee/eos/dest/eos3ujl --bundles_repo_path /home/dee/eos/repository --conda_env_name eos3ujl
15:08:14 | DEBUG    | Activating base environment
15:08:14 | DEBUG    | Current working directory: /home/dee/ersilia-project
15:08:14 | DEBUG    | Running bash /tmp/ersilia-gmfykfz3/script.sh 2>&1 | tee -a /tmp/ersilia-7nph50io/command_outputs.log
Collecting pandas==2.1.4
  Downloading pandas-2.1.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Collecting numpy<2,>=1.22.4 (from pandas==2.1.4)
  Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting python-dateutil>=2.8.2 (from pandas==2.1.4)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==2.1.4)
  Using cached pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.1 (from pandas==2.1.4)
  Downloading tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)
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Getting info from metadata
{'card': OrderedDict([('Identifier', 'eos3ujl'), ('Slug', 'mtb-permeability'), ('Status', 'In progress'), ('Title', 'Mtb Permeability'), ('Description', 'This model predicts the probability of a compound of passing the Mtb cell wall membrane. The classifier (permeable vs not permeable) model was trained on a dataset of 5368 molecules. It is a simple classifier (SVC) using Mordred descriptors.'), ('Mode', 'Pretrained'), ('Input', ['Compound']), ('Input Shape', 'Single'), ('Task', ['Classification']), ('Output', ['Probability']), ('Output Type', ['Float']), ('Output Shape', 'Single'), ('Interpretation', 'Probability of a compound passing the Mtb cell wall membrane'), ('Tag', ['M.tuberculosis', 'Permeability']), ('Publication', 'https://link.springer.com/article/10.1007/s11030-024-10952-3'), ('Source Code', 'https://github.com/PGlab-NIPER/MTB_Permeability'), ('License', 'GPL-3.0-or-later'), ('S3', 'https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos3ujl.zip'), ('DockerHub', 'https://hub.docker.com/r/ersiliaos/eos3ujl'), ('Docker Architecture', ['AMD64', 'ARM64'])]), 'model_id': 'eos3ujl', 'Slug': 'mtb-permeability', 'api_list': ['run']}
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Copying model
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File downloaded and saved to /home/dee/eos/repository/eos3ujl/20241023-0f8d918d-c70b-4966-a690-b5bea6328fae/static/favicon.ico
Getting info from metadata
{'card': OrderedDict([('Identifier', 'eos3ujl'), ('Slug', 'mtb-permeability'), ('Status', 'In progress'), ('Title', 'Mtb Permeability'), ('Description', 'This model predicts the probability of a compound of passing the Mtb cell wall membrane. The classifier (permeable vs not permeable) model was trained on a dataset of 5368 molecules. It is a simple classifier (SVC) using Mordred descriptors.'), ('Mode', 'Pretrained'), ('Input', ['Compound']), ('Input Shape', 'Single'), ('Task', ['Classification']), ('Output', ['Probability']), ('Output Type', ['Float']), ('Output Shape', 'Single'), ('Interpretation', 'Probability of a compound passing the Mtb cell wall membrane'), ('Tag', ['M.tuberculosis', 'Permeability']), ('Publication', 'https://link.springer.com/article/10.1007/s11030-024-10952-3'), ('Source Code', 'https://github.com/PGlab-NIPER/MTB_Permeability'), ('License', 'GPL-3.0-or-later'), ('S3', 'https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos3ujl.zip'), ('DockerHub', 'https://hub.docker.com/r/ersiliaos/eos3ujl'), ('Docker Architecture', ['AMD64', 'ARM64'])]), 'model_id': 'eos3ujl', 'Slug': 'mtb-permeability', 'api_list': ['run']}

15:08:44 | DEBUG    | Activation done
15:08:44 | DEBUG    | Packing command successfully run inside eos3ujl conda environment
15:08:44 | DEBUG    | Creating model symlink bundle > dest
15:08:44 | DEBUG    | Creating symlink from /home/dee/eos/repository/eos3ujl/20241023-0f8d918d-c70b-4966-a690-b5bea6328fae/model
15:08:44 | DEBUG    | Creating symlink to /home/dee/eos/dest/eos3ujl/model
15:08:44 | INFO     | Could not create symbolic link from /home/dee/eos/dest/eos3ujl/data.h5 to /home/dee/eos/isaura/lake/eos3ujl_public.h5
15:08:44 | DEBUG    | Symlinks created
15:08:44 | DEBUG    | Getting model card of eos3ujl
15:08:44 | DEBUG    | Trying to get metadata from: /home/dee/eos/dest/eos3ujl
15:08:45 | DEBUG    | Card saved at /home/dee/eos/dest/eos3ujl/card.json
15:08:45 | DEBUG    | Saving slug mtb-permeability
15:08:45 | DEBUG    | Checking that autoservice works
15:08:45 | DEBUG    | Setting BentoML AutoService for eos3ujl
15:08:45 | DEBUG    | No service class provided, deciding automatically
15:08:45 | DEBUG    | No service class file exists in /home/dee/eos/repository/eos3ujl/20241023-0f8d918d-c70b-4966-a690-b5bea6328fae/service_class.txt
15:08:45 | DEBUG    | Pack method is: fastapi
15:08:45 | DEBUG    | Pack method is: fastapi
15:08:45 | DEBUG    | Setting virtual environment at /home/dee/eos/dest/eos3ujl
15:08:45 | DEBUG    | Pack method is: fastapi
15:08:46 | DEBUG    | Pack method is: fastapi
15:08:46 | DEBUG    | Service class: conda
15:08:46 | DEBUG    | Getting APIs from list file
15:08:46 | DEBUG    | Getting APIs from FastAPI
15:08:46 | DEBUG    | Sniffing model
15:08:46 | DEBUG    | Getting model size
15:08:46 | DEBUG    | Model size is 148.82936191558838 MB
15:08:46 | DEBUG    | Fetching eos3ujl done in time: 0:00:49.712118s
15:08:46 | INFO     | Fetching eos3ujl done successfully: 0:00:49.712118
15:08:46 | DEBUG    | Writing model source to file
👍 Model eos3ujl fetched successfully!
DhanshreeA commented 2 weeks ago

Closing due to issue not being reproducible.