Merge pull request #47 from dealii/cleanup

Cleanup and new versions of symengine and CGAL.
dealii · Feb 28, 2025 · 317d80e · 317d80e
2 parents 5310a0f + 80912f4
commit 317d80e
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diff --git a/.github/workflows/dependencies.yml b/.github/workflows/dependencies.yml
@@ -17,12 +17,12 @@ jobs:
       fail-fast: false
       matrix:
         system:
-          - ubuntu_version: "focal"
-            dealii_version: 9.4.0-1ubuntu2~bpo20.04.1~ppa1
-            tag: focal-v9.5.1
-          - ubuntu_version: "jammy"
-            dealii_version: 9.4.0-1ubuntu2~bpo22.04.1~ppa1
-            tag: jammy-v9.5.1
+          - ubuntu_version: jammy
+            dealii_version: 9.6.0-1~ubuntu22.04.1~ppa1
+            tag: jammy-v9.6.0
+          - ubuntu_version: noble
+            dealii_version: 9.6.0-1~ubuntu24.04.1~ppa1
+            tag: noble-v9.6.0
 
     steps:
       - name: Checkout code
@@ -47,7 +47,7 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Build and push Docker image of dependencies ${{ matrix.system.ubuntu_version }}
+      - name: Build and push Docker image of dealii/dependencies:${{ matrix.system.ubuntu_version }}
         uses: docker/build-push-action@v5
         with:
           context: ./dependencies/
@@ -56,8 +56,10 @@ jobs:
           build-args: |
             IMG=${{ matrix.system.ubuntu_version }}
             VERSION=${{ matrix.system.dealii_version}}
+            REPO=ppa:ginggs/deal.ii-9.6.0-backports 
+            CLANG_VERSION=16
           platforms: linux/arm64,linux/amd64
           push: true
           tags: |
             ghcr.io/${{ github.repository }}:${{ matrix.system.tag }}
-            dealii/dependencies:${{ matrix.tag }}
+            dealii/dependencies:${{ matrix.system.tag }}
diff --git a/Makefile b/Makefile
@@ -15,136 +15,28 @@
 
 # Use no-cache option to force rebuild
 # DOCKER_BUILD=docker build --no-cache
-DOCKER_BUILD=docker build
+DOCKER_BUILD=docker buildx build --push --platform linux/amd64,linux/arm64 --output type=registry
+DOCKER_BUILD=docker buildx build --push --platform linux/arm64 --output type=registry
 
-# Repos:
-# ppa:ginggs/deal.ii-backports
-# ppa:ginggs/deal.ii-9.2.0-backports
-
-# Version 9.1.1
-v9.1.1-bionic:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.1.1-bionic \
-		--build-arg VERSION=9.1.1-2~ubuntu18.04.1~ppa1 \
-		--build-arg REPO=ppa:ginggs/deal.ii-backports \
-		bionic
-	docker push dealii/dealii:v9.1.1-bionic
-
-# Version 9.2.0 - Change to the correct package when it is available
-v9.2.0-bionic:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.2.0-bionic \
-		--build-arg VERSION=9.2.0-1~ubuntu18.04.1~ppa1 \
-		--build-arg REPO=ppa:ginggs/deal.ii-9.2.0-backports \
-		bionic
-	docker push dealii/dealii:v9.2.0-bionic
-
-v9.2.0-focal:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.2.0-focal \
-		--build-arg VERSION=9.2.0-1~ubuntu20.04.1~ppa1 \
-		--build-arg REPO=ppa:ginggs/deal.ii-9.2.0-backports \
-		--build-arg CLANG_VERSION=6 \
-		--build-arg CLANG_REPO=https://github.com/dealii/dealii/releases/download/v9.0.0/ \
-		focal
-	docker push dealii/dealii:v9.2.0-focal
-
-v9.3.0-focal:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.3.0-focal \
-		--build-arg VERSION=9.3.0-1~ubuntu20.04.1~ppa1 \
-		--build-arg REPO=ppa:ginggs/deal.ii-9.3.0-backports \
-		--build-arg CLANG_VERSION=11 \
-		--build-arg CLANG_REPO=https://github.com/dealii/dealii/releases/download/v9.3.0/ \
-		focal
-	docker push dealii/dealii:v9.3.0-focal
-	docker tag dealii/dealii:v9.3.0-focal dealii/dealii:latest
-	docker push dealii/dealii:latest
-
-v9.4.0-focal:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.4.0-focal \
-		--build-arg VERSION=9.4.0-1ubuntu2~bpo20.04.1~ppa1 \
-		--build-arg REPO=ppa:ginggs/deal.ii-9.4.0-backports \
-		--build-arg CLANG_VERSION=11 \
-		--build-arg CLANG_REPO=https://github.com/dealii/dealii/releases/download/v9.3.0/ \
-		focal
-	docker push dealii/dealii:v9.4.0-focal
-	docker tag dealii/dealii:v9.4.0-focal dealii/dealii:latest
-	docker push dealii/dealii:latest
-
-v9.4.0-jammy:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.4.0-jammy \
-		--build-arg VERSION=9.4.0-1ubuntu2~bpo22.04.1~ppa1 \
-		--build-arg REPO=ppa:ginggs/deal.ii-9.4.0-backports \
-		--build-arg CLANG_VERSION=11 \
-		--build-arg CLANG_REPO=https://github.com/dealii/dealii/releases/download/v9.3.0/ \
-		jammy
-	docker push dealii/dealii:v9.4.0-jammy
-
-dependencies-focal-v9.2.0:
-	$(DOCKER_BUILD) -t dealii/dependencies:focal-v9.2.0 \
- 		--build-arg IMG=focal \
-		--build-arg VERSION=9.2.0-1~ubuntu20.04.1~ppa1 \
-		--build-arg REPO=ppa:ginggs/deal.ii-9.2.0-backports \
-		--build-arg CLANG_VERSION=6 \
-		--build-arg CLANG_REPO=https://github.com/dealii/dealii/releases/download/v9.0.0/ \
-		dependencies
-	docker push dealii/dependencies:focal-v9.2.0
-
-dependencies-focal-v9.3.0:
-	$(DOCKER_BUILD) -t dealii/dependencies:focal-v9.3.0 \
- 		--build-arg IMG=focal \
-		--build-arg VERSION=9.3.0-1~ubuntu20.04.1~ppa1 \
-		--build-arg REPO=ppa:ginggs/deal.ii-9.3.0-backports \
-		--build-arg CLANG_VERSION=11 \
-		--build-arg CLANG_REPO=https://github.com/dealii/dealii/releases/download/v9.3.0/ \
-		dependencies
-	docker tag dealii/dependencies:focal dealii/dependencies:focal-v9.3.0
-	docker push dealii/dependencies:focal-v9.3.0
-
-dependencies-focal:
-	$(DOCKER_BUILD) -t dealii/dependencies:focal \
-		--build-arg IMG=focal \
-                --build-arg VERSION=9.4.0-1ubuntu2~bpo20.04.1~ppa1 \
-                --build-arg REPO=ppa:ginggs/deal.ii-9.4.0-backports \
-                --build-arg CLANG_VERSION=11 \
-                --build-arg CLANG_REPO=https://github.com/dealii/dealii/releases/download/v9.3.0/ \
-                dependencies
-	docker push dealii/dependencies:focal
 
 dependencies-jammy:
-	$(DOCKER_BUILD) -t dealii/dependencies:jammy \
+	$(DOCKER_BUILD) \
+		-t dealii/dependencies:jammy \
+		-t dealii/dependencies:jammy-v9.6.0 \
 		--build-arg IMG=jammy \
-                --build-arg VERSION=9.4.0-1ubuntu2~bpo22.04.1~ppa1 \
-                --build-arg REPO=ppa:ginggs/deal.ii-9.4.0-backports \
-                --build-arg CLANG_VERSION=11 \
-                --build-arg CLANG_REPO=https://github.com/dealii/dealii/releases/download/v9.3.0/ \
+                --build-arg VERSION=9.6.0-1~ubuntu22.04.1~ppa1 \
+                --build-arg REPO=ppa:ginggs/deal.ii-9.6.0-backports \
                 dependencies
-	docker push dealii/dependencies:jammy
-	docker tag dealii/dependencies:jammy dealii/dependencies:latest
-	docker tag dealii/dependencies:jammy dealii/dependencies:jammy-v9.4.0
-	docker push dealii/dependencies:latest
-	docker push dealii/dependencies:jammy-v9.4.0
-
-v9.4.2-focal:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.4.2-focal \
-		--build-arg IMG=focal \
-		--build-arg VER=v9.4.2 \
-		--build-arg PROCS=80 \
-		github
-	docker push dealii/dealii:v9.4.2-focal
 
-v9.4.2-jammy:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.4.2-jammy \
-		--build-arg IMG=jammy \
-		--build-arg VER=v9.4.2 \
-		--build-arg PROCS=80 \
-		github
-	docker push dealii/dealii:v9.4.2-jammy
-
-v9.5.0-focal:
-	$(DOCKER_BUILD) -t dealii/dealii:v9.5.0-focal \
-                --build-arg IMG=focal \
-                --build-arg VER=v9.5.0 \
-                --build-arg PROCS=12 \
-                github
-	docker push dealii/dealii:v9.5.0-focal
+dependencies-noble:
+	$(DOCKER_BUILD) \
+		-t dealii/dependencies:noble \
+		-t dealii/dependencies:noble-v9.6.0 \
+		-t dealii/dependencies:latest \
+		--build-arg IMG=noble \
+		--build-arg VERSION=9.6.0-1~ubuntu24.04.1~ppa1 \
+		--build-arg REPO=ppa:ginggs/deal.ii-9.6.0-backports \
+		dependencies
 
 v9.5.0-jammy:
 	$(DOCKER_BUILD) -t dealii/dealii:v9.5.0-jammy \
@@ -156,13 +48,20 @@ v9.5.0-jammy:
 	docker tag dealii/dealii:v9.5.0-jammy dealii/dealii:latest
 	docker push dealii/dealii:latest
 
-all: dependencies-focal v9.5.0-focal dependencies-jammy v9.5.0-jammy 
+v9.6.2-noble:
+	$(DOCKER_BUILD) -t dealii/dealii:v9.6.2-noble \
+		--build-arg IMG=noble \
+		--build-arg VER=v9.6.2 \
+		--build-arg PROCS=12 \
+		github
+	docker push dealii/dealii:v9.6.2-noble
+	docker tag dealii/dealii:v9.6.2-noble dealii/dealii:latest
+	docker push dealii/dealii:latest
+
+all: dependencies-noble v9.6.2-noble
 
 .PHONY: all \
-	v9.1.1-bionic v9.2.0-bionic \
-	v9.2.0-focal v9.3.0-focal v9.4.0-focal v9.4.1-focal v9.4.2-focal \
-	v9.5.0-focal \
-	v9.4.0-jammy v9.4.1-jammy v9.4.2-jammy \
+	dependencies-jammy \
+	dependencies-noble \
 	v9.5.0-jammy \
-	dependencies-focal-v9.2.0 dependencies-focal-v9.3.0 dependencies-focal \
-	dependencies-jammy
+	v9.6.2-noble
diff --git a/README.md b/README.md
@@ -8,27 +8,32 @@ Images are tagged with the ubuntu distribution they are based on.
 
 You can pull any of the images from dockerhub using (for example)
 
-    docker pull dealii/dealii:v9.5.0-jammy
+    docker pull dealii/dealii:v9.6.0-noble
 
 after which you could run an interactive shell in it:
 
-    docker run -i -t dealii/dealii:v9.5.0-jammy
+    docker run -i -t dealii/dealii:v9.6.0-noble
 
 This will drop you in an isolated environment where you can experiment with deal.II.
 
 Versions of interest:
-- ``dealii/dealii:v9.5.0-jammy`` - deal.II v9.5.0, Ubuntu 22.04
-- ``dealii/dealii:v9.5.0-focal`` - deal.II v9.5.0, Ubuntu 20.04
-- ``dealii/dealii:v9.4.2-jammy`` - deal.II v9.4.2, Ubuntu 22.04
-- ``dealii/dealii:v9.4.2-focal`` - deal.II v9.4.2, Ubuntu 20.04
 
-A list of all available images is here: 
+- ``dealii/dealii:v9.6.0-noble`` - deal.II v9.6.0, Ubuntu 24.04
+- ``dealii/dealii:v9.6.0-jammy`` - deal.II v9.6.0, Ubuntu 22.04
 
-https://hub.docker.com/r/dealii/dealii/tags/
+A list of all available images is here:
+
+<https://hub.docker.com/r/dealii/dealii/tags/>
 
 In addition there are images that only contain the deal.II dependencies, but
 not the library itself. These images are helpful to compile your own version
 of deal.II. All images containing only deal.II dependencies can be found at:
 
-https://hub.docker.com/r/dealii/dependencies/tags/
+<https://hub.docker.com/r/dealii/dependencies/tags/>
+
+# For developers
 
+If you want to update the dependencies image, open a pull request with the
+updated Dockerfile in the `dependencies` directory. The CI will build the image
+and push it to dockerhub. Notice that the image is built for all supported
+Ubuntu versions and tagged accordingly. The CI needs to be run manually.
diff --git a/dependencies/Dockerfile b/dependencies/Dockerfile
@@ -1,12 +1,9 @@
-ARG IMG=jammy
+ARG IMG=noble
 
 FROM ubuntu:$IMG
 
-LABEL maintainer="luca.heltai@gmail.com"
-
-ARG VERSION=9.4.0-1ubuntu2~bpo22.04.1~ppa1
-ARG REPO=ppa:ginggs/deal.ii-9.4.0-backports
-ARG CLANG_VERSION=11
+ARG VERSION=9.6.0-1~ubuntu24.04.1~ppa1
+ARG REPO=ppa:ginggs/deal.ii-9.6.0-backports
 
 USER root
 ENV DEBIAN_FRONTEND=noninteractive 
@@ -15,7 +12,6 @@ RUN apt-get update && apt-get install -y software-properties-common \
     && add-apt-repository $REPO \
     && apt-get update && \
     apt-get install -y \
-    clang-format-${CLANG_VERSION} \
     git \
     libboost-dev \
     libboost-python-dev \
@@ -42,8 +38,14 @@ RUN apt-get update && apt-get install -y software-properties-common \
     && rm -rf /var/lib/apt/lists/* \
     && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8
 
-ENV LANGUAGE en_US:en  
-ENV LC_ALL en_US.UTF-8
+ENV LANGUAGE=en_US:en  
+ENV LC_ALL=en_US.UTF-8
+
+RUN wget https://raw.githubusercontent.com/dealii/dealii/refs/heads/master/contrib/utilities/download_clang_format \
+    && chmod +x download_clang_format \
+    && ./download_clang_format \
+    && mv programs/clang-16/bin/clang-format /usr/local/bin/ \
+    && rm -rf download_clang_format programs
 
 # Symengine
 RUN cd /usr/src && \
@@ -56,7 +58,6 @@ RUN cd /usr/src && \
     -DBUILD_TESTS=off \
     -DINTEGER_CLASS=flint \
     -DWITH_BOOST=on  \
-    -DWITH_GMP=on \
     -DWITH_LLVM=on \
     -DWITH_MPC=on \
     -DWITH_MPFR=on \
@@ -67,10 +68,10 @@ RUN cd /usr/src && \
 
 # CGAL
 RUN cd /usr/src && \
-    wget https://github.com/CGAL/cgal/releases/download/v5.5.2/CGAL-5.5.2.tar.xz && \
-    tar xvf CGAL-5.5.2.tar.xz && \
-    rm -rf CGAL-5.5.2.tar.xz  && \
-    cd CGAL-5.5.2/  && \ 
+    wget https://github.com/CGAL/cgal/releases/download/v5.6.2/CGAL-5.6.2.tar.xz && \
+    tar xvf CGAL-5.6.2.tar.xz && \
+    rm -rf CGAL-5.6.2.tar.xz  && \
+    cd CGAL-5.6.2/  && \ 
     mkdir build && cd build && \
     cmake -GNinja .. -DCMAKE_INSTALL_PREFIX=/usr/ && \
     ninja install && cd ../ && rm -rf build 
@@ -83,28 +84,28 @@ RUN cd /usr/src && \
     cd vtk-v9.4.0/ && \ 
     mkdir build && cd build && \
     cmake -GNinja .. \
-        -DCMAKE_INSTALL_PREFIX=/usr/ \
-        -DCMAKE_BUILD_TYPE=Release \
-        -DBUILD_SHARED_LIBS=ON \
-        -DBUILD_TESTING=OFF \
-        -DVTK_EXTRA_COMPILER_WARNINGS=OFF \
-        -DVTK_GROUP_ENABLE_Imaging=DONT_WANT \
-        -DVTK_GROUP_ENABLE_MPI=DONT_WANT \
-        -DVTK_GROUP_ENABLE_Qt=DONT_WANT \
-        -DVTK_GROUP_ENABLE_Rendering=DONT_WANT \
-        -DVTK_GROUP_ENABLE_StandAlone=WANT \
-        -DVTK_GROUP_ENABLE_Views=DONT_WANT \
-        -DVTK_GROUP_ENABLE_Web=DONT_WANT \
-        -DVTK_USE_MPI=OFF \
-        -DVTK_WRAP_JAVA=OFF \
-        -DVTK_WRAP_PYTHON=OFF && \
+    -DCMAKE_INSTALL_PREFIX=/usr/ \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DBUILD_SHARED_LIBS=ON \
+    -DBUILD_TESTING=OFF \
+    -DVTK_EXTRA_COMPILER_WARNINGS=OFF \
+    -DVTK_GROUP_ENABLE_Imaging=DONT_WANT \
+    -DVTK_GROUP_ENABLE_MPI=DONT_WANT \
+    -DVTK_GROUP_ENABLE_Qt=DONT_WANT \
+    -DVTK_GROUP_ENABLE_Rendering=DONT_WANT \
+    -DVTK_GROUP_ENABLE_StandAlone=WANT \
+    -DVTK_GROUP_ENABLE_Views=DONT_WANT \
+    -DVTK_GROUP_ENABLE_Web=DONT_WANT \
+    -DVTK_USE_MPI=OFF \
+    -DVTK_WRAP_JAVA=OFF \
+    -DVTK_WRAP_PYTHON=OFF && \
     ninja install && cd ../ && rm -rf build
 
 RUN locale-gen en_US.UTF-8  
-ENV LANG en_US.UTF-8  
+ENV LANG=en_US.UTF-8  
 
 RUN ldconfig
-ENV PYTHONPATH "/usr/local/lib/python3.8/site-packages/"
+ENV PYTHONPATH="/usr/local/lib/python3.8/site-packages/"
 
 # add and enable the default user
 ARG USER=dealii
@@ -115,7 +116,7 @@ RUN adduser $USER sudo; echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
 # make sure everything is in place
 RUN chown -R $USER:$USER /home/$USER
 USER $USER
-ENV HOME /home/$USER
-ENV USER $USER
-ENV OMPI_MCA_btl "^vader"
+ENV HOME=/home/$USER
+ENV USER=$USER
+ENV OMPI_MCA_btl="^vader"
 WORKDIR $HOME
diff --git a/github/Dockerfile b/github/Dockerfile
@@ -15,7 +15,6 @@ RUN cd /usr/src \
     && cmake -GNinja \
     -DCMAKE_PREFIX_PATH="/usr/lib/x86_64-linux-gnu/hdf5/openmpi;/usr/include/hdf5/openmpi" \
     -DDEAL_II_ALLOW_AUTODETECTION=OFF \
-    -DDEAL_II_COMPILE_EXAMPLES=OFF \
     -DDEAL_II_COMPONENT_PYTHON_BINDINGS=ON \
     -DCMAKE_CXX_FLAGS="-std=c++17" \
     -DDEAL_II_WITH_64BIT_INDICES=OFF \