From 9f11cac3932f00e52966ef43050b2513037dfd05 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 24 Apr 2023 20:41:06 -0400
Subject: [PATCH] updated apptainer build definitions for almalinux 8/9

---
 tools/singularity/almalinux8.def | 110 +++++++++++++++++++++++++++++++
 tools/singularity/almalinux9.def |   2 +-
 2 files changed, 111 insertions(+), 1 deletion(-)
 create mode 100644 tools/singularity/almalinux8.def

diff --git a/tools/singularity/almalinux8.def b/tools/singularity/almalinux8.def
new file mode 100644
index 0000000000..cceb03dd9b
--- /dev/null
+++ b/tools/singularity/almalinux8.def
@@ -0,0 +1,110 @@
+BootStrap: docker
+From: library/almalinux:8
+
+%post
+        dnf -y install epel-release dnf-utils
+        dnf config-manager --set-enabled powertools
+        dnf -y update
+        dnf -y install vim-enhanced git file make cmake patch which file ninja-build \
+               ccache gcc-c++ gcc-gfortran clang libomp-devel gdb valgrind libubsan libasan libtsan \
+               eigen3-devel openblas-devel libpng-devel libjpeg-devel platform-python-devel \
+               openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
+               netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
+               enchant python3-virtualenv doxygen diffutils latexmk readline-devel \
+               texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \
+               texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
+               texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
+               texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
+               texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
+               blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel \
+               yaml-cpp-devel zstd libzstd-devel
+        dnf clean all
+
+        # we need to reset any module variables
+        # inherited from the host.
+        unset __LMOD_REF_COUNT__LMFILES_
+        unset __LMOD_REF_COUNT_PATH
+        unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
+        unset __LMOD_REF_COUNT_MANPATH
+        unset __LMOD_REF_COUNT_MODULEPATH
+        unset __LMOD_REF_COUNT_LOADEDMODULES
+        unset _LMFILES_
+        unset MODULEPATH
+        unset MODULESHOME
+        unset MODULEPATH_ROOT
+        unset LOADEDMODULES
+        unset LMOD_SYSTEM_DEFAULT_MODULES
+
+        # load MPI by default
+        . /etc/profile
+        module load mpi
+
+        # manually install Plumed
+        mkdir plumed
+        cd plumed
+        version=2.8.2
+        curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
+        tar -xzf plumed.tar.gz
+        cd plumed-${version}
+        ./configure --disable-doc --prefix=/usr
+        make
+        make install
+        # fix up installation for CentOS and Fedora
+        mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/
+        cd ../../
+        rm -rvf plumed
+
+        # create missing readline pkgconfig file
+        cat > /usr/lib64/pkgconfig/readline.pc <<EOF
+prefix=/usr
+exec_prefix=/usr
+libdir=/usr/lib64
+includedir=/usr/include
+
+Name: Readline
+Description: GNU Readline library for command line editing
+URL: http://tiswww.cwru.edu/php/chet/readline/rltop.html
+Version: 7.0
+Requires.private: ncurses
+Libs: -L\${libdir} -lreadline
+Cflags: -I\${includedir}/readline
+EOF
+        # set custom prompt indicating the container name
+        CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
+        cat >$CUSTOM_PROMPT_ENV <<EOF
+#!/bin/bash
+PS1="[almalinux8:\u@\h] \W> "
+EOF
+        chmod 755 $CUSTOM_PROMPT_ENV
+
+
+%environment
+        LC_ALL=C
+        export LC_ALL
+
+        # we need to reset any module variables
+        # inherited from the host.
+        unset __LMOD_REF_COUNT__LMFILES_
+        unset __LMOD_REF_COUNT_PATH
+        unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
+        unset __LMOD_REF_COUNT_MANPATH
+        unset __LMOD_REF_COUNT_MODULEPATH
+        unset __LMOD_REF_COUNT_LOADEDMODULES
+        unset _LMFILES_
+        unset MODULEPATH
+        unset MODULESHOME
+        unset MODULEPATH_ROOT
+        unset LOADEDMODULES
+        unset LMOD_SYSTEM_DEFAULT_MODULES
+
+        # load MPI by default
+        . /etc/profile
+        module load mpi
+        # tell OpenMPI to not try using Infiniband
+        OMPI_MCA_btl="^openib"
+        # do not warn about unused components as this messes up testing
+        OMPI_MCA_btl_base_warn_component_unused="0"
+        export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused
+
+%labels
+        Author akohlmey, rbberger
diff --git a/tools/singularity/almalinux9.def b/tools/singularity/almalinux9.def
index eacaf3b565..8b216d059b 100644
--- a/tools/singularity/almalinux9.def
+++ b/tools/singularity/almalinux9.def
@@ -9,7 +9,7 @@ From: library/almalinux:9
         dnf -y install vim-enhanced git file make cmake patch which file ninja-build \
                ccache gcc-c++ gcc-gfortran clang libomp-devel gdb valgrind libubsan libasan libtsan \
                eigen3-devel openblas-devel libpng-devel libjpeg-devel platform-python-devel \
-               openmpi-devel mpich-devel fftw-devel gsl-devel hdf5-devel \
+               openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
                netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
                enchant python3-virtualenv doxygen diffutils latexmk readline-devel \
                texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \