Port to AlmaLinux 9.3.

cmake/external/SHA256Digests.cmake

@@ -92,3 +92,4 @@ SET(centos-7-ParaView 45d545e75baf32c9fe30944781b4f6b172d4efd7d6cd794dcd19ec671c
 SET(centos-7-Qt 4308621ff9ec84585c3aead92a9d2de787b3c700323333b6e78ed45d04a0d2a4)
 SET(centos-7-ROOT 54298aa5f13dc2942925c10d755768f81f53d7135ac1a3e698e9b7ef1a3dfd1e)
 
+SET(almalinux-9.3-aarch64-ROOT f72e4abbfcaeca16cba862310d4dada2d6a7eda16e1044bcdaea9321e50ae48a)

util/installation/almalinux-9.3/Dockerfile

@@ -0,0 +1,52 @@
+# -----------------------------------------------------------------------------
+#
+# Copyright (C) 2021 CERN & University of Surrey for the benefit of the
+# BioDynaMo collaboration. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+#
+# See the LICENSE file distributed with this work for details.
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# -----------------------------------------------------------------------------
+
+FROM almalinux:9.3
+
+# workaround for https://github.com/containers/buildah/issues/1046
+RUN echo "" >> /etc/hosts && cat /etc/hosts && yum -y install setup
+
+# man required by ROOT
+# mesa-dri-drivers: OpenGL driver (software renderer)
+RUN dnf update -y && dnf install -y \
+  git \
+  sudo \
+  man \
+  wget \
+  xorg-x11-server-Xvfb \
+  mesa-dri-drivers
+
+RUN git config --system user.name "Test User" && \
+    git config --system user.email [email protected]
+
+# update user id and group id such that mapped volumes can be accessed with the
+# same rights as on the host. Files created by the container can also be
+# accessed on the host without chowning.
+ARG HOST_UID
+ARG HOST_GID
+
+RUN groupadd -g $HOST_GID testuser && \
+    useradd -u $HOST_UID -g $HOST_GID -m -c "Testuser" testuser && \
+    passwd --delete testuser && \
+    echo "testuser ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+
+USER testuser
+
+# preserve the environment variable BDM_LOCAL_LFS when calling scripts with
+# sudo
+RUN echo "Defaults env_keep += \"BDM_LOCAL_LFS\"" | sudo tee -a /etc/sudoers
+
+# the OpenGL capabilities can be incorrectly detected -> override version
+# https://python.develop-bugs.com/article/10118323/paraview+needs+higher+OpenGL+in+Mesa
+ENV MESA_GL_VERSION_OVERRIDE=3.3

util/installation/almalinux-9.3/package_list_extra

@@ -0,0 +1,14 @@
+doxygen
+graphviz
+libxml2-devel
+fontconfig-devel
+fontconfig
+freetype
+freetype-devel
+llvm-toolset-7
+llvm-toolset-7-clang-tools-extra
+llvm-toolset-7-llvm-devel
+llvm-toolset-7-llvm-static
+valgrind
+gsl-devel
+atlas-devel

util/installation/almalinux-9.3/package_list_required

@@ -0,0 +1,23 @@
+cmake
+git
+wget
+ninja-build
+bzip2-devel
+freeglut-devel
+libXext-devel
+libXt-devel
+libXpm-devel
+libXft-devel
+numactl-devel
+openmpi-devel
+zlib-devel
+lapack-devel
+blas-devel
+
+readline-devel
+sqlite-devel
+openssl-devel
+xz-devel
+libffi-devel
+findutils
+patch

util/installation/almalinux-9.3/prerequisites.sh

@@ -0,0 +1,81 @@
+#!/bin/bash
+# -----------------------------------------------------------------------------
+#
+# Copyright (C) 2021 CERN & University of Surrey for the benefit of the
+# BioDynaMo collaboration. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+#
+# See the LICENSE file distributed with this work for details.
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# -----------------------------------------------------------------------------
+
+# This script installs the required packages
+if [[ $# -ne 1 ]]; then
+  echo "ERROR: Wrong number of arguments.
+Description:
+    This script installs the prerequisites of BioDynaMo, but not BioDynaMo
+    itself. Script install.sh installs both prerequisites and BioDynaMo.
+Arguments:
+    <install_type>  all/required. If all is specified, then this script
+                    will install all the prerequisites."
+  exit 1
+fi
+
+BDM_PROJECT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/../../.."
+
+sudo -v
+
+sudo dnf update -y
+
+# Install required packages
+sudo dnf -y --enablerepo=crb install \
+  $(cat $BDM_PROJECT_DIR/util/installation/almalinux-9.3/package_list_required)
+
+if [ -n "${PYENV_ROOT}" ]; then
+  unset PYENV_ROOT
+fi
+
+# If PyEnv is not installed, install it
+if [ ! -f "$HOME/.pyenv/bin/pyenv" ]; then
+  echo "PyEnv was not found. Installing now..."
+  curl https://pyenv.run | bash
+fi
+export PYENV_ROOT="$HOME/.pyenv"
+export PATH="$PYENV_ROOT/bin:$PATH"
+eval "$(pyenv init --path)"
+eval "$(pyenv init -)"
+pyenv update
+
+PYVERS=3.9.1
+
+# If Python $PYVERS is not installed, install it
+if [ ! -f  "$HOME/.pyenv/versions/$PYVERS/lib/libpython3.so" ]; then
+  echo "Python $PYVERS was not found. Installing now..."
+  /usr/bin/env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install -f $PYVERS
+fi
+pyenv shell $PYVERS
+
+# Install optional packages
+if [ $1 == "all" ]; then
+  python -m pip install --upgrade pip
+  PIP_PACKAGES="markupsafe==2.0.1 nbformat jupyter metakernel jupyterlab nbformat==5.4.0 nbconvert==6.5.3 nbclient==0.6.6"
+  # Don't install --user: the packages should end up in the PYENV_ROOT directory
+  python -m pip install $PIP_PACKAGES
+  # SBML integration
+  #sudo bash -c 'cat << EOF  > /etc/yum.repos.d/springdale-7-SCL.repo
+#[SCL-core]
+#name=Springdale SCL Base 7.6 - x86_64
+#mirrorlist=http://springdale.princeton.edu/data/springdale/SCL/7.6/x86_64/mirrorlist
+##baseurl=http://springdale.princeton.edu/data/springdale/SCL/7.6/x86_64
+#gpgcheck=1
+#gpgkey=http://springdale.math.ias.edu/data/puias/7.6/x86_64/os/RPM-GPG-KEY-puias
+#EOF'
+  sudo dnf -y --enablerepo=crb install --nogpgcheck \
+    $(cat $BDM_PROJECT_DIR/util/installation/almalinux-9.3/package_list_extra)
+fi
+
+exit 0