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Port to almalinux-9 and ubuntu-24.04.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -27,3 +27,7 @@ libffi-devel | |
| findutils | ||
| patch | ||
| which | ||
| perl-Digest-SHA | ||
| xorg-x11-server-Xvfb | ||
| fontconfig | ||
| mesa-dri-drivers | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| # ----------------------------------------------------------------------------- | ||
| # | ||
| # 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 ubuntu:24.04 | ||
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||
| # man required by ROOT | ||
| RUN apt-get update && apt-get install -y \ | ||
| git \ | ||
| sudo \ | ||
| man \ | ||
| software-properties-common \ | ||
| wget \ | ||
| xvfb | ||
|
|
||
| # This will avoid tzdata package from requesting user interaction (tzdata is a | ||
| # dependency of one of the prerequisites of PyEnv) | ||
| RUN if ! [ -L /etc/localtime ]; then \ | ||
| sudo ln -fs /usr/share/zoneinfo/Europe/Berlin /etc/localtime; \ | ||
| fi | ||
|
|
||
| RUN git config --system user.name "Test User" && \ | ||
| git config --system user.email user@test.com | ||
|
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||
| # 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 | ||
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| USER testuser | ||
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| # 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| clang | ||
| clang-format | ||
| clang-tidy | ||
| doxygen | ||
| graphviz | ||
| libxml2-dev | ||
| llvm-14 | ||
| llvm-14-dev | ||
| llvm-14-runtime | ||
| valgrind | ||
| libgsl-dev |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| cmake | ||
| curl | ||
| freeglut3-dev | ||
| g++ | ||
| gcc | ||
| git | ||
| libblas-dev | ||
| libbz2-dev | ||
| liblapack-dev | ||
| libnuma-dev | ||
| libomp5 | ||
| libomp-dev | ||
| libopenmpi-dev | ||
| libpthread-stubs0-dev | ||
| make | ||
| wget | ||
| zlib1g-dev | ||
|
|
||
| libbz2-dev | ||
| libffi-dev | ||
| liblzma-dev | ||
| libreadline-dev | ||
| libsqlite3-dev | ||
| libssl-dev | ||
| python3-openssl | ||
| tk-dev | ||
| xz-utils | ||
| zlib1g-dev |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| jupyter | ||
| jupyter-client | ||
| jupyter-console | ||
| jupyter-core | ||
| jupyter-events | ||
| jupyter-server | ||
| jupyter-server-terminals | ||
| jupyterlab | ||
| jupyterlab-pygments | ||
| jupyterlab-server | ||
| jupyterlab-widgets | ||
| metakernel | ||
| nbclassic | ||
| nbclient | ||
| nbconvert | ||
| nbformat | ||
| markupsafe | ||
| beautifulsoup4 | ||
| ipython | ||
| traitlets | ||
| websocket-client | ||
| zipp |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| #!/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)/../../.." | ||
|
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||
| # Required to add Kitware ppa below | ||
| sudo apt-get update | ||
| sudo apt-get install apt-transport-https | ||
|
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| # Add ppa for newer CMake version | ||
| wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | sudo apt-key add - | ||
| CODENAME=$(grep -oP '(?<=^UBUNTU_CODENAME=).+' /etc/os-release | tr -d '"') | ||
| REPO="deb https://apt.kitware.com/ubuntu/ ${CODENAME} main" | ||
| sudo apt-add-repository "$REPO" | ||
|
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||
| # Update | ||
| sudo apt-get update | ||
| sudo apt install -y cmake-data=3.22.1-1ubuntu1.22.04.1 | ||
|
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| # Install required packages | ||
| sudo apt-get install -y \ | ||
| $(cat $BDM_PROJECT_DIR/util/installation/ubuntu-22.04/package_list_required) | ||
|
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||
| if [ -n "${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 | ||
|
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| PYVERS=3.9.1 | ||
|
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| # 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 | ||
|
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| # Install optional packages | ||
| if [ $1 == "all" ]; then | ||
| # Don't install --user: the packages should end up in the PYENV_ROOT directory | ||
| python -m pip install -r $BDM_PROJECT_DIR/util/installation/ubuntu-22.04/pip_packages.txt | ||
|
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| sudo apt-get install -y \ | ||
| $(cat $BDM_PROJECT_DIR/util/installation/ubuntu-22.04/package_list_extra) | ||
| fi | ||
|
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| exit 0 |