Upgrade all images (#215)

Description of changes: * migrate to Ubuntu 24.04, Debian 12 and Fedora 40 * install Kokkos libraries
espressomd · Apr 19, 2024 · 7843821 · 7843821
2 parents 3399039 + 2fc0dee
commit 7843821
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -9,7 +9,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        image: ['debian', 'fedora', 'ubuntu-22.04', 'ubuntu-wo-dependencies']
+        image:
+        - debian
+        - fedora
+        - ubuntu
+        - ubuntu-wo-dependencies
     steps:
     - uses: actions/checkout@main
     - name: Build and deploy

diff --git a/docker/Dockerfile-debian b/docker/Dockerfile-debian
@@ -1,29 +1,32 @@
-FROM debian:bullseye AS image_base
-RUN echo "deb http://deb.debian.org/debian bullseye-backports main" >> /etc/apt/sources.list && \
-    apt-get update && \
+FROM debian:bookworm AS image_base
+RUN apt-get update && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         apt-utils \
         build-essential \
-        curl \
+        cmake \
         ccache \
+        curl \
         cython3 \
         gdb \
         git \
-        libboost-dev libboost-serialization-dev libboost-mpi-dev libboost-filesystem-dev libboost-test-dev \
+        libboost-dev \
+        libboost-filesystem-dev \
+        libboost-mpi-dev \
+        libboost-serialization-dev \
+        libboost-test-dev \
         libfftw3-dev \
         libhdf5-openmpi-dev \
         libpython3-dev \
         openmpi-bin \
         python3 \
         python3-h5py \
         python3-numpy \
+        python3-packaging \
         python3-pip \
         python3-scipy \
         python3-setuptools \
         python3-vtk9 \
         vim && \
-    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends --target-release bullseye-backports \
-        cmake && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 

diff --git a/docker/Dockerfile-fedora b/docker/Dockerfile-fedora
@@ -1,4 +1,4 @@
-FROM fedora:36
+FROM fedora:40
 RUN dnf -y install \
   blas-devel \
   boost-devel \
@@ -7,6 +7,7 @@ RUN dnf -y install \
   cmake \
   environment-modules \
   fftw-devel \
+  fftw-mpich-devel \
   gcc \
   gcc-c++ \
   gdb \
@@ -18,8 +19,10 @@ RUN dnf -y install \
   python3 \
   python3-devel \
   python3-Cython \
+  python3-lxml \
   python3-numpy \
   python3-scipy \
+  python3-packaging \
   python3-pip \
   python3-setuptools \
   python3-h5py \

diff --git a/docker/Dockerfile-ubuntu b/docker/Dockerfile-ubuntu
@@ -0,0 +1,126 @@
+FROM ubuntu:noble
+RUN apt-get update && \
+    DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
+        apt-utils \
+        autoconf \
+        automake \
+        build-essential \
+        ccache \
+        clang-18 clang-tidy-18 clang-format-18 llvm-18 libclang-rt-18-dev \
+        cmake \
+        cmake-format \
+        curl \
+        cython3 \
+        doxygen \
+        ffmpeg \
+        gcc-12 g++-12 \
+        gcc-13 g++-13 \
+        gdb \
+        gfortran \
+        git \
+        gnupg \
+        graphviz \
+        ipython3 \
+        jq \
+        jupyter-client \
+        jupyter-core \
+        jupyter-nbconvert \
+        lcov \
+        libblas-dev \
+        libboost-dev \
+        libboost-filesystem-dev \
+        libboost-mpi-dev \
+        libboost-serialization-dev \
+        libboost-test-dev \
+        libdigest-sha-perl \
+        libfftw3-dev \
+        libfftw3-mpi-dev \
+        libgsl-dev \
+        libhdf5-openmpi-dev \
+        liblapack-dev \
+        libopenmpi-dev \
+        libthrust-dev \
+        libtool \
+        nvidia-cuda-toolkit \
+        openmpi-bin \
+        openssh-client \
+        perl \
+        pkg-config \
+        pre-commit \
+        python3 \
+        python3-dev \
+        pylint \
+        python3-coverage \
+        python3-dev \
+        python3-h5py \
+        python3-ipykernel \
+        python3-jinja2 \
+        python3-lxml \
+        python3-matplotlib \
+        python3-nbconvert \
+        python3-numpy \
+        python3-numpydoc \
+        python3-pint \
+        python3-pip \
+        python3-packaging \
+        python3-requests \
+        python3-scipy \
+        python3-setuptools \
+        python3-sympy \
+        python3-sphinx \
+        python3-sphinxcontrib.bibtex \
+        python3-tqdm \
+        python3-venv \
+        python3-vtk9 \
+        rsync \
+        texlive-base \
+        vim && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+COPY install-pfft.sh /tmp
+COPY install-scafacos.sh /tmp
+COPY install-kokkos.sh /tmp
+
+RUN sh /tmp/install-pfft.sh     && rm /tmp/install-pfft.sh && \
+    sh /tmp/install-scafacos.sh && rm /tmp/install-scafacos.sh && \
+    sh /tmp/install-kokkos.sh   && rm /tmp/install-kokkos.sh && \
+    ldconfig
+
+ENV NVIDIA_VISIBLE_DEVICES all
+ENV NVIDIA_DRIVER_CAPABILITIES compute,utility
+ENV JUPYTER_PLATFORM_DIRS 1
+
+COPY --chown=1000:1000 jupyter_nbconvert_config.json /tmp
+
+RUN userdel ubuntu && rm -rf /home/ubuntu && useradd -u 1000 -m espresso
+ENV HOME="/home/espresso"
+RUN echo | cpan && \
+    echo | cpan JSON::XS && \
+    chown -R espresso:espresso /home/espresso/.cpan/
+USER espresso
+ENV VIRTUAL_ENV "$HOME/venv"
+ENV PATH "$HOME/.local/bin:$VIRTUAL_ENV/bin:$PATH"
+RUN cd "${HOME}" && \
+  python3 -m venv --system-site-packages venv && \
+  . venv/bin/activate && \
+  python3 -m pip install --no-cache \
+    jupyterlab==4.0.13 \
+    pep8==1.7.1 \
+    autopep8==2.1.0 \
+    pycodestyle==2.11.1 \
+    sphinx-toggleprompt==0.5.2 && \
+  jupyter_config_root=$(jupyter --paths --json | jq ".config[0]") && \
+  jupyter_config_root=${jupyter_config_root#\"} && \
+  jupyter_config_root=${jupyter_config_root%\"} && \
+  jupyter_kernels_root=$(jupyter --paths --json | jq ".data[0]")/kernels && \
+  jupyter_kernels_root=${jupyter_kernels_root#\"} && \
+  jupyter_kernels_root=${jupyter_kernels_root%\"} && \
+  mkdir -p "${jupyter_config_root}" "${jupyter_kernels_root}" && \
+  mv "/tmp/jupyter_nbconvert_config.json" "${jupyter_config_root}/" && \
+  ln -s "${VIRTUAL_ENV}/share/jupyter/kernels/python3" "${jupyter_kernels_root}/python3" && \
+  deactivate && \
+  mkdir -p "${HOME}/.local/bin" && \
+  mkdir -p "${HOME}/.local/etc/alternatives" && \
+  mkdir -p "${HOME}/.local/var/lib/alternatives"
+WORKDIR /home/espresso
diff --git a/docker/Dockerfile-ubuntu-22.04 b/docker/Dockerfile-ubuntu-22.04
diff --git a/docker/Dockerfile-ubuntu-wo-dependencies b/docker/Dockerfile-ubuntu-wo-dependencies
@@ -1,4 +1,4 @@
-FROM ubuntu:jammy AS image_base
+FROM ubuntu:noble AS image_base
 RUN apt-get update && \
     DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
         apt-utils \
@@ -7,10 +7,14 @@ RUN apt-get update && \
         ccache \
         cmake \
         cython3 \
-        gcc-11 g++-11 \
+        gcc-13 g++-13 \
         gdb \
         git \
-        libboost-dev libboost-serialization-dev libboost-mpi-dev libboost-filesystem-dev libboost-test-dev \
+        libboost-dev \
+        libboost-filesystem-dev \
+        libboost-mpi-dev \
+        libboost-serialization-dev \
+        libboost-test-dev \
         libopenmpi-dev \
         openssh-client \
         openmpi-bin \
@@ -19,6 +23,7 @@ RUN apt-get update && \
         python3-h5py \
         python3-lxml \
         python3-numpy \
+        python3-packaging \
         python3-pip \
         python3-scipy \
         python3-setuptools \

diff --git a/docker/install-kokkos.sh b/docker/install-kokkos.sh
@@ -0,0 +1,15 @@
+#!/bin/sh
+
+set -e
+
+cd /tmp
+
+git clone -b 4.3.00 https://github.com/kokkos/kokkos
+cd kokkos/
+mkdir build
+cd build/
+cmake ..  -D Kokkos_ENABLE_CUDA=OFF -DKokkos_ENABLE_OPENMP=ON
+make -j $(nproc) install
+cd
+rm -r /tmp/kokkos
+ldconfig
diff --git a/docker/install-pfft.sh b/docker/install-pfft.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 
 set -e
 

diff --git a/docker/install-scafacos.sh b/docker/install-scafacos.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 
 set -e
 

diff --git a/docker/jupyter_nbconvert_config.json b/docker/jupyter_nbconvert_config.json
@@ -0,0 +1,7 @@
+{
+  "version": 1,
+  "Exporter": {
+    "require_js_url": "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js",
+    "mathjax_url": "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS_CHTML-full,Safe"
+  }
+}