Merge pull request #72 from yuqiyuqitan/docker_update

Docker update
yuqiyuqitan · Jan 27, 2025 · 6fbf9e5 · 6fbf9e5
2 parents 2818d2c + a8eab8a
commit 6fbf9e5
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Showing 8 changed files with 15 additions and 341 deletions.
diff --git a/Docker/old/Dockerfile b/Docker/old/Dockerfile
diff --git a/Docker/old/SPACEc_cpu b/Docker/old/SPACEc_cpu
diff --git a/Docker/old/SPACEc_gpu b/Docker/old/SPACEc_gpu
diff --git a/Docker/old/tutorial.Dockerfile b/Docker/old/tutorial.Dockerfile
diff --git a/Docker/old/tutorial_init.sh b/Docker/old/tutorial_init.sh
diff --git a/Docker/SPACEc_cpu → Docker/spacec_cpu_build.dockerfile b/Docker/SPACEc_cpu → Docker/spacec_cpu_build.dockerfile
@@ -1,6 +1,5 @@
 FROM debian:bullseye-slim
 
-# Fix (tzdata)
 ARG DEBIAN_FRONTEND=noninteractive
 
 # Update the package list and install dependencies
@@ -53,8 +52,8 @@ RUN mamba run -n spacec pip install networkx==3.2.* protobuf==3.20.0 numpy==1.24
 RUN mamba clean --all -f -y && \
     rm -rf /root/.cache/pip
 
-# Copy notebooks into the image
-COPY notebooks /notebooks
+# Copy notebooks into the image YOU CAN CHANGE THIS TO COPY YOUR OWN NOTEBOOKS
+COPY ../notebooks /notebooks
 WORKDIR /notebooks
 
 # Expose relevant ports

diff --git a/Docker/SPACEc_gpu → Docker/spacec_gpu_build.dockerfile b/Docker/SPACEc_gpu → Docker/spacec_gpu_build.dockerfile
@@ -1,9 +1,5 @@
-FROM nvidia/cuda:11.2.2-cudnn8-runtime
+FROM debian:bullseye-slim
 
-# Add the NVIDIA package repositories GPG key
-RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub
-
-# Fix (tzdata)
 ARG DEBIAN_FRONTEND=noninteractive
 
 # Update the package list and install dependencies
@@ -46,6 +42,8 @@ RUN apt-get update && \
     apt-get install -y build-essential gcc && \
     rm -rf /var/lib/apt/lists/*
 
+RUN mamba install -n spacec -c conda-forge cudatoolkit=11.2.2 cudnn=8.1.0.77 -y
+
 # Install SPACEc
 RUN mamba run -n spacec pip install spacec
 
@@ -55,6 +53,9 @@ RUN mamba run -n spacec pip install networkx==3.2.* protobuf==3.20.0 numpy==1.24
 # Install PyTorch
 RUN mamba run -n spacec pip install torch==1.12.1+cu113 torchvision==0.13.1+cu113 torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cu113
 
+# UNCOMMENT THE FOLLOWING LINES IF YOU ARE USING STELLAR
+# RUN mamba run -n spacec pip install torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.12.0+cu113.html
+
 # Install RAPIDS and related packages
 RUN mamba install -n spacec -c rapidsai -c conda-forge -c nvidia rapids=24.02 -y && \
     mamba run -n spacec pip install rapids-singlecell==0.9.5 pandas==1.5.3
@@ -63,8 +64,8 @@ RUN mamba install -n spacec -c rapidsai -c conda-forge -c nvidia rapids=24.02 -y
 RUN mamba clean --all -f -y && \
     rm -rf /root/.cache/pip
 
-# Copy notebooks into the image
-COPY notebooks /notebooks
+# Copy notebooks into the image YOU CAN CHANGE THIS TO COPY YOUR OWN NOTEBOOKS
+COPY ../notebooks /notebooks
 WORKDIR /notebooks
 
 # Expose relevant ports