add container definitions for Fedora 36 and Ubuntu 22.04LTS
This commit is contained in:
Axel Kohlmeyer
125
tools/singularity/fedora36_mingw.def
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125
tools/singularity/fedora36_mingw.def
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BootStrap: docker
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From: fedora:36
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%post
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dnf -y update
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dnf -y install vim-enhanced git file make cmake patch which file Lmod \
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ninja-build clang clang-tools-extra libomp-devel libubsan libasan libtsan \
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diffutils dos2unix findutils rsync python-devel libjpeg-devel libpng-devel \
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ccache gcc-c++ gcc-gfortran gdb valgrind eigen3-devel openblas-devel \
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openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
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netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
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readline-devel python3-pyyaml python3-Cython \
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mingw-filesystem-base mingw32-nsis mingw-binutils-generic \
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mingw32-filesystem mingw32-pkg-config \
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mingw64-filesystem mingw64-pkg-config \
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mingw32-crt mingw32-headers mingw32-binutils \
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mingw64-crt mingw64-headers mingw64-binutils \
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mingw32-cpp mingw32-gcc mingw32-gcc-gfortran mingw32-gcc-c++ \
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mingw64-cpp mingw64-gcc mingw64-gcc-gfortran mingw64-gcc-c++ \
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mingw32-libgomp mingw64-libgomp \
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mingw32-winpthreads mingw64-winpthreads \
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mingw32-eigen3 mingw64-eigen3 \
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mingw32-fftw mingw64-fftw \
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mingw32-libjpeg-turbo mingw64-libjpeg-turbo \
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mingw32-libpng mingw64-libpng \
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mingw32-python3 mingw64-python3 \
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mingw32-python3-numpy mingw64-python3-numpy \
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mingw32-python3-pyyaml mingw64-python3-pyyaml \
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mingw32-python3-setuptools mingw64-python3-setuptools \
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mingw32-readline mingw64-readline \
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mingw32-termcap mingw64-termcap \
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mingw32-zlib mingw64-zlib \
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mingw32-zstd mingw64-zstd \
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enchant python3-virtualenv doxygen latexmk \
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texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \
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texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
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texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
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texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
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texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng texlive-xindy \
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blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel \
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zstd libzstd-devel yaml-cpp-devel
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dnf clean all
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# enable Lmod and load MPI
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source /usr/share/lmod/lmod/init/profile
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module purge
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module load mpi
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# manually install Plumed
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mkdir plumed
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cd plumed
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version=2.7.4
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curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
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tar -xzf plumed.tar.gz
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cd plumed-${version}
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./configure --disable-doc --prefix=/usr
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make
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make install
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# fix up installation for CentOS and Fedora
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mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/
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cd ../../
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rm -rvf plumed
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# create missing termcap pkgconfig files
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cat > /usr/i686-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc <<EOF
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prefix=/usr/i686-w64-mingw32/sys-root/mingw
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exec_prefix=/usr/i686-w64-mingw32/sys-root/mingw
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libdir=/usr/i686-w64-mingw32/sys-root/mingw/lib
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includedir=/usr/i686-w64-mingw32/sys-root/mingw/include
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Name: Termcap
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Description: GNU/MinGW terminal feature database
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URL: ftp://ftp.gnu.org/gnu/termcap/
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Version: 1.3
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Libs: -L\${libdir} -ltermcap
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Cflags:
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EOF
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cat > /usr/x86_64-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc <<EOF
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prefix=/usr/x86_64-w64-mingw32/sys-root/mingw
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exec_prefix=/usr/x86_64-w64-mingw32/sys-root/mingw
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libdir=/usr/x86_64-w64-mingw32/sys-root/mingw/lib
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includedir=/usr/x86_64-w64-mingw32/sys-root/mingw/include
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Name: Termcap
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Description: GNU/MinGW terminal feature database
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URL: ftp://ftp.gnu.org/gnu/termcap/
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Version: 1.3
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Libs: -L\${libdir} -ltermcap
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Cflags:
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EOF
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# set custom prompt indicating the container name
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CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
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cat >$CUSTOM_PROMPT_ENV <<EOF
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#!/bin/bash
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PS1="[fedora36:\u@\h] \W> "
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EOF
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chmod 755 $CUSTOM_PROMPT_ENV
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%environment
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# we need to reset any module variables
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# inherited from the host.
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unset __LMOD_REF_COUNT__LMFILES_
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unset __LMOD_REF_COUNT_PATH
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unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
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unset __LMOD_REF_COUNT_MANPATH
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unset __LMOD_REF_COUNT_MODULEPATH
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unset __LMOD_REF_COUNT_LOADEDMODULES
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unset _LMFILES_
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unset MODULEPATH
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unset MODULESHOME
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unset MODULEPATH_ROOT
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unset LOADEDMODULES
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unset LMOD_SYSTEM_DEFAULT_MODULES
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# load MPI by default
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. /etc/profile
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module load mpi
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# tell OpenMPI to not try using Infiniband
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OMPI_MCA_btl="^openib"
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# do not warn about unused components as this messes up testing
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OMPI_MCA_btl_base_warn_component_unused="0"
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export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused
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%labels
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Author akohlmey, rbberger
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149
tools/singularity/ubuntu22.04.def
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149
tools/singularity/ubuntu22.04.def
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@ -0,0 +1,149 @@
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BootStrap: docker
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From: ubuntu:22.04
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%post
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export DEBIAN_FRONTEND=noninteractive
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apt-get update
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apt-get install --no-install-recommends -y software-properties-common
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# add-apt-repository ppa:openkim/latest
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apt-get update
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apt-get upgrade --no-install-recommends -y
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apt-get install --no-install-recommends -y \
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bc \
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build-essential \
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ccache \
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clang \
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cmake \
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cmake-curses-gui \
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curl \
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doxygen \
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enchant-2 \
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g++ \
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gcc \
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gfortran \
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git \
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hdf5-tools \
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less \
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libblas-dev \
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libeigen3-dev \
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libenchant-2-dev \
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libfftw3-dev \
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libgsl-dev \
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libhdf5-serial-dev \
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libhwloc-dev \
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libjpeg-dev \
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liblapack-dev \
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libnetcdf-dev \
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libomp-dev \
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libopenblas-dev \
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libnuma-dev \
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libpng-dev \
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libproj-dev \
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libreadline-dev \
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libvtk9-dev \
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libyaml-dev \
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libzstd-dev \
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make \
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mpi-default-bin \
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mpi-default-dev \
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ninja-build \
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python3-dev \
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python3-pip \
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python3-pkg-resources \
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python3-setuptools \
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python3-virtualenv \
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python3-venv \
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rsync \
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ssh \
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texlive \
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texlive-latex-recommended \
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texlive-formats-extra \
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texlive-pictures \
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texlive-publishers \
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texlive-science \
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dvipng \
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latexmk \
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xindy \
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vim-nox \
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virtualenv \
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voro++-dev \
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wget \
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xxd \
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valgrind \
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gdb \
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zstd \
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libyaml-cpp-dev \
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libkim-api-dev \
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gpg-agent \
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# openkim-models
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# ###########################################################################
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# # KIM-API
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# ###########################################################################
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#
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# # workaround for installing files in /usr/share/doc inside of a container
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# sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
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# apt-get install -y libkim-api-doc
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# sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
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#
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# # install KIM models
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# KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples
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# gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz
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# gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz
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#
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# kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003
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# kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ
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# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar
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# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ
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# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003
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# kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu
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###########################################################################
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# Plumed
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###########################################################################
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export PLUMED_PKG_VERSION=2.7.4
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mkdir plumed
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cd plumed
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curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_PKG_VERSION}/plumed-src-${PLUMED_PKG_VERSION}.tgz
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tar -xzf plumed.tar.gz
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cd plumed-${PLUMED_PKG_VERSION}
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./configure --disable-doc --prefix=/usr
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make
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make install
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cd ../../
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rm -rvf plumed
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###########################################################################
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# Customizations
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###########################################################################
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# set custom prompt indicating the container name
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CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
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cat >$CUSTOM_PROMPT_ENV <<EOF
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#!/bin/bash
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PS1="[ubuntu22.04:\u@\h] \W> "
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EOF
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chmod 755 $CUSTOM_PROMPT_ENV
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###########################################################################
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# Cleanup
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###########################################################################
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# clean cache
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rm -rf /var/lib/apt/lists/*
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%environment
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LC_ALL=C
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export LC_ALL
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export PATH=/usr/lib/ccache:$PATH
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# tell OpenMPI to not try using Infiniband
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OMPI_MCA_btl="^openib"
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# do not warn about unused components as this messes up testing
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OMPI_MCA_btl_base_warn_component_unused="0"
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export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused
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%labels
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Author akohlmey, rbberger
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