updated pytorch and some other packages on top of image with cuda <= …

…2.12

build-local-docker.sh

@@ -10,17 +10,17 @@ echo "tensorflow_version=$tensorflow_version"
 echo "tag=$tag"
 echo "image=$image"
 
-## CPU version
+### CPU version
 #DOCKER_BUILDKIT=1 docker buildx build --no-cache -t ghcr.io/pharmbio/$image:${tag} \
 #             --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-jupyter \
 #             -f docker/env.cuda.Dockerfile . || exit 1
+#
 
 # GPU version
-DOCKER_BUILDKIT=1 docker buildx build --no-cache -t ghcr.io/pharmbio/$image:${tag}-gpu \
+DOCKER_BUILDKIT=1 docker buildx build -t ghcr.io/pharmbio/$image:${tag}-gpu \
              --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-gpu-jupyter \
              -f docker/env.cuda.Dockerfile . || exit 1
 
-echo Push image with command:
+echo "Push with this command"
 echo docker push "ghcr.io/pharmbio/$image:${tag}-gpu"
 
-#docker push "ghcr.io/pharmbio/$image:$tag-devel"

build-push-local-docker.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+#set -xv
+
+git_branch="$(git branch --show-current)"
+tag=$git_branch
+tensorflow_version="${git_branch#tf-}" # remove prefix
+tensorflow_version="${tensorflow_version%-*}" # remove suffix
+image="pharmbio-notebook"
+echo "tensorflow_version=$tensorflow_version"
+echo "tag=$tag"
+echo "image=$image"
+
+## CPU version
+DOCKER_BUILDKIT=1 docker buildx build --no-cache -t ghcr.io/pharmbio/$image:${tag} \
+             --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-jupyter \
+             -f docker/env.cuda.Dockerfile . || exit 1
+
+docker push "ghcr.io/pharmbio/$image:${tag}"
+
+# GPU version
+DOCKER_BUILDKIT=1 docker buildx build -t ghcr.io/pharmbio/$image:${tag}-gpu \
+             --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-gpu-jupyter \
+             -f docker/env.cuda.Dockerfile . || exit 1
+
+echo docker push "ghcr.io/pharmbio/$image:${tag}-gpu"
+

docker/env.cuda.Dockerfile

@@ -55,17 +55,12 @@ COPY requirements.txt .
 RUN python3 -m pip install --no-cache-dir --upgrade pip && \
     python3 -m pip install --no-cache-dir -r requirements.txt
 
-RUN echo "Installing for CUDA framework" 
+RUN echo "Installing for CUDA framework"
 RUN python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cu121 \ 
                 torch==2.4.1 \
                 torchvision \
                 torchaudio
 
-
-# RUN python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cu121 \ 
-#         torch==2.2.1 \
-#         torchvision \
-#         torchaudio;
 # RUN python3 -m pip install \
 #         --extra-index-url=https://pypi.nvidia.com \
 #         cudf-cu12==24.6.* dask-cudf-cu12==24.6.* cuml-cu12==24.6.* \
@@ -74,8 +69,6 @@ RUN python3 -m pip install --no-cache-dir --index-url https://download.pytorch.o
 #         raft-dask-cu12==24.6.* cuvs-cu12==24.6.*; 
 
 
-
-
 # Add pharmbio templates, examples and misc
 #WORKDIR /pharmbio/
 #COPY README.md .

requirements.txt

@@ -29,3 +29,4 @@ fastparquet
 #umap-learn
 #torchsummary
 scanpy
+jupyterlab