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Fix broken Docker recipe and update dependencies #7

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merged 2 commits into from
Dec 13, 2023
Merged

Fix broken Docker recipe and update dependencies #7

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878d71c
Fix broken Dockerfile due to old jax
tuncK Nov 23, 2023
72ef870
Upgrade cuda to 12.2
tuncK Nov 23, 2023
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35 changes: 18 additions & 17 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
FROM nvidia/cuda:11.8.0-cudnn8-runtime-ubuntu22.04

# CUDA12 and tensorflow 2.12 in pypi are incompatible
# FROM nvidia/cuda:12.1.1-cudnn8-runtime-ubuntu22.04
FROM nvidia/cuda:12.2.2-cudnn8-runtime-ubuntu22.04
# ^ If doing an upgrade, ensure cuda/cudnn versions are supported by the
# Tensorflow versions specified below.

# Version of python to be installed and used
ENV PYTHON_VERSION=3.10
Expand Down Expand Up @@ -85,8 +84,8 @@ RUN python$PYTHON_VERSION -m pip install \
bqplot==0.12.39 \
elyra==3.15.0 \
galaxy-ie-helpers==0.2.7 \
jax==0.3.25 \
jaxlib==0.3.25 \
jax==0.4.20\
jaxlib==0.4.20\
jupyter_server==1.24.0 \
jupyterlab==3.6.5 \
jupyterlab-nvdashboard==0.8.0 \
Expand All @@ -99,30 +98,32 @@ RUN python$PYTHON_VERSION -m pip install \
nbclassic==1.0.0 \
nibabel==5.1.0 \
numba==0.57.1 \
onnx==1.12.0 \
onnx==1.15.0 \
onnx-tf==1.10.0 \
onnxruntime==1.15.1 \
opencv-python==4.7.0.72 \
tensorflow-cpu==2.11.0 \
onnxruntime==1.16.3 \
opencv-python==4.8.1.78 \
tensorflow-cpu==2.15.0 \
tensorrt==8.6.1 \
tf2onnx==1.14.0 \
tf2onnx==1.15.1 \
skl2onnx==1.14.1 \
scikit-image==0.21.0 \
scikit-image==0.22.0 \
seaborn==0.12.2 \
voila==0.4.1 \
"colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" && \
&& \
# As of Nov 2023, colabfold requires 0.3.25 <= jax < 0.4.0, which leads to build errors.
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@anuprulez you need to decide if we can remove that.

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Strictly speaking, tensorflow errors have been an issue for the past release as well and we now have another IT with a separate container (v. 0.2) that provides the colabfold service.

Option 2: If we want to keep it, I could try to provide colabfold out of a conda env installed in this container so that Tensorflow et al. still work.

@anuprulez ?

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Some how I do not get this email even though I am subscribed to this repo. Not even in my spam. Sorry for that!

I will have a look at it today :)

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I agree that Colabfold has issues with the latest versions of TensorFlow, maybe with CUDA as well. We can remove it from v0.3 and later versions of this Docker container. We already have it on v0.2 in case it is needed for my defense.
@tuncK @bgruening

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@bgruening, shall we merge this?

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Sure.

#"colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" && \
rm -r ~/.cache/pip

RUN sed -i -e "s/jax.tree_flatten/jax.tree_util.tree_flatten/g" $PYTHON_LIB_PATH/alphafold/model/mapping.py && \
sed -i -e "s/jax.tree_unflatten/jax.tree_util.tree_unflatten/g" $PYTHON_LIB_PATH/alphafold/model/mapping.py
#RUN sed -i -e "s/jax.tree_flatten/jax.tree_util.tree_flatten/g" $PYTHON_LIB_PATH/alphafold/model/mapping.py && \
# sed -i -e "s/jax.tree_unflatten/jax.tree_util.tree_unflatten/g" $PYTHON_LIB_PATH/alphafold/model/mapping.py

# Cache the CPU-optimised version of tensorflow
RUN mv $PYTHON_LIB_PATH/tensorflow $PYTHON_LIB_PATH/tensorflow-CPU-cached

# Install GPU version of tensorflow
RUN python$PYTHON_VERSION -m pip install \
tensorflow==2.11.0 \
tensorflow_probability==0.20.1 && \
tensorflow==2.15.0 \
tensorflow_probability==0.23.0 && \
rm -r ~/.cache/pip

# Cache the GPU version of tensorflow
Expand Down