aws-samples / aws-samples/amazon-sagemaker-protein-folding-workflows

alphafold docker build failing

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Description

...
Step 7/20 : RUN wget -q -P /tmp https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
---> Running in d87251b97d57
PREFIX=/opt/conda
Unpacking payload ...

Installing base environment...

Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
Removing intermediate container d87251b97d57
---> 7e4cbdfb38dc
Step 8/20 : ENV PATH="/opt/conda/bin:$PATH"
---> Running in 2156b4e87d66
Removing intermediate container 2156b4e87d66
---> 19b9006ce9d0
Step 9/20 : RUN conda install -qy conda==4.13.0 && conda install -y -c conda-forge openmm=7.5.1 cudatoolkit==${CUDA_VERSION} pdbfixer pip python=3.8 && conda clean --all --force-pkgs-dirs --yes
---> Running in 02478a06183c
Channels:

  • defaults
    Platform: linux-64
    Collecting package metadata (repodata.json): ...working... done
    Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:

  • package conda-4.13.0-py310h06a4308_0 requires python >=3.10,<3.11.0a0, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ conda ==4.13.0 * is installable with the potential options
│ ├─ conda 4.13.0 would require
│ │ └─ python >=3.10,<3.11.0a0 *, which can be installed;
│ ├─ conda 4.13.0 would require
│ │ └─ python >=3.7,<3.8.0a0 *, which can be installed;
│ ├─ conda 4.13.0 would require
│ │ └─ python >=3.8,<3.9.0a0 , which can be installed;
│ └─ conda 4.13.0 would require
│ └─ python >=3.9,<3.10.0a0 , which can be installed;
└─ pin on python 3.12.
=
* is not installable because it requires
└─ python =3.12 *, which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:

  • python=3.12

The command '/bin/bash -o pipefail -c conda install -qy conda==4.13.0 && conda install -y -c conda-forge openmm=7.5.1 cudatoolkit==${CUDA_VERSION} pdbfixer pip python=3.8 && conda clean --all --force-pkgs-dirs --yes' returned a non-zero code: 1

[Container] 2025/02/10 13:40:18.240894 Command did not exit successfully docker build -t $IMAGE_REPO_NAME:$IMAGE_TAG . --file ./Dockerfile.alphafold exit status 1
[Container] 2025/02/10 13:40:18.249050 Phase complete: BUILD State: FAILED
[Container] 2025/02/10 13:40:18.249069 Phase context status code: COMMAND_EXECUTION_ERROR Message: Error while executing command: docker build -t $IMAGE_REPO_NAME:$IMAGE_TAG . --file ./Dockerfile.alphafold. Reason: exit status 1
[Container] 2025/02/10 13:40:18.302258 Entering phase POST_BUILD
[Container] 2025/02/10 13:40:18.303316 Running command echo Build completed on date
Build completed on Mon Feb 10 13:40:18 UTC 2025

[Container] 2025/02/10 13:40:18.310577 Running command echo Pushing the Docker image...
Pushing the Docker image...

[Container] 2025/02/10 13:40:18.316715 Running command docker push $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$IMAGE_REPO_NAME:$IMAGE_TAG
The push refers to repository [729286525078.dkr.ecr.us-east-1.amazonaws.com/sagemaker-studio-alphafold]
An image does not exist locally with the tag: 729286525078.dkr.ecr.us-east-1.amazonaws.com/sagemaker-studio-alphafold

[Container] 2025/02/10 13:40:18.346486 Command did not exit successfully docker push $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$IMAGE_REPO_NAME:$IMAGE_TAG exit status 1
[Container] 2025/02/10 13:40:18.350578 Phase complete: POST_BUILD State: FAILED
[Container] 2025/02/10 13:40:18.350597 Phase context status code: COMMAND_EXECUTION_ERROR Message: Error while executing command: docker push $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$IMAGE_REPO_NAME:$IMAGE_TAG. Reason: exit status 1

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with Dockerfile.alphafold and reproduce the failure using docker build -t $IMAGE_REPO_NAME:$IMAGE_TAG . --file ./Dockerfile.alphafold. Read the conda installation step and its Python 3.8 request alongside the reported Python 3.12 pin conflict. Done means the image builds successfully and the subsequent ECR push no longer fails because the image is missing.

Written by the indexing model from the issue text.

Assessment

Tech stack
aws, docker, python
Domain
build-system, cloud, devops
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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